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)