RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780143|ref|YP_003064556.1| DNA-directed RNA polymerase
subunit beta [Candidatus Liberibacter asiaticus str. psy62]
(1386 letters)
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 1288 bits (3334), Expect = 0.0
Identities = 602/1388 (43%), Positives = 879/1388 (63%), Gaps = 62/1388 (4%)
Query: 12 RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
R+R F K P +++P+L+ +Q+ SYD FL + G++ FKS+FPI
Sbjct: 10 RLRADFTKTPTDLEVPNLLLLQRDSYDSFLY----SKDGKESGIEKVFKSIFPIQDEHNR 65
Query: 72 AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAK-SIKDIKEQSI 130
LE+ EF K+ V + + R +TY++PLKI +RLI+++ D +G K IKDIKEQSI
Sbjct: 66 ITLEYAGCEFGKSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKNGIKDIKEQSI 125
Query: 131 YMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGL 190
++ ++PLMT+ +F+I G++R+VV+QLHRSPG+ F ++ S KL+Y +IIPD+G
Sbjct: 126 FIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESSTS-LNKLIYTGQIIPDRGS 184
Query: 191 WMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLS 250
W+ E+DSKD+++ RI++RRKVPVT A+ ++I+ FYP + D + P +
Sbjct: 185 WLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFA 244
Query: 251 AADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAE 310
+ D ++ L D G+ ++ +GKKLTS +K LKE ++++ D L ++AE
Sbjct: 245 SLD--ANQRMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAE 301
Query: 311 DIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTD----- 365
++ G+ E+ ++ +D+ LE+I +++ I+ ++ ++A I ++ D
Sbjct: 302 PVMVGK--EVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLK 359
Query: 366 ------KNKDRKD-ALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNM 418
K D A + I++VM+PGD T VA+ LFFD ++YDL+ VGR+KMN
Sbjct: 360 LLKQTEKIDDENALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNH 419
Query: 419 RLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLG 478
+L L PD + + EDII +K L+ ++N +G IDD D+LGNRR+R+VGE+L N+ G
Sbjct: 420 KLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSG 479
Query: 479 LLRMERSIKERIS--SVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRIT 536
L++M+++IK++++ S DS+MP DL+N+K + S + EFF QLSQ + N LS +T
Sbjct: 480 LVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVT 539
Query: 537 HTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYG 596
H RRLSALG+GG+ + R G E RDVHPTHYGRICP ET EG NIGL+++L++F RVN G
Sbjct: 540 HKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLG 599
Query: 597 FIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILV 656
FIE PY+KV DGKV + +YL+A++E++ IA A++ +DE+G+ +L+ R GE +L
Sbjct: 600 FIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLN 659
Query: 657 PREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGME 716
+ K+ +D S +V +AASLIPFLE+DD+NR LMG NMQRQAVPLL+++AP VGTG+E
Sbjct: 660 EKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIE 719
Query: 717 SVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCV 776
++A+ S AI A RAG+VE++D+ I I + +D Y L K R+NQNT
Sbjct: 720 KIIARDSWGAIKANRAGVVEKIDSKNIYILGE----GKEEAYIDAYSLQKNLRTNQNTSF 775
Query: 777 NQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSE 836
NQ P+VKVGD+V IIADGPS D G+LALG+N+ VAFMPW+GYNFED++++SER+ +
Sbjct: 776 NQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKD 835
Query: 837 DVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVG 896
D+FTS HI E EV AR+ K G EE T DIP+V EE L ++DE GI+ VG V+ G ILVG
Sbjct: 836 DIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVG 895
Query: 897 KITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERS 956
K +PKGE TPEE+LLRAIFG+KA V + SL P + GTV+DV++F + G +K+ R
Sbjct: 896 KTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDARV 955
Query: 957 ISVEREQIELLARDKDDEQVILDRNIYSRLMEILC----GQNAVSGPKGFKKSTVLS--- 1009
+S E+ L + D +L+R R+ +L + K +K+ +
Sbjct: 956 LSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEPFSHNGKDYKEGDQIPKEE 1015
Query: 1010 ---------SDLISEYPRSQWWQFAVQDEKVQRNVESLKVQYETSKSILEDRFKNKIEKI 1060
+ L+ +Y + VQ + E K + K +L + + K+ +
Sbjct: 1016 IASINRFTLASLVKKYSKE-----------VQNHYEITKNNFLEQKKVLGEEHEEKLSIL 1064
Query: 1061 QWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDI 1120
+ D +P GV++ VK+++A KR ++ GDKMAGRHGNKGIVS I+P DMP+ DG PVDI
Sbjct: 1065 EKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDI 1124
Query: 1121 VLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGS 1180
VLNPLGVPSRMN+GQI E HLG GK+I S++ D K LR+ + ++ +
Sbjct: 1125 VLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLED-KTKDFAKELRAKMLEIANAIN 1183
Query: 1181 HTEK-----ISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSI 1235
+ + + D+ +L A+ W GV ++ PVF+G +E + +A + G+
Sbjct: 1184 EKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMD 1243
Query: 1236 LYDGLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLG 1295
LYDG TGE V VGY+YM+KL+H+V +KV+ARSTG YSLVT QP+GGK+ GGQR G
Sbjct: 1244 LYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFG 1303
Query: 1296 EMEVWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQ 1355
EMEVW ++AYGAA+ L+EMLTIKSDD+ GR Y +I G E+ PE+F VL KE+Q
Sbjct: 1304 EMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQ 1363
Query: 1356 ALGLSIDL 1363
+L L I++
Sbjct: 1364 SLALDINI 1371
Score = 29.5 bits (66), Expect = 6.2
Identities = 22/91 (24%), Positives = 42/91 (46%), Gaps = 11/91 (12%)
Query: 256 VGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNG 315
V V D T E + + + S L++ L+E+ + G + ED+++
Sbjct: 2168 VSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEER-----------IFGRVLLEDVIDP 2216
Query: 316 ETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
T EI + A +IDE+ +++ + I+ I I
Sbjct: 2217 ITNEILLYADTLIDEEGAKKVVEAGIKSITI 2247
>gnl|CDD|179007 PRK00405, rpoB, DNA-directed RNA polymerase subunit beta; Reviewed.
Length = 1112
Score = 1171 bits (3032), Expect = 0.0
Identities = 427/660 (64%), Positives = 519/660 (78%), Gaps = 23/660 (3%)
Query: 288 LKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPIL 347
KE+ K + + + L G +AEDIV+ ETGE+ EA D I E+
Sbjct: 219 EKEEFGKEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITEE---------------- 262
Query: 348 YVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYD 407
+ YIRNTL D R++AL++IYR +RPG+ T A S+ LFFD +YD
Sbjct: 263 -----LDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYD 317
Query: 408 LSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSV 467
LS VGR K+N +L LD +DVR + KEDIIA IK L++LRNGKG +DDID+LGNRRVRSV
Sbjct: 318 LSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSV 377
Query: 468 GEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEE 527
GE+L+NQ+R+GL RMER+++ER+S D+D++ PQDLINAKPVV+A+ EFF SSQLSQ +
Sbjct: 378 GELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMD 437
Query: 528 HVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLT 587
N LS +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL
Sbjct: 438 QTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLA 497
Query: 588 SFARVNAYGFIETPYRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFC 647
++ARVN YGFIETPYRKV DGKVT+++VYL+A EE+N IAQAN+ LDEDG F +ELV
Sbjct: 498 TYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTA 557
Query: 648 RCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAE 707
R GE +LVP E++D++D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVPLL+ E
Sbjct: 558 RYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPE 617
Query: 708 APFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKF 767
AP VGTGME VA+ SGA +VAKR G+VE VDA RIV+R E LDP GVDIY L+KF
Sbjct: 618 APLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEE--LDPGEDGVDIYNLIKF 675
Query: 768 QRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSM 827
QRSNQNTC+NQRP+VKVGD V + D++ADGPSTD G+LALG+N+LVAFMPW+GYNFED++
Sbjct: 676 QRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAI 735
Query: 828 LISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAE 887
LISER+V EDVFTSIHIEE+E+ ARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +GAE
Sbjct: 736 LISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAE 795
Query: 888 VNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNR 947
V PGDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DV+DTSLRVP G GTV+DV++F R
Sbjct: 796 VKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR 855
Score = 518 bits (1338), Expect = e-147
Identities = 183/308 (59%), Positives = 216/308 (70%), Gaps = 54/308 (17%)
Query: 1059 KIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPV 1118
+I+ GD++PPGV ++VKV++A KR IQ GDKMAGRHGNKG+VSRILP EDMP+L+DGTPV
Sbjct: 855 RIEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPV 914
Query: 1119 DIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGT 1178
DIVLNPLGVPSRMN+GQI ETHLGWA GLG
Sbjct: 915 DIVLNPLGVPSRMNIGQILETHLGWAAKGLG----------------------------- 945
Query: 1179 GSHTEKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYD 1238
K +TPVFDGA EE I +L A L E G++ LYD
Sbjct: 946 ---------------------IK----FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYD 980
Query: 1239 GLTGEPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEME 1298
G TGEPFDRPVTVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+ GGQR GEME
Sbjct: 981 GRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 1040
Query: 1299 VWCIQAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALG 1358
VW ++AYGAAY LQEMLT+KSDDVVGRT+VYE+IV G + E G PESFNVLVKE+Q+LG
Sbjct: 1041 VWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLG 1100
Query: 1359 LSIDLENS 1366
L ++L +
Sbjct: 1101 LDVELLDE 1108
Score = 360 bits (926), Expect = 2e-99
Identities = 132/279 (47%), Positives = 190/279 (68%), Gaps = 19/279 (6%)
Query: 6 VFNGLGRVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPI 65
+ G R+RK FGK E++++P+L+E+Q S+D FL +++ P+ +EGL+ F+S+FPI
Sbjct: 4 SYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPI 60
Query: 66 TAFSGAAMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDI 125
F+G LEFVSYE PK+DV++C R LTY+ PL++ LRLI K +I
Sbjct: 61 EDFNGNLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVKLRLI---------NKETGEI 111
Query: 126 KEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRII 185
KEQ +YMGD+PLMT++GTF+I G +R++VSQLHRSPG++FDHDK + S SGKLLY+ RII
Sbjct: 112 KEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKTS-SGKLLYSARII 170
Query: 186 PDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFW 245
P +G W++ EFD KDI++VRIDRRRK+PVT L ALG EEIL FY K + + +
Sbjct: 171 PYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKEIEV- 229
Query: 246 CFPLSAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGL 284
+ ++G ++ +VD +TGE + E+ ++T L
Sbjct: 230 -----PVEYLLGKVLAEDIVDEETGEVLAEANDEITEEL 263
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 1123 bits (2907), Expect = 0.0
Identities = 552/1186 (46%), Positives = 793/1186 (66%), Gaps = 40/1186 (3%)
Query: 28 DLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFD 87
DL++VQK SYD F P + NE L+ F ++FPI A +EF+S D PK+D
Sbjct: 31 DLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYD 85
Query: 88 VDDCLWRDLTYAVPLKITLRLIVF----DVDEFTGAKS----------IKDIKEQSIYMG 133
+C+ R +T++ + ++RL++ +DE+ K IK I+EQ ++
Sbjct: 86 ESECIKRGITFSAQVIASIRLVIMQDGISLDEYKSIKESGDHSKLATVIKSIEEQEVHFC 145
Query: 134 DLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLWMD 193
+LP+MT GTF+I G+++++VSQ+HRSPG+ FD DKG+ SGKL+Y+ R+IP +G W+D
Sbjct: 146 ELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKLIYSARVIPYRGSWLD 205
Query: 194 IEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAAD 253
IEFD KD ++ RIDR+RK+P++ L ALG+ + +IL FY KI Y + D W P D
Sbjct: 206 IEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVP-D 264
Query: 254 LMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIV 313
G ++ L+D++ G ++++ ++TS L K L + +K + D +CGL++AED++
Sbjct: 265 KFKGVRLPFDLMDVE-GNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLI 323
Query: 314 NGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPILYVDSVNNNAYIRNTLVTDKNKDRKDA 373
+ + + AG+ I + ++++ I +I +L +D+++ YI NTL D+N +DA
Sbjct: 324 DSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDA 383
Query: 374 LLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKYDLSTVGRVKMNMRLNLDTPDDVRHIRK 433
L +IY+V+RPG+V + E F LFF + YDLS +GR+K+N L L+ +D+ +
Sbjct: 384 LYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTH 443
Query: 434 EDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSV 493
EDII I++ +V LR+G+G++DDID+LGNRRVRSVGE ++NQ+R GLL++ER++ + +S+
Sbjct: 444 EDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS 503
Query: 494 DIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRLSALGQGGVARAR 553
+D V P D IN K + + + +FF SSQLSQ + N LS ITH RRLSALG GG+ R R
Sbjct: 504 SLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRER 563
Query: 554 AGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARVNAYGFIETPYRKVCDGKVTND 613
AG E+RDVHPTHYGRICP ET EG NIGL++SL +AR+N YGFIE+PYRKV + VT+
Sbjct: 564 AGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQ 623
Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
+ YLSA++E YIA ++ LDE+ F +++++CR AG ++V +++ +ID SPKQV+S
Sbjct: 624 IEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVIS 683
Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPLLKAEAPFVGTGMESVVAKSSGAAIVAKRAG 733
+AASLIPFLENDD+NR LMG NMQRQAVPLLK AP V TGMES VA SGA ++AKR G
Sbjct: 684 VAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDG 743
Query: 734 IVEQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQRPLVKVGDEVRRNDI 793
IV+ D+ IVIR+ + + + VDIY L KFQRSN NTC+NQ+PLV VGD V+ D+
Sbjct: 744 IVDSSDSNSIVIRAFDKE-RVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDV 802
Query: 794 IADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSEDVFTSIHIEEFEVMARD 853
IADGP+ + G+LALG+N+LVAFM W GYNFEDS++IS +V +D+FTSIHIEEFE + D
Sbjct: 803 IADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHD 862
Query: 854 TKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPMTPEEKLL 913
T LG E+ITR IP V+EE L ++D+ GI+ +G V PG ILVGK+TPK + PE KLL
Sbjct: 863 TPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLL 922
Query: 914 RAIFGEKAVDVRDTSLRVPSGVSGTVVDVRIFNRHGIDKNERSISVEREQIELLARDKDD 973
IFGEK+ D D+SL V GTV+DV++F R G+++NER++ +++++I +++D
Sbjct: 923 MTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDY 982
Query: 974 EQVILDRNIYSRLMEILCGQNAVSGPKGFKKSTVLSSDLISEYPRSQWWQFAVQDEKVQR 1033
+ Y L ++L SG + +K R QWW ++++ +
Sbjct: 983 IINVTSEYFYDELKKLLIN----SGSQDREK--------FDSIEREQWWGIGLKNQSISE 1030
Query: 1034 NVESLKVQYETSKSILEDRFKNKIEKIQWGDDMPPGVLRVVKVFVAMKRPIQSGDKMAGR 1093
V+SLK ++ S +FK K+EK+ G D+P GV VKVF+A+K +Q GDKMAGR
Sbjct: 1031 QVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGR 1090
Query: 1094 HGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRMNVGQIFETHLGWACVGLGKKIK 1153
HGNKG++SR++P EDMP+L+DGTPVDI+LNPLGVPSRMNVGQI ETH+GWAC LG+K+
Sbjct: 1091 HGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVG 1150
Query: 1154 SLINDY-KANGDI-SPLRSF----LEKVIGTGSHTEKISDYDDDSV 1193
+++++ K +RS K +KI + DDD +
Sbjct: 1151 NILDEINKIKSAFCKGIRSLNDDNFTKFAAAYLDNKKIENIDDDEI 1196
Score = 251 bits (643), Expect = 7e-67
Identities = 121/239 (50%), Positives = 167/239 (69%), Gaps = 9/239 (3%)
Query: 1148 LGKKIKSLINDY--KANGDISPLRSFLEKVIGTGSHTE---KISDYDDDSVLRVAEQWKS 1202
L ++ L+ +Y S LR+FL +V GS+ I D D++++ A + +
Sbjct: 1209 LNDELNELVENYLNSCKSAYSNLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRD 1268
Query: 1203 GVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTVGYIYMLKLNHM 1262
G+PV+ PVF+G +E I + +A LD SGQ++LYDG +GE FDR VTVGY+YMLKL+H+
Sbjct: 1269 GIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHL 1328
Query: 1263 VSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTIKSDDV 1322
V K++ARS G YSLVTQQPLGGKS+ GGQR GEME W +QAYGAAY LQEMLT+KSDD+
Sbjct: 1329 VDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDI 1388
Query: 1323 VGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNSAKMEEIPDFN 1381
GR ++YESI+ G+ FE G PESFNV++KE+++L L++DL+ +N +E+I N
Sbjct: 1389 NGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLK----QNDVVIEDISHTN 1443
Score = 32.3 bits (73), Expect = 0.85
Identities = 21/77 (27%), Positives = 38/77 (49%)
Query: 260 VSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGE 319
++ LVD+ V + K +GL+ +G + + G A DI N T E
Sbjct: 2217 LTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKE 2276
Query: 320 IYIEAGDVIDEKSLEEI 336
+ ++AG++IDE +++I
Sbjct: 2277 LLVKAGELIDEDKVKQI 2293
>gnl|CDD|162660 TIGR02013, rpoB, DNA-directed RNA polymerase, beta subunit. This
model describes orthologs of the beta subunit of
Bacterial RNA polymerase. The core enzyme consists of
two alpha chains, one beta chain, and one beta' subunit.
Length = 1065
Score = 980 bits (2535), Expect = 0.0
Identities = 401/607 (66%), Positives = 492/607 (81%), Gaps = 3/607 (0%)
Query: 347 LYVDSVNNNAYIRNTLVTDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFDSDKY 406
L ++ + + YIRNTL D ++AL++IYR +RPG+ T A S+ LFFD +Y
Sbjct: 212 LILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRY 271
Query: 407 DLSTVGRVKMNMRLNLDTPDDVRHIRKEDIIAIIKILVDLRNGKGTIDDIDNLGNRRVRS 466
DL VGR K+N +L LD P+D+ + KEDIIA IK L+ LRNGKG IDDID+LGNRR+RS
Sbjct: 272 DLGRVGRYKLNKKLGLDVPEDIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRS 331
Query: 467 VGEMLKNQYRLGLLRMERSIKERISSVDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLE 526
VGE+L+NQ+R+GL RMER ++ER+S+ D D++ PQDLINAKP+ +A+ EFF SSQLSQ
Sbjct: 332 VGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFM 391
Query: 527 EHVNSLSRITHTRRLSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSL 586
+ N L+ +TH RRLSALG GG+ R RAG E+RDVHPTHYGRICP ET EG NIGL++SL
Sbjct: 392 DQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSL 451
Query: 587 TSFARVNAYGFIETPYRKVCDGK--VTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEEL 644
+++ARVN YGFIETPYRKV DGK VT++V YL+A EE+N IAQAN+ LDE+G F E+L
Sbjct: 452 STYARVNEYGFIETPYRKVKDGKVVVTDEVDYLTADEEDNYVIAQANAPLDENGRFVEDL 511
Query: 645 VFCRCAGEEILVPREKIDFIDASPKQVVSIAASLIPFLENDDSNRVLMGCNMQRQAVPLL 704
V R GE LV +++D++D SPKQVVS+AASLIPFLE+DD+NR LMG NMQRQAVPLL
Sbjct: 512 VVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLL 571
Query: 705 KAEAPFVGTGMESVVAKSSGAAIVAKRAGIVEQVDAIRIVIRSVEGDLDPSTSGVDIYRL 764
++EAP VGTGME+ VA+ SGA IVAKR G+VE VDA RIVIR E D D G+DIYRL
Sbjct: 572 RSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDE-DEDEPDGGIDIYRL 630
Query: 765 MKFQRSNQNTCVNQRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFE 824
+K+QRSNQ+TC+NQRP+V VGD V D++ADGPSTDLG+LALGRN+LVAFMPW+GYN+E
Sbjct: 631 LKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYE 690
Query: 825 DSMLISERMVSEDVFTSIHIEEFEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICV 884
D++LISER+V +DVFTSIHIEE+EV ARDTKLGPEEITRDIPNVSEE L+N+DE GI+ +
Sbjct: 691 DAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRI 750
Query: 885 GAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
GAEV GDILVGK+TPKGE+ +TPEEKLLRAIFGEKA DVRDTSLRVP GV GTV+DV++
Sbjct: 751 GAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKV 810
Query: 945 FNRHGID 951
F+R D
Sbjct: 811 FSRKQGD 817
Score = 444 bits (1143), Expect = e-124
Identities = 181/301 (60%), Positives = 211/301 (70%), Gaps = 51/301 (16%)
Query: 1063 GDDMPPGVLRVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVL 1122
GD++PPGV ++VKV++A KR IQ GDKMAGRHGNKG+VS+ILP EDMPFL+DGTPVDIVL
Sbjct: 816 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVL 875
Query: 1123 NPLGVPSRMNVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHT 1182
NPLGVPSRMN+GQI ETHLGWA LG+K
Sbjct: 876 NPLGVPSRMNIGQILETHLGWAGKRLGRK------------------------------- 904
Query: 1183 EKISDYDDDSVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTG 1242
GVP++TPVFDGA EE I L A L G+ LYDG TG
Sbjct: 905 --------------------GVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTG 944
Query: 1243 EPFDRPVTVGYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCI 1302
E FDRPVTVGY+YMLKL+H+V DK++ARSTG YSLVTQQPLGGK+ GGQR GEMEVW +
Sbjct: 945 EQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWAL 1004
Query: 1303 QAYGAAYVLQEMLTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSID 1362
+AYGAAY LQEMLT+KSDDVVGRT+ YE+IV G + E G PESFNVL+KE+Q+LGL I+
Sbjct: 1005 EAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIE 1064
Query: 1363 L 1363
L
Sbjct: 1065 L 1065
Score = 282 bits (724), Expect = 3e-76
Identities = 106/218 (48%), Positives = 151/218 (69%), Gaps = 7/218 (3%)
Query: 12 RVRKFFGKNPEIIDIPDLIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGA 71
R+R FGK PE++++P+L+E+Q SYD FL + P++R EGL+ FKS+FPI ++G
Sbjct: 3 RIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGN 62
Query: 72 AMLEFVSYEFDPPKFDVDDCLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIY 131
LE++SY PK+ V++C R LTY+ PLK+ LRLI + D K+IKEQ +Y
Sbjct: 63 IELEYLSYRLGEPKYSVEECKERGLTYSAPLKVKLRLINKEEDG------TKEIKEQDVY 116
Query: 132 MGDLPLMTKDGTFVIKGIQRIVVSQLHRSPGIHFDHDKGRASLSGKLLYACRIIPDQGLW 191
MGD+PLMT GTF+I G +R+VVSQLHRSPG+ F +K SGK+L++ RIIP +G W
Sbjct: 117 MGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDTHK-SGKVLFSARIIPYRGSW 175
Query: 192 MDIEFDSKDIIHVRIDRRRKVPVTSFLMALGMDSEEIL 229
++ E D KD+++VRIDR+RK+P T L ALG + ++
Sbjct: 176 LEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI 213
>gnl|CDD|132709 TIGR03670, rpoB_arch, DNA-directed RNA polymerase subunit B. This
model represents the archaeal version of DNA-directed RNA
polymerase subunit B (rpoB) and is observed in all
archaeal genomes.
Length = 599
Score = 180 bits (459), Expect = 2e-45
Identities = 95/309 (30%), Positives = 140/309 (45%), Gaps = 70/309 (22%)
Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
++VKV V R + GDK A RHG KG++ I+P EDMPF +DG D+++NP +PSRM
Sbjct: 340 KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRM 399
Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
VGQ+ E + K+ +L
Sbjct: 400 TVGQLLEM--------IAGKVAAL------------------------------------ 415
Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
G V F+G EE + L G+ ++YDG+TGE + + +
Sbjct: 416 ----------EGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFI 465
Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
G IY KL+HMV+DK++ARS G ++T+QP G++ GG R GEME + +GAA +L
Sbjct: 466 GVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLL 525
Query: 1312 QEMLTIKSDDVV--------------GRTRVYESIVAGNDT--FETGTPESFNVLVKEMQ 1355
+E L +SD V R V G +F +L+ E++
Sbjct: 526 KERLLDESDKYVVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPVEMSYAFKLLLDELK 585
Query: 1356 ALGLSIDLE 1364
+LG+S LE
Sbjct: 586 SLGISPRLE 594
Score = 75.4 bits (186), Expect = 9e-14
Identities = 54/172 (31%), Positives = 77/172 (44%), Gaps = 22/172 (12%)
Query: 778 QRPLVKVGDEVRRNDIIADGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVSED 837
Q+PLVK R ++I D G+N +VA M + GYN ED++++++ +
Sbjct: 178 QKPLVKT----RVLELI------GYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 227
Query: 838 VFTSIHIEEFEVMARDTKLGPE-EITRDIPNV----SEEGLKNIDECGIICVGAEVNPGD 892
+ S +E R G E P+V EE K++DE GI+ EV GD
Sbjct: 228 LARSTFFRTYEAEERRYPGGQEDRFEIPEPDVRGYRGEEAYKHLDEDGIVYPEVEVKGGD 287
Query: 893 ILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
+L+GK +P P EE G RDTS+ V G G V V I
Sbjct: 288 VLIGKTSP----PRFLEE---LRELGLVTERRRDTSVTVRHGEKGIVDKVII 332
Score = 45.4 bits (108), Expect = 1e-04
Identities = 28/90 (31%), Positives = 39/90 (43%), Gaps = 23/90 (25%)
Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
+ YL A EEEN YIA L + + E ID P ++
Sbjct: 92 IEYLDAEEEENAYIALDPEELTPEHTHLE---------------------ID--PSAILG 128
Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
I AS IP+ E++ S R MG M +Q++ L
Sbjct: 129 IIASTIPYPEHNQSPRNTMGAAMAKQSLGL 158
>gnl|CDD|181473 PRK08565, PRK08565, DNA-directed RNA polymerase subunit B;
Provisional.
Length = 1103
Score = 177 bits (452), Expect = 1e-44
Identities = 91/309 (29%), Positives = 139/309 (44%), Gaps = 70/309 (22%)
Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
++VKV V R + GDK A RHG KG++ ++P EDMPF +DG D+++NP +PSRM
Sbjct: 844 KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRM 903
Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
VGQ+ E+ + K+ +L
Sbjct: 904 TVGQLLES--------IAGKVAAL------------------------------------ 919
Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
G V F G EE + L G ++YDG TGE P+ +
Sbjct: 920 ----------EGRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFI 969
Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
G +Y KL+HMV+DK++AR+ G ++T+QP G++ GG R GEME C+ +GAA +L
Sbjct: 970 GVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLL 1029
Query: 1312 QEMLTIKSDDVV--------------GRTRVYESIVAGNDT--FETGTPESFNVLVKEMQ 1355
+E L SD R Y + G+ +F +L++E+
Sbjct: 1030 KERLLDSSDKTTIYVCELCGHIAWYDRRKNKYVCPIHGDKGNISPVEVSYAFKLLLQELM 1089
Query: 1356 ALGLSIDLE 1364
++G+S L+
Sbjct: 1090 SMGISPRLK 1098
Score = 83.5 bits (207), Expect = 4e-16
Identities = 54/188 (28%), Positives = 97/188 (51%), Gaps = 29/188 (15%)
Query: 422 LDTPDDVRHIRKEDIIA-IIKILVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLL 480
L T + R I+K + + L++L G+ DD D+ N+R+R G++L +R+
Sbjct: 293 LGTSPEDR-IKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFK 351
Query: 481 RMERSIKERISS-------VDIDSVMPQDLINAKPVVSAVCEFFCSSQ--------LSQL 525
++ + +K ++ +D+ +++ D+I + + A+ ++ +SQL
Sbjct: 352 QLVKDLKYQLEKSYARGRKLDLRAIVRPDIITER-IRHAL-----ATGNWVGGRTGVSQL 405
Query: 526 EEHVNSLSRITHTRR-LSALGQGGVARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVS 584
+ N LS ++H RR +S L +R + E RD+H T +GRICP ET EG N GLV
Sbjct: 406 LDRTNYLSTLSHLRRVVSPL-----SRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVK 460
Query: 585 SLTSFARV 592
+L A++
Sbjct: 461 NLALMAQI 468
Score = 68.4 bits (168), Expect = 1e-11
Identities = 56/175 (32%), Positives = 82/175 (46%), Gaps = 28/175 (16%)
Query: 778 QRPLVKVGDEVRRNDIIA--DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
QRPLV + R +II D P+ G+N +VA + + GYN ED++++++ +
Sbjct: 682 QRPLV----QTRALEIIGYNDRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASIE 729
Query: 836 EDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNVS----EEGLKNIDECGIICVGAEVNP 890
+ S +E R G E +I PNV EE + +DE GI+ EV
Sbjct: 730 RGLARSTFFRTYETEERKYPGGQEDKIEIPEPNVRGYRGEEYYRKLDEDGIVSPEVEVKG 789
Query: 891 GDILVGKITPKGESP-MTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTVVDVRI 944
GD+L+GK +P P E + L E+ RDTS+ V G G V V I
Sbjct: 790 GDVLIGKTSP----PRFLEELEELSLGLQER----RDTSVTVRHGEKGIVDTVLI 836
Score = 52.3 bits (126), Expect = 9e-07
Identities = 45/242 (18%), Positives = 81/242 (33%), Gaps = 71/242 (29%)
Query: 29 LIEVQKASYDHFLMMNIAPDERPNEGLQAAFKSVFPITAFSGAAMLEFVSYEFDPPKFDV 88
L+ SY+ F+ GLQ I + P+
Sbjct: 14 LVRQHLDSYNDFI----------ERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKE 63
Query: 89 DD----------CLWRDLTYAVPLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLM 138
D R+LTYA PL +T+ + ++ + + + +GDLP+M
Sbjct: 64 ADGSERPITPMEARLRNLTYAAPLYLTMIPVENGIEY----------EPEEVKIGDLPIM 113
Query: 139 TKD------------------------GTFVIKGIQRIVVSQLHRSPG-IHFDHDKGRAS 173
K G F+I G +R++VSQ +P + D + +S
Sbjct: 114 VKSKICPLSGLSPDELIEIGEDPKDPGGYFIINGSERVIVSQEDLAPNRVLVDKGEAGSS 173
Query: 174 -------LSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDR-RRKVPVTSFLMALGMDS 225
+S + Y ++ +E I+V K+P + ALG+++
Sbjct: 174 ITHTAKVISSRAGYRAQVT--------VERRKDGTIYVSFPAVPGKIPFVILMRALGLET 225
Query: 226 EE 227
+
Sbjct: 226 DR 227
Score = 38.8 bits (91), Expect = 0.011
Identities = 26/90 (28%), Positives = 37/90 (41%), Gaps = 23/90 (25%)
Query: 614 VVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVS 673
+ YL A EEEN Y+A L T E EI P ++
Sbjct: 596 IEYLDAEEEENAYVALDPEDL------TPEHTHL-----EIWPP------------AILG 632
Query: 674 IAASLIPFLENDDSNRVLMGCNMQRQAVPL 703
I AS+IP+ E++ S R M +Q++ L
Sbjct: 633 ITASIIPYPEHNQSPRNTYQAAMAKQSLGL 662
>gnl|CDD|180893 PRK07225, PRK07225, DNA-directed RNA polymerase subunit B';
Validated.
Length = 605
Score = 169 bits (430), Expect = 5e-42
Identities = 97/309 (31%), Positives = 147/309 (47%), Gaps = 70/309 (22%)
Query: 1072 RVVKVFVAMKRPIQSGDKMAGRHGNKGIVSRILPCEDMPFLKDGTPVDIVLNPLGVPSRM 1131
R+VKV V R + GDK A RHG KG++ I+P EDMPF + G D+++NP +PSRM
Sbjct: 346 RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRM 405
Query: 1132 NVGQIFETHLGWACVGLGKKIKSLINDYKANGDISPLRSFLEKVIGTGSHTEKISDYDDD 1191
VG + E +G K+ SL
Sbjct: 406 TVGHVLEM--------IGGKVGSL------------------------------------ 421
Query: 1192 SVLRVAEQWKSGVPVSTPVFDGADEEAINSMLRMADLDESGQSILYDGLTGEPFDRPVTV 1251
G V F G DEE + L + +G+ ++YDG+TGE + + V
Sbjct: 422 ----------EGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFV 471
Query: 1252 GYIYMLKLNHMVSDKVYARSTGSYSLVTQQPLGGKSNRGGQRLGEMEVWCIQAYGAAYVL 1311
G IY KL+HMV++K++ARS G ++T+QP G++ GG R GEME + +GAA +L
Sbjct: 472 GVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLL 531
Query: 1312 QEMLTIKSDDVV-------GRTRVYESI-------VAGNDT--FETGTPESFNVLVKEMQ 1355
+E L +SD V G +Y+ + G +T + +F +L+ E++
Sbjct: 532 KERLLDESDKVEIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVEMSYAFKLLLDELK 591
Query: 1356 ALGLSIDLE 1364
+LG++ LE
Sbjct: 592 SLGIAPRLE 600
Score = 62.7 bits (153), Expect = 6e-10
Identities = 49/169 (28%), Positives = 77/169 (45%), Gaps = 26/169 (15%)
Query: 778 QRPLVKVGDEVRRNDIIA--DGPSTDLGDLALGRNMLVAFMPWHGYNFEDSMLISERMVS 835
Q PLVK + +II + P+ G+N +VA M + GYN ED++++++ +
Sbjct: 184 QVPLVKT----QTQEIIGFDERPA--------GQNFVVAVMSYEGYNIEDALIMNKASIE 231
Query: 836 EDVFTSIHIEEFEVMARDTKLGPE-EITRDIPNV----SEEGLKNIDECGIICVGAEVNP 890
+ S +E R G E +V EE +++DE G++ EV
Sbjct: 232 RGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKDVRGYRGEEAYRHLDEDGLVNPETEVKE 291
Query: 891 GDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDTSLRVPSGVSGTV 939
GD+L+GK +P P EE FG R+TS+ + SG G V
Sbjct: 292 GDVLIGKTSP----PRFLEEP---DDFGISPEKRRETSVTMRSGEEGIV 333
Score = 45.0 bits (107), Expect = 1e-04
Identities = 28/88 (31%), Positives = 40/88 (45%), Gaps = 23/88 (26%)
Query: 616 YLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKIDFIDASPKQVVSIA 675
YL A EEEN YIA L E+ + E ID P ++ I
Sbjct: 100 YLDAEEEENAYIAVYEEDLTEEHTHLE---------------------ID--PSLILGIG 136
Query: 676 ASLIPFLENDDSNRVLMGCNMQRQAVPL 703
A +IP+ E++ S R+ MG M +Q++ L
Sbjct: 137 AGMIPYPEHNASPRITMGAGMIKQSLGL 164
>gnl|CDD|150971 pfam10385, RNA_pol_Rpb2_45, RNA polymerase beta subunit external 1
domain. RNA polymerases catalyse the DNA-dependent
polymerisation of RNA. Prokaryotes contain a single RNA
polymerase compared with three in eukaryotes (not
including mitochondrial or chloroplast polymerases).
This domain in prokaryotes spans the gap between domains
4 and 5 of the yeast protein. It is also known as the
external 1 region of the polymerase and is bound in
association with the external 2 region.
Length = 66
Score = 109 bits (275), Expect = 6e-24
Identities = 38/66 (57%), Positives = 51/66 (77%)
Query: 602 YRKVCDGKVTNDVVYLSAMEEENRYIAQANSSLDEDGSFTEELVFCRCAGEEILVPREKI 661
YRKV +GKVT+++VYL+A EEE IAQAN+ LDEDG F ++LV R GE +LVP E++
Sbjct: 1 YRKVKNGKVTDEIVYLTADEEEGYVIAQANAPLDEDGKFVDDLVIARYRGEFVLVPPEEV 60
Query: 662 DFIDAS 667
D++D S
Sbjct: 61 DYMDVS 66
>gnl|CDD|181986 PRK09606, PRK09606, DNA-directed RNA polymerase subunit B'';
Validated.
Length = 494
Score = 71.5 bits (176), Expect = 2e-12
Identities = 48/164 (29%), Positives = 85/164 (51%), Gaps = 23/164 (14%)
Query: 443 LVDLRNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIK---ERISS------- 492
+L G+ DD D+ N+R++ G+++++ +R+ R+ R +K ER +
Sbjct: 317 CFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSI 376
Query: 493 ---VDIDSVMPQDLINAKPVVSAVCEFFCSSQLSQLEEHVNSLSRITHTRRL-SALGQGG 548
V D V+ + L +A + V + +SQL + + ++ ++H RR+ S L
Sbjct: 377 KTAVRSD-VLTERLEHAMATGNWVGG---RTGVSQLLDRTDYMATLSHLRRVVSPL---- 428
Query: 549 VARARAGVEMRDVHPTHYGRICPAETSEGHNIGLVSSLTSFARV 592
+R++ E RD+HPT +GRICP+ET EG N GLV + +
Sbjct: 429 -SRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEI 471
>gnl|CDD|179068 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 41.2 bits (98), Expect = 0.002
Identities = 17/42 (40%), Positives = 29/42 (69%)
Query: 305 GLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
G +AED+V+ ETGE+ + AG +IDE+ ++I + I ++ I
Sbjct: 808 GRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKI 849
Score = 33.1 bits (77), Expect = 0.48
Identities = 22/79 (27%), Positives = 30/79 (37%), Gaps = 21/79 (26%)
Query: 724 GAAIVAKRAGIV----EQVDAIRIVIRSVEGDLDPSTSGVDIYRLMKFQRSNQNTCVNQR 779
G AI+A+ G V E RIVI +G+ Y + K +
Sbjct: 927 GPAIIAEIDGTVSFGKETKGKRRIVITPDDGE-------EREYLIPK----------GKH 969
Query: 780 PLVKVGDEVRRNDIIADGP 798
LV+ GD V D + DG
Sbjct: 970 LLVQEGDHVEAGDKLTDGS 988
>gnl|CDD|162830 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain.
Length = 1140
Score = 37.3 bits (87), Expect = 0.027
Identities = 16/47 (34%), Positives = 28/47 (59%)
Query: 300 SDCLCGLYVAEDIVNGETGEIYIEAGDVIDEKSLEEIFHSEIRDIPI 346
D + G Y AED+ + +TG++ EA +I E+ E+I +S I + +
Sbjct: 795 KDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKV 841
Score = 31.2 bits (71), Expect = 2.0
Identities = 13/55 (23%), Positives = 28/55 (50%)
Query: 250 SAADLMVGAKVSSSLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLC 304
S D +VG + + D DTG+ + E+ +T + + ++ G++ + + S C
Sbjct: 793 SLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTC 847
>gnl|CDD|178458 PLN02867, PLN02867, Probable galacturonosyltransferase.
Length = 535
Score = 36.0 bits (83), Expect = 0.069
Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 1/62 (1%)
Query: 1315 LTIKSDDVVGRTRVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSRTKNS-AK 1373
++K + + R V G+ ESFN LVKEM + I RTK K
Sbjct: 90 TSLKLREELTRALVEAKEQDDGGRGTKGSTESFNDLVKEMTSNRQDIKAFAFRTKAMLLK 149
Query: 1374 ME 1375
ME
Sbjct: 150 ME 151
>gnl|CDD|182871 PRK10966, PRK10966, exonuclease subunit SbcD; Provisional.
Length = 407
Score = 30.7 bits (70), Expect = 2.5
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 6/32 (18%)
Query: 1332 IVAGNDTFETGTPES-----FNVLVKEMQALG 1358
IVAG D F+TG+P S +N V +Q G
Sbjct: 44 IVAG-DIFDTGSPPSYARELYNRFVVNLQQTG 74
>gnl|CDD|162415 TIGR01549, HAD-SF-IA-v1, haloacid dehalogenase superfamily,
subfamily IA, variant 1 with third motif having Dx(3-4)D
or Dx(3-4)E. HAD subfamilies caused by an overly broad
single model.
Length = 154
Score = 30.8 bits (70), Expect = 2.6
Identities = 26/96 (27%), Positives = 37/96 (38%), Gaps = 10/96 (10%)
Query: 263 SLVDIDTGEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVAEDIVNGETGEIYI 322
L+ D E I L LK LKE G+K LGI S+ + I
Sbjct: 55 ELLGYDAEEAYIRGAADL----LKRLKEAGIK-LGIISNGSLRAQKLLLRKHLGDYFDLI 109
Query: 323 EAGDVIDEKSLEEIFHSEIRDI----PILYV-DSVN 353
D K EIF + + + +L+V D++N
Sbjct: 110 LGSDEFGAKPEPEIFLAALESLGLPPEVLHVGDNLN 145
>gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerD, one of two closely related
chromosomal proteins along with XerC (TIGR02224). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and with homologs of XerD on other replicons,
the chomosomal copy was preferred for building this
model. This model does not detect all XerD, as some
apparent XerD examples score below the trusted and noise
cutoff scores. XerC and XerD interact with cell division
protein FtsK.
Length = 291
Score = 29.9 bits (68), Expect = 4.7
Identities = 25/90 (27%), Positives = 32/90 (35%), Gaps = 19/90 (21%)
Query: 899 TPKGESP----MTPEE--KLLRAIFGEKAVDVRD---------TSLRVPSGVSGTVVDV- 942
PK +T EE LL A + + +RD T LRV V + DV
Sbjct: 94 PPKVARKLPKVLTVEEVEALLAAPDVDTPLGLRDRAMLELLYATGLRVSELVGLRLEDVN 153
Query: 943 ---RIFNRHGIDKNERSISVEREQIELLAR 969
G ER + + E IE L R
Sbjct: 154 LDEGFVRVRGKGNKERLVPLGEEAIEALER 183
>gnl|CDD|179764 PRK04172, pheS, phenylalanyl-tRNA synthetase subunit alpha;
Provisional.
Length = 489
Score = 29.8 bits (68), Expect = 4.7
Identities = 33/159 (20%), Positives = 55/159 (34%), Gaps = 39/159 (24%)
Query: 847 FEVMARDTKLGPEEITRDIPNVSEEGLKNIDECGIICVGAEVNPGDILVGKITPKGESPM 906
E +A L PE + R + E+GL ++E V V +T +G+
Sbjct: 23 LEELAEKLGLPPEAVMRAAEWLEEKGLVKVEE--------RV----EEVYVLTEEGKKYA 70
Query: 907 ---TPEEKLLRAIFGEKAV---DVRDTSLRVPSGVSGTVVDVRI----FNRHG------- 949
PE +LL A+ V ++++ L +V I R G
Sbjct: 71 EEGLPERRLLNALKDGGEVSLDELKEALLDKK--------EVGIALGNLARKGWAKIEKG 122
Query: 950 --IDKNERSISVEREQIELLARDKDDEQVILDRNIYSRL 986
I K + E + ++ LA +E D + L
Sbjct: 123 KVILKPDAYEDPEEKALKALAEGDKEELSEEDLKVLKEL 161
>gnl|CDD|182181 PRK09983, pflD, putative formate acetyltransferase 2; Provisional.
Length = 765
Score = 29.8 bits (67), Expect = 4.8
Identities = 29/113 (25%), Positives = 48/113 (42%), Gaps = 14/113 (12%)
Query: 1264 SDKVYARSTGSYSLVTQQP------LGGKSNRGGQRLGEMEVWCIQAYGAAYVLQEMLTI 1317
+D V RST S P LGG + G + + C+ AY + + Q L +
Sbjct: 305 NDIVLLRSTSSARYFAGFPTGYTALLGGLTENGRSAVNVLSFLCLDAYQSVQLPQPNLGV 364
Query: 1318 KSDDVVGRT---RVYESIVAGNDTFETGTPESFNVLVKEMQALGLSIDLENSR 1367
+++ ++ + E+I G TG P+ FN V L + LE++R
Sbjct: 365 RTNALIDTPFLMKTAETIRLG-----TGIPQIFNDEVVVPAFLNRGVSLEDAR 412
>gnl|CDD|178449 PLN02858, PLN02858, fructose-bisphosphate aldolase.
Length = 1378
Score = 29.8 bits (67), Expect = 5.6
Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 446 LRNGKGTIDDIDNLGNR-RVRSVGEMLKNQ-----YRLGLLR--MERSIKERISSVDIDS 497
L+ G+ TI+DI + + R+ GE + Y+ LR +E K RIS+ + S
Sbjct: 772 LQGGRYTINDIHYVADSDRLVPAGETEFAKDASFGYKSSNLREWVEEKTKGRISANSVQS 831
Query: 498 VMPQDLINAKPVVSAVCEFFCS 519
+ Q L P AVCE CS
Sbjct: 832 ISIQLLRKGGP--DAVCEHLCS 851
>gnl|CDD|165256 PHA02946, PHA02946, ankyin-like protein; Provisional.
Length = 446
Score = 29.6 bits (66), Expect = 5.7
Identities = 34/125 (27%), Positives = 53/125 (42%), Gaps = 26/125 (20%)
Query: 101 PLKITLRLIVFDVDEFTGAKSIKDIKEQSIYMGDLPLMTKDGTFVIKGIQRIVVSQLHRS 160
PL I V +VD D+ +Q+ + GD PL T +IK + S
Sbjct: 211 PLHIVCSKTVKNVDIINLLLPSTDVNKQNKF-GDSPL-----TLLIKTL----------S 254
Query: 161 PGIHFDHDKGRASLSGKLLYACRIIPDQGLWMDIEFDSKDIIHVRIDRRRKVPVTSFLMA 220
P A L KLL +I DQ + + I +D D++ + D+ ++ T F MA
Sbjct: 255 P----------AHLINKLLSTSNVITDQTVNICIFYDRDDVLEIINDKGKQYDSTDFKMA 304
Query: 221 LGMDS 225
+ + S
Sbjct: 305 VEVGS 309
>gnl|CDD|180251 PRK05776, PRK05776, DNA topoisomerase I; Provisional.
Length = 670
Score = 29.6 bits (67), Expect = 6.3
Identities = 21/88 (23%), Positives = 33/88 (37%), Gaps = 23/88 (26%)
Query: 208 RRRKVPVTSFLMALGMDSEEILSTFYPKIVYSQRGDFWCFPLSAADLMVGAKVSSSLVDI 267
+ + VT LG E+L ++P IV + + L I
Sbjct: 510 NGKYIEVTP----LGFGVAEVLEKYFPDIV---------------SVELTRDFEEKLEMI 550
Query: 268 DTG----EQVIESGKKLTSGLLKSLKEK 291
TG E+VIE K+ + LL+ K+
Sbjct: 551 RTGKATREEVIEEAKETLNKLLEEFKKN 578
>gnl|CDD|152076 pfam11640, TAN, Telomere-length maintenance and DNA damage repair.
ATM is a large protein kinase, in humans, critical for
responding to DNA double-strand breaks (DSBs). Tel1, the
orthologue from budding yeast, also regulates responses
to DSBs. Tel1 is important for maintaining viability and
for phosphorylation of the DNA damage signal transducer
kinase Rad53 (an orthologue of mammalian CHK2). In
addition to functioning in the response to DSBs,
numerous findings indicate that Tel1/ATM regulates
telomeres. The overall domain structure of Tel1/ATM is
shared by proteins of the phosphatidylinositol 3-kinase
(PI3K)-related kinase (PIKK) family, but this family
carries a unique and functionally important TAN sequence
motif, near its N-terminal, LxxxKxxE/DRxxxL. which is
conserved specifically in the Tel1/ATM subclass of the
PIKKs. The TAN motif is essential for both telomere
length maintenance and Tel1 action in response to DNA
damage. It is classified as an EC:2.7.11.1.
Length = 154
Score = 29.3 bits (66), Expect = 6.7
Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 7/56 (12%)
Query: 358 IRNTLVTDKNKDRKDALLDIYRVMRPGDVSTF-------SVAESMFNFLFFDSDKY 406
+ N L +DK KDR DAL + +++ + + E++F + + KY
Sbjct: 9 LVNLLSSDKIKDRNDALDLLENILKSNEEGKRLNDKQFHKIFEALFRLIEKEKSKY 64
>gnl|CDD|184898 PRK14905, PRK14905, triosephosphate isomerase/PTS system
glucose/sucrose-specific transporter subunit IIB;
Provisional.
Length = 355
Score = 29.2 bits (65), Expect = 6.7
Identities = 29/107 (27%), Positives = 53/107 (49%), Gaps = 12/107 (11%)
Query: 270 GEQVIESGKKLTSGLLKSLKEKGVKFLGITSDCLCGLYVA-EDIVNGETGEI-----YIE 323
GE + + ++ +L++ + G+ G++++ L L++A E + G I Y +
Sbjct: 136 GETLEQKNYNISDEVLRTQLKIGLH--GVSAEQLPHLFIAYEPVWAIGEGGIPASAEYAD 193
Query: 324 AGDVIDEKSLEEIFHSEIRDIPILYVDSVN-NNAYIRNTLVTDKNKD 369
I ++ L E+F E + IP+LY SVN NA N L+ + D
Sbjct: 194 EKHAIIKQCLFELFAEESKKIPVLYGGSVNLENA---NELIMKPHID 237
>gnl|CDD|162617 TIGR01945, rnfC, electron transport complex, RnfABCDGE type, C
subunit. The six subunit complex RnfABCDGE in
Rhodobacter capsulatus encodes an apparent NADH
oxidoreductase responsible for electron transport to
nitrogenase, necessary for nitrogen fixation. A closely
related complex in E. coli, RsxABCDGE (Reducer of SoxR),
reduces the 2Fe-2S-containing superoxide sensor SoxR,
active as a transcription factor when oxidized. This
family of putative NADH oxidoreductase complexes exists
in many of the same species as the related NQR, a
Na(+)-translocating NADH-quinone reductase, but is
distinct. This model describes the C subunit.
Length = 435
Score = 29.2 bits (66), Expect = 7.0
Identities = 9/22 (40%), Positives = 12/22 (54%)
Query: 779 RPLVKVGDEVRRNDIIADGPST 800
P+VKVGD+V + IA
Sbjct: 44 EPIVKVGDKVLKGQKIAKADGF 65
>gnl|CDD|183339 PRK11856, PRK11856, branched-chain alpha-keto acid dehydrogenase
subunit E2; Reviewed.
Length = 411
Score = 29.4 bits (67), Expect = 7.7
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 781 LVKVGDEVRRNDIIAD 796
LVKVGD V+ +A+
Sbjct: 23 LVKVGDTVKEGQPLAE 38
>gnl|CDD|183749 PRK12792, flhA, flagellar biosynthesis protein FlhA; Reviewed.
Length = 694
Score = 28.9 bits (65), Expect = 8.7
Identities = 16/48 (33%), Positives = 24/48 (50%), Gaps = 2/48 (4%)
Query: 880 GIICVGAEVNPGDILVGKITPKGESPMTPEEKLLRAIFGEKAVDVRDT 927
G + E+ PG++LV + G P P E++ FG KA+ V D
Sbjct: 422 GTVVATQELRPGELLV--VVGDGPRPDVPGEEVREPAFGMKALWVPDA 467
>gnl|CDD|162721 TIGR02135, phoU_full, phosphate transport system regulatory protein
PhoU. This model describes PhoU, a regulatory protein
of unknown mechanism for high-affinity phosphate ABC
transporter systems. The protein consists of two copies
of the domain described by Pfam model pfam01895.
Deletion of PhoU activates constitutive expression of
the phosphate ABC transporter and allows phosphate
transport, but causes a growth defect and so likely has
some second function.
Length = 212
Score = 28.8 bits (65), Expect = 9.3
Identities = 24/88 (27%), Positives = 39/88 (44%), Gaps = 9/88 (10%)
Query: 436 IIAIIKILVDL-RNGKGTIDDIDNLGNRRVRSVGEMLKNQYRLGLLRMERSIKERISSVD 494
II+IIKI DL R G D N+ R +R E K ++ L +M + + +
Sbjct: 78 IISIIKISSDLERIG----DYAVNIAKRALRLKEEDAKPKHLEELEKMGKLALKMLKDA- 132
Query: 495 IDSVMPQDLINAKPVVS---AVCEFFCS 519
+D+ + +D A+ V V E +
Sbjct: 133 LDAFLNKDAELARQVAEMDERVDELYRQ 160
>gnl|CDD|182054 PRK09736, PRK09736, 5-methylcytosine-specific restriction enzyme
subunit McrC; Provisional.
Length = 352
Score = 28.8 bits (65), Expect = 9.5
Identities = 15/52 (28%), Positives = 24/52 (46%), Gaps = 6/52 (11%)
Query: 355 NAYIRNTLV----TDKNKDRKDALLDIYRVMRPGDVSTFSVAESMFNFLFFD 402
N I++TL D +KD KD L + G VST + +++L +
Sbjct: 106 NRIIKSTLELLIRHDIDKDIKDRLRSLLVYF--GGVSTIDPSRIEWSYLQYG 155
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.319 0.137 0.395
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 22,995,504
Number of extensions: 1578384
Number of successful extensions: 3164
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3126
Number of HSP's successfully gapped: 67
Length of query: 1386
Length of database: 5,994,473
Length adjustment: 105
Effective length of query: 1281
Effective length of database: 3,725,633
Effective search space: 4772535873
Effective search space used: 4772535873
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 63 (28.0 bits)