|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
13-770 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 851.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 13 VIQDRETALDFIGRRgTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFG 92
Cdd:PRK08565 253 IAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYA 331
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 93 KKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGeqkkamSSRAGVSQV 172
Cdd:PRK08565 332 NKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQL 405
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 173 LNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWG 252
Cdd:PRK08565 406 LDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELG 485
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 253 MEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSM--IRDIREKELKIFTDAGRVYRPLFIV 330
Cdd:PRK08565 486 VVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV 565
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 331 EDDEslghkeLKVRKGHIAKLmateyqdieggfeDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneend 410
Cdd:PRK08565 566 ENGK------PKLTREHVEKL-------------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP-------- 618
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 411 ldvdpakrirvSHhattfTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ 490
Cdd:PRK08565 619 -----------EH-----THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQ 682
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 491 KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrT 570
Cdd:PRK08565 683 RPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--E 760
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 571 NTLRMKHG--TYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQ 648
Cdd:PRK08565 761 PNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESP 840
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 649 DGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALS 728
Cdd:PRK08565 841 EGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALE 920
|
730 740 750 760
....*....|....*....|....*....|....*....|..
gi 396941823 729 GNEGDASPFTDITVEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:PRK08565 921 GRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEK 962
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
63-770 |
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: 752.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 63 RKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKT 142
Cdd:cd00653 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKP 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 143 ITSGLKYALATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQ 221
Cdd:cd00653 288 ITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 222 ACGLVKNLSLMSCISvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinp 301
Cdd:cd00653 367 NCGLVKNLALMARIS----------------------------------------------------------------- 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 302 evsmirdirekelkiftdaGRVYRPLFIVEDDeslghkelkvrkghiaklmateyqdieggfedveeytwssllneglve 381
Cdd:cd00653 382 -------------------GRIERPYRIVEKE------------------------------------------------ 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 382 yidaeeeesiliamqpedlepaeaneendldvdpakrirvshhattFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQS 461
Cdd:cd00653 395 ----------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 462 AMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 541
Cdd:cd00653 429 NMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFF 508
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 542 RSLFFRSYMDQEKKYGMSITETFekpqRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAY 621
Cdd:cd00653 509 RSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKA 584
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 622 HSKRDASTPLRSTENGIVDQVLVTT---NQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVP 698
Cdd:cd00653 585 RDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPP 664
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 396941823 699 DLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:cd00653 665 DIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEP 736
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
270-770 |
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: 572.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 270 VFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDEslghkeLKVRKGHIA 349
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGK------PKLTREHVE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 350 KLMateyqdiEGgfedveEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneendldvdpakrirvSHhattfT 429
Cdd:TIGR03670 75 KLK-------EG------ELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTP-------------------EH-----T 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 430 HCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPA 509
Cdd:TIGR03670 118 HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPA 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 510 GQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrTNTLRMKHG--TYDKLDDDG 587
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLDEDG 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 588 LIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG 667
Cdd:TIGR03670 276 IVYPEVEVKGGDVLIGKTSPPRFLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELG 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 668 DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISK 747
Cdd:TIGR03670 356 DKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRK 435
|
490 500
....*....|....*....|...
gi 396941823 748 LLREHGYQS*GFEVMYNGHTGKK 770
Cdd:TIGR03670 436 ELLKLGFKPDGKEVMYDGITGEK 458
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
443-770 |
2.07e-151 |
|
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: 446.21 E-value: 2.07e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 443 ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSG 522
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYTG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 523 YNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMsITETFEKPqrtntLRMKHGTYDKLDDDGLIAPGVRVSGEDVII 602
Cdd:pfam00562 82 YNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-IEEITRDI-----PNVSEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 603 GKTTPISPDEE--ELGQRTAYHsKRDASTPLRSTENGIVDQVLV-TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT 679
Cdd:pfam00562 156 GKVGPTELTKLlrAIFGEKARD-VKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 680 IGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFT--DITVEGISKLLREHGYQS* 757
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314
|
330
....*....|...
gi 396941823 758 GFEVMYNGHTGKK 770
Cdd:pfam00562 315 GKEVLYDGRTGEP 327
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
14-770 |
1.78e-148 |
|
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: 459.96 E-value: 1.78e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 14 IQDRETALDFIGRRgtaLGIKKEKRIQYAKDILQKEF-------LPHI---------TQLEGFESR--KAFFLGYMINRL 75
Cdd:COG0085 216 TKTQEEALLEIYRK---LRPGEPPTIERAEQLLDNLFfdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYL 292
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 76 LLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIfRYmQRTVEEAHDFNMKLAINAKTITSGLKYALATGn 155
Cdd:COG0085 293 LELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS- 369
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 156 wgeqkkamssraGVSQVLNRYTYSSTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVK 227
Cdd:COG0085 370 ------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIG 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 228 NLSLMscisvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkGDINPEvsmir 307
Cdd:COG0085 434 SLALY----------------------------------------------------------------ARVNEY----- 444
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 308 direkelkiftdaGRVYRPLFIVEDdeslGhkelKVRKGhiaklmateyqdieggfedveeytwssllneglVEYIDAEE 387
Cdd:COG0085 445 -------------GFIETPYRKVEN----G----KVTDE---------------------------------IEYLTADE 470
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 388 EESILIAMQPEDLePAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQA 467
Cdd:COG0085 471 EENYYIAQANAPL-DEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQA 549
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 468 MGVFLTNynvrmdtmANILYYP--------------QKPLgtTRAMEYLK------------FRELPAGQNAIVAIACYS 521
Cdd:COG0085 550 VPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPI--VRVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWE 619
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 522 GYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKY--GMSITeTFEKPqrtntlrmKHG--TYDKLDDDGLIAPGVRVSG 597
Cdd:COG0085 620 GYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTklGPEEI-TRDIP--------NVSeeALRNLDEDGIIRIGAEVKG 690
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 598 EDVIIGKTTP-----ISPDEEELgqRTAYHSK----RDASTPLRSTENGIVDQVLVTTNQDG-------LKFVKVRVRTT 661
Cdd:COG0085 691 GDILVGKVTPkgeteLTPEERLL--RAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQK 768
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 662 KIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDIT 741
Cdd:COG0085 769 RKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAP 848
|
810 820
....*....|....*....|....*....
gi 396941823 742 VEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:COG0085 849 EEEIRELLEKAGLPPDGKEVLYDGRTGEP 877
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
13-770 |
0e+00 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 851.17 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 13 VIQDRETALDFIGRRgTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFG 92
Cdd:PRK08565 253 IAATVEDALDYIGKR-VAIGQPREYRIERAEQILDKYLLPHLGTSPEDRIKKAYFLGQMASKLLELYLGRREPDDKDHYA 331
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 93 KKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGeqkkamSSRAGVSQV 172
Cdd:PRK08565 332 NKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITERIRHALATGNWV------GGRTGVSQL 405
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 173 LNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWG 252
Cdd:PRK08565 406 LDRTNYLSTLSHLRRVVSPLSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISVGVDEEEVEEILYELG 485
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 253 MEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSM--IRDIREKELKIFTDAGRVYRPLFIV 330
Cdd:PRK08565 486 VVPVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISDEVNVayIETGEINEVYVNCDSGRVRRPLIVV 565
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 331 EDDEslghkeLKVRKGHIAKLmateyqdieggfeDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneend 410
Cdd:PRK08565 566 ENGK------PKLTREHVEKL-------------KKGELTFDDLVKMGVIEYLDAEEEENAYVALDPEDLTP-------- 618
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 411 ldvdpakrirvSHhattfTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQ 490
Cdd:PRK08565 619 -----------EH-----THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRIRTDTRGHLLHYPQ 682
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 491 KPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrT 570
Cdd:PRK08565 683 RPLVQTRALEIIGYNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEDKIEIP--E 760
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 571 NTLRMKHG--TYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQ 648
Cdd:PRK08565 761 PNVRGYRGeeYYRKLDEDGIVSPEVEVKGGDVLIGKTSPPRFLEELEELSLGLQERRDTSVTVRHGEKGIVDTVLITESP 840
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 649 DGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALS 728
Cdd:PRK08565 841 EGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALE 920
|
730 740 750 760
....*....|....*....|....*....|....*....|..
gi 396941823 729 GNEGDASPFTDITVEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:PRK08565 921 GRFVDATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEK 962
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
63-770 |
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: 752.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 63 RKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKT 142
Cdd:cd00653 208 KRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKP 287
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 143 ITSGLKYALATGNWGeQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNT-PIGRDGKLAKPRQLHNTHWGLVCPAETPEGQ 221
Cdd:cd00653 288 ITSGIKEFLATGNWG-SKRFLMQRSGLSQVLDRLNPLSELSHKRRISSlGLFRERKGFEVRDLHPSHWGRICPIETPEGE 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 222 ACGLVKNLSLMSCISvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkgdinp 301
Cdd:cd00653 367 NCGLVKNLALMARIS----------------------------------------------------------------- 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 302 evsmirdirekelkiftdaGRVYRPLFIVEDDeslghkelkvrkghiaklmateyqdieggfedveeytwssllneglve 381
Cdd:cd00653 382 -------------------GRIERPYRIVEKE------------------------------------------------ 394
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 382 yidaeeeesiliamqpedlepaeaneendldvdpakrirvshhattFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQS 461
Cdd:cd00653 395 ----------------------------------------------VTHIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 462 AMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLF 541
Cdd:cd00653 429 NMQKQAVGTPALNQQYRMDTKLYLLLYPQKPLVGTGIEEYIAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFF 508
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 542 RSLFFRSYMDQEKKYGMSITETFekpqRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAY 621
Cdd:cd00653 509 RSIHYKKYEIELRKTKNGPEEIT----RGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIFGEKA 584
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 622 HSKRDASTPLRSTENGIVDQVLVTT---NQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVP 698
Cdd:cd00653 585 RDVRDTSLKYPGGEKGIVDDVKIFSrelNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPP 664
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 396941823 699 DLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:cd00653 665 DIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEP 736
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
270-770 |
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: 572.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 270 VFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDEslghkeLKVRKGHIA 349
Cdd:TIGR03670 1 VYLNGRLIGYHDDPEELVEEVRKLRRSGKLSQEVNVAYYEETNEVYINCDAGRIRRPLIVVENGK------PKLTREHVE 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 350 KLMateyqdiEGgfedveEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPaeaneendldvdpakrirvSHhattfT 429
Cdd:TIGR03670 75 KLK-------EG------ELTWDDLVKQGVIEYLDAEEEENAYIALDPEELTP-------------------EH-----T 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 430 HCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPA 509
Cdd:TIGR03670 118 HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRIRLDTRGHLLHYPQKPLVKTRVLELIGYDDRPA 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 510 GQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPqrTNTLRMKHG--TYDKLDDDG 587
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERRYPGGQEDRFEIP--EPDVRGYRGeeAYKHLDEDG 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 588 LIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG 667
Cdd:TIGR03670 276 IVYPEVEVKGGDVLIGKTSPPRFLEELREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKLVKVRVRDLRIPELG 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 668 DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISK 747
Cdd:TIGR03670 356 DKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRK 435
|
490 500
....*....|....*....|...
gi 396941823 748 LLREHGYQS*GFEVMYNGHTGKK 770
Cdd:TIGR03670 436 ELLKLGFKPDGKEVMYDGITGEK 458
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
268-770 |
0e+00 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 538.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 268 TRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESlghkelKVRKGH 347
Cdd:PRK07225 5 AKVYVNGKLIGTHDDPEELVEEIREARRSGEISEEVNVSYKEETNEVIINTDAGRARRPLIVVENGEP------LLTEEH 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 348 IAKLmateyqdiEGGfedveEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAeaneendldvdpakrirvshHatt 427
Cdd:PRK07225 79 IEKL--------KNG-----ELTFDDLVKQGVIEYLDAEEEENAYIAVYEEDLTEE--------------------H--- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 428 fTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL 507
Cdd:PRK07225 123 -THLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKLRPDTRGHLLHYPQVPLVKTQTQEIIGFDER 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 508 PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTntLRMKHG--TYDKLDD 585
Cdd:PRK07225 202 PAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEDRFEIPDKD--VRGYRGeeAYRHLDE 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 586 DGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQ 665
Cdd:PRK07225 280 DGLVNPETEVKEGDVLIGKTSPPRFLEEPDDFGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRLVKVRVRDLRIPE 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 666 IGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGI 745
Cdd:PRK07225 360 LGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDL 439
|
490 500
....*....|....*....|....*
gi 396941823 746 SKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:PRK07225 440 REALEKLGFEHTGKEVMYDGITGEK 464
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
443-770 |
2.07e-151 |
|
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: 446.21 E-value: 2.07e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 443 ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSG 522
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGIYTLNKFYRSDQNTYVLCYPQKPLVKTGAVEAGGFGELPLGQNAIVAVMSYTG 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 523 YNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMsITETFEKPqrtntLRMKHGTYDKLDDDGLIAPGVRVSGEDVII 602
Cdd:pfam00562 82 YNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKLGP-IEEITRDI-----PNVSEEALKKLDEDGIVRVGAEVKPGDILV 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 603 GKTTPISPDEE--ELGQRTAYHsKRDASTPLRSTENGIVDQVLV-TTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGT 679
Cdd:pfam00562 156 GKVGPTELTKLlrAIFGEKARD-VKDTSLKVPPGEEGVVDDVIVfELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGV 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 680 IGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFT--DITVEGISKLLREHGYQS* 757
Cdd:pfam00562 235 VSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDgaSTEVEDIGELLEKAGYNYY 314
|
330
....*....|...
gi 396941823 758 GFEVMYNGHTGKK 770
Cdd:pfam00562 315 GKEVLYDGRTGEP 327
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
14-770 |
1.78e-148 |
|
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: 459.96 E-value: 1.78e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 14 IQDRETALDFIGRRgtaLGIKKEKRIQYAKDILQKEF-------LPHI---------TQLEGFESR--KAFFLGYMINRL 75
Cdd:COG0085 216 TKTQEEALLEIYRK---LRPGEPPTIERAEQLLDNLFfdpkrydLAHVgrykinkklGLDVPPEDRvlTAEDIVATIKYL 292
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 76 LLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIfRYmQRTVEEAHDFNMKLAINAKTITSGLKYALATGn 155
Cdd:COG0085 293 LELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVV-RE-RMTTQDVEAITPQSLINIRPVVAAIKEFFGSS- 369
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 156 wgeqkkamssraGVSQVLNRYTYSSTLSHLRRTNT----PIGRDgklaKP----RQLHNTHWGLVCPAETPEGQACGLVK 227
Cdd:COG0085 370 ------------QLSQFMDQTNPLSELTHKRRLSAlgpgGLSRE----RAgfevRDVHPSHYGRMCPIETPEGPNIGLIG 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 228 NLSLMscisvgtdpmpiitflsewgmepledyvphqspdatrvfvngvwhgvhrnparlmetlrtlrrkGDINPEvsmir 307
Cdd:COG0085 434 SLALY----------------------------------------------------------------ARVNEY----- 444
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 308 direkelkiftdaGRVYRPLFIVEDdeslGhkelKVRKGhiaklmateyqdieggfedveeytwssllneglVEYIDAEE 387
Cdd:COG0085 445 -------------GFIETPYRKVEN----G----KVTDE---------------------------------IEYLTADE 470
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 388 EESILIAMQPEDLePAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQA 467
Cdd:COG0085 471 EENYYIAQANAPL-DEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQA 549
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 468 MGVFLTNynvrmdtmANILYYP--------------QKPLgtTRAMEYLK------------FRELPAGQNAIVAIACYS 521
Cdd:COG0085 550 VPLLRPE--------APLLHYPlqkfqrsnqgtcinQRPI--VRVGDRVEkgdvladgpatdNGELALGQNLLVAFMPWE 619
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 522 GYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKY--GMSITeTFEKPqrtntlrmKHG--TYDKLDDDGLIAPGVRVSG 597
Cdd:COG0085 620 GYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTklGPEEI-TRDIP--------NVSeeALRNLDEDGIIRIGAEVKG 690
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 598 EDVIIGKTTP-----ISPDEEELgqRTAYHSK----RDASTPLRSTENGIVDQVLVTTNQDG-------LKFVKVRVRTT 661
Cdd:COG0085 691 GDILVGKVTPkgeteLTPEERLL--RAIFGEKarevRDTSLRVPHGEKGKVIDVKVFSREEGdelppgvNKLVRVYVAQK 768
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 662 KIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDIT 741
Cdd:COG0085 769 RKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAP 848
|
810 820
....*....|....*....|....*....
gi 396941823 742 VEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:COG0085 849 EEEIRELLEKAGLPPDGKEVLYDGRTGEP 877
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
14-256 |
1.07e-64 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 223.67 E-value: 1.07e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 14 IQDRETALDFIGRRGtALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGK 93
Cdd:PRK09606 257 VDTQEEALEYIGKRV-APGQTKEYRIKRAEYVIDRYLLPHLGVEPEVRRAKAHYLGRMAEACFELALGRREEDDKDHYAN 335
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 94 KRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWgeqkkaMSSRAGVSQVL 173
Cdd:PRK09606 336 KRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELSIKTAVRSDVLTERLEHAMATGNW------VGGRTGVSQLL 409
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 174 NRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 253
Cdd:PRK09606 410 DRTDYMATLSHLRRVVSPLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVKEILKELGV 489
|
...
gi 396941823 254 EPL 256
Cdd:PRK09606 490 EPE 492
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
1-145 |
8.96e-61 |
|
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: 210.31 E-value: 8.96e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 1 LEMLKPCVEDGFVI--QDRETALDFIGRRGTA---LGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRL 75
Cdd:pfam04563 247 QEELLPSLEEGFKIriQTQEQALDYIGGRGRAifrMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYFIGYMIRRL 326
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 76 LLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITS 145
Cdd:pfam04563 327 LLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPITS 396
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
86-770 |
1.21e-42 |
|
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: 167.53 E-value: 1.21e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 86 DDRDHFGKKRLDLAGPLLAQLFKTLFKKltkdifryMQRTVEE---AHDFNmKLA----INAKTITSGLKYALATGNwge 158
Cdd:TIGR02013 319 DDIDHLGNRRIRSVGELLQNQFRVGLAR--------MERIVRErmsTQDTD-TLTpqdlINAKPISAAIKEFFGSSQ--- 386
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 159 qkkamssragVSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSlmsc 234
Cdd:TIGR02013 387 ----------LSQFMDQTNPLAELTHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLS---- 452
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 235 isvgtdpmpiiTFlsewgmepledyvphqspdaTRVfvngvwhgvhrNPARLMETlrtlrrkgdinPevsmirdirekel 314
Cdd:TIGR02013 453 -----------TY--------------------ARV-----------NEYGFIET-----------P------------- 466
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 315 kiftdagrvYRplfiveddeslghkelKVRKGhiaklmateyqdiEGGFEDVeeytwssllneglVEYIDAEEEESILIA 394
Cdd:TIGR02013 467 ---------YR----------------KVKDG-------------KVVVTDE-------------IDYLTADEEDNYVIA 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 395 mqpedlePAEAN-EENDLDVDPAKRIRVSHHATTF-----THCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAM 468
Cdd:TIGR02013 496 -------QANAPlDENGRFVEDLVVARYRGEITLVspdqvDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAV 568
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 469 -------------------------------GV---------FLTNYNVRMDTMANILYYP--------------QKPL- 493
Cdd:TIGR02013 569 pllrseaplvgtgmeakvardsgavivakrgGVveyvdakriVIRYDEDEEEPDGGIDIYRllkyqrsnqdtcinQRPIv 648
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 494 --------GTTRAMEYLKFR-ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSY--MDQEKKYGMS-IT 561
Cdd:TIGR02013 649 svgdrveaGDVLADGPSTDLgELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYevEARDTKLGPEeIT 728
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 562 EtfEKPQrtntlrMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPIS----PDEEELgQRTAYHSK----RDASTPLRS 633
Cdd:TIGR02013 729 R--DIPN------VSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGetelTPEEKL-LRAIFGEKardvRDTSLRVPP 799
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 634 TENGIVDQVLVTTNQDG-------LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHA 706
Cdd:TIGR02013 800 GVEGTVIDVKVFSREQGdelppgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLG 879
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 396941823 707 IPSRMTVAHLIECLLSKVAALSGNEGD--ASP-FTDITVEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:TIGR02013 880 VPSRMNIGQILETHLGWAGKRLGRKGVpiATPvFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQ 946
|
|
| RNA_pol_Rpb2_4 |
pfam04566 |
RNA polymerase Rpb2, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
270-331 |
2.85e-32 |
|
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: 119.01 E-value: 2.85e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 396941823 270 VFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVE 331
Cdd:pfam04566 1 VFLNGNLIGVHRDPEELVETLRKLRRSGKISEEVSIVRDIREKEVRINTDGGRVCRPLIIVE 62
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
171-233 |
1.36e-29 |
|
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: 111.46 E-value: 1.36e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 396941823 171 QVLNRYTYSSTLSHLRRTNTPIG---RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMS 233
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNSPRGglfREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYA 66
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
72-721 |
2.33e-29 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 125.59 E-value: 2.33e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 72 INRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF----KTLFKKLTKDIFRYMQRTVEeahDFNMklaINAKTITSGL 147
Cdd:CHL00207 284 IDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFriglKRLERILRNRMTICDIDSLS---KFNL---INPKPLIALI 357
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 148 KYALAtgnwgeqkkamSSRagVSQVLNRYTYSSTLSHLRRTNT--PIGRDgKLAKP---RQLHNTHWGLVCPAETPEGQA 222
Cdd:CHL00207 358 REFFG-----------SSQ--LSQYMDQTNPLSELTHKRRISIlgPGGLD-KDRISfavRDIHPSHYGRICPIETPEGPN 423
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 223 CGLVKnlSLMSCISVGTDPMPIITFLsewgmepledyvphqspdatRVFVNGVWhgVHRNPARLMETLRTLRRkgdINPE 302
Cdd:CHL00207 424 CGLIG--SLATNARINKFGFIETPFY--------------------KVINGKVK--KFGNPIYLTADSEDLYR---IAPN 476
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 303 vsmirDIREKELKIFTDagrvyrplfiveddeslghKELKVRKGHIAKLmateyqdieggfedveeytwssllneglvey 382
Cdd:CHL00207 477 -----DINLNKNNYFKK-------------------NIIPVRYKQEFKT------------------------------- 501
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 383 IDAEEEESILIAmqpedlepaeaneendldvdpakrirvshhattfthceihPSMILGVAASIIPFPDHNQSPRNTYQSA 462
Cdd:CHL00207 502 VNPSKVDFIAIS----------------------------------------PIQVFSIAESLIPFLEHNDANRALMGSN 541
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 463 MGKQAMG---------------------------------VFLTNYNVRMDTMAN--ILYYPQK-------------PL- 493
Cdd:CHL00207 542 MQRQAVPllypekpivgtgyekqialdsgmtiisltegivVSVSAYKIIIQDDNNryIHYYLQKyqrsnqntcinyrPIv 621
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 494 --------GTTRAM-EYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFrsymdqeKKYGMSITETF 564
Cdd:CHL00207 622 wvgekiniGQILADgSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHI-------EKYEIELRQTK 694
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 565 EKPQRTNTLRMKHGTYD--KLDDDGLIAPGVRVSGEDVIIGKTTPIS----PDEEELGQRTAYHSKRDA-STPLRSTENG 637
Cdd:CHL00207 695 LGSEEITRNIPNVSEYSlkNLDENGIISIGSKVLAGDILVGKITPKGesdqLPEGKLLRAIFGEKAKDVkDTSLRMPNGG 774
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 638 ---IVDQVLVTTNQ-DGLKF---VKVRVRTTKIP--QIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIP 708
Cdd:CHL00207 775 ygrVIKVEIFSRSKgDELKFgyyLKIRVFIAQIRkiQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVP 854
|
730
....*....|...
gi 396941823 709 SRMTVAHLIECLL 721
Cdd:CHL00207 855 SRMNVGQLFECLL 867
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-97 |
9.84e-29 |
|
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: 113.60 E-value: 9.84e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 1 LEMLKPCVEDGFVIQDRETALDFIGRrGTALGIKKEKRIQYAKDILQK-----EFLPHITQLEGFESR--KAFFLGYMIN 73
Cdd:pfam04561 83 LELLKPELEEAENIYTQEEALDYIGK-GFALRRGEEPRLQRAREILYSrdpkyNLNKHLGLNEPFENErlKAQDILYMID 161
|
90 100
....*....|....*....|....
gi 396941823 74 RLLLCALDRKDQDDRDHFGKKRLD 97
Cdd:pfam04561 162 RLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
506-770 |
2.02e-25 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 112.89 E-value: 2.02e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 506 ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLffrsymdqekkygmSITEtFEKPQRtNTlrmKHG----TYD 581
Cdd:PRK00405 712 ELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSI--------------HIEE-YEIEAR-DT---KLGpeeiTRD 772
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 582 ----------KLDDDGLIAPGVRVSGEDVIIGKTTP-----ISPdEEEL-----GQRTAYHskRDAStpLR--STENGIV 639
Cdd:PRK00405 773 ipnvseealrNLDESGIVRIGAEVKPGDILVGKVTPkgeteLTP-EEKLlraifGEKARDV--KDTS--LRvpHGEEGTV 847
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 640 DQVLV-TTNQDG-------LKFVKVRV---RttKIpQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIP 708
Cdd:PRK00405 848 IDVKVfTRIEQGdelppgvNKLVKVYIaqkR--KI-QVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVP 924
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 396941823 709 SRMTVAHLIECLLSKVAALSGNEGdASP-FTDITVEGISKLLREHGYQS*GFEVMYNGHTGKK 770
Cdd:PRK00405 925 SRMNIGQILETHLGWAAKGLGIKF-ATPvFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEP 986
|
|
| RNA_pol_Rpb2_5 |
pfam04567 |
RNA polymerase Rpb2, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
371-435 |
3.15e-22 |
|
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: 90.29 E-value: 3.15e-22
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 396941823 371 WSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEaneendldvdpaKRIRVSHHATTFTHCEIHP 435
Cdd:pfam04567 1 WSDLLREGVIEYLDAEEEETSMIAMTPEDLEESS------------REEREGPYAHTYTHCEIHP 53
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
506-721 |
1.34e-20 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 97.28 E-value: 1.34e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 506 ELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRsymdqekKYGMSITETFEKPQR-TN--------TLRmk 576
Cdd:CHL00001 648 ELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIR-------KYEIQTHVTSQGPERiTKeiphleahLLR-- 718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 577 HgtydkLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEE-----------LGQRTAyhSKRDasTPLRSTENG---IVDQV 642
Cdd:CHL00001 719 N-----LDKNGIVMLGSWVETGDILVGKLTPQEAEESSyapegrllraiFGIQVS--TSKE--TCLKLPIGGrgrVIDVR 789
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 643 LVTTNQDGLKFVK-VRV---RTTKIpQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIE 718
Cdd:CHL00001 790 WIQKKGGSSYNPEtIHVyilQKREI-QVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFE 868
|
...
gi 396941823 719 CLL 721
Cdd:CHL00001 869 CLL 871
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
86-731 |
3.97e-18 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 89.98 E-value: 3.97e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 86 DDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIfRYMQRTVEEAHDFNMKL-AINAKTITSGLKYALATGNwgeqkkams 164
Cdd:PRK09603 455 DDRDHLGNRRIRAVGELLANELHSGLVKMQKTI-KDKLTTMSGAFDSLMPHdLVNSKMITSTIMEFFMGGQ--------- 524
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 165 sragVSQVLNRYTYSSTLSHLRRTNTpIGrDGKLAK------PRQLHNTHWGLVCPAETPEGQACGLVKNLSlmscisvg 238
Cdd:PRK09603 525 ----LSQFMDQTNPLSEVTHKRRLSA-LG-EGGLVKdrvgfeARDVHPTHYGRICPIETPEGQNIGLINTLS-------- 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 239 tdpmpiiTFlsewgmepledyvphqspdaTRVfvngvwhgvhrnparlmetlrtlrrkgdinpevsmirdirekelkifT 318
Cdd:PRK09603 591 -------TF--------------------TRV-----------------------------------------------N 596
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 319 DAGRVYRPLfiveddeslghkeLKVRKGHIAklmateyqdieggfedveeytwssllneGLVEYIDAEEEESILIAMQPE 398
Cdd:PRK09603 597 DLGFIEAPY-------------KKVVDGKVV----------------------------GETIYLTAIQEDSHIIAPAST 635
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 399 DLEPAEANEENDLDVDPAKRIRVSHHaTTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNV- 477
Cdd:PRK09603 636 PIDEEGNILGDLIETRVEGEIVLNEK-SKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIv 714
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 478 -------------------------RMDTM-----------ANILYYP-QKPLGTTRAMEY------------------- 501
Cdd:PRK09603 715 gtgiekiiardswgaikanragvveKIDSKniyilgegkeeAYIDAYSlQKNLRTNQNTSFnqvpivkvgdkveagqiia 794
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 502 ----LKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRS--LFFRSYMDQEKKYGmsITETFEKPQRTNTLRM 575
Cdd:PRK09603 795 dgpsMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSthIYEKEVDARELKHG--VEEFTADIPDVKEEAL 872
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 576 KHgtydkLDDDGLIAPGVRVSGEDVIIGKTTP---ISPDEEELGQRTAYHSK---------------------------- 624
Cdd:PRK09603 873 AH-----LDESGIVKVGTYVSAGMILVGKTSPkgeIKSTPEERLLRAIFGDKaghvvnkslycppslegtvidvkvftkk 947
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 625 ---RDAST-------------------------------------PLRS------------------------------- 633
Cdd:PRK09603 948 gyeKDARVlsayeeekakldmehfdrltmlnreellrvssllsqaILEEpfshngkdykegdqipkeeiasinrftlasl 1027
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 634 --------------TENGIVDQ--VLVTTNQDGL--------------KFVKVRVRTTKIPQIGDKFASRHGQKGTIGIT 683
Cdd:PRK09603 1028 vkkyskevqnhyeiTKNNFLEQkkVLGEEHEEKLsilekddilpngviKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNI 1107
|
810 820 830 840
....*....|....*....|....*....|....*....|....*...
gi 396941823 684 YRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNE 731
Cdd:PRK09603 1108 VPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQ 1155
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
71-718 |
1.16e-14 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 78.51 E-value: 1.16e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 71 MINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEE---AHDFnmklaINAKTITSGL 147
Cdd:PRK14844 449 IVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDkvsPSDF-----INPKVLTNVL 523
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 148 KyalatgnwgeqkkAMSSRAGVSQVLNRYTYSSTLSHLRRTNT--PIG--RDGKLAKPRQLHNTHWGLVCPAETPEGQAC 223
Cdd:PRK14844 524 R-------------DFFNSSQLSQFMDQTNPLSEITHKRRLSAlgPGGltRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 224 GLVKNLSLMSCISvgtdpmpiitflsEWGM--EPLEDYVPHQSPDATRvFVNGVWHGVHR---------NPARLMETLRT 292
Cdd:PRK14844 591 GLINSLAIYARIN-------------KYGFieSPYRKVVNRVVTDQIE-YLSAIDEGLYYiadtsakldENNCFVDDMLY 656
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 293 LRRKGDI----NPEVSMIrDIREKELkIFTDAGRVyrPlFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEE 368
Cdd:PRK14844 657 CRYAGSFvmvsSDQVSYI-DVSPKQV-ISVAASLI--P-FLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVAS 731
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 369 YTWSSLL--NEGLVeyiDAEEEESILI-AMQPEDLepaeaneeNDLDVD--PAKRIRVSHHATTFthceihpsmilgvaa 443
Cdd:PRK14844 732 GSGAVVLakRDGIV---DSSDSNSIVIrAFDKERV--------NYLDVDiyHLRKFQRSNHNTCI--------------- 785
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 444 siipfpdhNQSPRntyqsamgkqamgVFLTNYNVRMDTMANilyYPQKPLGttrameylkfrELPAGQNAIVAIACYSGY 523
Cdd:PRK14844 786 --------NQKPL-------------VCVGDYVKEGDVIAD---GPAINSG-----------ELALGQNLLVAFMSWQGY 830
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 524 NQEDSMIMNQSSIDRGLFRSLFFRSY--------MDQEKkygmsITETFEKPQRTNtlrMKHgtydkLDDDGLIAPGVRV 595
Cdd:PRK14844 831 NFEDSIIISSEVVKKDLFTSIHIEEFecvvhdtpLGSEK-----ITRAIPGVNEEN---LYH-----LDDSGIVKIGTRV 897
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 596 SGEDVIIGKTTP------------------------------ISPDEE--------------ELGQRtAYHSKRDASTPL 631
Cdd:PRK14844 898 GPGYILVGKVTPkpslslppetkllmtifgeksfdcadsslyTSPDVEgtvidvqvftrrgvEENER-ALLIKQKEINDF 976
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 396941823 632 RSTENGIVD-----------QVLVTT-NQDGLKF---------------------------------------------- 653
Cdd:PRK14844 977 EKERDYIINvtseyfydelkKLLINSgSQDREKFdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkvek 1056
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 396941823 654 --------------VKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIE 718
Cdd:PRK14844 1057 lhegydlpqgvsmsVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILE 1135
|
|
| |
