|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
55-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 863.50 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 55 TIKATLPYIKSEIPIVIVFRALGVVSDEDILNHICYDrkdTQMLEMLKPCIEEAF-VIQDREVALDFIGKRGnSQGITRD 133
Cdd:PRK08565 200 TIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLD---PEIQQELLPSLEQASsIAATVEDALDYIGKRV-AIGQPRE 275
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 134 KRIKYARDIMQKELLPHISQVEGSETRKAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTK 213
Cdd:PRK08565 276 YRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVK 355
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 214 DVYKYLQKCVESNREFNLTLGVKSTTLTNGLRYSLATGNWGeqkkaaSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDG 293
Cdd:PRK08565 356 DLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQ 429
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 294 KIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVFVNGVW 373
Cdd:PRK08565 430 PHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRL 509
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 374 VGVHRDPAHLVSTVMSLRRRGLISHEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdakspnkGSLVLTKELVSRLE 450
Cdd:PRK08565 510 IGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLK 581
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 451 DDKdlpadmdpdekaakiMGWDGLIKRGVVEYLDAEEEETVMIVMTPEDLdisrqlqagyqLPETtddpnkrvkaplnpt 530
Cdd:PRK08565 582 KGE---------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPEH--------------- 620
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 531 ahtwTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSMEFLKF 610
Cdd:PRK08565 621 ----THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGY 696
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 611 RELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSVVEQFEKPmrSDTLKLKHG--TYDK 688
Cdd:PRK08565 697 NDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRK 774
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 689 LDDDGLVAPGVRISGEDIIIGKTEP--IAPDSEELGQRTKlhVKRDKSTPLRTTENGLVDKVMLSTNAEGLRFVKVRTRT 766
Cdd:PRK08565 775 LDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRD 852
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 767 TKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEV 846
Cdd:PRK08565 853 LRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGE 932
|
810 820 830 840
....*....|....*....|....*....|....*....|....*..
gi 45545327 847 TVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:PRK08565 933 PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
97-893 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 764.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 97 MLEMLKPCIEEAFVIQDREVAL-DFIGKRGNSQGITRDKRIKYARDIM--------QKELLPHISQvegsetrKAFFLGY 167
Cdd:cd00653 143 NQEQRSPNVIIVEDSKGKRIYTkTSIPSYSPYRGSWLEVKSDKKKDRIyvridlkrQEEALKYIGK-------RFEDLIY 215
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 168 MVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLRYS 247
Cdd:cd00653 216 MIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEF 295
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 248 LATGNWGeQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 326
Cdd:cd00653 296 LATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNL 374
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 327 ALMCCVTvgspsepiidfmvqrnmeileeyeplrspnatkvfvngvwvgvhrdpahlvstvmslrrrglishevslvrdi 406
Cdd:cd00653 375 ALMARIS------------------------------------------------------------------------- 381
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 407 rdrefkiftdaGRVCRPLFVIDNDakspnkgslvltkelvsrleddkdlpadmdpdekaakimgwdglikrgvveyldae 486
Cdd:cd00653 382 -----------GRIERPYRIVEKE-------------------------------------------------------- 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 487 eeetvmivmtpedldisrqlqagyqlpettddpnkrvkaplnptahtWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQ 566
Cdd:cd00653 395 -----------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQ 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 567 SAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGL 646
Cdd:cd00653 428 SNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGF 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 647 FRSLYYRTYTDQEKRVGmsvvEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRISGEDIIIGKTEPIAPDSEELGQRTK 726
Cdd:cd00653 508 FRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEK 583
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 727 LHVKRDKSTPLRTTENGLVDKVMLST---NAEGLRFVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIV 803
Cdd:cd00653 584 ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIP 663
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 804 PDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFL 883
Cdd:cd00653 664 PDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFV 743
|
810
....*....|
gi 45545327 884 GPTYYQRLRH 893
Cdd:cd00653 744 GPVYYQRLKH 753
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
367-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 564.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 367 VFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdakspnkGSLVLTKELV 446
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 447 SRLeddkdlpadmdpdeKAAKIMgWDGLIKRGVVEYLDAEEEETVMIVMTPEDLdisrqlqagyqlpetTDDpnkrvkap 526
Cdd:TIGR03670 74 EKL--------------KEGELT-WDDLVKQGVIEYLDAEEEENAYIALDPEEL---------------TPE-------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 527 lnptaHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSME 606
Cdd:TIGR03670 116 -----HT--HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLE 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 607 FLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSVVEQFEKPmrSDTLKLKHG-- 684
Cdd:TIGR03670 189 LIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGee 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 685 TYDKLDDDGLVAPGVRISGEDIIIGKTEPiaP----DSEELGQRTKlhVKRDKSTPLRTTENGLVDKVMLSTNAEGLRFV 760
Cdd:TIGR03670 267 AYKHLDEDGIVYPEVEVKGGDVLIGKTSP--PrfleELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKLV 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 761 KVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDA 840
Cdd:TIGR03670 343 KVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDG 422
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|...
gi 45545327 841 TPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:TIGR03670 423 TPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
548-893 |
4.50e-156 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 462.00 E-value: 4.50e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 548 CASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 627
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 628 GYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSvVEQFEKPMRSDTLKLKHgtydkLDDDGLVAPGVRISGEDII 707
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI-EEITRDIPNVSEEALKK-----LDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 708 IGKTEPIAPDSE---ELGQrtKLHVKRDKSTPLRTTENGLVDKVML-STNAEGLRFVKVRTRTTKIPQIGDKFASRHGQK 783
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGE--KARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 784 GTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVT--VDSVSRLLREHGYQ 861
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYN 312
|
330 340 350
....*....|....*....|....*....|..
gi 45545327 862 SRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
64-893 |
9.08e-146 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 456.88 E-value: 9.08e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 64 KSEIPIVIVFRALGVVSDEDILNHIcydrKDTQMLEMLKPCIEEAfVIQDREVALDFIGKRgnsQGITRDKRIKYARDIM 143
Cdd:COG0085 174 KRKIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRK---LRPGEPPTIERAEQLL 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 144 QKEL-------LPHI---------SQVEGSETR--KAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFR 205
Cdd:COG0085 246 DNLFfdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFR 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 206 TLFNKLTKDVyKYlQKCVESNREFNLTLGVKSTTLTNGLRYSLATGnwgeqkkaasskaGVSQVLNRYTFASTLSHLRRT 285
Cdd:COG0085 326 VGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRL 390
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 286 NT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVTvgspsepiidfmvqrnmeileEYe 357
Cdd:COG0085 391 SAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------------EY- 444
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 358 plrspnatkvfvngvwvgvhrdpahlvstvmslrrrglishevslvrdirdrefkiftdaGRVCRPLFVIDNdakspnkG 437
Cdd:COG0085 445 ------------------------------------------------------------GFIETPYRKVEN-------G 457
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 438 slVLTKElvsrleddkdlpadmdpdekaakimgwdglikrgvVEYLDAEEEETVMIVMTPEDLD-----ISRQLQAGYQL 512
Cdd:COG0085 458 --KVTDE-----------------------------------IEYLTADEEENYYIAQANAPLDedgnfLEERVLVRYRG 500
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 513 PETTDDPNKrvkaplnptaHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFsermdnafNIL 592
Cdd:COG0085 501 EEVLVPPEE----------VD--YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEA--------PLL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 593 YYP--------------QKPLAttRSMEFLK------------FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGL 646
Cdd:COG0085 561 HYPlqkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 647 FRSLYYRTYTDQEKR--VGMSVVeQFEKPMRSDTLklkhgtYDKLDDDGLVAPGVRISGEDIIIGKTEP---IAPDSEEL 721
Cdd:COG0085 639 LTSIHIEEYEIEARDtkLGPEEI-TRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEER 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 722 GQR----TKLHVKRDKSTPLRTTENGLVDKVMLSTNAEG-------LRFVKVRTRTTKIPQIGDKFASRHGQKGTIGITY 790
Cdd:COG0085 712 LLRaifgEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRIL 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 791 RQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTVDSVSRLLREHGYQSRGFEVMYN 870
Cdd:COG0085 792 PQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYD 871
|
890 900
....*....|....*....|...
gi 45545327 871 GHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:COG0085 872 GRTGEPFDNPVTVGYMYYLKLHH 894
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
55-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 863.50 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 55 TIKATLPYIKSEIPIVIVFRALGVVSDEDILNHICYDrkdTQMLEMLKPCIEEAF-VIQDREVALDFIGKRGnSQGITRD 133
Cdd:PRK08565 200 TIYVSFPAVPGKIPFVILMRALGLETDRDIVYAVSLD---PEIQQELLPSLEQASsIAATVEDALDYIGKRV-AIGQPRE 275
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 134 KRIKYARDIMQKELLPHISQVEGSETRKAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTK 213
Cdd:PRK08565 276 YRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVK 355
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 214 DVYKYLQKCVESNREFNLTLGVKSTTLTNGLRYSLATGNWGeqkkaaSSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDG 293
Cdd:PRK08565 356 DLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQLLDRTNYLSTLSHLRRVVSPLSRGQ 429
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 294 KIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMVQRNMEILEEYEPLRSPNATKVFVNGVW 373
Cdd:PRK08565 430 PHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELGVVPVEEAREEEYISWSRVYLNGRL 509
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 374 VGVHRDPAHLVSTVMSLRRRGLISHEVSlVRDIRDREFK---IFTDAGRVCRPLFVIDNdakspnkGSLVLTKELVSRLE 450
Cdd:PRK08565 510 IGYHPDGEELAEKIRELRRSGKISDEVN-VAYIETGEINevyVNCDSGRVRRPLIVVEN-------GKPKLTREHVEKLK 581
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 451 DDKdlpadmdpdekaakiMGWDGLIKRGVVEYLDAEEEETVMIVMTPEDLdisrqlqagyqLPETtddpnkrvkaplnpt 530
Cdd:PRK08565 582 KGE---------------LTFDDLVKMGVIEYLDAEEEENAYVALDPEDL-----------TPEH--------------- 620
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 531 ahtwTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSMEFLKF 610
Cdd:PRK08565 621 ----THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQRPLVQTRALEIIGY 696
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 611 RELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSVVEQFEKPmrSDTLKLKHG--TYDK 688
Cdd:PRK08565 697 NDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--EPNVRGYRGeeYYRK 774
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 689 LDDDGLVAPGVRISGEDIIIGKTEP--IAPDSEELGQRTKlhVKRDKSTPLRTTENGLVDKVMLSTNAEGLRFVKVRTRT 766
Cdd:PRK08565 775 LDEDGIVSPEVEVKGGDVLIGKTSPprFLEELEELSLGLQ--ERRDTSVTVRHGEKGIVDTVLITESPEGNKLVKVRVRD 852
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 767 TKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEV 846
Cdd:PRK08565 853 LRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGE 932
|
810 820 830 840
....*....|....*....|....*....|....*....|....*..
gi 45545327 847 TVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:PRK08565 933 PEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHH 979
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
97-893 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 764.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 97 MLEMLKPCIEEAFVIQDREVAL-DFIGKRGNSQGITRDKRIKYARDIM--------QKELLPHISQvegsetrKAFFLGY 167
Cdd:cd00653 143 NQEQRSPNVIIVEDSKGKRIYTkTSIPSYSPYRGSWLEVKSDKKKDRIyvridlkrQEEALKYIGK-------RFEDLIY 215
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 168 MVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTKDVYKYLQKCVESNREFNLTLGVKSTTLTNGLRYS 247
Cdd:cd00653 216 MIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEF 295
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 248 LATGNWGeQKKAASSKAGVSQVLNRYTFASTLSHLRRTNT-PIGRDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 326
Cdd:cd00653 296 LATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNL 374
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 327 ALMCCVTvgspsepiidfmvqrnmeileeyeplrspnatkvfvngvwvgvhrdpahlvstvmslrrrglishevslvrdi 406
Cdd:cd00653 375 ALMARIS------------------------------------------------------------------------- 381
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 407 rdrefkiftdaGRVCRPLFVIDNDakspnkgslvltkelvsrleddkdlpadmdpdekaakimgwdglikrgvveyldae 486
Cdd:cd00653 382 -----------GRIERPYRIVEKE-------------------------------------------------------- 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 487 eeetvmivmtpedldisrqlqagyqlpettddpnkrvkaplnptahtWTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQ 566
Cdd:cd00653 395 -----------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQ 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 567 SAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGL 646
Cdd:cd00653 428 SNMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGF 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 647 FRSLYYRTYTDQEKRVGmsvvEQFEKPMRSDTLKLKHGTYDKLDDDGLVAPGVRISGEDIIIGKTEPIAPDSEELGQRTK 726
Cdd:cd00653 508 FRSIHYKKYEIELRKTK----NGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEK 583
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 727 LHVKRDKSTPLRTTENGLVDKVMLST---NAEGLRFVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIV 803
Cdd:cd00653 584 ARDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIP 663
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 804 PDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFL 883
Cdd:cd00653 664 PDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFV 743
|
810
....*....|
gi 45545327 884 GPTYYQRLRH 893
Cdd:cd00653 744 GPVYYQRLKH 753
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
367-893 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 564.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 367 VFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdakspnkGSLVLTKELV 446
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVEN-------GKPKLTREHV 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 447 SRLeddkdlpadmdpdeKAAKIMgWDGLIKRGVVEYLDAEEEETVMIVMTPEDLdisrqlqagyqlpetTDDpnkrvkap 526
Cdd:TIGR03670 74 EKL--------------KEGELT-WDDLVKQGVIEYLDAEEEENAYIALDPEEL---------------TPE-------- 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 527 lnptaHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSME 606
Cdd:TIGR03670 116 -----HT--HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLE 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 607 FLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSVVEQFEKPmrSDTLKLKHG-- 684
Cdd:TIGR03670 189 LIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGee 266
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 685 TYDKLDDDGLVAPGVRISGEDIIIGKTEPiaP----DSEELGQRTKlhVKRDKSTPLRTTENGLVDKVMLSTNAEGLRFV 760
Cdd:TIGR03670 267 AYKHLDEDGIVYPEVEVKGGDVLIGKTSP--PrfleELREFGLVTE--RRRDTSVTVRHGEKGIVDKVIITETEEGNKLV 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 761 KVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDA 840
Cdd:TIGR03670 343 KVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDG 422
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|...
gi 45545327 841 TPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:TIGR03670 423 TPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHH 475
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
365-893 |
3.29e-179 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 530.69 E-value: 3.29e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 365 TKVFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVIDNdakspnkGSLVLTKE 444
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVEN-------GEPLLTEE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 445 LVSRLEDDKdlpadmdpdekaakiMGWDGLIKRGVVEYLDAEEEETVMIVMTPEDLdisrqlqagyqlpetTDDpnkrvk 524
Cdd:PRK07225 78 HIEKLKNGE---------------LTFDDLVKQGVIEYLDAEEEENAYIAVYEEDL---------------TEE------ 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 525 aplnptaHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRS 604
Cdd:PRK07225 122 -------HT--HLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQT 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 605 MEFLKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSVVEQFEKPmrSDTLKLKHG 684
Cdd:PRK07225 193 QEIIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIP--DKDVRGYRG 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 685 --TYDKLDDDGLVAPGVRISGEDIIIGKTEPiaP----DSEELGQRTKlhVKRDKSTPLRTTENGLVDKVMLSTNAEGLR 758
Cdd:PRK07225 271 eeAYRHLDEDGLVNPETEVKEGDVLIGKTSP--PrfleEPDDFGISPE--KRRETSVTMRSGEEGIVDTVILTETEEGSR 346
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 759 FVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEG 838
Cdd:PRK07225 347 LVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRV 426
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*
gi 45545327 839 DATPFTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:PRK07225 427 DGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHH 481
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
548-893 |
4.50e-156 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 462.00 E-value: 4.50e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 548 CASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFSERMDNAFNILYYPQKPLATTRSMEFLKFRELPAGQNAIVAIACYS 627
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYT 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 628 GYNQEDSVIMNQSSIDRGLFRSLYYRTYTDQEKRVGMSvVEQFEKPMRSDTLKLKHgtydkLDDDGLVAPGVRISGEDII 707
Cdd:pfam00562 81 GYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGPI-EEITRDIPNVSEEALKK-----LDEDGIVRVGAEVKPGDIL 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 708 IGKTEPIAPDSE---ELGQrtKLHVKRDKSTPLRTTENGLVDKVML-STNAEGLRFVKVRTRTTKIPQIGDKFASRHGQK 783
Cdd:pfam00562 155 VGKVGPTELTKLlraIFGE--KARDVKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQK 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 784 GTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVT--VDSVSRLLREHGYQ 861
Cdd:pfam00562 233 GVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGASteVEDIGELLEKAGYN 312
|
330 340 350
....*....|....*....|....*....|..
gi 45545327 862 SRGFEVMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:pfam00562 313 YYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKH 344
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
64-893 |
9.08e-146 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 456.88 E-value: 9.08e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 64 KSEIPIVIVFRALGVVSDEDILNHIcydrKDTQMLEMLKPCIEEAfVIQDREVALDFIGKRgnsQGITRDKRIKYARDIM 143
Cdd:COG0085 174 KRKIPVTVLLRALGLETDEEILEAF----GDDPIQEYILATLEKD-NTKTQEEALLEIYRK---LRPGEPPTIERAEQLL 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 144 QKEL-------LPHI---------SQVEGSETR--KAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFR 205
Cdd:COG0085 246 DNLFfdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFR 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 206 TLFNKLTKDVyKYlQKCVESNREFNLTLGVKSTTLTNGLRYSLATGnwgeqkkaasskaGVSQVLNRYTFASTLSHLRRT 285
Cdd:COG0085 326 VGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS-------------QLSQFMDQTNPLSELTHKRRL 390
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 286 NT----PIGRDgkiaKP----RQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVTvgspsepiidfmvqrnmeileEYe 357
Cdd:COG0085 391 SAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVN---------------------EY- 444
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 358 plrspnatkvfvngvwvgvhrdpahlvstvmslrrrglishevslvrdirdrefkiftdaGRVCRPLFVIDNdakspnkG 437
Cdd:COG0085 445 ------------------------------------------------------------GFIETPYRKVEN-------G 457
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 438 slVLTKElvsrleddkdlpadmdpdekaakimgwdglikrgvVEYLDAEEEETVMIVMTPEDLD-----ISRQLQAGYQL 512
Cdd:COG0085 458 --KVTDE-----------------------------------IEYLTADEEENYYIAQANAPLDedgnfLEERVLVRYRG 500
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 513 PETTDDPNKrvkaplnptaHTwtHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIFLTNFsermdnafNIL 592
Cdd:COG0085 501 EEVLVPPEE----------VD--YMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEA--------PLL 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 593 YYP--------------QKPLAttRSMEFLK------------FRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGL 646
Cdd:COG0085 561 HYPlqkfqrsnqgtcinQRPIV--RVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDV 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 647 FRSLYYRTYTDQEKR--VGMSVVeQFEKPMRSDTLklkhgtYDKLDDDGLVAPGVRISGEDIIIGKTEP---IAPDSEEL 721
Cdd:COG0085 639 LTSIHIEEYEIEARDtkLGPEEI-TRDIPNVSEEA------LRNLDEDGIIRIGAEVKGGDILVGKVTPkgeTELTPEER 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 722 GQR----TKLHVKRDKSTPLRTTENGLVDKVMLSTNAEG-------LRFVKVRTRTTKIPQIGDKFASRHGQKGTIGITY 790
Cdd:COG0085 712 LLRaifgEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRIL 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 791 RQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGDATPFTEVTVDSVSRLLREHGYQSRGFEVMYN 870
Cdd:COG0085 792 PQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYD 871
|
890 900
....*....|....*....|...
gi 45545327 871 GHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:COG0085 872 GRTGEPFDNPVTVGYMYYLKLHH 894
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-242 |
1.59e-94 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 303.15 E-value: 1.59e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 1 RSAANIVQVFKKSD-AKTPYVAEIRSAVEKGSRLISSMQIKLHskgEGAKGGfgqTIKATLPYIKSEIPIVIVFRALGVV 79
Cdd:pfam04563 155 HRSRNHPIVFKKADpKKRGSVASVRSSAEISVRPDSTSWVNVL---EYLSNG---TIYFKFPYIKKEIPIVIILRALGFT 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 80 SDEDILNHICYDRKDTQMLEMLKPCIEEAFVI--QDREVALDFIGKRGNSQ---GITRDKRIKYARDIMQKELLPHISQV 154
Cdd:pfam04563 229 SDREIFELICYDVNDQQLQEELLPSLEEGFKIriQTQEQALDYIGGRGRAIfrmGRPREPRIKYAEEILQKEVLPHLGTY 308
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 155 EGSETRKAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTKDVYKYLQKCVESNREFNLTLG 234
Cdd:pfam04563 309 ELDETKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLL 388
|
....*...
gi 45545327 235 VKSTTLTN 242
Cdd:pfam04563 389 VNAKPITS 396
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
58-357 |
9.77e-82 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 272.21 E-value: 9.77e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 58 ATLPYIKSEIPIVIVFRALGVVSDEDILNHICYDRK-DTQMLEMLkpciEEAfVIQDREVALDFIGKRGNSqGITRDKRI 136
Cdd:PRK09606 208 VSFPSVPGSIPFVILMRALGLETDEEIVEAVSDDPEiVKFMLENL----EEA-EVDTQEEALEYIGKRVAP-GQTKEYRI 281
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 137 KYARDIMQKELLPHISQVEGSETRKAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTKDVy 216
Cdd:PRK09606 282 KRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDV- 360
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 217 KY-LQKCVESNREFNLTLGVKSTTLTNGLRYSLATGNWgeqkkaASSKAGVSQVLNRYTFASTLSHLRRTNTPIGRDGKI 295
Cdd:PRK09606 361 KYqLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLLDRTDYMATLSHLRRVVSPLSRSQPH 434
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545327 296 AKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVTVGSPSEPIIDFMvqRNMEILEEYE 357
Cdd:PRK09606 435 FEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEIL--KELGVEPERG 494
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
3-194 |
1.72e-48 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 170.22 E-value: 1.72e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 3 AANIVQVFKKSDaktpyvaeiRSAVEKGSRLISSMQIKLHSKGEGakggFGQTIKATLPYIKSEIPIVIVFRALGVVSDE 82
Cdd:pfam04561 1 RSNGIYVEKELD---------KNGIIATYTSSLISNRGSWLKLEI----DGKTLIWSRPSKKRKIPIVIFLKALGLVSDR 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 83 DILNHICYDRKDTQMLEMLKPCIEEAFVIQDREVALDFIGKrGNSQGITRDKRIKYARDIMQK-----ELLPHISQVEGS 157
Cdd:pfam04561 68 EILDRLCYDFNDPQMLELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPF 146
|
170 180 190
....*....|....*....|....*....|....*....
gi 45545327 158 ETR--KAFFLGYMVHRMLQVTLGRRDPDDRDHFGKKRLD 194
Cdd:pfam04561 147 ENErlKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
64-893 |
1.05e-36 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 149.81 E-value: 1.05e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 64 KSEIPIVIVFRALGVVSDEDILNHIcyDRKDTQMLEMLK-PCI--EEAFVI----------QDREVALDFIGKRGNSQ-- 128
Cdd:TIGR02013 193 KRKLPATVLLRALGYTIDTLILNRL--GSGEYIRNTLRKdPTNseEEALVEiyrklrpgepPTVEAARSLLENLFFDPkr 270
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 129 -GITRDKRIKyardiMQKELLPHISQVEGSETrKAFFLGYMVHrMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTL 207
Cdd:TIGR02013 271 yDLGRVGRYK-----LNKKLGLDVPESIGVLT-KEDIIATIKY-LIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVG 343
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 208 FNKLTKDVYKYLqkcveSNREFNltlGVKSTTLTNGLRYSLATgnwgeQKKAASSKagVSQVLNRYTFASTLSHLRRTNT 287
Cdd:TIGR02013 344 LARMERIVRERM-----STQDTD---TLTPQDLINAKPISAAI-----KEFFGSSQ--LSQFMDQTNPLAELTHKRRLSA 408
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 288 --PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMCCVT----VGSPSEPIIDFMVQRNMEI-----LE 354
Cdd:TIGR02013 409 lgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNeygfIETPYRKVKDGKVVVTDEIdyltaDE 488
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 355 EYEPLRSPNATKVFVNGvwvgvhrdpaHLVSTVMSLRRRGlishEVSLVR----DIRDREFKIFTDAGRVCRPlFVIDND 430
Cdd:TIGR02013 489 EDNYVIAQANAPLDENG----------RFVEDLVVARYRG----EITLVSpdqvDYMDVSPKQVVSVAASLIP-FLEHDD 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 431 AKSPNKGSlVLTKELVSRLEDDKDLPAD-MDpdEKAAKIMGWDGLIKR-GVVEYLDAEEeetvMIVMTPEDLDISRQLQA 508
Cdd:TIGR02013 554 ANRALMGS-NMQRQAVPLLRSEAPLVGTgME--AKVARDSGAVIVAKRgGVVEYVDAKR----IVIRYDEDEEEPDGGID 626
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 509 GYQLPEttddpNKRVKAplnptahtwthceihpsmilGVCasiipfpdHNQSPrntyqsamgkqamgifLTNFSERMdNA 588
Cdd:TIGR02013 627 IYRLLK-----YQRSNQ--------------------DTC--------INQRP----------------IVSVGDRV-EA 656
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 589 FNILyypqkplATTRSMEFlkfRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYyrtytdqekrvgmsvVE 668
Cdd:TIGR02013 657 GDVL-------ADGPSTDL---GELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIH---------------IE 711
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 669 QFEKPMRsDTlklKHG----TYD----------KLDDDGLVAPGVRISGEDIIIGKTEP---IAPDSEE------LGQRT 725
Cdd:TIGR02013 712 EYEVEAR-DT---KLGpeeiTRDipnvseealrNLDENGIVRIGAEVKAGDILVGKVTPkgeTELTPEEkllraiFGEKA 787
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 726 KlHVkRDKSTPLRTTENGLVDKVMLSTNAEG-------LRFVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFT 798
Cdd:TIGR02013 788 R-DV-RDTSLRVPPGVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFL 865
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 799 SEGIVPDLIINPHAIPSRMTIAHLIECQLSKVSSLRGYEGD--ATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGR 875
Cdd:TIGR02013 866 EDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGE 945
|
890
....*....|....*...
gi 45545327 876 KLVAQVFLGPTYYQRLRH 893
Cdd:TIGR02013 946 QFDRPVTVGYMYMLKLHH 963
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
367-428 |
1.83e-31 |
|
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain.
Pssm-ID: 428012 [Multi-domain] Cd Length: 62 Bit Score: 117.08 E-value: 1.83e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 45545327 367 VFVNGVWVGVHRDPAHLVSTVMSLRRRGLISHEVSLVRDIRDREFKIFTDAGRVCRPLFVID 428
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
268-330 |
1.60e-30 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 114.55 E-value: 1.60e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 45545327 268 QVLNRYTFASTLSHLRRTNTPIG---RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLALMC 330
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
172-893 |
7.39e-29 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 124.43 E-value: 7.39e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 172 MLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTKDVYKYLQKCVESNRE-FNLtlgVKSTTLTNGLRYSLAt 250
Cdd:CHL00207 287 LINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSkFNL---INPKPLIALIREFFG- 362
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 251 gnwgeqkkaaSSKagVSQVLNRYTFASTLSHLRRTNT--PIGRDG-KIAKP-RQLHNTHWGLVCPAETPEGQACGLVKNL 326
Cdd:CHL00207 363 ----------SSQ--LSQYMDQTNPLSELTHKRRISIlgPGGLDKdRISFAvRDIHPSHYGRICPIETPEGPNCGLIGSL 430
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 327 AlmccvtvgspsepiidfmvqrnmeileeyeplrspnaTKVFVNgvwvgvhrdpahlvstvmslrRRGLISHEVSLVRDI 406
Cdd:CHL00207 431 A-------------------------------------TNARIN---------------------KFGFIETPFYKVING 452
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 407 RDREFKIFTdagrvcrplfvidndakspnkgslvltkelvsrleddkdlpadmdpdekaakimgwdglikrgvveYLDAE 486
Cdd:CHL00207 453 KVKKFGNPI------------------------------------------------------------------YLTAD 466
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 487 EEETVMIvmTPEDLDISR-------QLQAGYQLPETTDDPNKRVKAPLNPTAhtwthceihpsmILGVCASIIPFPDHNQ 559
Cdd:CHL00207 467 SEDLYRI--APNDINLNKnnyfkknIIPVRYKQEFKTVNPSKVDFIAISPIQ------------VFSIAESLIPFLEHND 532
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 560 SPRNTYQSAMGKQAM-------------------------------GI--FLTNFSERMDNAFN--ILYYPQK------- 597
Cdd:CHL00207 533 ANRALMGSNMQRQAVpllypekpivgtgyekqialdsgmtiislteGIvvSVSAYKIIIQDDNNryIHYYLQKyqrsnqn 612
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 598 ------P-------------LATTRSMeflKFRELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYtDQ 658
Cdd:CHL00207 613 tcinyrPivwvgekinigqiLADGSDI---DNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKY-EI 688
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 659 EKRVGMSVVEQFEKpmrsDTLKLKHGTYDKLDDDGLVAPGVRISGEDIIIGKTEPiAPDSEELGQ---------RTKLHV 729
Cdd:CHL00207 689 ELRQTKLGSEEITR----NIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITP-KGESDQLPEgkllraifgEKAKDV 763
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 730 KrDKSTPLRTTENGLVDKVMLSTNAEGLR-----FVKVRTRTTKIP--QIGDKFASRHGQKGTIG-ITYRQeDMPFTSEG 801
Cdd:CHL00207 764 K-DTSLRMPNGGYGRVIKVEIFSRSKGDElkfgyYLKIRVFIAQIRkiQVGDKLAGRHGNKGIISrILPRQ-DMPYLPDG 841
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 802 IVPDLIINPHAIPSRMTIAHLIECQLskvsslrGYEGD-------ATPFTEVTVDSVSRLLREHGYQSRGFE-------- 866
Cdd:CHL00207 842 TPPDIILNPLGVPSRMNVGQLFECLL-------GLAGDnlnkrfkILPFDEMYGSEYSRILINNKLNQASIKnneywlfn 914
|
810 820 830
....*....|....*....|....*....|....
gi 45545327 867 -------VMYNGHTGRKLVAQVFLGPTYYQRLRH 893
Cdd:CHL00207 915 syhpgkmVLRDGRTGYKFKNPVTVGIAYMLKLIH 948
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
471-541 |
8.51e-25 |
|
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pssm-ID: 428013 [Multi-domain] Cd Length: 53 Bit Score: 97.61 E-value: 8.51e-25
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 45545327 471 WDGLIKRGVVEYLDAEEEETVMIVMTPEDLDISRQLQAGYqlpettddpnkrvkaplnPTAHTWTHCEIHP 541
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESSREEREG------------------PYAHTYTHCEIHP 53
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
612-893 |
1.37e-23 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 107.49 E-value: 1.37e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 612 ELPAGQNAIVAIACYSGYNQEDSVIMNQssidrglfRSLYYRTYTdqekrvgmSV-VEQFEKPMRsDTlklKHG----TY 686
Cdd:PRK00405 712 ELALGQNVLVAFMPWNGYNFEDAILISE--------RLVKEDVFT--------SIhIEEYEIEAR-DT---KLGpeeiTR 771
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 687 D----------KLDDDGLVAPGVRISGEDIIIGKTEP---IAPDSEE------LGQRTKlHVKrDKStpLR--TTENGLV 745
Cdd:PRK00405 772 DipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeTELTPEEkllraiFGEKAR-DVK-DTS--LRvpHGEEGTV 847
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 746 -DKVMLSTNAEG-------LRFVKV-----RtrttKIpQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHA 812
Cdd:PRK00405 848 iDVKVFTRIEQGdelppgvNKLVKVyiaqkR----KI-QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLG 922
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 813 IPSRMTIAHLIECQLSKVSSLRGYEGdATP-FTEVTVDSVSRLLREHGYQSRGFEVMYNGHTGRKLVAQVFLGPTYYQRL 891
Cdd:PRK00405 923 VPSRMNIGQILETHLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKL 1001
|
..
gi 45545327 892 RH 893
Cdd:PRK00405 1002 HH 1003
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
612-878 |
2.37e-19 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 93.81 E-value: 2.37e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 612 ELPAGQNAIVAIACYSGYNQEDSVIMNQSSIDRGLFRSLYYRTYtDQEKRVGMSVVEQFEKPM-RSDTLKLKHgtydkLD 690
Cdd:CHL00001 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY-EIQTHVTSQGPERITKEIpHLEAHLLRN-----LD 721
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 691 DDGLVAPGVRISGEDIIIGKTEPIAPDSEELGQRTKL-------HVKRDKSTPLRTTENG---LVD------KVMLSTNA 754
Cdd:CHL00001 722 KNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLlraifgiQVSTSKETCLKLPIGGrgrVIDvrwiqkKGGSSYNP 801
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 755 EGLRFVKVRTRttKIpQIGDKFASRHGQKGTIG-ITYRQeDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLskvssl 833
Cdd:CHL00001 802 ETIHVYILQKR--EI-QVGDKVAGRHGNKGIISkILPRQ-DMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLL------ 871
|
250 260 270 280
....*....|....*....|....*....|....*....|....*
gi 45545327 834 rGYEGDatpftevtvdsvsrLLREHgYQSRGFEVMYNGHTGRKLV 878
Cdd:CHL00001 872 -GLAGD--------------LLNRH-YRIAPFDERYEQEASRKLV 900
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
169-830 |
1.01e-13 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 75.73 E-value: 1.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 169 VHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAglfrtlfNKLTKDVYKyLQKCVESnrefnltlgvKSTTLTNGLRySL 248
Cdd:PRK09603 441 VKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLA-------NELHSGLVK-MQKTIKD----------KLTTMSGAFD-SL 501
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 249 ATGNWGEQKKAASS------KAGVSQVLNRYTFASTLSHLRRTNTpIGRDGKIA-----KPRQLHNTHWGLVCPAETPEG 317
Cdd:PRK09603 502 MPHDLVNSKMITSTimeffmGGQLSQFMDQTNPLSEVTHKRRLSA-LGEGGLVKdrvgfEARDVHPTHYGRICPIETPEG 580
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 318 QACGLVKNLALMCCVT----VGSPSEPIIDFMVQRNMEIL---EEYEPLRSPNATKVFVNGvwvgvhrdpaHLVSTVMSL 390
Cdd:PRK09603 581 QNIGLINTLSTFTRVNdlgfIEAPYKKVVDGKVVGETIYLtaiQEDSHIIAPASTPIDEEG----------NILGDLIET 650
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 391 RRRG-LISHEVSLVrDIRDREFKIFTDAGRVCRPlFVIDNDAKSPNKGSlVLTKELVSRLEDDKdlPADMDPDEKAAKIM 469
Cdd:PRK09603 651 RVEGeIVLNEKSKV-TLMDLSSSMLVGVAASLIP-FLEHDDANRALMGT-NMQRQAVPLLRSDA--PIVGTGIEKIIARD 725
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 470 GWDGL--IKRGVVEYLDA-------EEEETVMIvmtpEDLDISRQLQAgyqlpettddpNKRVKAPLNPTAHTWTHCEIH 540
Cdd:PRK09603 726 SWGAIkaNRAGVVEKIDSkniyilgEGKEEAYI----DAYSLQKNLRT-----------NQNTSFNQVPIVKVGDKVEAG 790
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 541 ------PSMILGvcasiipfpdhnqsprntyQSAMGKQAMGIFLT----NF------SERM--DNAFNILYYPQKPLAT- 601
Cdd:PRK09603 791 qiiadgPSMDRG-------------------ELALGKNVRVAFMPwngyNFedaivvSERItkDDIFTSTHIYEKEVDAr 851
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 602 ---------TRSMEFLKFRELP-AGQNAIVAIACY--SG-------------------------YNQEDSVIMNQS---- 640
Cdd:PRK09603 852 elkhgveefTADIPDVKEEALAhLDESGIVKVGTYvsAGmilvgktspkgeikstpeerllraiFGDKAGHVVNKSlycp 931
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 641 ------SIDRGLFRSLYY----RTYTDQEKRVGMSVVEQFEKPM---RSDTLKLKHG-TYDKLDDDGLVAPGVRISGEDI 706
Cdd:PRK09603 932 pslegtVIDVKVFTKKGYekdaRVLSAYEEEKAKLDMEHFDRLTmlnREELLRVSSLlSQAILEEPFSHNGKDYKEGDQI 1011
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 707 IIGKTEPIAPDSeeLGQRTKLHVKRDKSTPLRTTENGLVDKVMLSTNAEG---------------LRFVKVRTRTTKIPQ 771
Cdd:PRK09603 1012 PKEEIASINRFT--LASLVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEklsilekddilpngvIKKVKLYIATKRKLK 1089
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*....
gi 45545327 772 IGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRMTIAHLIECQLSKV 830
Cdd:PRK09603 1090 VGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLV 1148
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
168-827 |
2.16e-13 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 74.66 E-value: 2.16e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 168 MVHRMLQVTLGRRDPDDRDHFGKKRLDLAGPLMAGLFRTLFNKLTKDVYKYLQkcVESNREFNLTLGVKSTTLTNGLRYS 247
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMS--TSSLDKVSPSDFINPKVLTNVLRDF 526
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 248 LatgnwgeqkkaasSKAGVSQVLNRYTFASTLSHLRRTNT--PIG--RDGKIAKPRQLHNTHWGLVCPAETPEGQACGLV 323
Cdd:PRK14844 527 F-------------NSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNIGLI 593
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 324 KNLALMCCVT----VGSPSEPIIDFMVQRNMEILEEYEPlrspnatkvfvngvwvGVHrdpaHLVSTVMSLrrrglishe 399
Cdd:PRK14844 594 NSLAIYARINkygfIESPYRKVVNRVVTDQIEYLSAIDE----------------GLY----YIADTSAKL--------- 644
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 400 vslvrdirdREFKIFTDAGRVCRplfvidndakspNKGSLVltkelvsrleddkdlpadmdpdekaakimgwdgLIKRGV 479
Cdd:PRK14844 645 ---------DENNCFVDDMLYCR------------YAGSFV---------------------------------MVSSDQ 670
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 480 VEYLDAEEEETVMIV--MTP--EDLDISRQLQAGYQLPETTddPNKRVKAPLNPTAHTWTHCEIHPSMILGVCASIIPFP 555
Cdd:PRK14844 671 VSYIDVSPKQVISVAasLIPflENDDANRALMGSNMQRQAV--PLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSS 748
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 556 DHNQSPRNTYQSAmGKQAMGIFLTNFSERMDNAFNILyYPQKPLatTRSMEFLK------------FRELPAGQNAIVAI 623
Cdd:PRK14844 749 DSNSIVIRAFDKE-RVNYLDVDIYHLRKFQRSNHNTC-INQKPL--VCVGDYVKegdviadgpainSGELALGQNLLVAF 824
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 624 ACYSGYNQEDSVIMNQSSIDRGLFRSLYyrtytdqekrvgmsvVEQFE-----KPMRSDTLK-----LKHGTYDKLDDDG 693
Cdd:PRK14844 825 MSWQGYNFEDSIIISSEVVKKDLFTSIH---------------IEEFEcvvhdTPLGSEKITraipgVNEENLYHLDDSG 889
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 694 LVAPGVRISGEDIIIGKTEP------------------------------IAPDSE--------------ELGQRTKLhV 729
Cdd:PRK14844 890 IVKIGTRVGPGYILVGKVTPkpslslppetkllmtifgeksfdcadsslyTSPDVEgtvidvqvftrrgvEENERALL-I 968
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 730 KRDKSTPLRTTENGLVD-----------KVMLSTNAE----------------GLR------------------------ 758
Cdd:PRK14844 969 KQKEINDFEKERDYIINvtseyfydelkKLLINSGSQdrekfdsiereqwwgiGLKnqsiseqvkslkkdfdekvshaia 1048
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 45545327 759 ---------------------FVKVRTRTTKIPQIGDKFASRHGQKGTIGITYRQEDMPFTSEGIVPDLIINPHAIPSRM 817
Cdd:PRK14844 1049 qfkrkveklhegydlpqgvsmSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRM 1128
|
810
....*....|
gi 45545327 818 TIAHLIECQL 827
Cdd:PRK14844 1129 NVGQILETHV 1138
|
|
| |
