|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
15-1067 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2031.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFL-------EKGLIEELQNFSPISDYTGKLELHFIgeDYRLKRPRHDVEEAKRRDATFASQMYVTC 87
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFV--SYELGEPKYDVEECKERGLTYSAPLRVKL 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 88 RLINKETGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDK--NGRRTYNASVIPNRGAWLKFET 165
Cdd:PRK00405 102 RLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFEF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 166 DKNNLLYVRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQSSIDSAND----------------------------- 216
Cdd:PRK00405 182 DPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKEIEVPVEyllgkvlaedivdeetgevlaeandeite 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 217 -------------EGINSEDQALLELYKKLRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDEVRTL 283
Cdd:PRK00405 262 eldgpyirntlekDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 284 THEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPL 363
Cdd:PRK00405 342 TKEDIIATIKYLINLRNGKG--EVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPV 419
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 364 VAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATH 443
Cdd:PRK00405 420 VAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATY 499
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 444 ARVNEYGFIETPFWEVNNGRVNKEgnPVYLSADLEDECRVAPGDVATDKDGNILANLIPVRYRQDFEKVPPHQVDYVQLS 523
Cdd:PRK00405 500 ARVNEYGFIETPYRKVVDGKVTDE--IVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVS 577
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 524 PVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVK- 602
Cdd:PRK00405 578 PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRv 657
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 603 -----DTEGNEHFHyLQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGGEIALGQNVLIAYMPWEGYNYEDAIL 677
Cdd:PRK00405 658 eeldpGEDGVDIYN-LIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAIL 736
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 678 VSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPP 757
Cdd:PRK00405 737 ISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTP 816
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 758 EEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTR-EQGDELPPGANMVVRVYVAQRRKIQVGDKMAGRHGNKGII 836
Cdd:PRK00405 817 EEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVV 896
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 837 SRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDemyGAekSHQTVQAFLEEAskq 916
Cdd:PRK00405 897 SRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFD---GA--KEEEIKELLEEA--- 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 917 pgkawvyNPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRLGEMEV 996
Cdd:PRK00405 969 -------GLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1041
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2021943934 997 WALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKE 1067
Cdd:PRK00405 1042 WALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
15-1065 |
0e+00 |
|
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: 1849.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFigEDYRLKRPRHDVEEAKRRDATFASQMYVTCRLINKET 94
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKET 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 95 GEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVR 174
Cdd:COG0085 91 GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVR 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 175 VDKTRKINAHVLMRAMGL-SDNDVVDKLRHPEFYQSSIDSANDEGINSEDQALLELYKKLRPGEPPSVSGGQQLLHSRFF 253
Cdd:COG0085 171 IDRKRKIPVTVLLRALGLeTDEEILEAFGDDPIQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFF 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 254 DPKRYDLGRVGRYKINKKLRLTVPDEVRTLTHEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGL 333
Cdd:COG0085 251 DPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGER--EPDDIDHLGNRRVRLVGELLQNQFRVGL 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 334 NRLERIIKERMTVGETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVR 413
Cdd:COG0085 329 SRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVR 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 414 DIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEGnpVYLSADLEDECRVAPGDVATDKD 493
Cdd:COG0085 409 DVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEI--EYLTADEEENYYIAQANAPLDED 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 494 GNILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVgtgles 573
Cdd:COG0085 487 GNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPLL------ 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 574 qvardsgmvpitkvngivsyvdaneivvkdtegnehfHY-LQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGG 652
Cdd:COG0085 561 -------------------------------------HYpLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNG 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 653 EIALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIR 732
Cdd:COG0085 604 ELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIR 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 733 IGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRV 812
Cdd:COG0085 684 IGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRV 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 813 YVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVP 892
Cdd:COG0085 764 YVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPV 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 893 FDEMYGAEkshqtVQAFLEEAskqpgkawvyNPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPY 972
Cdd:COG0085 844 FDGAPEEE-----IRELLEKA----------GLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPY 908
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 973 SLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQ 1052
Cdd:COG0085 909 SLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQ 988
|
1050
....*....|...
gi 2021943934 1053 SLGLDIGVYTDEG 1065
Cdd:COG0085 989 SLGLDVEVLSEDG 1001
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1058 |
0e+00 |
|
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: 1816.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 10 KTATYLPDLVEVQRASFKWFL----------EKGLIEELQNFSPISDYTGKLELHFIgeDYRLKRPRHDVEEAKRRDATF 79
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYL--SYRLGEPKYSVEECKERGLTY 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 80 ASQMYVTCRLINKE---TGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD--KNGRRTYNASVI 154
Cdd:TIGR02013 90 SAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLFSARII 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 155 PNRGAWLKFETDKNNLLYVRVDKTRKINAHVLMRAMGLSDNDV-VDKLRHPEFYQSSIDSandEGINSEDQALLELYKKL 233
Cdd:TIGR02013 170 PYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLiLNRLGSGEYIRNTLRK---DPTNSEEEALVEIYRKL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 234 RPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDEVRTLTHEDVLSTIDYLInlELDIGGASLDDIDHL 313
Cdd:TIGR02013 247 RPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLI--KLRNGKGEIDDIDHL 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 314 GNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKR 393
Cdd:TIGR02013 325 GNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 394 RISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEGNPVYL 473
Cdd:TIGR02013 405 RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTDEIDYL 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 474 SADLEDECRVAPGDVATDKDGNILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQ 553
Cdd:TIGR02013 485 TADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQ 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 554 RQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDTE------GNEHFHYLQKYQRSNQDTCLNQ 627
Cdd:TIGR02013 565 RQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEdeeepdGGIDIYRLLKYQRSNQDTCINQ 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 628 RPIVQIGDQVISGQVLADGSACEGGEIALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGP 707
Cdd:TIGR02013 645 RPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGP 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 708 EEITREIPNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGR 787
Cdd:TIGR02013 725 EEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGT 804
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 788 VLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRM 867
Cdd:TIGR02013 805 VIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRM 884
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 868 NVGQVFELLMGWAASNLNcrvkvvpfdeMYGAEKSHQTVQAFLEEASKQPGKAWVYNPDdpGKLLLKDGRTGEPFDQPVA 947
Cdd:TIGR02013 885 NIGQILETHLGWAGKRLG----------RKGVPIATPVFDGASEEEIKEYLEKAGLPRD--GKVRLYDGRTGEQFDRPVT 952
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 948 VGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALN 1027
Cdd:TIGR02013 953 VGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYE 1032
|
1050 1060 1070
....*....|....*....|....*....|.
gi 2021943934 1028 AIVKGKPIPRPGTPESFKVLMRELQSLGLDI 1058
Cdd:TIGR02013 1033 AIVKGENVPEPGIPESFNVLIKELQSLGLDI 1063
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
18-1058 |
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: 1002.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 18 LVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFIGEDYRLKRPRH---------DVEEAKRRDATFASQMYVTCR 88
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVeeggvtrklTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 89 LINKETGEIKEQEVFIGELPLMTE------------------------RGTFIINGAERVIVNQIVRSPGVYFKDeqDKN 144
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 145 GRRTY----NASVIPNRGAWLKFETD-KNNLLYVRVDKTRKinahvlmramglsdndvvdklrhpefyqssidsandegi 219
Cdd:cd00653 159 GKRIYtktsIPSYSPYRGSWLEVKSDkKKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 220 nseDQALLELYKKLrpgeppsvsggqqllhsrffdpkrydlgrvgrykinkklrltvpdevrtlthEDVLSTIDYLINLE 299
Cdd:cd00653 200 ---EEALKYIGKRF----------------------------------------------------EDLIYMIRKLILLV 224
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 300 LDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDS--LTPAQLVNPKPLVAAIKEFFGSSQ-- 375
Cdd:cd00653 225 LGKG--KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwg 302
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 376 ----------LSQFMDQTNPLAELTHKRRISAlgpGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHAR 445
Cdd:cd00653 303 skrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMAR 379
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 446 VNeyGFIETPFWEVNNgrvnkegnpvylsadledecrvapgdvatdkdgnilanlipvryrqdfekvpphQVDYVQLSPV 525
Cdd:cd00653 380 IS--GRIERPYRIVEK------------------------------------------------------EVTHIEISPS 403
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 526 QVISVATSLIPFLEHDDANRALMGSNMQRQAVP----------------LLRPERPLVGTGLESQVARdsgmvpitkvng 589
Cdd:cd00653 404 QILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAF------------ 471
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 590 ivsyvdaneivvkdtegnehfhylqkyqrsnqdtclnqrpivqigdqvisgqvladgsacegGEIALGQNVLIAYMPWEG 669
Cdd:cd00653 472 --------------------------------------------------------------GELPLGQNAIVAVMSYSG 489
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 670 YNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITR-EIPNISEESLNNLDEMGIIRIGAFVESGDILVGKVT 748
Cdd:cd00653 490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKIT 569
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 749 PKGESDQPPeekllraIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREqgdeLPPGANMVVRVYVAQRRKIQVGDKMAG 828
Cdd:cd00653 570 PKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFAS 638
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 829 RHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDEMYGAEKSHqtvqa 908
Cdd:cd00653 639 RHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISE----- 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 909 FLEEASKQPgkawvynpddPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGG 988
Cdd:cd00653 714 LLGEAGLNY----------YGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGG 783
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 989 QRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV----------KGKPIPRPGTPESFKVLMRELQSLGLDI 1058
Cdd:cd00653 784 QRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDP 863
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
584-985 |
2.23e-168 |
|
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: 500.13 E-value: 2.23e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 584 ITKVNGIVSYVDANEIVVKDTEGNE--HFHYLQKYQRSNQDT---CLNQRPIVQIGDQVISGQvladgsacegGEIALGQ 658
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQamGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEAGGF----------GELPLGQ 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 659 NVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEkyEIEARQTKLGP-EEITREIPNISEESLNNLDEMGIIRIGAFV 737
Cdd:pfam00562 71 NAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEV 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 738 ESGDILVGKVTPkgesdqPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTreqgdeLPPGANMVVRVYVAQR 817
Cdd:pfam00562 149 KPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQK 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 818 RKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDemy 897
Cdd:pfam00562 217 RKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD--- 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 898 GAEKSHQTVQAFLEEAskqpgkawVYNPDdpGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQ 977
Cdd:pfam00562 294 GASTEVEDIGELLEKA--------GYNYY--GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTR 363
|
....*...
gi 2021943934 978 QPLGGKAQ 985
Cdd:pfam00562 364 QPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
15-1067 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2031.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFL-------EKGLIEELQNFSPISDYTGKLELHFIgeDYRLKRPRHDVEEAKRRDATFASQMYVTC 87
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFV--SYELGEPKYDVEECKERGLTYSAPLRVKL 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 88 RLINKETGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDK--NGRRTYNASVIPNRGAWLKFET 165
Cdd:PRK00405 102 RLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFEF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 166 DKNNLLYVRVDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQSSIDSAND----------------------------- 216
Cdd:PRK00405 182 DPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKEIEVPVEyllgkvlaedivdeetgevlaeandeite 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 217 -------------EGINSEDQALLELYKKLRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDEVRTL 283
Cdd:PRK00405 262 eldgpyirntlekDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 284 THEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPL 363
Cdd:PRK00405 342 TKEDIIATIKYLINLRNGKG--EVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPV 419
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 364 VAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATH 443
Cdd:PRK00405 420 VAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATY 499
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 444 ARVNEYGFIETPFWEVNNGRVNKEgnPVYLSADLEDECRVAPGDVATDKDGNILANLIPVRYRQDFEKVPPHQVDYVQLS 523
Cdd:PRK00405 500 ARVNEYGFIETPYRKVVDGKVTDE--IVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVS 577
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 524 PVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVK- 602
Cdd:PRK00405 578 PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRv 657
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 603 -----DTEGNEHFHyLQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGGEIALGQNVLIAYMPWEGYNYEDAIL 677
Cdd:PRK00405 658 eeldpGEDGVDIYN-LIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAIL 736
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 678 VSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPP 757
Cdd:PRK00405 737 ISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTP 816
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 758 EEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTR-EQGDELPPGANMVVRVYVAQRRKIQVGDKMAGRHGNKGII 836
Cdd:PRK00405 817 EEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVV 896
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 837 SRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDemyGAekSHQTVQAFLEEAskq 916
Cdd:PRK00405 897 SRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFD---GA--KEEEIKELLEEA--- 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 917 pgkawvyNPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRLGEMEV 996
Cdd:PRK00405 969 -------GLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1041
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2021943934 997 WALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDIGVYTDEGKE 1067
Cdd:PRK00405 1042 WALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
15-1065 |
0e+00 |
|
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: 1849.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFigEDYRLKRPRHDVEEAKRRDATFASQMYVTCRLINKET 94
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEF--GDYRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKET 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 95 GEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVR 174
Cdd:COG0085 91 GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVR 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 175 VDKTRKINAHVLMRAMGL-SDNDVVDKLRHPEFYQSSIDSANDEGINSEDQALLELYKKLRPGEPPSVSGGQQLLHSRFF 253
Cdd:COG0085 171 IDRKRKIPVTVLLRALGLeTDEEILEAFGDDPIQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFF 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 254 DPKRYDLGRVGRYKINKKLRLTVPDEVRTLTHEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGL 333
Cdd:COG0085 251 DPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGER--EPDDIDHLGNRRVRLVGELLQNQFRVGL 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 334 NRLERIIKERMTVGETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVR 413
Cdd:COG0085 329 SRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVR 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 414 DIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEGnpVYLSADLEDECRVAPGDVATDKD 493
Cdd:COG0085 409 DVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEI--EYLTADEEENYYIAQANAPLDED 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 494 GNILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVgtgles 573
Cdd:COG0085 487 GNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPLL------ 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 574 qvardsgmvpitkvngivsyvdaneivvkdtegnehfHY-LQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGG 652
Cdd:COG0085 561 -------------------------------------HYpLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNG 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 653 EIALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIR 732
Cdd:COG0085 604 ELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIR 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 733 IGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRV 812
Cdd:COG0085 684 IGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRV 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 813 YVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVP 892
Cdd:COG0085 764 YVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPV 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 893 FDEMYGAEkshqtVQAFLEEAskqpgkawvyNPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPY 972
Cdd:COG0085 844 FDGAPEEE-----IRELLEKA----------GLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPY 908
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 973 SLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQ 1052
Cdd:COG0085 909 SLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQ 988
|
1050
....*....|...
gi 2021943934 1053 SLGLDIGVYTDEG 1065
Cdd:COG0085 989 SLGLDVEVLSEDG 1001
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1058 |
0e+00 |
|
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: 1816.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 10 KTATYLPDLVEVQRASFKWFL----------EKGLIEELQNFSPISDYTGKLELHFIgeDYRLKRPRHDVEEAKRRDATF 79
Cdd:TIGR02013 12 PEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYL--SYRLGEPKYSVEECKERGLTY 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 80 ASQMYVTCRLINKE---TGEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD--KNGRRTYNASVI 154
Cdd:TIGR02013 90 SAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLFSARII 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 155 PNRGAWLKFETDKNNLLYVRVDKTRKINAHVLMRAMGLSDNDV-VDKLRHPEFYQSSIDSandEGINSEDQALLELYKKL 233
Cdd:TIGR02013 170 PYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLiLNRLGSGEYIRNTLRK---DPTNSEEEALVEIYRKL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 234 RPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKKLRLTVPDEVRTLTHEDVLSTIDYLInlELDIGGASLDDIDHL 313
Cdd:TIGR02013 247 RPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLI--KLRNGKGEIDDIDHL 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 314 GNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKR 393
Cdd:TIGR02013 325 GNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKR 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 394 RISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEGNPVYL 473
Cdd:TIGR02013 405 RLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTDEIDYL 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 474 SADLEDECRVAPGDVATDKDGNILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQ 553
Cdd:TIGR02013 485 TADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQ 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 554 RQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNGIVSYVDANEIVVKDTE------GNEHFHYLQKYQRSNQDTCLNQ 627
Cdd:TIGR02013 565 RQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEdeeepdGGIDIYRLLKYQRSNQDTCINQ 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 628 RPIVQIGDQVISGQVLADGSACEGGEIALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGP 707
Cdd:TIGR02013 645 RPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGP 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 708 EEITREIPNISEESLNNLDEMGIIRIGAFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGR 787
Cdd:TIGR02013 725 EEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGT 804
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 788 VLDVRIYTREQGDELPPGANMVVRVYVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRM 867
Cdd:TIGR02013 805 VIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRM 884
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 868 NVGQVFELLMGWAASNLNcrvkvvpfdeMYGAEKSHQTVQAFLEEASKQPGKAWVYNPDdpGKLLLKDGRTGEPFDQPVA 947
Cdd:TIGR02013 885 NIGQILETHLGWAGKRLG----------RKGVPIATPVFDGASEEEIKEYLEKAGLPRD--GKVRLYDGRTGEQFDRPVT 952
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 948 VGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALN 1027
Cdd:TIGR02013 953 VGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYE 1032
|
1050 1060 1070
....*....|....*....|....*....|.
gi 2021943934 1028 AIVKGKPIPRPGTPESFKVLMRELQSLGLDI 1058
Cdd:TIGR02013 1033 AIVKGENVPEPGIPESFNVLIKELQSLGLDI 1063
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
15-1078 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1658.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFIGEDYRLKRPRHDVEEAKRRDATFASQMYVTCRLINKET 94
Cdd:CHL00207 7 LPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFINLKT 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 95 GEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVR 174
Cdd:CHL00207 87 NKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIR 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 175 VDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQSSIDSANDEGINSEDQALLELYKKLRPGEPPSVSGGQQLLHSRFFD 254
Cdd:CHL00207 167 IDKNRKKPLIIFLKALGLTDQDIYSRLTKSEFLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFFD 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 255 PKRYDLGRVGRYKINKKLRLTVPDEVRTLTHEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGLN 334
Cdd:CHL00207 247 PKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKG--NFDDIDHLKNRRVRSVGELLQNQFRIGLK 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 335 RLERIIKERMTVGETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRD 414
Cdd:CHL00207 325 RLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRD 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 415 IHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEGNPVYLSADLEDECRVAPGDVATDKDG 494
Cdd:CHL00207 405 IHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIAPNDINLNKNN 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 495 NILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLESQ 574
Cdd:CHL00207 485 YFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQ 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 575 VARDSGMVPITKVNGIVSYVDANEIVVKDTEGNEHFHYLQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGGEI 654
Cdd:CHL00207 565 IALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSEL 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 655 ALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIRIG 734
Cdd:CHL00207 645 ALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIG 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 735 AFVESGDILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREQGDELPPGANMVVRVYV 814
Cdd:CHL00207 725 SKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFI 804
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 815 AQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFD 894
Cdd:CHL00207 805 AQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFD 884
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 895 EMYGAEKSHQTVQAFLEEASKQPGKAWVYNPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSL 974
Cdd:CHL00207 885 EMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSL 964
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 975 VTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQSL 1054
Cdd:CHL00207 965 VTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSL 1044
|
1050 1060 1070
....*....|....*....|....*....|..
gi 2021943934 1055 GLDIGVY----TDEGK----EVDLMQDINPRR 1078
Cdd:CHL00207 1045 GLDIEAYkienFLEGQrleiEINLMENYKYFR 1076
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
15-1061 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1579.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFIGEDYRLKRPRHDVEEAKRRDATFASQMYVTCRLINKET 94
Cdd:CHL00001 12 IPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGLIWKKS 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 95 GEIKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDKNGRRTYNASVIPNRGAWLKFETDKNNLLYVR 174
Cdd:CHL00001 92 RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKARIWAR 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 175 VDKTRKINAHVLMRAMGLSDNDVVDKLRHPEFYQSSIDSANDEGINSEDQALLELYKKL-RPGEPPSVSGG-QQLLHSRF 252
Cdd:CHL00001 172 VSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLNDKEKKKIGSKENAILEFYQQFaCVGGDPVFSESlCKELQKKF 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 253 FDpKRYDLGRVGRYKINKKLRLTVPDEVRTLTHEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVG 332
Cdd:CHL00001 252 FQ-QRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMG--TLDDIDHLKNKRIRSVADLLQDQFGLA 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 333 LNRLERIIKERMTVGETDSL--TPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGF 410
Cdd:CHL00001 329 LNRLENAVRGTICGAIRRKLipTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASF 408
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 411 AVRDIHPSHYGRLCPIETPEGPNAGLINSLATHARVNEYGFIETPFWEVNNgrVNKEGNPVYLSADLEDECRVAPGDVAT 490
Cdd:CHL00001 409 RVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISE--RSKEERMVYLSPSEDEYYMIAAGNSLA 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 491 DKDGNILANLIPVRYRQDFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTG 570
Cdd:CHL00001 487 LNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTG 566
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 571 LESQVARDSGMVPITKVNGIVSYVDANEIVVKdTEGNEHFHYLQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACE 650
Cdd:CHL00001 567 LERQVALDSGVVAIAEHEGKIIYTDTDKIILS-GNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATV 645
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 651 GGEIALGQNVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGI 730
Cdd:CHL00001 646 GGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGI 725
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 731 IRIGAFVESGDILVGKVTPK--GESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRiytREQGDELPPGANM 808
Cdd:CHL00001 726 VMLGSWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR---WIQKKGGSSYNPE 802
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 809 VVRVYVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRV 888
Cdd:CHL00001 803 TIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHY 882
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 889 KVVPFDEMYGAEKSHQTVQAFLEEASKQPGKAWVYNPDDPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARS 968
Cdd:CHL00001 883 RIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARS 962
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 969 TGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRP-GTPESFKVL 1047
Cdd:CHL00001 963 SGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLL 1042
|
1050
....*....|....
gi 2021943934 1048 MRELQSLGLDIGVY 1061
Cdd:CHL00001 1043 VRELRSLALELNHF 1056
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1067 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1057.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFL------EKGLIEELQNFSPISDYTGKLELHFIGEDYrlKRPRHDVEEAKRRDATFASQMYVTCR 88
Cdd:PRK09603 24 VPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPIQDEHNRITLEYAGCEF--GKSKYTVREAMERGITYSIPLKIKVR 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 89 LI----NKETGE------IKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQD--KNGRRTYNASVIPN 156
Cdd:PRK09603 102 LIlwekDTKSGEkngikdIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESstSLNKLIYTGQIIPD 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 157 RGAWLKFETDKNNLLYVRVDKTRKINAHVLMRAMGLSDNDVVdKLRHP-------------EFYQSSIDS---------- 213
Cdd:PRK09603 182 RGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDII-KMFYPlvkvryendkyliPFASLDANQrmefdlkdpq 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 214 ---------------------------------------------------------------------------AND-- 216
Cdd:PRK09603 261 gkiillagkkltsrkikelkenhlewveypmdillnrhlaepvmvgkevlldmltqldknklekihdlgvqefviINDla 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 217 ------------------------EGINSE-DQALLELYKKLRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYKINKK 271
Cdd:PRK09603 341 lghdasiihsfsadseslkllkqtEKIDDEnALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHK 420
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 272 LRLTVPDEVRTLTHEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTV--GET 349
Cdd:PRK09603 421 LGLHVPDYITTLTHEDIITTVKYLMKIKNNQG--KIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTmsGAF 498
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 350 DSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPIETP 429
Cdd:PRK09603 499 DSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETP 578
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 430 EGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEgnPVYLSADLEDECRVAPGDVATDKDGNILANLIPVRYRQDF 509
Cdd:PRK09603 579 EGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGE--TIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEI 656
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 510 EKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKVNG 589
Cdd:PRK09603 657 VLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAG 736
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 590 IVSYVDANEIVV--KDTEGNEHFHY-LQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGGEIALGQNVLIAYMP 666
Cdd:PRK09603 737 VVEKIDSKNIYIlgEGKEEAYIDAYsLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMP 816
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 667 WEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIRIGAFVESGDILVGK 746
Cdd:PRK09603 817 WNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGK 896
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 747 VTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTR------------------------------ 796
Cdd:PRK09603 897 TSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKkgyekdarvlsayeeekakldmehfdrltm 976
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 --------------------------------------------------------------------------------
Cdd:PRK09603 977 lnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslvkkyskevqnhyeitknnfleqkkvlgee 1056
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 797 --------EQGDELPPGANMVVRVYVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMN 868
Cdd:PRK09603 1057 heeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMN 1136
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 869 VGQVFELLMGWAASNLNCRVKvvpfdEMYgaekSHQTVQAFLEEASKQPGKAWVYNPDDP-------------------- 928
Cdd:PRK09603 1137 IGQILEMHLGLVGKEFGKQIA-----SML----EDKTKDFAKELRAKMLEIANAINEKDPltihalencsdeelleyakd 1207
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 929 --------------------------------GKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVT 976
Cdd:PRK09603 1208 wskgvkmaipvfegisqekfyklfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVT 1287
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 977 QQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGL 1056
Cdd:PRK09603 1288 HQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLAL 1367
|
1370
....*....|.
gi 2021943934 1057 DIGVYTDEGKE 1067
Cdd:PRK09603 1368 DINIFGDDVDE 1378
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
18-1058 |
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: 1002.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 18 LVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFIGEDYRLKRPRH---------DVEEAKRRDATFASQMYVTCR 88
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVeeggvtrklTPNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 89 LINKETGEIKEQEVFIGELPLMTE------------------------RGTFIINGAERVIVNQIVRSPGVYFKDeqDKN 144
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 145 GRRTY----NASVIPNRGAWLKFETD-KNNLLYVRVDKTRKinahvlmramglsdndvvdklrhpefyqssidsandegi 219
Cdd:cd00653 159 GKRIYtktsIPSYSPYRGSWLEVKSDkKKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 220 nseDQALLELYKKLrpgeppsvsggqqllhsrffdpkrydlgrvgrykinkklrltvpdevrtlthEDVLSTIDYLINLE 299
Cdd:cd00653 200 ---EEALKYIGKRF----------------------------------------------------EDLIYMIRKLILLV 224
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 300 LDIGgaSLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVGETDS--LTPAQLVNPKPLVAAIKEFFGSSQ-- 375
Cdd:cd00653 225 LGKG--KLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwg 302
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 376 ----------LSQFMDQTNPLAELTHKRRISAlgpGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHAR 445
Cdd:cd00653 303 skrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMAR 379
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 446 VNeyGFIETPFWEVNNgrvnkegnpvylsadledecrvapgdvatdkdgnilanlipvryrqdfekvpphQVDYVQLSPV 525
Cdd:cd00653 380 IS--GRIERPYRIVEK------------------------------------------------------EVTHIEISPS 403
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 526 QVISVATSLIPFLEHDDANRALMGSNMQRQAVP----------------LLRPERPLVGTGLESQVARdsgmvpitkvng 589
Cdd:cd00653 404 QILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAF------------ 471
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 590 ivsyvdaneivvkdtegnehfhylqkyqrsnqdtclnqrpivqigdqvisgqvladgsacegGEIALGQNVLIAYMPWEG 669
Cdd:cd00653 472 --------------------------------------------------------------GELPLGQNAIVAVMSYSG 489
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 670 YNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITR-EIPNISEESLNNLDEMGIIRIGAFVESGDILVGKVT 748
Cdd:cd00653 490 YNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKIT 569
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 749 PKGESDQPPeekllraIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREqgdeLPPGANMVVRVYVAQRRKIQVGDKMAG 828
Cdd:cd00653 570 PKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE----LNDGGNKLVKVYIRQKRKPQIGDKFAS 638
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 829 RHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDEMYGAEKSHqtvqa 908
Cdd:cd00653 639 RHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISE----- 713
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 909 FLEEASKQPgkawvynpddPGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGG 988
Cdd:cd00653 714 LLGEAGLNY----------YGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGG 783
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 989 QRLGEMEVWALEAYGAAYTLQELLTVKSDDMQGRNEALNAIV----------KGKPIPRPGTPESFKVLMRELQSLGLDI 1058
Cdd:cd00653 784 QRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDP 863
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1058 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 980.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 15 LPDLVEVQRASFKWFLEKGLIEE-----LQNFSPISDYTGKLELHFIgeDYRLKRPRHDVEEAKRRDATFASQMYVTCRL 89
Cdd:PRK14844 29 LLDLVKVQKESYDSFTPKNKGNErleviFHTIFPINDPLHRATIEFI--SCRVDDPKYDESECIKRGITFSAQVIASIRL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 90 IN-------------KETGE----------IKEQEVFIGELPLMTERGTFIINGAERVIVNQIVRSPGVYFKDEQDK--- 143
Cdd:PRK14844 107 VImqdgisldeyksiKESGDhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKtyn 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 144 NGRRTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAHVLMRAMGLSDNDVVDK-------LRH---------PEFY 207
Cdd:PRK14844 187 SGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRfyekikyIKHkdgwkvpfvPDKF 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 208 QSS-----------------------------------------------------IDSAN------------------- 215
Cdd:PRK14844 267 KGVrlpfdlmdvegnvllkanvritsrlakklydnelkeylvpfdsicglflaedlIDSASstkilsagesikledikkl 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 216 ----------------------------DEGINSEDqALLELYKKLRPGEPPSVSGGQQLLHSRFFDPKRYDLGRVGRYK 267
Cdd:PRK14844 347 ellsideisvlnidnlsvgpyilntlflDENMSYQD-ALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLK 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 268 INKKLRLTVPDEVRTLTHEDVLSTIDYLINLEldIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERMTVG 347
Cdd:PRK14844 426 LNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLR--DGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS 503
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 348 ETDSLTPAQLVNPKPLVAAIKEFFGSSQLSQFMDQTNPLAELTHKRRISALGPGGLTRERAGFAVRDIHPSHYGRLCPIE 427
Cdd:PRK14844 504 SLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIE 583
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 428 TPEGPNAGLINSLATHARVNEYGFIETPFWEVNNGRVNKEGNpvYLSADLEDECRVAPGDVATDKDGNILANLIPVRYRQ 507
Cdd:PRK14844 584 TPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIE--YLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAG 661
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 508 DFEKVPPHQVDYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVPLLRPERPLVGTGLESQVARDSGMVPITKV 587
Cdd:PRK14844 662 SFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKR 741
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 588 NGIVSYVDANEIVVK--DTEGNEHF----HYLQKYQRSNQDTCLNQRPIVQIGDQVISGQVLADGSACEGGEIALGQNVL 661
Cdd:PRK14844 742 DGIVDSSDSNSIVIRafDKERVNYLdvdiYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLL 821
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 662 IAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTKLGPEEITREIPNISEESLNNLDEMGIIRIGAFVESGD 741
Cdd:PRK14844 822 VAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGY 901
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 742 ILVGKVTPKGESDQPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTR------------------------- 796
Cdd:PRK14844 902 ILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRrgveenerallikqkeindfekerd 981
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 797 ----------------------------------------------------------------------------EQGD 800
Cdd:PRK14844 982 yiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklHEGY 1061
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 801 ELPPGANMVVRVYVAQRRKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWA 880
Cdd:PRK14844 1062 DLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 881 ASNLNCRV-----------------------------KVVPFD---------------------------------EMY- 897
Cdd:PRK14844 1142 CKKLGEKVgnildeinkiksafckgirslnddnftkfAAAYLDnkkienidddeitasvlntpnknalndelnelvENYl 1221
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 898 -GAEKSHQTVQAFL-------------------------EEASKQPGKAWVYNP-------------------DDPGKLL 932
Cdd:PRK14844 1222 nSCKSAYSNLRNFLievyscgsnvsicnnirdisdnnliEFARKLRDGIPVAAPvfegpkdeqiaklfelaglDNSGQAV 1301
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 933 LKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQRLGEMEVWALEAYGAAYTLQELL 1012
Cdd:PRK14844 1302 LYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEML 1381
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|....*.
gi 2021943934 1013 TVKSDDMQGRNEALNAIVKGKPIPRPGTPESFKVLMRELQSLGLDI 1058
Cdd:PRK14844 1382 TVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNV 1427
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
584-985 |
2.23e-168 |
|
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: 500.13 E-value: 2.23e-168
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 584 ITKVNGIVSYVDANEIVVKDTEGNE--HFHYLQKYQRSNQDT---CLNQRPIVQIGDQVISGQvladgsacegGEIALGQ 658
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQamGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEAGGF----------GELPLGQ 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 659 NVLIAYMPWEGYNYEDAILVSERMVTDDLYTSVHIEkyEIEARQTKLGP-EEITREIPNISEESLNNLDEMGIIRIGAFV 737
Cdd:pfam00562 71 NAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEV 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 738 ESGDILVGKVTPkgesdqPPEEKLLRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTreqgdeLPPGANMVVRVYVAQR 817
Cdd:pfam00562 149 KPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIKMVKVYIRQK 216
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 818 RKIQVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDemy 897
Cdd:pfam00562 217 RKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD--- 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 898 GAEKSHQTVQAFLEEAskqpgkawVYNPDdpGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQ 977
Cdd:pfam00562 294 GASTEVEDIGELLEKA--------GYNYY--GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTR 363
|
....*...
gi 2021943934 978 QPLGGKAQ 985
Cdd:pfam00562 364 QPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
18-1057 |
3.37e-122 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 402.41 E-value: 3.37e-122
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 18 LVEVQRASFKWFLEKGLIEELQNFSPISDYTGKLELHFigEDYRLKRPR----HDVE------EAKRRDATFASQMYVTC 87
Cdd:PRK08565 14 LVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVL--GKIRVGEPEikeaDGSErpitpmEARLRNLTYAAPLYLTM 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 88 RLINkETGEIKEQEVFIGELPLMTER------------------------GTFIINGAERVIVNQIVRSPGVYFKDEQDK 143
Cdd:PRK08565 92 IPVE-NGIEYEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNRVLVDKGEA 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 144 NGRRTYNASVIPNRG---AWLKFETDKNNLLYVRVDKTR-KINAHVLMRAMGL-SDNDVVDKLR-HPEFYQ---SSIDSA 214
Cdd:PRK08565 171 GSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAVPgKIPFVILMRALGLeTDRDIVYAVSlDPEIQQellPSLEQA 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 215 NDEGINSEDqALLELYKKLRPGEPPSV--SGGQQLLHSRFF-----DP-----KRYDLGRVGRykinkKLrltvpdevrt 282
Cdd:PRK08565 251 SSIAATVED-ALDYIGKRVAIGQPREYriERAEQILDKYLLphlgtSPedrikKAYFLGQMAS-----KL---------- 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 283 lthedvlstidylinLELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERM--TVGETDSLTPAQLVNP 360
Cdd:PRK08565 315 ---------------LELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLekSYARGRKLDLRAIVRP 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 361 KPLVAAIKEFF-------GSSQLSQFMDQTNPLAELTHKRRIsaLGPggLTRERAGFAVRDIHPSHYGRLCPIETPEGPN 433
Cdd:PRK08565 380 DIITERIRHALatgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPN 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 434 AGLINSLATHAR----VNEYGFIET-------PFWEVNnGRVNKEGNPVYL-----------------------SADLED 479
Cdd:PRK08565 456 CGLVKNLALMAQisvgVDEEEVEEIlyelgvvPVEEAR-EEEYISWSRVYLngrligyhpdgeelaekirelrrSGKISD 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 480 ECRVAPGD--------VATDkDGNILANLIPVRY------RQDFEKVP-------------------------------P 514
Cdd:PRK08565 535 EVNVAYIEtgeinevyVNCD-SGRVRRPLIVVENgkpkltREHVEKLKkgeltfddlvkmgvieyldaeeeenayvaldP 613
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 515 HQV----DYVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVpllrperplvgtGLESqvardsgmvpitkvngi 590
Cdd:PRK08565 614 EDLtpehTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSL------------GLYA----------------- 664
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 591 vsyvdANEIVVKDTEGneHF-HYlqkyqrsnqdtclNQRPIVQIGDQVISGqvLADGSAceggeialGQNVLIAYMPWEG 669
Cdd:PRK08565 665 -----ANFRIRTDTRG--HLlHY-------------PQRPLVQTRALEIIG--YNDRPA--------GQNAVVAVLSYTG 714
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 670 YNYEDAILVSERMVTDDLYTSVHIEKYEIEARQTkLGPEEITREIP--NIS----EESLNNLDEMGIIRIGAFVESGDIL 743
Cdd:PRK08565 715 YNIEDAIIMNKASIERGLARSTFFRTYETEERKY-PGGQEDKIEIPepNVRgyrgEEYYRKLDEDGIVSPEVEVKGGDVL 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 744 VGKVTPkgesdqP---PEEKLLRAIFGEKardvRDNSLRVPKTEKGRVLDVRIYTREQGDELppganmvVRVYVAQRRKI 820
Cdd:PRK08565 794 IGKTSP------PrflEELEELSLGLQER----RDTSVTVRHGEKGIVDTVLITESPEGNKL-------VKVRVRDLRIP 856
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 821 QVGDKMAGRHGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDEmygaE 900
Cdd:PRK08565 857 ELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYG----E 932
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 901 KSHQTVQAFLEEASKQPGKAWVYnpddpgklllkDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPL 980
Cdd:PRK08565 933 PEEELRKELLKLGYKPDGTEVMY-----------DGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPT 1001
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 981 GGKAQQGGQRLGEMEVWALEAYGAAYTLQELLTVKSD-------DMQGRNEALNAIvKGKPI-PRPG---------TPES 1043
Cdd:PRK08565 1002 EGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDkttiyvcELCGHIAWYDRR-KNKYVcPIHGdkgnispveVSYA 1080
|
1210
....*....|....
gi 2021943934 1044 FKVLMRELQSLGLD 1057
Cdd:PRK08565 1081 FKLLLQELMSMGIS 1094
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
519-1057 |
6.00e-72 |
|
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: 251.10 E-value: 6.00e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 519 YVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVpllrperplvgtGLESqvardsgmvpitkvngivsyvdANE 598
Cdd:TIGR03670 118 HLEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSL------------GLYA----------------------ANY 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 599 IVVKDTEGnehfHYLQkYQrsnqdtclnQRPIVQIGDQVISGqvLADGSAceggeialGQNVLIAYMPWEGYNYEDAILV 678
Cdd:TIGR03670 164 RIRLDTRG----HLLH-YP---------QKPLVKTRVLELIG--YDDRPA--------GQNFVVAVMSYEGYNIEDALIM 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 679 SERMVTDDLYTSVHIEKYEIEARQTKLGpEEITREIPNI------SEESLNNLDEMGIIRIGAFVESGDILVGKVTPkge 752
Cdd:TIGR03670 220 NKASIERGLARSTFFRTYEAEERRYPGG-QEDRFEIPEPdvrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP--- 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 753 sdqpP---EEkllRAIFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREQGDELppganmvVRVYVAQRRKIQVGDKMAGR 829
Cdd:TIGR03670 296 ----PrflEE---LREFGLVTERRRDTSVTVRHGEKGIVDKVIITETEEGNKL-------VKVRVRDLRIPELGDKFASR 361
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 830 HGNKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASNLNCRVKVVPFDEmygaEKSHQTVQAF 909
Cdd:TIGR03670 362 HGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEG----EPEEELRKEL 437
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 910 LEEASKQPGKAWVYnpddpgklllkDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQ 989
Cdd:TIGR03670 438 LKLGFKPDGKEVMY-----------DGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGL 506
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 990 RLGEMEVWALEAYGAAYTLQELLTVKSD-------DMQGRNEALNAIvKGKPI-PRPG---------TPESFKVLMRELQ 1052
Cdd:TIGR03670 507 RFGEMERDVLIGHGAAMLLKERLLDESDkyvvyvcENCGHIAWEDKR-KGTAYcPVCGetgdispveMSYAFKLLLDELK 585
|
....*
gi 2021943934 1053 SLGLD 1057
Cdd:TIGR03670 586 SLGIS 590
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
519-1057 |
4.95e-65 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 231.77 E-value: 4.95e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 519 YVQLSPVQVISVATSLIPFLEHDDANRALMGSNMQRQAVpllrperplvgtGLESqvardsgmvpitkvngivsyvdANE 598
Cdd:PRK07225 124 HLEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSL------------GLPA----------------------ANY 169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 599 IVVKDTEGneHF-HYLQKyqrsnqdtclnqrPIVQIGDQVISGQvladgsacegGEIALGQNVLIAYMPWEGYNYEDAIL 677
Cdd:PRK07225 170 KLRPDTRG--HLlHYPQV-------------PLVKTQTQEIIGF----------DERPAGQNFVVAVMSYEGYNIEDALI 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 678 VSERMVTDDLYTSVHIEKYEIEARQTKLGPEEiTREIPNI------SEESLNNLDEMGIIRIGAFVESGDILVGKVTPKG 751
Cdd:PRK07225 225 MNKASIERGLGRSHFFRTYEGEERRYPGGQED-RFEIPDKdvrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPPR 303
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 752 ESDQPPEekllraiFGEKARDVRDNSLRVPKTEKGRVLDVRIYTREQGDELppganmvVRVYVAQRRKIQVGDKMAGRHG 831
Cdd:PRK07225 304 FLEEPDD-------FGISPEKRRETSVTMRSGEEGIVDTVILTETEEGSRL-------VKVRVRDLRIPELGDKFASRHG 369
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 832 NKGIISRILPREDMPYLPDGTPVDIVLNPLGVPSRMNVGQVFELLMGWAASnLNC-RVKVVPFdemygaeksHQTVQAFL 910
Cdd:PRK07225 370 QKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGS-LEGrRVDGTAF---------SGEDEEDL 439
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 911 EEASKQPGkawvYNPDdpGKLLLKDGRTGEPFDQPVAVGYSHFLKLVHLVDDKIHARSTGPYSLVTQQPLGGKAQQGGQR 990
Cdd:PRK07225 440 REALEKLG----FEHT--GKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLR 513
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 991 LGEMEVWALEAYGAAYTLQELLTVKSDDMQ-------GRNEALNAIVKGKPIPRPGTPES---------FKVLMRELQSL 1054
Cdd:PRK07225 514 FGEMERDVLIGHGAAMLLKERLLDESDKVEiyvcakcGMIAIYDKKRNRKYCPICGEETDiypvemsyaFKLLLDELKSL 593
|
...
gi 2021943934 1055 GLD 1057
Cdd:PRK07225 594 GIA 596
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
18-363 |
2.47e-44 |
|
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: 166.02 E-value: 2.47e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 18 LVEVQRASFKWFLE---KGLIEE---LQNFSPISDYTG---KLELHFigEDYRLKRPRHDV----------EEAKRRDAT 78
Cdd:pfam04563 2 LVRQQLDSFNEFVDndlQKIIDEnalIESEFEIQHPGEngdKLSLKF--GQIRLGKPMFDEtdgstreiypQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 79 FASQMYVTCRLINKETGEIKEQEVFIGELPLMTE------------------------RGTFIINGAERVIVNQIVRS-- 132
Cdd:pfam04563 80 YSAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRsnacilsgateselvklgecpldpGGYFIINGSEKVIVAQEHRSrn 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 133 -PGVYFKDEQDK---NGRRTYNA--SVIPNRGAWLKF-ETDKNNLLYVRVDKTRK-INAHVLMRAMG-LSDNDVVDKLRH 203
Cdd:pfam04563 160 hPIVFKKADPKKrgsVASVRSSAeiSVRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGfTSDREIFELICY 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 204 PE---FYQS----SIDSANDEGINSEDQALlelykklrpgeppsvsggqQLLHSRFFDPKRYDLGRVGRYKINKKLRLTv 276
Cdd:pfam04563 240 DVndqQLQEellpSLEEGFKIRIQTQEQAL-------------------DYIGGRGRAIFRMGRPREPRIKYAEEILQK- 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 277 pdevRTLTHEDVLST--------IDYLIN--LELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIKERM-- 344
Cdd:pfam04563 300 ----EVLPHLGTYELdetkkayfIGYMIRrlLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLqk 375
|
410
....*....|....*....
gi 2021943934 345 TVGETDSLTPAQLVNPKPL 363
Cdd:pfam04563 376 VLGSPDDLMLQLLVNAKPI 394
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
17-448 |
3.26e-44 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 168.20 E-value: 3.26e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 17 DLVEVQRASFKWFLEKGLIEelqnfspISDYTGKLELHfIGEDYRLKRPRHDVE-----------------EAKRRDATF 79
Cdd:PRK09606 17 RLVRHHIDSYNDFVDNGLQK-------IIDEQGPIETE-IEDGVYVELGKIRVGkpvvkeadgsereiypmEARLRNLTY 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 80 ASQMYVTCRLInKETGEIKEQEVFIGELPLM-------------TER-----------GTFIINGAERVIVNQIVRSPGV 135
Cdd:PRK09606 89 SAPLYLEMSPV-EGGEEEEPEEVYIGELPVMvgskicnlyglseEELievgedpldpgGYFIVNGSERVLMTLEDLAPNK 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 136 YFKDEQDKNGRRTYNASVIPNRG---AWLKFETDKNNLLYV---RVdkTRKINAHVLMRAMGL-SDNDVVDKL-RHPEFY 207
Cdd:PRK09606 168 ILVEKDERYGDRIEVAKVFSQRRgyrALVTVERNRDGLLEVsfpSV--PGSIPFVILMRALGLeTDEEIVEAVsDDPEIV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 208 QSSIDSANDEGINSEDQALLELYKKLRPGEPpsvsggqqllhsrffdpKRYDLGRvGRYKINKKL--RLTVPDEVRtlth 285
Cdd:PRK09606 246 KFMLENLEEAEVDTQEEALEYIGKRVAPGQT-----------------KEYRIKR-AEYVIDRYLlpHLGVEPEVR---- 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 286 edvLSTIDYLIN-----LELDIGGASLDDIDHLGNRRVRSVGELLQNQVRVGLNRLERIIK---ERMTVGETDsLTPAQL 357
Cdd:PRK09606 304 ---RAKAHYLGRmaeacFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqlERANMRNRE-LSIKTA 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 358 VNPKPLVAAIKEFF-------GSSQLSQFMDQTNPLAELTHKRRISAlgpgGLTRERAGFAVRDIHPSHYGRLCPIETPE 430
Cdd:PRK09606 380 VRSDVLTERLEHAMatgnwvgGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPE 455
|
490
....*....|....*...
gi 2021943934 431 GPNAGLINSLATHARVNE 448
Cdd:PRK09606 456 GPNCGLVKNFAQMVEIST 473
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
131-319 |
6.22e-42 |
|
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: 151.73 E-value: 6.22e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 131 RSPGVYFKDEQDKNGR-RTYNASVIPNRGAWLKFETDKNNLLYVRVDKTRKINAHVLMRAMGL-SDNDVVDKLRHPEFYQ 208
Cdd:pfam04561 1 RSNGIYVEKELDKNGIiATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLvSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 209 SSIDSANDE-----GINSEDQALLELYK--KLRPGEPPSVSGGQQLLHSRFfdpkrydlgrvGRYKINKKLRLTVPDEVR 281
Cdd:pfam04561 81 QMLELLKPEleeaeNIYTQEEALDYIGKgfALRRGEEPRLQRAREILYSRD-----------PKYNLNKHLGLNEPFENE 149
|
170 180 190
....*....|....*....|....*....|....*...
gi 2021943934 282 TLTHEDVLSTIDYLINLELDIGgaSLDDIDHLGNRRVR 319
Cdd:pfam04561 150 RLKAQDILYMIDRLLNLKLGRR--KPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
378-445 |
3.84e-36 |
|
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: 130.72 E-value: 3.84e-36
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2021943934 378 QFMDQTNPLAELTHKRRISAlGPGGLTRERAGFAVRDIHPSHYGRLCPIETPEGPNAGLINSLATHAR 445
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
987-1063 |
4.30e-33 |
|
RNA polymerase Rpb2, domain 7; 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 comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 122.70 E-value: 4.30e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 987 GGQRLGEMEVWALEAYGAAYTLQELLTVKSD----DMQGRNEALNA-----IVKGKPIPRPGT-PESFKVLMRELQSLGL 1056
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGYiPESFKLLFQELQSLGI 80
|
....*..
gi 2021943934 1057 DIGVYTD 1063
Cdd:pfam04560 81 DPRLLLE 87
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
459-523 |
2.45e-19 |
|
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pssm-ID: 463067 [Multi-domain] Cd Length: 66 Bit Score: 82.80 E-value: 2.45e-19
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2021943934 459 VNNGRVNKEgnPVYLSADLEDECRVAPGDVATDKDGNILANLIPVRYRQDFEKVPPHQVDYVQLS 523
Cdd:pfam10385 4 VEDGKVTDE--IVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
583-648 |
8.87e-04 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 43.52 E-value: 8.87e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2021943934 583 PITKVNGIVSYV----DANEIVVKDTEGNEHFHYLQKyqrsnqdtclNQRPIVQIGDQVISGQVLADGSA 648
Cdd:PRK00566 930 IIAEIDGTVSFGketkGKRRIVITPDDGEEREYLIPK----------GKHLLVQEGDHVEAGDKLTDGSI 989
|
|
| |
