RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780142|ref|YP_003064555.1| DNA-directed RNA polymerase
subunit beta' [Candidatus Liberibacter asiaticus str. psy62]
(1398 letters)
>gnl|CDD|179068 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 1716 bits (4448), Expect = 0.0
Identities = 596/1019 (58%), Positives = 731/1019 (71%), Gaps = 50/1019 (4%)
Query: 18 FDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYK 77
FD+++I +ASP KI S SYGE+KKPETINYRT KPERDGLFC RIFGP KDYEC+CGKYK
Sbjct: 7 FDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYK 66
Query: 78 RMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVE 137
R++YKGIICE+CGVEVT S VRR+RM HI+LA+PVAH WF KSLPSRI LL MSL+D+E
Sbjct: 67 RVRYKGIICERCGVEVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLE 126
Query: 138 RVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQ 197
RVLYFESYVV+DPG + LEK Q+LTEEEY EA+ ++G D+F+A MGA+AI ELL +DL+
Sbjct: 127 RVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYG-DEFVAKMGAEAIKELLKNIDLE 185
Query: 198 NLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVAL 257
A LR++L ++ S +RKK +KRLK+V++F SGN P WMI+ LPV+PPDLRPLV L
Sbjct: 186 AEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
Query: 258 DFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRV 317
D GRFA SDLNDLYRRVI RNNRL RL L APEII+RNEKRMLQE+VDALFDNGR R
Sbjct: 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRP 305
Query: 318 VTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALE 377
VTG N RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV GPEL+LHQCGLPK MALE
Sbjct: 306 VTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALE 365
Query: 378 LFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQ 437
LFKPF+ +L ++G +T+K AKK VE+E PEVWDVL EV+ +H VLLNRAP+LHRL +Q
Sbjct: 366 LFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEVIKEHPVLLNRAPTLHRLGIQ 425
Query: 438 AFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPAS 497
AFEP +I GKAIQLHPLVC +NADFDGDQMAV+ +S EAQ EARVLMLS+NN+L PA+
Sbjct: 426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
Query: 498 GAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSV 557
G P+ VPSQDMVLGL YL+ EG GEGM+F+ E A EN V LH++I+ R S
Sbjct: 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITS- 544
Query: 558 DKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKST 617
K+ +TT GR+I EILP + F N+ + KK IS +++ +YR G K T
Sbjct: 545 -------KKLVETTVGRVIFNEILPE--GLPFINVNKPLKKKEISKIINEVYRRYGLKET 595
Query: 618 VAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGE 677
V F D + LGF+YA SGIS G DDI++P K++II EA+K V E E QY GLIT GE
Sbjct: 596 VIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGE 655
Query: 678 KYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQL 737
+YNKV+D+W K TD+V + MM + + Q+ N I+MM+ SGARGS Q+RQL
Sbjct: 656 RYNKVIDIWSKATDEVAKAMMKNLSK--------DQESFNPIYMMADSGARGSASQIRQL 707
Query: 738 GGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRL 797
GMRGL+AKPSGEIIE+PI+S+F+ GL E+F S G RKGL D ++TA SGYL+RRL
Sbjct: 708 AGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRL 767
Query: 798 VDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKA 857
VDVAQ+ +V + DC T +G+ +T I++ G+V+ L R+LGR +D+++P T E IV A
Sbjct: 768 VDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPA 827
Query: 858 GQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAA 917
G LI E ++IE+ GI V+IRS LTCE+ GVC CYGRDLA G LVN+GEAVGVIAA
Sbjct: 828 GTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAA 887
Query: 918 QSIGEPGTQLTMRTFHLGG---------------AVTVMDRSFIESPCDGIVKIKNRNVC 962
QSIGEPGTQLTMRTFH GG A + I + DG V
Sbjct: 888 QSIGEPGTQLTMRTFHTGGVDITGGLPRVAELFEARKPKGPAII-AEIDGTVSF------ 940
Query: 963 RNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEW--DPH 1019
+ ++ E+ + I G L V +G +E G ++++ DPH
Sbjct: 941 -------GKETKGKRRIVITPDDGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPH 992
Score = 417 bits (1076), Expect = e-117
Identities = 150/246 (60%), Positives = 182/246 (73%), Gaps = 2/246 (0%)
Query: 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP 1186
DIT GLPRVAELFEAR+PK AI+AEI GT+ + K K R+VI P D E EY IP
Sbjct: 908 DITGGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITP--DDGEEREYLIP 965
Query: 1187 KNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHK 1246
K KH +Q+GDHVE GD + DG+ P DILR+ GVEA+ +YL+NEVQ+VYRL+GV IN K
Sbjct: 966 KGKHLLVQEGDHVEAGDKLTDGSIDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDK 1025
Query: 1247 HIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITK 1306
HIEV+VR ML+KV ITDP DT+++ G+ VDR E EE NR L +GK+ + P+L GITK
Sbjct: 1026 HIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITK 1085
Query: 1307 ASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRV 1366
ASL T+SF+SAASFQETT+VLTEAAI GKVD L G KENVI+GR IPAGTG + +V
Sbjct: 1086 ASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKV 1145
Query: 1367 AMNRDQ 1372
D+
Sbjct: 1146 EPAVDE 1151
Score = 28.9 bits (66), Expect = 9.4
Identities = 25/106 (23%), Positives = 33/106 (31%), Gaps = 41/106 (38%)
Query: 1023 IITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVV 1082
II E+ GTV F G KR+ IV+T ++G
Sbjct: 930 IIAEIDGTVSFGKETKG--------------KRR----------------IVITPDDGEE 959
Query: 1083 LKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDI 1128
+ + +P L V G V GD L I DI
Sbjct: 960 RE--------YLIPKGKHLLVQEGDHVEAGDKLTDGSIDP---HDI 994
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 1596 bits (4133), Expect = 0.0
Identities = 752/1356 (55%), Positives = 995/1356 (73%), Gaps = 10/1356 (0%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
+ F+ V ISIASP I +SYGEI+ T NYRTFK E+ GLFC +IFGP+ D EC+CGK
Sbjct: 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGK 1505
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRD 135
YK+ +++G ICEKCGVEVT S VRR+RM HI+LASPVAH WFLKSLPSRI LL MSLRD
Sbjct: 1506 YKKRRHRGRICEKCGVEVTSSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRD 1565
Query: 136 VERVLYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALD 195
+E +LY ++Y+V+DP +S EK +I++E+ Y EA +G D F+AM G +AI ELL LD
Sbjct: 1566 IENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGIDSFVAMQGVEAIRELLTRLD 1625
Query: 196 LQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLV 255
L + LR +L +S RRKKIIKRL+IV++FI SGN P WMI+ +P+LPPDLRPLV
Sbjct: 1626 LHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLV 1685
Query: 256 ALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHK 315
+L+ GR A SDLN YR +I RNNRL +L SL+ PEI+IRNEKRMLQE+VD+LFDN R
Sbjct: 1686 SLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRN 1745
Query: 316 RVVTGANRRPL-KSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLM 374
+V A KS+SDMLKGKQGRFR NLLGKRVDYSGRSVIV GP L+L+QCGLPK M
Sbjct: 1746 ALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRM 1805
Query: 375 ALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRL 434
ALELFKPF+Y++L+ G T+K A K + E+PEVWD+L EV+ +H VLLNRAP+LHRL
Sbjct: 1806 ALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEEVIKEHPVLLNRAPTLHRL 1865
Query: 435 SMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494
+QAFEP +I GKAIQLHPLVC +NADFDGDQMAV+ IS EAQLEARVLM+STNN+L
Sbjct: 1866 GIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
Query: 495 PASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRY 554
P++G P+ VPS+D+VLG+ YL T+ E + F EV H+L + + +HS I+ R
Sbjct: 1926 PSNGRPIIVPSKDIVLGIYYL-TLQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRM 1984
Query: 555 KSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQ 614
+ ++ G + K TTPGR+I+ +I P+H + FD+ NQ + K I+++VD +YR+CGQ
Sbjct: 1985 EYINSSGETHYKTICTTPGRLILWQIFPKHENLGFDLINQVLTVKEITSIVDLVYRNCGQ 2044
Query: 615 KSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLIT 674
+TVAF D LM LGF YA SG+SF + D+++PE+K + A +K++ QY DGLIT
Sbjct: 2045 SATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLIT 2104
Query: 675 RGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQM 734
R E+YNKV+D W K TD + +M+ I + K NS++MM +SGARGS QM
Sbjct: 2105 RSERYNKVIDEWSKCTDMIANDMLKAISIYD------GNSKYNSVYMMVNSGARGSTSQM 2158
Query: 735 RQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLS 794
+QL GMRGL+ KPSGEIIE+PI S+F+ GL FE+F S G RKGL D ++TA+SGYL+
Sbjct: 2159 KQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLT 2218
Query: 795 RRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECI 854
RRLVDV+QNC+V + DC TK GL + V+ +V SL S VLGRTA +DI NP+T E +
Sbjct: 2219 RRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELL 2278
Query: 855 VKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGV 914
VKAG+LI E V +I G+ V+IRS LTCE S GVC LCYGRDLA G +V++GEAVGV
Sbjct: 2279 VKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGV 2338
Query: 915 IAAQSIGEPGTQLTMRTFHLGGAVTV-MDRSFIESPCDGIVKIKNRNVCRNSTNDLISMG 973
IAAQS+GEPGTQLTMRTFH+GG +T ++ S I + + +K+ N N+ + + I +
Sbjct: 2339 IAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIVIS 2398
Query: 974 RNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGF 1033
R+ + ++D G E+ H + YGAKL+VD+GG ++ G +++EWDP+T PIITE +GTV +
Sbjct: 2399 RSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSY 2458
Query: 1034 EDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARGTDARW 1093
+DL DGIS+ E + ESTGI+ + V DW+ S NL+P IV+ D+NG V+ A G +A +
Sbjct: 2459 QDLKDGISITEVMDESTGISSKVVKDWKLYSGGANLRPRIVLLDDNGKVMTLASGVEACY 2518
Query: 1094 FLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEARRPKNHAILAEI 1153
F+P+ A+L+V GQKV GDV+ R P S KT+DIT GLPRV ELFEARRPK HAI++EI
Sbjct: 2519 FIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARRPKEHAIVSEI 2578
Query: 1154 SGTIRI-KRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVP 1212
G + +++ + K ++I+P ++ + P EY + ++KH + +GD V KGD ++DG+P
Sbjct: 2579 DGYVAFSEKDRRGKRSILIKPVDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLMDGDPDL 2638
Query: 1213 QDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILG 1272
DILR+ G+EALA Y+I+E+Q+VYRL+GV I++KH+EV+++ MLQKVEITDP DT Y++G
Sbjct: 2639 HDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVG 2698
Query: 1273 DNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAI 1332
+++D++EV+ N +++ GK+ + PILQGIT+ASL+T SFISAASFQETTKVLTEAA
Sbjct: 2699 ESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAF 2758
Query: 1333 AGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAM 1368
GK D L G KENVIVGR IPAGTG I+++ R +++
Sbjct: 2759 CGKSDPLSGLKENVIVGRLIPAGTGLIMNKVRALSL 2794
>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 = 1335 bits (3458), Expect = 0.0
Identities = 551/1023 (53%), Positives = 707/1023 (69%), Gaps = 56/1023 (5%)
Query: 20 SVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKRM 79
+++ISIASP I + SYGE+KKPETINYRT KPE+DGLFC +IFGP KD+EC CGKYK++
Sbjct: 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKI 60
Query: 80 KYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVERV 139
+YKG++CE+CGVEVT S VRR+RM HI+LA+PVAH W+ K LPSRI LL ++ +++E V
Sbjct: 61 RYKGVVCERCGVEVTESKVRRERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESV 120
Query: 140 LYFESYVVVDPGLSSLEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNL 199
LYFE+YVV+DPG + L+K ++L E EY E + ++G D F A MGA+AI ELL +DL
Sbjct: 121 LYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYG-DGFRAGMGAEAIKELLEKIDLDKE 179
Query: 200 ALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDF 259
L+ QL +S S +RKK++KRL+IV++F SGN P WM++ +PV+PP+LRP+V LD
Sbjct: 180 IEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDG 239
Query: 260 GRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVT 319
GRFA SDLNDLYRRVI RNNRL RL L APEII+RNEKRMLQE+VDALFDNGR + V
Sbjct: 240 GRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVV 299
Query: 320 GANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELF 379
G N RPLKSLSDMLKGKQGRFR NLLGKRVDYSGRSVIV GPEL+++QCGLPK MALELF
Sbjct: 300 GKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELF 359
Query: 380 KPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAF 439
KPF+ +L + + +K AKK +E+E PEVWDVL +V+ +H VLLNRAP+LHRL +QAF
Sbjct: 360 KPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKEHPVLLNRAPTLHRLGIQAF 419
Query: 440 EPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGA 499
EP ++ GKAI+LHPLVC +NADFDGDQMAV+ +SPEAQ EAR LML++NN+L+P G
Sbjct: 420 EPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGK 479
Query: 500 PVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDK 559
P+ PSQDMVLGL YL+T G GEG +F+++ E A +N V LH+ I R
Sbjct: 480 PIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTS---- 535
Query: 560 DGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVA 619
+I +TT GR+I EILP D N+ + KK IS+++D +Y G + T
Sbjct: 536 -----GEILETTVGRVIFNEILPEGFPYIND--NEPLSKKEISSLIDLLYEVHGIEETAE 588
Query: 620 FCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKY 679
D + LGF+YA SG + DI+VP+ K +I+ EADK V + + YN GLIT E+Y
Sbjct: 589 MLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERY 648
Query: 680 NKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGG 739
KVV +W +T DKVT+ MM +K+ K N IFMM+ SGARG+I Q RQL G
Sbjct: 649 RKVVSIWSETKDKVTDAMMKLLKK--------DTYKFNPIFMMADSGARGNISQFRQLAG 700
Query: 740 MRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVD 799
MRGL+AKPSG+IIE PI+S F+ GL E+F S G RKGL D ++TA SGYL+RRLVD
Sbjct: 701 MRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVD 760
Query: 800 VAQNCVVNQVDCNTKKGLTITHIVD-SGQVVYSLGSRVLGRTALDDIINPLTNECIVKAG 858
VAQ+ VV + DC T++G+ + IV+ +++ SL R++GR + +D+ +P T + I +A
Sbjct: 761 VAQDVVVREEDCGTEEGIEVEAIVEGKDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEAN 820
Query: 859 QLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQ 918
LI E +IE GI V++RS LTCES GVC CYGRDLA G LV +GEAVGVIAAQ
Sbjct: 821 TLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQ 880
Query: 919 SIGEPGTQLTMRTFHLGG--------------------AVTVMDRSFIESPCDGIVKIKN 958
SIGEPGTQLTMRTFH GG A T D++ I + DG V+I
Sbjct: 881 SIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFEARTPKDKAVI-AEVDGTVEIIE 939
Query: 959 RNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE--W 1016
V +N + I D + E+ + I +GA+L V DG + G +++E
Sbjct: 940 DIV-KNKRV----------VVIKDEND-EEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSI 987
Query: 1017 DPH 1019
DPH
Sbjct: 988 DPH 990
Score = 321 bits (824), Expect = 1e-87
Identities = 134/244 (54%), Positives = 170/244 (69%), Gaps = 3/244 (1%)
Query: 1121 SSAKTKDITSGLPRVAELFEARRPKNHAILAEISGTIRIKRN-YKNKSRVVIEPFEDGVE 1179
+ + DIT GLPRV ELFEAR PK+ A++AE+ GT+ I + KNK VVI+ D E
Sbjct: 899 VAGASGDITQGLPRVKELFEARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDEND--E 956
Query: 1180 PAEYFIPKNKHFYLQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLE 1239
+Y IP ++DGD V GD + +G+ P D+LRIKG++A+ YL+ EVQ+VYRL+
Sbjct: 957 EKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQ 1016
Query: 1240 GVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSP 1299
GV IN KHIEV+VR ML+KV ITD D+ + G+ +D E E NR L +QGKK S P
Sbjct: 1017 GVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIP 1076
Query: 1300 ILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
L GITKASL T+SF+SAASFQETTKVLT+AAI GKVD L G KENVI+G IPAGTG
Sbjct: 1077 QLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLK 1136
Query: 1360 LHEK 1363
+++
Sbjct: 1137 TYKE 1140
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 1118 bits (2893), Expect = 0.0
Identities = 504/937 (53%), Positives = 672/937 (71%), Gaps = 30/937 (3%)
Query: 14 DDR--GFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYEC 71
DDR F S ++++ASP KI S SYGE+KKPETINYRT KPERDGLFC +IFGP KDYEC
Sbjct: 1390 DDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYEC 1449
Query: 72 ICGKYKRMKYKGI-ICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLG 130
+CGKYK+ ++K I CEKCGV +T S VRR RM HI+LA+PVAH W++ SLPSRI TLLG
Sbjct: 1450 LCGKYKKPRFKDIGTCEKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLG 1509
Query: 131 MSLRDVERVLYFESYVVVDPGLSSLE--------KYQILTEEEYVEAVSQFGQDQFIAMM 182
+ ++D+ERVLY+E+Y+V +PG ++ + KY IL EE+Y ++ F+A M
Sbjct: 1510 VKMKDLERVLYYEAYIVKEPGEAAYDNEGTKLVMKYDILNEEQYQNISRRYEDRGFVAQM 1569
Query: 183 GADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIR 242
G +AI +LL +DL L +L++++ ++S ++KK+IKRLK+V+SF+ SGN P WM++
Sbjct: 1570 GGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLT 1629
Query: 243 KLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQ 302
LPVLPPDLRPLVALD G+FA SD+N+LYRRVI RN RL RL L APEII+RNEKRMLQ
Sbjct: 1630 VLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQ 1689
Query: 303 ESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGPE 362
E+VD LFDNGR V GAN+RPLKSLS+++KGKQGRFR NLLGKRVD+SGRSVIV GP
Sbjct: 1690 EAVDVLFDNGRSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPN 1749
Query: 363 LQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQHV 422
L++ +CGLPK MALELFKP L ++LE++GY +T+KQAK+ +E++ EVW+ L E+ +
Sbjct: 1750 LKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSNEVWECLQEITEGYP 1809
Query: 423 VLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEA 482
VLLNRAP+LH+ S+QAF PK+I GKAIQLHPLVC+ +NADFDGDQMAV+ +S EA E
Sbjct: 1810 VLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAEC 1869
Query: 483 RVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENK 542
+VLMLS+ N+L PASG V +PSQDMVLGL YLS G GE LF+ + E+ A++ K
Sbjct: 1870 KVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTK 1929
Query: 543 IVTLHSKIRGRYKSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNIS 602
+ +H+KIR +D+ I T+ GRMII ILP I D+ N+ M KK+I
Sbjct: 1930 ELDIHAKIR----VLDQ-----GNIIATSAGRMIIKSILPDF--IPTDLWNRPMKKKDIG 1978
Query: 603 AMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVK 662
+VD +++ G T F D+L LGFRYA +GIS +DII P+ K+K++ +A VK
Sbjct: 1979 VLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVK 2038
Query: 663 EYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMM 722
+ + QY+ GL+T E+YNK++D W + DK+++EMM I ++ NSI+MM
Sbjct: 2039 KIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA--------KDKEGFNSIYMM 2090
Query: 723 SHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLD 782
+ SGARGS Q+RQL MRGL+ KP G IIE+PI S+FK GL E+F S G RKGL D
Sbjct: 2091 ADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLAD 2150
Query: 783 VVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTAL 842
++TA++GYL+R+L+DV+QN V DC T +G+ IT I +++ L R+ GR L
Sbjct: 2151 TALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLL 2210
Query: 843 DDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLAR 902
+D+I+P+TNE ++ A LI E ++ + GI+S+ IR+ +TC++ +GVC CYG +L
Sbjct: 2211 EDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGE 2270
Query: 903 GSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVT 939
G + GEAVGV+AAQSIGEPGTQLT+RTFH+GG +
Sbjct: 2271 GKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTAS 2307
Score = 308 bits (791), Expect = 5e-84
Identities = 154/403 (38%), Positives = 241/403 (59%), Gaps = 31/403 (7%)
Query: 980 ILDMSGQEQYSHRIMYGAKLFVDDGGVIECGQRISE-----------WDPHTFPIITEVS 1028
I D +G+E H I G+++ +DD + IS+ WDP+ PII +
Sbjct: 2496 IADDNGREAARHYIARGSEILIDDNSEVSANSVISKPTTNTFKTIATWDPYNTPIIADFK 2555
Query: 1029 GTVGFEDLVDGISVIESIGESTGIAKRKVIDWRFASRSQNLKPAIVVTDENGVVLKSARG 1088
G V F D++ G++V E E+TGI V D+ + KP++ + A G
Sbjct: 2556 GKVSFVDIIAGVTVAEKEDENTGITSLVVNDYIPSG----YKPSLFLE--------GANG 2603
Query: 1089 TDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGLPRVAELFEAR--RPKN 1146
+ R+FL +++S G V +VLA++P ++ K++DIT GLPRV+ELFEAR +PK+
Sbjct: 2604 EEIRYFLEPKTSIAISDGSSVEQAEVLAKIPKATVKSRDITGGLPRVSELFEARKPKPKD 2663
Query: 1147 HAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206
AIL+E+ G + + +NK +++ +DG +YF+ K K + + V G+ +
Sbjct: 2664 VAILSEVDGIVSFGKPIRNKEHIIVTS-KDG-RSMDYFVDKGKQILVHADEFVHAGEAMT 2721
Query: 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPAD 1266
DG DILRI G + L Y+++EVQ+VYR +GV+I KHIE++V ML++V I D D
Sbjct: 2722 DGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGD 2781
Query: 1267 TEYILGDNVDRIEVEELN-RSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTK 1325
+++I GD V + +E N R +A +G+ ++ P+L GIT+A++ + S ISAASFQETTK
Sbjct: 2782 SKFIEGDLVSKKLFKEENARVIALKGEPAIA-EPVLLGITRAAIGSDSIISAASFQETTK 2840
Query: 1326 VLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAM 1368
VLTEA+IA K D L+ KENV++GR IP GTG +++ +++ +
Sbjct: 2841 VLTEASIAMKKDFLEDLKENVVLGRMIPVGTG--MYKNKKIVL 2881
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 829 bits (2142), Expect = 0.0
Identities = 414/908 (45%), Positives = 565/908 (62%), Gaps = 67/908 (7%)
Query: 155 LEKYQILTEEEYVEAVSQFGQDQFIAMMGADAIYELLIALDLQNLALTLRDQLSKSSSIF 214
+E Q++++E + F MGA+A+ +LL A+DL+ A LR ++
Sbjct: 232 IEPKQLISDEALYREMRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQ- 290
Query: 215 RRKKIIKRLKIVDSFITSGNNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRV 274
+R+K +KRLK+VD+F+ SGN+P MI+ +PV+PPDLRP+V LD GRFA SDLNDLYRRV
Sbjct: 291 KREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRV 350
Query: 275 IGRNNRLMRLKSLHAPEIIIRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLK 334
I RNNRL RL L APEII+ NEKRMLQE+VD+LFDNGR R VTG RPLKSL+DMLK
Sbjct: 351 INRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLADMLK 410
Query: 335 GKQGRFRTNLLGKRVDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVS 394
GKQGRFR NLLGKRVDYSGRSVIV GP L+LHQCGLP MALELFKPF+ +L + Y +
Sbjct: 411 GKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAA 470
Query: 395 TVKQAKKFVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPL 454
+K AK+ V++ VWDVL EV+ H VLLNRAP+LHRL +QAFEP ++ GKAI+LHPL
Sbjct: 471 NIKAAKRAVDRGASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPL 530
Query: 455 VCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCY 514
VC +NADFDGDQMAV+ +S +AQ EARVLMLS+NN+ PA G P+TVP+QDM++G+ Y
Sbjct: 531 VCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYY 590
Query: 515 LSTVHEGDPGEGMLFADMGEVYHALE-NKIVTLHSKI----------RGRYKSVDKDGNS 563
L+T +G GEG FAD + +A + + L +KI RG Y D +
Sbjct: 591 LTTERDGFEGEGRTFADFDDALNAYDARADLDLQAKIVVRLSRDMTVRGSYG--DLEETK 648
Query: 564 ISKIYDTTPGRMIIGEILPRHHEISFDICNQEMIKKNISAMVDTIYRHCGQKSTVAFCDD 623
+ +TT GR+I ++LP + N +M+KK+I +V+ D
Sbjct: 649 AGERIETTVGRIIFNQVLPE----DYPYLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDG 704
Query: 624 LMRLGFRYACSSGISFGKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVV 683
+ + GF YA +G++ D +P+ K +I+AEAD+ V + Y DG ++ E++ +VV
Sbjct: 705 IKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVV 764
Query: 684 DLWGKTTDKVTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGMRGL 743
D+W + T++V E M+A FD + N I+MM+ SGARG+I Q+RQL GMRGL
Sbjct: 765 DIWTEATEEVGEAMLA-----GFD-------EDNPIYMMADSGARGNIKQIRQLAGMRGL 812
Query: 744 IAKPSGEIIESPIRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVAQN 803
+A GEII+ PI+++F+ GL E+F S G RKGL+D +RTA SGYL+RRLVDVAQ+
Sbjct: 813 MADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQD 872
Query: 804 CVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINPLTNECIVKAGQLILE 863
+V + DC T +G+T + G V +L +GR L+D+ +P E ++ AG I
Sbjct: 873 VIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDP-NGEVLLSAGDYI-- 925
Query: 864 SHVNEIEK---CGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAAQSI 920
++++++ G+ V+IR+ +TC + GVC CYG DLA VN+G AVG+IAAQSI
Sbjct: 926 ESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSI 985
Query: 921 GEPGTQLTMRTFHLGG--------AVTVMDRSFIESPCDGIVKIKNRNVCRNSTNDL-IS 971
GEPGTQLTMRTFH GG + + F K K V + L I+
Sbjct: 986 GEPGTQLTMRTFHSGGVAGDDITQGLPRVAELF------EARKPKGEAVLAEISGTLQIT 1039
Query: 972 MGRNT-TLQILDMSGQEQ-----YSHRIMYGAKLFVDDGGVIECGQRISEW--DPHTFPI 1023
+ TL I D G + + M G V+DG + GQ+I+ +PH
Sbjct: 1040 GDKTEKTLTIHDQDGNSREYVVSARVQFMPG----VEDGVEVRVGQQITRGSVNPHDLLR 1095
Query: 1024 ITEVSGTV 1031
+T+ + T+
Sbjct: 1096 LTDPNTTL 1103
Score = 229 bits (586), Expect = 4e-60
Identities = 117/233 (50%), Positives = 155/233 (66%), Gaps = 5/233 (2%)
Query: 1127 DITSGLPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIP 1186
DIT GLPRVAELFEAR+PK A+LAEISGT++I + K + + I + EY +
Sbjct: 1006 DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGD-KTEKTLTIHDQDGNSR--EYVVS 1062
Query: 1187 KNKHFY--LQDGDHVEKGDYILDGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVAIN 1244
F ++DG V G I G+ P D+LR+ Y++++VQ+VY +GV IN
Sbjct: 1063 ARVQFMPGVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDIN 1122
Query: 1245 HKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGI 1304
KHIEV+ R ML+KV +T+P D++Y+ G V+R E E+ +L +GK+ P+L GI
Sbjct: 1123 DKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGI 1182
Query: 1305 TKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTG 1357
TKASL T S++SAASFQETTKVLT+AAI GKVD L G KENVI+G+ IPAGTG
Sbjct: 1183 TKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
Score = 216 bits (551), Expect = 4e-56
Identities = 83/136 (61%), Positives = 109/136 (80%)
Query: 14 DDRGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECIC 73
D FD++RIS+AS I S S+GE+KKPETINYRT KPE+DGLFC +IFGP KD+EC C
Sbjct: 5 DVTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECAC 64
Query: 74 GKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSL 133
GKYKR+++KGI+CE+CGVEVT + VRR+RM HI+LA+PV+H W+ K PSR+ LL +
Sbjct: 65 GKYKRIRFKGIVCERCGVEVTRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKP 124
Query: 134 RDVERVLYFESYVVVD 149
+D+E+VLYF SY++
Sbjct: 125 KDLEKVLYFASYIITS 140
>gnl|CDD|179452 PRK02625, rpoC1, DNA-directed RNA polymerase subunit gamma;
Provisional.
Length = 627
Score = 763 bits (1972), Expect = 0.0
Identities = 330/617 (53%), Positives = 431/617 (69%), Gaps = 51/617 (8%)
Query: 10 NPWTDDRGFDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCA 60
N T++R FD V+I +ASP +I GE+ KPETINYRT KPE DGLFC
Sbjct: 2 NLRTENR-FDYVKIGLASPERIRQWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCE 60
Query: 61 RIFGPIKDYECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKS 120
+IFGP KD+EC CGKYKR++++GI+CE+CGVEVT S VRR RM I LA+PV H W+LK
Sbjct: 61 KIFGPSKDWECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKG 120
Query: 121 LPSRISTLLGMSLRDVERVLYFESYVVVDPGLSSLEKY-QILTEEEYVEAVSQ-FGQDQF 178
+PS ++ LL M LRDVE+++YF YVV+DPG KY Q+LTE++++E Q + +D
Sbjct: 121 IPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYKQLLTEDQWLEIEDQIYAEDSE 180
Query: 179 I-----AMMGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSG 233
+ +GA+A+ LL L+L+ A LR++++ S +R K+IKRL+++D+FI +G
Sbjct: 181 LEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATG 239
Query: 234 NNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEII 293
+ P WM++ +PV+PPDLRP+V LD GRFA SDLNDLYRRVI RNNRL RL+ + APEII
Sbjct: 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEII 299
Query: 294 IRNEKRMLQESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSG 353
+RNEKRMLQE+VDAL DNGR R V GAN RPLKSLSD+++GKQGRFR NLLGKRVDYSG
Sbjct: 300 VRNEKRMLQEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSG 359
Query: 354 RSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDV 413
RSVIV GP+L++HQCGLPK MA+ELF+PF+ +L ++G V+ +K AKK +++ PEVW V
Sbjct: 360 RSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADPEVWQV 419
Query: 414 LAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAV 473
L EV+ H VLLNRAP+LHRL +QAFEP ++ G+AIQLHPLVC +NADFDGDQMAV+
Sbjct: 420 LEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVP 479
Query: 474 ISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEGDP-GEGMLFADM 532
+S EAQ EAR+LML++NN+L PA+G P+ PSQDMVLG YL+ + G G G FA +
Sbjct: 480 LSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQKGAGRYFASL 539
Query: 533 GEVYHALENKIVTLHSKIRGRYKS--------------------------------VDKD 560
+V A E + LH+ + R+ D+D
Sbjct: 540 EDVIMAFEQGRIDLHAWVWVRFNGEVEDDDEDTEPLKTETLEDGTRIEQYRYRRDRFDED 599
Query: 561 GNSISKIYDTTPGRMII 577
GN IS+ TT GR+I+
Sbjct: 600 GNLISQYILTTVGRVIM 616
>gnl|CDD|131440 TIGR02387, rpoC1_cyan, DNA-directed RNA polymerase, gamma subunit.
The RNA polymerase gamma subunit, encoded by the rpoC1
gene, is found in cyanobacteria and corresponds to the
N-terminal region the beta' subunit, encoded by rpoC, in
other bacteria. The equivalent subunit in plastids and
chloroplasts is designated beta', while the product of
the rpoC2 gene is designated beta''.
Length = 619
Score = 705 bits (1820), Expect = 0.0
Identities = 322/613 (52%), Positives = 431/613 (70%), Gaps = 50/613 (8%)
Query: 18 FDSVRISIASPAKIASLS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKD 68
FD V+I+IASP ++ GE+ KPETINYRT KPE DGLFC +IFGP KD
Sbjct: 2 FDYVKITIASPERVMEWGQRTLPNGQVVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKD 61
Query: 69 YECICGKYKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTL 128
+EC CGKYKR++++GI+CE+CGVEVT S VRR RM +I LA+PV H W+LK +PS +S L
Sbjct: 62 WECHCGKYKRVRHRGIVCERCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSIL 121
Query: 129 LGMSLRDVERVLYFESYVVVDPGLSSLEKY-QILTEEEYVEAVSQ-FGQDQFI-----AM 181
L M LRDVE+++YF +YVV++PG + KY Q+LTE++++E Q + +D +
Sbjct: 122 LDMPLRDVEQIVYFNAYVVLNPGNAKNLKYKQLLTEDQWLEIEDQIYAEDSELENEEVVG 181
Query: 182 MGADAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMII 241
+GA+A+ +LL L+L+ +A LR++++ S +R K+IKRL+++D+FI + + P WM++
Sbjct: 182 IGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
Query: 242 RKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRML 301
+PV+PPDLRP+V LD GRFA SDLNDLYRRVI RNNRL RL+ + APEII+RNEKRML
Sbjct: 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRML 300
Query: 302 QESVDALFDNGRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVIVAGP 361
QE+VDAL DNGR R V GAN RPLKSLSD+++GKQGRFR NLLGKRVDYSGRSVIV GP
Sbjct: 301 QEAVDALIDNGRRGRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGP 360
Query: 362 ELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWDVLAEVVHQH 421
+L++HQCGLPK MA+ELF+PF+ +L ++G V+ +K AKK +++ E+W VL EV+ H
Sbjct: 361 KLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRADDEIWSVLQEVITGH 420
Query: 422 VVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLE 481
V+LNRAP+LHRL +QAFEP ++ G+AIQLHPLVC +NADFDGDQMAV+ +S EAQ E
Sbjct: 421 PVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
Query: 482 ARVLMLSTNNLLHPASGAPVTVPSQDMVLGLCYLSTVHEG-DPGEGMLFADMGEVYHALE 540
AR+LML++NN+L PA+G P+ PSQDMVLG YL+ ++ G + G G F+ + + HA E
Sbjct: 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEKGRGRYFSSLEDAIHAYE 540
Query: 541 NKIVTLHSKI--------------------------------RGRYKSVDKDGNSISKIY 568
+ + LH I R D+DG IS+
Sbjct: 541 DGRIDLHDWIWVRFNGEVETNDPLDEPIKSEDLSDGTRIEQWTYRRDRFDEDGALISQYI 600
Query: 569 DTTPGRMIIGEIL 581
TT GR+I+ +
Sbjct: 601 LTTTGRIIMNHTI 613
>gnl|CDD|128909 smart00663, RPOLA_N, RNA polymerase I subunit A N-terminus.
Length = 295
Score = 418 bits (1076), Expect = e-117
Identities = 150/296 (50%), Positives = 186/296 (62%), Gaps = 24/296 (8%)
Query: 238 WMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNE 297
WMI+ LPV PP LRP V+LD GRFA DL L R +I RNNRL RL L APE IIRNE
Sbjct: 2 WMILTVLPVPPPCLRPSVSLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPEHIIRNE 61
Query: 298 KRMLQESVDALFDNG--RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRS 355
KR+LQE+VD LFDN R +G RPLKSLS LKGK+GRFR NLLGKRVD+S RS
Sbjct: 62 KRLLQEAVDTLFDNEGLPRARQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARS 118
Query: 356 VIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKK------------------GYVSTVK 397
VI P L+L++ G+PK +ALEL P + L G + +K
Sbjct: 119 VITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGPNGAKYIIRGKKTNLK 178
Query: 398 QAKK-FVEKERPEVWDVLAEVVHQHVVLLNRAPSLHRLSMQAFEPKIISGKAIQLHPLVC 456
AK+ + K V V+ VVL NR P+LHR+S+QA +++ GK I+L+PLVC
Sbjct: 179 LAKRSKIAKHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVC 238
Query: 457 AGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPSQDMVLGL 512
+ YNADFDGD+M ++ S EA+ EAR LML NN+L P +G P+ P QDM+LGL
Sbjct: 239 SPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGL 294
>gnl|CDD|179447 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 377 bits (971), Expect = e-105
Identities = 199/562 (35%), Positives = 300/562 (53%), Gaps = 62/562 (11%)
Query: 592 CNQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKE 651
N+ + KK + ++ +++ G T D+L LGFRYA +G+S DD+ VP +K
Sbjct: 4 RNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKR 63
Query: 652 KIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETG 711
++ +A++ + E +Y G IT E++ KV+D W +T +++ +E++ + + DP
Sbjct: 64 DLLEQAEEEITATEERYRRGEITEVERFQKVIDTWNETNERLKDEVVKNFR--QNDP--- 118
Query: 712 RQKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQ 771
+NS++MM+ SGARG++ Q+RQL GMRGL+A P GEII+ PI+++F+ GL E+
Sbjct: 119 ----LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTVTEYVI 174
Query: 772 SCVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYS 831
S G RKGL+D +RTA SGYL+RRLVDV+Q+ +V + DC T +G+ + + D +V+
Sbjct: 175 SSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIP 234
Query: 832 LGSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGV 891
LG R+LGR +D+++P E I + I +IEK G+ V +RS LTCE++R V
Sbjct: 235 LGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSV 293
Query: 892 CVLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCD 951
C CYG LA LV++GEAVG+IAAQSIGEPGTQLTMRTFH GG T + SP
Sbjct: 294 CRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFA 353
Query: 952 GIV----KIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRIMYGAKLFVDDGGVI 1007
G V K++ R + + + L + + I G+ LFVDDG +
Sbjct: 354 GTVEFGKKLRTRPYRTRHGVEALQAEVDFDLVLKPSGKGKPQKIEITQGSLLFVDDGQTV 413
Query: 1008 ECGQRISE---------WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKVI 1058
E Q ++E + T +I +++G V F DL+ + G +T A+R +
Sbjct: 414 EADQLLAEVAAGAVKKSTEKATKDVICDLAGEVRFADLIPE-EKTDRQGNTTRKAQRGGL 472
Query: 1059 DWRFASRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLA-- 1116
W + NL P A VS G +V GDVLA
Sbjct: 473 LWVLSGDVYNLPP--------------------------GAEPVVSNGDRVEEGDVLAET 506
Query: 1117 ----------RLPISSAKTKDI 1128
RL SS ++++
Sbjct: 507 KLVSEHGGVVRLRESSGDSREV 528
Score = 259 bits (664), Expect = 4e-69
Identities = 133/307 (43%), Positives = 174/307 (56%), Gaps = 24/307 (7%)
Query: 1073 IVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGL 1132
+ V L+ R + + A+L V G V GD LA L AKT DI GL
Sbjct: 928 VEAVSGGSVTLRLGR----PYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGL 983
Query: 1133 PRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRV-VIEPFEDGVEPAEYFIPKNKHF 1191
PR+ EL EAR+PK ILA+ GT++IK V VIE DG EY I ++
Sbjct: 984 PRIEELLEARKPKESCILAKKPGTVQIKYGDDESVDVKVIE--SDGTI-TEYPILPGQNV 1040
Query: 1192 YLQDGDHVEKGDYILDGNPVPQDILRI----------------KGVEALASYLINEVQEV 1235
+ DG V+ G+ + DG P ++L I + ++ L +L+NEVQ V
Sbjct: 1041 MVSDGQQVDAGEPLTDGPINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNV 1100
Query: 1236 YRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLV 1295
Y+ +GV I+ KHIEV+VR M KV I D DT + G+ ++ +VE++N ++A G
Sbjct: 1101 YQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPA 1160
Query: 1296 SFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAG 1355
++P+L GITKASL T SFISAASFQETT+VLTEAAI GK D L G KENVI+GR IPAG
Sbjct: 1161 EYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAG 1220
Query: 1356 TGAILHE 1362
TG E
Sbjct: 1221 TGFSGFE 1227
>gnl|CDD|162831 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria.
Length = 1227
Score = 351 bits (903), Expect = 6e-97
Identities = 211/621 (33%), Positives = 312/621 (50%), Gaps = 81/621 (13%)
Query: 593 NQEMIKKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEK 652
N+ + KK + ++ Y+ G T A D L LGFRYA +G+S DD+ VP +K+
Sbjct: 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQD 63
Query: 653 IIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMARIKRVEFDPETGR 712
++ A+K ++ E +Y G IT E++ KV+D W T +++ +E++ ++ DP
Sbjct: 64 LLEAAEKEIRATEERYRRGEITEVERFQKVIDTWNGTNEELKDEVVNNFRQT--DP---- 117
Query: 713 QKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESPIRSHFKGGLCGFEFFQS 772
+NS++MM+ SGARG++ Q+RQL GMRGL+A P GEII+ PI+++F+ GL E+ S
Sbjct: 118 ---LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTVTEYVIS 174
Query: 773 CVGGRKGLLDVVMRTASSGYLSRRLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSL 832
G RKGL+D +RTA SGYL+RRLVDV+Q+ +V + DC T++ + + + + + + SL
Sbjct: 175 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI-SL 233
Query: 833 GSRVLGRTALDDIINPLTNECIVKAGQLILESHVNEIEKCGIRSVRIRSALTCESSRGVC 892
G R+LGR +D+++P E IV I IE GI V +RS LTCE++R VC
Sbjct: 234 GDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVC 292
Query: 893 VLCYGRDLARGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDG 952
CYG LA LV++GEAVG+IAAQSIGEPGTQLTMRTFH GG T + S DG
Sbjct: 293 RKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDG 352
Query: 953 IV----KIKNRNVCRNSTNDLISMGRNTTLQILDMSGQEQYSHRI--MYGAKLFVDDGGV 1006
V K++ R D + L I + I G+ LFV+DG
Sbjct: 353 TVEFGKKLRTRGYRTRHGEDAKQVEVAGLLIIKPTGSITNKAQEIEVTQGSLLFVEDGQT 412
Query: 1007 IECGQRISE---------WDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRKV 1057
++ GQ ++E + T + ++++G V F D V + G +T IA+R
Sbjct: 413 VDAGQLLAEIALGAVRKSTEKATKDVASDLAGEVKF-DKVVPEEKTDRQGNTTRIAQRGG 471
Query: 1058 IDWRFASRSQNLKP--------------------AIVVTDENGVVLKSARGTDARWFLPV 1097
+ W + NL P + T+ GVV D+R +
Sbjct: 472 LIWVLSGEVYNLPPGAEPVVKNGDRVEQGTVLAETKLSTEHGGVVRLPESVGDSREVEII 531
Query: 1098 DA------------------------------LLSVSPGQKVSTGDVLARLPISSAKTKD 1127
A L +PG KV G V+A L +T
Sbjct: 532 TASVLLDQAKVIEESSQGRELYHIETADGQRFRLKAAPGTKVQNGQVVAELIDDRYRTT- 590
Query: 1128 ITSGLPRVA--ELFEARRPKN 1146
T GL + A E+ + + K
Sbjct: 591 -TGGLLKYAGVEVAKKGKAKQ 610
Score = 237 bits (607), Expect = 1e-62
Identities = 129/308 (41%), Positives = 178/308 (57%), Gaps = 21/308 (6%)
Query: 1072 AIVVTDENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSG 1131
I + V+L+ R + + A+L + G V GD LA L AKT DI G
Sbjct: 925 EIEEVASDYVILRIGR----PYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQG 980
Query: 1132 LPRVAELFEARRPKNHAILAEISGTIRIKRNYKNKSRVVIEPFEDGVEPAEYFIPKNKHF 1191
LPR+ EL EAR+PK ILA+ G +++K ++S V I+ E +EY + ++
Sbjct: 981 LPRIEELLEARKPKEACILAKRPGVVQVKYGTDDES-VSIKVIERDGTISEYPLLPGQNI 1039
Query: 1192 YLQDGDHVEKGDYILDGNPVPQDILRI----------------KGVEALASYLINEVQEV 1235
+ DG V G+ + DG P DIL + + ++ + +L+NEVQ V
Sbjct: 1040 MVSDGQQVTGGEPLTDGPINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNV 1099
Query: 1236 YRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQGKKLV 1295
Y+ +GV I+ KHIEV+VR M KV I D DT + G+ V+ +VE++N ++A G
Sbjct: 1100 YQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPA 1159
Query: 1296 SFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAG 1355
++P+L GITKASL T SFISAASFQETT+VLTEAAI GK D L G KENVI+GR IPAG
Sbjct: 1160 QYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAG 1219
Query: 1356 TGAILHEK 1363
TG +E+
Sbjct: 1220 TGFSSYEE 1227
>gnl|CDD|162833 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 868
Score = 275 bits (705), Expect = 5e-74
Identities = 241/905 (26%), Positives = 369/905 (40%), Gaps = 198/905 (21%)
Query: 19 DSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGKYKR 78
S++ + SP +I +S E+ +T + + P GL R G I+
Sbjct: 5 GSIKFGLLSPEEIRKMSVVEVVTADTYDDDGY-PIEGGLMDPR-LGVIE----------- 51
Query: 79 MKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRDVER 138
G+ C+ CG +V HI+LA PV H F K I +L + R R
Sbjct: 52 ---PGLRCKTCGGKV---GECPGHFGHIELARPVVHVGFAKE----IYKILRATCRKCGR 101
Query: 139 VL--------YFESYVVVDPGLSSLEKYQILTEEEYVEAVSQF-----GQDQF-IAMMGA 184
+ Y E + L L E+ EA + G++Q I
Sbjct: 102 ITLTEEEIEQYLEKINKLKEEGGDLAS--TLIEKIVKEAAKRMKCPHCGEEQKKIKFEKP 159
Query: 185 DAIYELLIALDLQNLALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSGNNPGWMIIRKL 244
YE D++ +R++L K + +++ P WM++ L
Sbjct: 160 TYFYEEGKEGDVKLTPSEIRERLEKIPD--------EDAELL-GINPKVARPEWMVLTVL 210
Query: 245 PVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIRNEKRMLQES 304
PV P +RP + L+ G + DL +I N RL AP++II + +LQ
Sbjct: 211 PVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYH 270
Query: 305 VDALFDN-------GRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKRVDYSGRSVI 357
V FDN RH+ RPLK+L+ LKGK+GRFR NL GKRV++S R+VI
Sbjct: 271 VATYFDNELPGIPPARHRS------GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVI 324
Query: 358 VAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVSTVKQAKKFVEKERPEVWD----- 412
P + +++ G+P+ +A EL P + + +++V P+ W
Sbjct: 325 SPDPNISINEVGVPEQIAKELTVPERVTPW-------NIDELREYVLNG-PDSWPGANYV 376
Query: 413 ----------------VLAE------VVHQH-----VVLLNRAPSLHRLSMQAFEPKIIS 445
LAE VV +H +VL NR PSLHR+SM + K++
Sbjct: 377 IRPDGRRIKIRDENKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLP 436
Query: 446 GKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHPASGAPVTVPS 505
GK +L+ VC YNADFDGD+M ++ + EA+ EAR LML ++L P G P+
Sbjct: 437 GKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGI 496
Query: 506 QDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRYKSVDKDGNSIS 565
D + G YL T + + EV L Y +
Sbjct: 497 HDYISGA-YLLTHK-----STLFTKE--EVQTILGV----------AGYFGDPPEPAIEK 538
Query: 566 KIYDTTPGRMIIGEILPR----------------------HHEISFDICNQEMI-----K 598
T G+ I LP H+ I N +++ K
Sbjct: 539 PKEYWT-GKQIFSAFLPEDLNFEGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDK 597
Query: 599 KNISA----MVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESK---- 650
K I A ++ I R G ++ F D + RL R+ G + G DDI +P+
Sbjct: 598 KAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEI 657
Query: 651 EKIIAEA----DKMVKEYENQYNDGLITRGEK---YNKVVDLWGKTTDKVTEEMMARIKR 703
E++I +A D +++ Y N + L R + K++++ GK D+ E +
Sbjct: 658 EELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGE-----VAE 712
Query: 704 VEFDPETGRQKKMNSIFMMSHSGARGSIHQMRQLGGM------------RGLIAK----- 746
DPE N +M+ +GARGS+ + Q+ M RG +
Sbjct: 713 KYLDPE-------NHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHF 765
Query: 747 PSGEIIESP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSRRLVDVA 801
G+I +RS FK GL E+F GGR+GL+D +RT+ SGY+ RRL++
Sbjct: 766 KKGDI--GAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINAL 823
Query: 802 QNCVV 806
Q+ V
Sbjct: 824 QDLYV 828
>gnl|CDD|181474 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 262 bits (673), Expect = 3e-70
Identities = 197/672 (29%), Positives = 293/672 (43%), Gaps = 153/672 (22%)
Query: 236 PGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEIIIR 295
P WM++ LPV P +RP + L+ G+ + DL +I N RL AP++II
Sbjct: 206 PEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIE 265
Query: 296 NEKRMLQESVDALFDN-------GRHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGKR 348
+ +LQ V FDN RH+ RPLK+L+ LKGK+GRFR NL GKR
Sbjct: 266 DLWELLQYHVTTYFDNEIPGIPPARHRS------GRPLKTLAQRLKGKEGRFRGNLSGKR 319
Query: 349 VDYSGRSVIVAGPELQLHQCGLPKLMALELFKPFLYAQLEKKGYVST--VKQAKKFVEKE 406
V++S R+VI P L +++ G+P+ +A EL P V+ +++ +++V
Sbjct: 320 VNFSARTVISPDPNLSINEVGVPEAIAKELTVPE---------RVTEWNIEELREYVLNG 370
Query: 407 RPEVW---------------------DVLAE------VVHQH-----VVLLNRAPSLHRL 434
PE + LAE +V +H +VL NR PSLHR+
Sbjct: 371 -PEKHPGANYVIRPDGRRIKLTDKNKEELAEKLEPGWIVERHLIDGDIVLFNRQPSLHRM 429
Query: 435 SMQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLH 494
S+ A +++ GK +L+ VC YNADFDGD+M ++ + EA+ EAR+LML ++L
Sbjct: 430 SIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILS 489
Query: 495 PASGAPVTVPSQDMVLGLCYLSTVHEGDPGEGMLFADMGEVYHALENKIVTLHSKIRGRY 554
P G P+ QD + G YL T + LF E L
Sbjct: 490 PRYGGPIIGGIQDHISGA-YLLTR------KSTLF-TKEEALDLLR----------AAGI 531
Query: 555 KSVDKDGNSISKIYDTTPGRMIIGEILPRHHEISF--------DICNQEMI--------- 597
+ + +I G+ I LP+ + F D C +E
Sbjct: 532 DELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIK 591
Query: 598 ----------KKNISA----MVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDD 643
KK I A ++D I + G + F D + RL R+ G + G DD
Sbjct: 592 NGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDD 651
Query: 644 I-IVPESKEKI---IAEADKMVKEYENQYNDGLI------TRGEKY-NKVVDLWGKTTDK 692
I E+KE+I I EA+K V+E Y +G + T E K++ + GK D+
Sbjct: 652 EDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDE 711
Query: 693 VTEEMMARIKRVEFDPETGRQKKMNSIFMMSHSGARGS---IHQMRQLGG---------M 740
I + N +M+ +GARGS + QM G
Sbjct: 712 A-----GEIAEKYLGLD-------NPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIR 759
Query: 741 RGLIAK-----PSGEIIESP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASS 790
RG + G++ +RS +K GL EFF +GGR+GL+D +RT+ S
Sbjct: 760 RGYRDRTLPHFKPGDL--GAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQS 817
Query: 791 GYLSRRLVDVAQ 802
GY+ RRL++ Q
Sbjct: 818 GYMQRRLINALQ 829
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 257 bits (657), Expect = 2e-68
Identities = 256/1102 (23%), Positives = 432/1102 (39%), Gaps = 196/1102 (17%)
Query: 16 RGFDSVRISIASPAKIASLSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECICGK 75
+ D + + SPA + + EI PE + P + GL R+ G I+
Sbjct: 7 KAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIE-------- 56
Query: 76 YKRMKYKGIICEKCGVEVTLSSVRRDRMAHIDLASPVAHPWFLKSLPSRISTLLGMSLRD 135
G C CG L++ HI+LA PV H F+ I LL +
Sbjct: 57 ------PGQKCLTCG---NLAANCPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHK 103
Query: 136 VERVLYFESYVVVDPGLSSLEKY-----QILTEEEYVEAVSQF--------------GQD 176
++ + + V + + ++E +E V G
Sbjct: 104 CAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIEEVRDQVKVYAKKAKECPHCGAP 163
Query: 177 QFIAMMGADAIYELLIALDLQN---LALTLRDQLSKSSSIFRRKKIIKRLKIVDSFITSG 233
Q + + +++ L + +RD K II + F
Sbjct: 164 QHELEF--EEPTIFIEKTEIEEHRLLPIEIRDIFEK---------IIDDDLELIGFDPKK 212
Query: 234 NNPGWMIIRKLPVLPPDLRPLVALDFGRFAASDLNDLYRRVIGRNNRLMRLKSLHAPEII 293
P W +++ V P RP + L+ G + DL + +I N +L K AP +I
Sbjct: 213 ARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLI 272
Query: 294 IRNEKRMLQESVDALFDNG------RHKRVVTGANRRPLKSLSDMLKGKQGRFRTNLLGK 347
+ +E LQ FDN H + + RPLKSL LKGK+GRFR NL+GK
Sbjct: 273 VEDEVDHLQYHTSTFFDNATAGIPQAHHK----GSGRPLKSLFQRLKGKEGRFRGNLIGK 328
Query: 348 RVDYSGRSVIVAGPELQLHQCGLPKLMALELFKP---------------------FLYAQ 386
RVD+S R+VI P + + + G+P+ +A++L P F A
Sbjct: 329 RVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGAN 388
Query: 387 LEKKGYVSTVKQAKKFVEKERPEVWDVLAE------VVHQH-----VVLLNRAPSLHRLS 435
+KG K F+E + + AE +V +H +V+ NR PSLH+LS
Sbjct: 389 AIRKGDG--TKIRLDFLEDKGKDALREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLS 446
Query: 436 MQAFEPKIISGKAIQLHPLVCAGYNADFDGDQMAVYAVISPEAQLEARVLMLSTNNLLHP 495
+ A K++ G +LHP VC YNADFDGD+M ++ +A+ EA LM +NL+ P
Sbjct: 447 ILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISP 506
Query: 496 ASGAPVTVPSQDMVLGLCYLSTVHEG--DPGEGMLFADMGEVYHALENKIVTLHSKIRGR 553
+G P+ QD + YL T + D E A + + L +
Sbjct: 507 RTGGPIIGALQDFITAA-YLITKDDALFDKNEASNIAMLAGITDPLPEPAIKTKDGPAWT 565
Query: 554 YKS-----VDKDGN--SISKIYDTT------PGRMIIGEILPRHHEISFDICNQEMI--- 597
K + KD N I+K P + G +L + E+ + + +I
Sbjct: 566 GKQLFSLFLPKDFNFEGIAKWSAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNIIGAL 625
Query: 598 KKNISAMVDTIYRHCGQKSTVAFCDDLMRLGFRYACSSGISFGKDDIIVPESKEKIIAEA 657
+ +++D I + G+ + F + ++ + + G S G D+I+P+ ++ I +
Sbjct: 626 VEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIED- 684
Query: 658 DKMVKEYENQYND-GLITRGEKYNKVVDLWGKTTDKVT-----EEMMARIKRVEFDPETG 711
+ + ++ + K + + ++ K +++ EE + E D
Sbjct: 685 -----DIQGMKDEVSDLIDQRKITRKITIY-KGKEELLRGMKEEEALEADIVNELDKARD 738
Query: 712 RQKKM--------NSIFMMSHSGARGSIHQMRQLGG--------MRGLIAKPSGEIIE-- 753
+ N+ +M+ +GARGS+ + Q+ G R G + E
Sbjct: 739 KAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTGGRLHEGY 798
Query: 754 -------------SP-----IRSHFKGGLCGFEFFQSCVGGRKGLLDVVMRTASSGYLSR 795
+P ++++++ GL EFF +GGR+GL+D RT SGY R
Sbjct: 799 KDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQR 858
Query: 796 RLVDVAQNCVVNQVDCNTKKGLTITHIVDSGQVVYSLGSRVLGRTALDDIINP---LTNE 852
RL + ++ + + D + HI+ Q + + + N + +
Sbjct: 859 RLANALEDIRL-EYDETVRD--PHGHII---QFKFGEDGIDPQKLDHGEAFNLERIIEKQ 912
Query: 853 CIVKAGQLILESHVNEIEKCGIRSVRIRSALTCE--------SSRGVCVLCY-GRDLARG 903
I G+ + + E+ K ++ + +C G++
Sbjct: 913 KIEDRGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELEAICAEGKEGFEK 972
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGA----VTVMDRSFIE------SPCDGI 953
+ V G+A+G+I+AQSI EPGTQ+T+RTFH G VT FIE P
Sbjct: 973 AKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPT 1032
Query: 954 VKIKNRNVCRNSTNDLISMGRN 975
+ I + C+ I + RN
Sbjct: 1033 MDIYLDDECKEDIEKAIEIARN 1054
Score = 46.6 bits (110), Expect = 4e-05
Identities = 28/146 (19%), Positives = 65/146 (44%), Gaps = 32/146 (21%)
Query: 1214 DILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGD 1273
+I G+EA + + NE+ + +G+ +++++I +V M +
Sbjct: 1198 EIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSR--------------G 1243
Query: 1274 NVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIA 1333
++ I ++ G+K S ++ A+F+ TT + AA+
Sbjct: 1244 TIEAIGLQAAGVRHGFAGEK------------------DSPLAKAAFEITTHTIAHAALG 1285
Query: 1334 GKVDTLDGFKENVIVGRSIPAGTGAI 1359
G+++ + G + +I+G++IP G+G +
Sbjct: 1286 GEIEKIKGILDALIMGQNIPIGSGKV 1311
>gnl|CDD|179818 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 71.0 bits (175), Expect = 2e-12
Identities = 27/33 (81%), Positives = 29/33 (87%)
Query: 904 SLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
SLV GEAVGV+AAQSIGEPGTQ+TMRTFH G
Sbjct: 54 SLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG 86
Score = 58.3 bits (142), Expect = 1e-08
Identities = 44/146 (30%), Positives = 68/146 (46%), Gaps = 44/146 (30%)
Query: 1215 ILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRH-MLQKVEITDPADTEYILGD 1273
I + G+EA + +I E++ +G ++V +RH ML AD G
Sbjct: 268 IEEVLGIEAARNAIIEEIKNTLEEQG-------LDVDIRHIMLV-------ADMMTWDG- 312
Query: 1274 NVDRIEVEELNRSLAQQGKKLVSFSPILQGIT--KASLQTKSFISAASFQETTKVLTEAA 1331
EV ++ R G++ KAS+ ++ A+F+ T K L +AA
Sbjct: 313 -----EVRQIGR----------------HGVSGEKASV-----LARAAFEVTVKHLLDAA 346
Query: 1332 IAGKVDTLDGFKENVIVGRSIPAGTG 1357
+ G+VD L G EN+IVG+ IP GTG
Sbjct: 347 VRGEVDELKGVTENIIVGQPIPLGTG 372
>gnl|CDD|162832 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 367
Score = 66.2 bits (162), Expect = 6e-11
Identities = 30/79 (37%), Positives = 41/79 (51%), Gaps = 10/79 (12%)
Query: 858 GQLILESHVNEIEKCGIRSVRIRSALTCESSRGVCVLCYGRDLARGSLVNVGEAVGVIAA 917
+ +L+ ++K I + Y R SL++ GEAVG++AA
Sbjct: 3 PEKLLKELEETVKKREISDKEELDEIIKRVEEE-----YLR-----SLIDPGEAVGIVAA 52
Query: 918 QSIGEPGTQLTMRTFHLGG 936
QSIGEPGTQ+TMRTFH G
Sbjct: 53 QSIGEPGTQMTMRTFHYAG 71
Score = 54.7 bits (132), Expect = 2e-07
Identities = 32/93 (34%), Positives = 53/93 (56%), Gaps = 13/93 (13%)
Query: 1280 VEELNRSLAQQG-----------KKLVSFSPILQGITKASL--QTKSFISAASFQETTKV 1326
+EE+ R+L +QG L+++ ++ I + + + S ++ A+F+ T K
Sbjct: 270 IEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARAAFEVTVKH 329
Query: 1327 LTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
L +AAI G+VD L G EN+IVG+ IP GTG +
Sbjct: 330 LLDAAIRGEVDELAGVIENIIVGQPIPLGTGDV 362
>gnl|CDD|184891 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 62.9 bits (153), Expect = 6e-10
Identities = 23/34 (67%), Positives = 27/34 (79%)
Query: 905 LVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAV 938
V+ EAVG++AAQSIGEPGTQ+TMRTFH G
Sbjct: 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVA 211
Score = 57.9 bits (140), Expect = 2e-08
Identities = 43/149 (28%), Positives = 67/149 (44%), Gaps = 41/149 (27%)
Query: 1214 DILRIK---GVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYI 1270
DI+ I G+EA + +I+E + + +G+ ++ +HI +V AD
Sbjct: 388 DIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLV-------------ADMMTF 434
Query: 1271 LGDNVDRIEVEELNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEA 1330
G V+ + R GI S + S ++ A+F+ T K L A
Sbjct: 435 DG------SVKAIGR----------------HGI---SGEKSSVLARAAFEITGKHLLRA 469
Query: 1331 AIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359
I G+VD L G EN+IVG+ I GTGA+
Sbjct: 470 GILGEVDKLAGVAENIIVGQPITLGTGAV 498
>gnl|CDD|184892 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 52.6 bits (126), Expect = 8e-07
Identities = 50/189 (26%), Positives = 87/189 (46%), Gaps = 46/189 (24%)
Query: 1185 IPKNKHFYLQDGDHVEKGDYIL--DGNPVPQDILRIKGVEALASYL--INEVQEVYRLEG 1240
IP + ++ +H +Y+L G+ + +++ +I+GV+ + I E+QEV +E
Sbjct: 688 IPGIERVLVKKEEHENDEEYVLYTQGSNL-REVFKIEGVDTSRTTTNNIIEIQEVLGIEA 746
Query: 1241 V----------AINHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNRSLAQQ 1290
+ + +EV +RH++ +I AD E V+ + R
Sbjct: 747 ARNAIINEMMNTLEQQGLEVDIRHLMLVADIMT-ADGE-----------VKPIGR----- 789
Query: 1291 GKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGR 1350
G+ + + S ++ A+F+ET K L +AA G+VD L G ENVIVG+
Sbjct: 790 -----------HGV---AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGK 835
Query: 1351 SIPAGTGAI 1359
I GTG +
Sbjct: 836 PIKLGTGCV 844
Score = 41.0 bits (96), Expect = 0.002
Identities = 17/28 (60%), Positives = 23/28 (82%)
Query: 902 RGSLVNVGEAVGVIAAQSIGEPGTQLTM 929
+LV EAVG++AAQSIGEPGTQ+++
Sbjct: 50 LNALVEPYEAVGIVAAQSIGEPGTQMSL 77
>gnl|CDD|162918 TIGR02551, SpaO_YscQ, type III secretion system apparatus protein
YscQ/HrcQ. Genes in this family are found in type III
secretion operons. The gene (YscQ) in Yersinia is
essential for YOPs secretion, while SpaO in Shigella is
involved in the Surface Presentation of Antigens
apparatus found on the virulence plasmid, and HrcQ is
involved in the Harpin secretory system in organisms
like Pseudomonas syringae.
Length = 298
Score = 32.8 bits (75), Expect = 0.68
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 882 ALTCESSRGVCVLCYGRDLARGSLVNVGEAVGV 914
L V + GR L RG LV+VG +GV
Sbjct: 261 ELNVPVDGPVRLRANGRLLGRGELVDVGGRLGV 293
>gnl|CDD|185275 PRK15377, PRK15377, E3 ubiquitin-protein ligase SopA; Provisional.
Length = 782
Score = 31.6 bits (71), Expect = 1.7
Identities = 21/145 (14%), Positives = 40/145 (27%), Gaps = 27/145 (18%)
Query: 1253 RHMLQKVEITDPADTEYILGDNVDRIEV-EELNRSLAQQGKKLVSFSPILQGITKASLQT 1311
+ + PAD L D R E EEL + + + + I + +
Sbjct: 159 LSLQATSSPSSPADWAKKLTDARLRQEAGEELTYA----DRDFSNAD--FRNINFSKINP 212
Query: 1312 KSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAILHEKRRVAMNRD 1371
F+ ++ + T E R
Sbjct: 213 SGFM-----LRDGDIIKGFNFSNSKFTYSDISH-------------LHFDECRFTYSTLS 254
Query: 1372 QMILKERSNFSQNEDLKNTAIQGSI 1396
++ + FS N D+ +++ SI
Sbjct: 255 DVVC-SNTKFS-NSDMNEASLKYSI 277
>gnl|CDD|161785 TIGR00239, 2oxo_dh_E1, 2-oxoglutarate dehydrogenase, E1 component.
The E1 ortholog from Corynebacterium glutamicum is
unusual in having an N-terminal extension that resembles
the dihydrolipoamide succinyltransferase (E2) component
of 2-oxoglutarate dehydrogenase.
Length = 929
Score = 31.0 bits (70), Expect = 2.4
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 1266 DTEYILGDNVDRIEVEE--LNRSLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQET 1323
D +Y +G + ++ +LA L SP++ G T+A L + E+
Sbjct: 287 DVKYHMGRFSSDFTTDGKLVHLALAFNPSHLEIVSPVVIGSTRARLDRLN-----DSPES 341
Query: 1324 TKVLT-----EAAIAGK 1335
TKVL +AA AG+
Sbjct: 342 TKVLAILIHGDAAFAGQ 358
>gnl|CDD|151414 pfam10967, DUF2769, Protein of unknown function (DUF2769). This
family of proteins have no known function.
Length = 54
Score = 30.8 bits (70), Expect = 3.0
Identities = 15/41 (36%), Positives = 16/41 (39%), Gaps = 10/41 (24%)
Query: 51 KPERDGLFCARIFGPIKDYECICGKYKRMKYKGIICEKCGV 91
K E LFCAR G +K KG IC C V
Sbjct: 11 KCEEKKLFCAR--G--------NSFACIIKEKGCICPACPV 41
>gnl|CDD|180603 PRK06522, PRK06522, 2-dehydropantoate 2-reductase; Reviewed.
Length = 304
Score = 29.8 bits (68), Expect = 5.3
Identities = 19/80 (23%), Positives = 28/80 (35%), Gaps = 29/80 (36%)
Query: 1214 DILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRH--------------MLQ-- 1257
++L AL L+ EV V EGV ++ +E V + MLQ
Sbjct: 202 ELLADPDYRALIRALMEEVAAVAEAEGVHLS---VEEVREYVRQVIQKTAANTSSMLQDL 258
Query: 1258 ----KVEITDPADTEYILGD 1273
EI + I+G
Sbjct: 259 EAGRPTEI------DAIVGY 272
>gnl|CDD|178832 PRK00059, prsA, peptidylprolyl isomerase; Provisional.
Length = 336
Score = 29.7 bits (67), Expect = 5.4
Identities = 15/62 (24%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 640 GKDDIIVPESKEKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDLWGKTTDKVTEEMMA 699
K+ ++P S+E++ E DK + E + Q+N+ E++ + + G T + E +
Sbjct: 103 AKELKLIP-SEEELNKEVDKKINEIKKQFNND----EEQFEEALKATGFTEETFKEYLKN 157
Query: 700 RI 701
+I
Sbjct: 158 QI 159
>gnl|CDD|180005 PRK05305, PRK05305, phosphatidylserine decarboxylase; Provisional.
Length = 206
Score = 29.8 bits (68), Expect = 5.9
Identities = 15/27 (55%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 1094 FLPVDALLSVSPGQKVSTGD-VLARLP 1119
+LP+ VS GQKV G+ VLARLP
Sbjct: 180 YLPLGTEPLVSVGQKVVAGETVLARLP 206
>gnl|CDD|184764 PRK14608, PRK14608, 4-diphosphocytidyl-2-C-methyl-D-erythritol
kinase; Provisional.
Length = 290
Score = 29.4 bits (67), Expect = 6.5
Identities = 10/24 (41%), Positives = 13/24 (54%)
Query: 1095 LPVDALLSVSPGQKVSTGDVLARL 1118
LP + V+PG V+T DV L
Sbjct: 167 LPSLPAVLVNPGVPVATPDVFRAL 190
>gnl|CDD|149559 pfam08546, ApbA_C, Ketopantoate reductase PanE/ApbA C terminal. This
is a family of 2-dehydropantoate 2-reductases also known
as ketopantoate reductases, EC:1.1.1.169. The reaction
catalysed by this enzyme is: (R)-pantoate + NADP(+) <=>
2-dehydropantoate + NADPH. AbpA catalyses the NADPH
reduction of ketopantoic acid to pantoic acid in the
alternative pyrimidine biosynthetic (APB) pathway. ApbA
and PanE are allelic. ApbA, the ketopantoate reductase
enzyme is required for the synthesis of thiamine via the
APB biosynthetic pathway.
Length = 125
Score = 29.5 bits (67), Expect = 7.1
Identities = 20/84 (23%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 1214 DILRIKGVEALASYLINEVQEVYRLEGVAINHKHIEVVVRHMLQKVEITDPADTEYILGD 1273
++L L L++E V R EGVA+ E + + +V PA+ +L D
Sbjct: 29 ELLDSPEARELIRALMDEAVAVARAEGVALP----EDDLVEAVLRVARKTPANKSSMLQD 84
Query: 1274 NVDR---IEVEELNRSLAQQGKKL 1294
++ E++ +N + + +KL
Sbjct: 85 -IEAGRPTEIDAINGYVVRLARKL 107
>gnl|CDD|148987 pfam07683, CobW_C, Cobalamin synthesis protein cobW C-terminal
domain. This family of proteins contains P47K, a
Pseudomonas chlororaphis protein needed for nitrile
hydratase expression, and the cobW gene product, which
may be involved in cobalamin biosynthesis in Pseudomonas
denitrificans. This family represents the C-terminal
domain.
Length = 94
Score = 29.5 bits (67), Expect = 7.1
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 4/38 (10%)
Query: 1206 LDGNPVPQDILRIKGVEALAS----YLINEVQEVYRLE 1239
L+ +P+ ILR KG+ LA + V LE
Sbjct: 21 LEDLLLPEGILRAKGILWLAGRPDPLVFQGVGGRLSLE 58
>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 1740
Score = 29.0 bits (64), Expect = 8.2
Identities = 31/111 (27%), Positives = 48/111 (43%), Gaps = 13/111 (11%)
Query: 651 EKIIAEADKMVKEYENQYNDGLITRGEKYNKVVDL---WGKTTDKVTEEMMARIKRVEFD 707
EK + E K + + N+ DG I E +V+L + ++ R K+ E
Sbjct: 37 EKKLDEVVKRIVQRINELYDGKIPHIENIQDIVELELMRAGLFEVAKAYILYRKKKAEIR 96
Query: 708 PETGR---QKKMNSIFMMSHSGARGSIHQMRQLGGMRGLIAKPSGEIIESP 755
E R +K+++ I R SI+ +R L R L +G IIESP
Sbjct: 97 EEKKRILNKKELDEI------DKRFSINALRVLAS-RYLKKDENGNIIESP 140
>gnl|CDD|162685 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily of
the penicillin binding proteins includes the member from
E. coli designated penicillin-binding protein 1C. Members
have both transglycosylase and transpeptidase domains and
are involved in forming cross-links in the late stages of
peptidoglycan biosynthesis. All members of this subfamily
are presumed to have the same basic function.
Length = 727
Score = 28.9 bits (65), Expect = 8.6
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 1064 SRSQNLKPAIVVTDENGVVLKSARGTDARWFLPVDALLSVSP 1105
+ + VV D +G +L++ D +W LPV L +SP
Sbjct: 3 PLLFHRPSSTVVLDRHGTLLRALLANDGQWRLPVP-LEDISP 43
>gnl|CDD|184948 PRK14986, PRK14986, glycogen phosphorylase; Provisional.
Length = 815
Score = 29.0 bits (65), Expect = 8.6
Identities = 13/28 (46%), Positives = 20/28 (71%), Gaps = 1/28 (3%)
Query: 564 ISKIYDTTPGRMIIGEILPRHHEISFDI 591
+S+ +T P M+ G+ILPRH +I F+I
Sbjct: 362 MSEALETWPVDML-GKILPRHLQIIFEI 388
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
0.320 0.137 0.395
Gapped
Lambda K H
0.267 0.0680 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 23,024,893
Number of extensions: 1572129
Number of successful extensions: 3199
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3124
Number of HSP's successfully gapped: 65
Length of query: 1398
Length of database: 5,994,473
Length adjustment: 105
Effective length of query: 1293
Effective length of database: 3,725,633
Effective search space: 4817243469
Effective search space used: 4817243469
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 (21.8 bits)
S2: 63 (28.1 bits)