|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
2-1054 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1807.95 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 2 LSINRNAGMFVLPDFKQIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGELYRLEIPKFNEREAVYQSATYSSNL 81
Cdd:CHL00001 1 MLRDGNEGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 82 YAPAYLVDKKRGIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYT--LSVQG--VYTATIICNSGKSFKL 157
Cdd:CHL00001 81 YVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRseLDHNGisVYTGTIISDWGGRLEL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 158 ELDRQGCLWVRVGRNSKAPLLLLLIALGLEMRYI------PPMIVQR-TKKLNQLLLCVEDAKIDLCKRLKlkqkttqIE 230
Cdd:CHL00001 161 EIDRKARIWARVSRKQKISILVLLSAMGLNLREIldnvcyPEIFLSFlNDKEKKKIGSKENAILEFYQQFA-------CV 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 231 LGvtDPIYS----------LFLKPYELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKH 300
Cdd:CHL00001 234 GG--DPVFSeslckelqkkFFQQRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKN 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 301 KRVKWVSDLFCVQLNMALKKLNVAVHTNLNKMEARISRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKR 380
Cdd:CHL00001 312 KRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGR 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 381 KLSLLGPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTNSMQGHVIDMLP 460
Cdd:CHL00001 392 KLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSP 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 461 GEDEYSTIATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQ 540
Cdd:CHL00001 472 SEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQ 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 541 AVPLLKLERPIVGTGIESQVALDSGTVITAVQECKIHNVDATQIAYVPKDsfELLYINLLNYERSNNATCLHQRPIVECG 620
Cdd:CHL00001 552 AVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNG--DTLSIPLVMYQRSNKNTCMHQKPQVRRG 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 621 ETVQKGQLIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQI 700
Cdd:CHL00001 630 KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEI 709
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 701 PHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKQSEGLLHTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVR 780
Cdd:CHL00001 710 PHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 781 WITRDNHLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFEC 860
Cdd:CHL00001 790 WIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFEC 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 861 LLGLAGGYLNQHYRIMPFDERYGRESSRKLVFSELYKASQTTNYPWIFEPDSPGKSRLFDGRTGEVFNQPVTVGRAYMFK 940
Cdd:CHL00001 870 LLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILK 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 941 LIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLV 1020
Cdd:CHL00001 950 LIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTI 1029
|
1050 1060 1070
....*....|....*....|....*....|....
gi 108796736 1021 PKPIGTSDCLGVLIRELQCLGIQLDHTMLSQHNM 1054
Cdd:CHL00001 1030 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNF 1063
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
13-1042 |
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: 1019.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 13 LPDFKQIQIDSFRHFLTDL----------LRLELQRFGTIKHANQQLEFKLLGelYRLEIPKFNEREAVYQSATYSSNLY 82
Cdd:TIGR02013 17 VPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPIEDYTGNIELEYLS--YRLGEPKYSVEECKERGLTYSAPLK 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 83 APAYLVDKKR---GIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYTLSV------QGVYTATIICNSGK 153
Cdd:TIGR02013 95 VKLRLINKEEdgtKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKdttksgKVLFSARIIPYRGS 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 154 SFKLELDRQGCLWVRVGRNSKAPLLLLLIALGLEMRYI-------PPMIvqRTKKLNQLLLCVEDAKIDLCKRLKLKQKT 226
Cdd:TIGR02013 175 WLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLilnrlgsGEYI--RNTLRKDPTNSEEEALVEIYRKLRPGEPP 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 227 TqIELGVTDpIYSLFLKP--YELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVK 304
Cdd:TIGR02013 253 T-VEAARSL-LENLFFDPkrYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIR 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 305 WVSDLFCVQlnmalkklnvaVHTNLNKMEARI-SRMSLKSV--------VSSNAIATTFFRFVASYQLSQFLDQTNPLSE 375
Cdd:TIGR02013 331 SVGELLQNQ-----------FRVGLARMERIVrERMSTQDTdtltpqdlINAKPISAAIKEFFGSSQLSQFMDQTNPLAE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 376 IVHKRKLSLLGPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTNSMQGH- 454
Cdd:TIGR02013 400 LTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTd 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 455 VIDMLPGEDEYS-TIATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALM 533
Cdd:TIGR02013 480 EIDYLTADEEDNyVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALM 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 534 GSNMQRQAVPLLKLERPIVGTGIESQVALDSGTVITAVQECKIHNVDATQI------AYVPKDSFELLYiNLLNYERSNN 607
Cdd:TIGR02013 560 GSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIvirydeDEEEPDGGIDIY-RLLKYQRSNQ 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 608 ATCLHQRPIVECGETVQKGQLIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEAR 687
Cdd:TIGR02013 639 DTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEAR 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 688 ETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKqSEGLLhTPESKLLQDILGVQAFGTQDTCLK 767
Cdd:TIGR02013 719 DTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPK-GETEL-TPEEKLLRAIFGEKARDVRDTSLR 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 768 VPTRGEGRVIDVRWITR---DNHLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLS 844
Cdd:TIGR02013 797 VPPGVEGTVIDVKVFSReqgDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLN 876
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 845 PLGVPSRMNVGQVFECLLGLAGGYLNQHyrimpfderyGRESSRKLVFSELYKASQTTNYPWIFEPDspGKSRLFDGRTG 924
Cdd:TIGR02013 877 PLGVPSRMNIGQILETHLGWAGKRLGRK----------GVPIATPVFDGASEEEIKEYLEKAGLPRD--GKVRLYDGRTG 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 925 EVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHA 1004
Cdd:TIGR02013 945 EQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1024
|
1050 1060 1070
....*....|....*....|....*....|....*...
gi 108796736 1005 TARAEAPNAIVTGNLVPKPiGTSDCLGVLIRELQCLGI 1042
Cdd:TIGR02013 1025 VGRTKAYEAIVKGENVPEP-GIPESFNVLIKELQSLGL 1061
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
13-1042 |
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: 1000.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 13 LPDFKQIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGelYRLEIPKFNEREAVYQSATYSSNLYAPAYLVDKKR 92
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGD--YRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKET 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 93 GIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYT----LSVQGVYTATIICNSGKSFKLELDRQGCLWVR 168
Cdd:COG0085 91 GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVeeedKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVR 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 169 VGRNSKAPLL--------------LLLIALGLEMRYIPPMIVQRTKKLnqlllcVEDAKIDLCKRLKLKQKTTqIELGVT 234
Cdd:COG0085 171 IDRKRKIPVTvllralgletdeeiLEAFGDDPIQEYILATLEKDNTKT------QEEALLEIYRKLRPGEPPT-IERAEQ 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 235 DpIYSLFLKP--YELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCV 312
Cdd:COG0085 244 L-LDNLFFDPkrYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQN 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 313 QLNMALKKLNVAVHTNLNKMEARisRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGPGGLTP 392
Cdd:COG0085 323 QFRVGLSRMERVVRERMTTQDVE--AITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSR 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 393 RTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTnsmqGHV---IDML-PGEDEYSTI 468
Cdd:COG0085 401 ERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVEN----GKVtdeIEYLtADEEENYYI 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 469 ATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLE 548
Cdd:COG0085 477 AQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 549 RPivgtgiesqvaldsgtvitavqeckihnvdatqiayvpkdsfeLLYINLLNYERSNNATCLHQRPIVECGETVQKGQL 628
Cdd:COG0085 557 AP-------------------------------------------LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDV 593
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 629 IADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQIPHLNAHVL 708
Cdd:COG0085 594 LADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEAL 673
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 709 RHLDETGVVSLGAWVETGDVLVGKLTAKqSEGLLhTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITRDN-- 786
Cdd:COG0085 674 RNLDEDGIIRIGAEVKGGDILVGKVTPK-GETEL-TPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEgd 751
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 787 -HLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLA 865
Cdd:COG0085 752 eLPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWA 831
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 866 GGYLNQHYRIMPFDERYGREssrklVFSELYKAsqttnypwIFEPDspGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQV 945
Cdd:COG0085 832 AALLGRRVATPVFDGAPEEE-----IRELLEKA--------GLPPD--GKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMV 896
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 946 DDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLVPKPiG 1025
Cdd:COG0085 897 DDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEP-G 975
|
1050
....*....|....*..
gi 108796736 1026 TSDCLGVLIRELQCLGI 1042
Cdd:COG0085 976 IPESFKVLLKELQSLGL 992
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
18-1042 |
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: 763.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 18 QIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGELYRLEIPKFNE---------REAVYQSATYSSNLYAPAYLV 88
Cdd:cd00653 3 KQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIRLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 89 DKKRGIIQKQTVFLGSIPLM------------------------SARGTFVIRGVSRCIVSQLLRSPGIYYTLSVQG--V 142
Cdd:cd00653 83 VNDKGKIKEQEVFIGEIPIMlrsklcnlngltpeeliklgecplDPGGYFIINGTEKVIINQEQRSPNVIIVEDSKGkrI 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 143 YTATIICNSGKSFKLELDrqgclwvrvgrnskaplllllialglemryippmivqrtkklnqlllcvedakidlckrLKL 222
Cdd:cd00653 163 YTKTSIPSYSPYRGSWLE-----------------------------------------------------------VKS 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 223 KQKTTQIELgvtdpiyslflkpyelgrmgRLNLNKRLNLRvseFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKR 302
Cdd:cd00653 184 DKKKDRIYV--------------------RIDLKRQEEAL---KYIGKRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKR 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 303 VKWVSDLFCVQLNMALKKLNVAVHTNLNKMEARISRMSLKSVVSSNAIATTFFRFVASYQ------------LSQFLDQT 370
Cdd:cd00653 241 VRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRL 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 371 NPLSEIVHKRKLSllgPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIgdNGAIKTSLYKVctns 450
Cdd:cd00653 321 NPLSELSHKRRIS---SLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARI--SGRIERPYRIV---- 391
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 451 mqghvidmlpgedeystiatesclvvanssnqfqsipaqhrREFVTLRwdEIGfrntlPVHSFSVGVVLIPFLEHDDATR 530
Cdd:cd00653 392 -----------------------------------------EKEVTHI--EIS-----PSQILSVAASLIPFPEHNQSPR 423
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 531 ALMGSNMQRQAVP----------------LLKLERPIVGTGIESQVALDsgtvitavqeckihnvdatqiayvpkdsfel 594
Cdd:cd00653 424 NLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG------------------------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 595 lyinllnyersnnatclhqrpivecgetvqkgqliadgsatvdgELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVY 674
Cdd:cd00653 473 --------------------------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFF 508
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 675 TSLHIERYEAEARETNQAIETITK-QIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKQSEGLLHtpeskllqdI 753
Cdd:cd00653 509 RSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP---------I 579
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 754 LGVQAFGTQDTCLKVPTRGEGRVIDVRWITRDNhLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYL 833
Cdd:cd00653 580 FGEKARDVRDTSLKYPGGEKGIVDDVKIFSREL-NDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT 658
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 834 QDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDERYGRESSRKLVFSELykasqttNYPwifepdsp 913
Cdd:cd00653 659 EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGL-------NYY-------- 723
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 914 GKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVL 993
Cdd:cd00653 724 GKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLL 803
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*...
gi 108796736 994 QELLTTKSDHATARAEAPNAIV-TGNLVPKPIGTSDC--------LGVLIRELQCLGI 1042
Cdd:cd00653 804 QERLTIKSDDVVARVCVKCGIIlSANLCRLCKKGTNIskvgipyaFKLLFQELQSMNI 861
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
519-970 |
1.40e-134 |
|
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: 411.15 E-value: 1.40e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 519 LIPFLEHDDATRALMGSNMQRQAVpllklerpivgtGIesqvaldsgtvitavqeckihnvdatqiayvpkdsfellyIN 598
Cdd:pfam00562 4 LIPFVDHNQSPRNTYQCAMGKQAM------------GI----------------------------------------YT 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 599 LLNYERSNNAT---CLHQRPIVECGeTVQKGQLiadgsatvdGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYT 675
Cdd:pfam00562 32 LNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFT 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 676 SLHIERYEAEaRETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAkqsegllhTPESKLLQDILG 755
Cdd:pfam00562 102 SIHIKEIEAR-KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGP--------TELTKLLRAIFG 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 756 VQAFGTQDTCLKVPTRGEGRVIDVRWITRDNHllGHRKVIhVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQD 835
Cdd:pfam00562 173 EKARDVKDTSLKVPPGEEGVVDDVIVFELPPG--GIKMVK-VYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTED 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 836 GTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDeryGRESSRKLVFSELYKASqttnypwiFEPDspGK 915
Cdd:pfam00562 250 GIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAG--------YNYY--GK 316
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 108796736 916 SRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSR 970
Cdd:pfam00562 317 EVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
2-1054 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1807.95 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 2 LSINRNAGMFVLPDFKQIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGELYRLEIPKFNEREAVYQSATYSSNL 81
Cdd:CHL00001 1 MLRDGNEGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 82 YAPAYLVDKKRGIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYT--LSVQG--VYTATIICNSGKSFKL 157
Cdd:CHL00001 81 YVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRseLDHNGisVYTGTIISDWGGRLEL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 158 ELDRQGCLWVRVGRNSKAPLLLLLIALGLEMRYI------PPMIVQR-TKKLNQLLLCVEDAKIDLCKRLKlkqkttqIE 230
Cdd:CHL00001 161 EIDRKARIWARVSRKQKISILVLLSAMGLNLREIldnvcyPEIFLSFlNDKEKKKIGSKENAILEFYQQFA-------CV 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 231 LGvtDPIYS----------LFLKPYELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKH 300
Cdd:CHL00001 234 GG--DPVFSeslckelqkkFFQQRCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKN 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 301 KRVKWVSDLFCVQLNMALKKLNVAVHTNLNKMEARISRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKR 380
Cdd:CHL00001 312 KRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGR 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 381 KLSLLGPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTNSMQGHVIDMLP 460
Cdd:CHL00001 392 KLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSP 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 461 GEDEYSTIATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQ 540
Cdd:CHL00001 472 SEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQ 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 541 AVPLLKLERPIVGTGIESQVALDSGTVITAVQECKIHNVDATQIAYVPKDsfELLYINLLNYERSNNATCLHQRPIVECG 620
Cdd:CHL00001 552 AVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNG--DTLSIPLVMYQRSNKNTCMHQKPQVRRG 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 621 ETVQKGQLIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQI 700
Cdd:CHL00001 630 KCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEI 709
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 701 PHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKQSEGLLHTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVR 780
Cdd:CHL00001 710 PHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 781 WITRDNHLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFEC 860
Cdd:CHL00001 790 WIQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFEC 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 861 LLGLAGGYLNQHYRIMPFDERYGRESSRKLVFSELYKASQTTNYPWIFEPDSPGKSRLFDGRTGEVFNQPVTVGRAYMFK 940
Cdd:CHL00001 870 LLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILK 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 941 LIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLV 1020
Cdd:CHL00001 950 LIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTI 1029
|
1050 1060 1070
....*....|....*....|....*....|....
gi 108796736 1021 PKPIGTSDCLGVLIRELQCLGIQLDHTMLSQHNM 1054
Cdd:CHL00001 1030 PKPEDAPESFRLLVRELRSLALELNHFLVSEKNF 1063
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
13-1042 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1073.96 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 13 LPDFKQIQIDSFRHFLTDL-------LRLELQRFGTIKHANQQLEFKLLGelYRLEIPKFNEREAVYQSATYSSNLYAPA 85
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLQLDvppedegLEEVFRSIFPIEDFNGNLSLEFVS--YELGEPKYDVEECKERGLTYSAPLRVKL 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 86 YLVDKKRGIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYY------TLSVQGVYTATIICNSGKSFKLEL 159
Cdd:PRK00405 102 RLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFdhdkdkTSSGKLLYSARIIPYRGSWLEFEF 181
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 160 DRQGCLWVRVGRNSKAP---------------------LLLLLIALGLEMRYIPPMIVQRTKKLNQ--LLLCVEDAKIDL 216
Cdd:PRK00405 182 DPKDILYVRIDRRRKLPvtvllralgysdeeildlfyeKEEFGKEIEVPVEYLLGKVLAEDIVDEEtgEVLAEANDEITE 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 217 CKRLKLKQKTTQIELGVT---------------DP---------IYSLFLKP--YELGRMGRLNLNKRLNLRVSEFEILL 270
Cdd:PRK00405 262 ELDGPYIRNTLEKDPTSSreealveiyrrlrpgEPptveaarslLENLFFDPkrYDLSKVGRYKLNKKLGLDEDEDVRVL 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 271 RSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQlnmalkklnvaVHTNLNKMEaRI--SRMSL------- 341
Cdd:PRK00405 342 TKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQ-----------FRIGLSRME-RAvrERMSLqdldtlt 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 342 -KSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQN 420
Cdd:PRK00405 410 pQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPN 489
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 421 AGVVNSFTICAHIGDNGAIKTSLYKVcTNsmqGHVIDmlpgEDEYSTIATESCLVVA------NSSNQF--QSIPAQHRR 492
Cdd:PRK00405 490 IGLINSLATYARVNEYGFIETPYRKV-VD---GKVTD----EIVYLTADEEDNYVIAqanaplDEDGRFvdELVTARYKG 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 493 EFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLERPIVGTGIESQVALDSGTVITAVQ 572
Cdd:PRK00405 562 EFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKR 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 573 ECKIHNVDATQI--AYVPKDSFEL---LYiNLLNYERSNNATCLHQRPIVECGETVQKGQLIADGSATVDGELALGKNVL 647
Cdd:PRK00405 642 DGVVEYVDASRIvvRVEELDPGEDgvdIY-NLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVL 720
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 648 VAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGD 727
Cdd:PRK00405 721 VAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGD 800
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 728 VLVGKLTAKqSEGLLhTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITR----DNhlL--GHRKVIHVYILQ 801
Cdd:PRK00405 801 ILVGKVTPK-GETEL-TPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRieqgDE--LppGVNKLVKVYIAQ 876
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 802 ERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDER 881
Cdd:PRK00405 877 KRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGA 956
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 882 YGREssrklVFSELYKASqttnypwifePDSPGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVT 961
Cdd:PRK00405 957 KEEE-----IKELLEEAG----------LPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVT 1021
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 962 QQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLVPKPiGTSDCLGVLIRELQCLG 1041
Cdd:PRK00405 1022 QQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEP-GIPESFNVLVKELQSLG 1100
|
.
gi 108796736 1042 I 1042
Cdd:PRK00405 1101 L 1101
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
10-1044 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1038.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 10 MFVLPDFKQIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGELYRLEIPKFNEREAVYQSATYSSNLYAPAYLVD 89
Cdd:CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFIN 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 90 KKRGIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYTLSV----QGVYTATIICNSGKSFKLELDRQGCL 165
Cdd:CHL00207 84 LKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIkknsNKIYSATLIPNRGSWIKFELDKNKEI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 166 WVRVGRNSKAPLLLLLIALGLEMRYI-PPMIVQRTKKLNQLLLCV------EDAKIDLCKRLKLKQKTTQieLGVTDPIY 238
Cdd:CHL00207 164 WIRIDKNRKKPLIIFLKALGLTDQDIySRLTKSEFLKKLKPILLNsnsytnEEILLEIYKNLSPIEPATV--NDANQNLF 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 239 SLFLKP--YELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQLNM 316
Cdd:CHL00207 242 SRFFDPknYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRI 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 317 ALKKLNVAVHTNLNKMEarISRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGPGGLTPRTAR 396
Cdd:CHL00207 322 GLKRLERILRNRMTICD--IDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRIS 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 397 FRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTNSMQGHV----IDMLPgEDEYStIATES 472
Cdd:CHL00207 400 FAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGnpiyLTADS-EDLYR-IAPND 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 473 CLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLERPIV 552
Cdd:CHL00207 478 INLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIV 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 553 GTGIESQVALDSGTVITAVQECKIHNVDATQIAYVPKDSFELLYiNLLNYERSNNATCLHQRPIVECGETVQKGQLIADG 632
Cdd:CHL00207 558 GTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHY-YLQKYQRSNQNTCINYRPIVWVGEKINIGQILADG 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 633 SATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQIPHLNAHVLRHLD 712
Cdd:CHL00207 637 SDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLD 716
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 713 ETGVVSLGAWVETGDVLVGKLTAKQSEGLLhtPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITR---DNHLL 789
Cdd:CHL00207 717 ENGIISIGSKVLAGDILVGKITPKGESDQL--PEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRskgDELKF 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 790 GHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYL 869
Cdd:CHL00207 795 GYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNL 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 870 NQHYRIMPFDERYGRESSRKLVFSELYKASQTTNYPWIFEPDSPGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKI 949
Cdd:CHL00207 875 NKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKI 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 950 HARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLVPKPiGTSDC 1029
Cdd:CHL00207 955 HARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKP-GTPES 1033
|
1050
....*....|....*
gi 108796736 1030 LGVLIRELQCLGIQL 1044
Cdd:CHL00207 1034 FKVLMRELQSLGLDI 1048
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
13-1042 |
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: 1019.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 13 LPDFKQIQIDSFRHFLTDL----------LRLELQRFGTIKHANQQLEFKLLGelYRLEIPKFNEREAVYQSATYSSNLY 82
Cdd:TIGR02013 17 VPNLLEIQLDSYDWFLQQDtppekrkeegLEEVFKSIFPIEDYTGNIELEYLS--YRLGEPKYSVEECKERGLTYSAPLK 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 83 APAYLVDKKR---GIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYTLSV------QGVYTATIICNSGK 153
Cdd:TIGR02013 95 VKLRLINKEEdgtKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKdttksgKVLFSARIIPYRGS 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 154 SFKLELDRQGCLWVRVGRNSKAPLLLLLIALGLEMRYI-------PPMIvqRTKKLNQLLLCVEDAKIDLCKRLKLKQKT 226
Cdd:TIGR02013 175 WLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLilnrlgsGEYI--RNTLRKDPTNSEEEALVEIYRKLRPGEPP 252
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 227 TqIELGVTDpIYSLFLKP--YELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVK 304
Cdd:TIGR02013 253 T-VEAARSL-LENLFFDPkrYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIR 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 305 WVSDLFCVQlnmalkklnvaVHTNLNKMEARI-SRMSLKSV--------VSSNAIATTFFRFVASYQLSQFLDQTNPLSE 375
Cdd:TIGR02013 331 SVGELLQNQ-----------FRVGLARMERIVrERMSTQDTdtltpqdlINAKPISAAIKEFFGSSQLSQFMDQTNPLAE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 376 IVHKRKLSLLGPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTNSMQGH- 454
Cdd:TIGR02013 400 LTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTd 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 455 VIDMLPGEDEYS-TIATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALM 533
Cdd:TIGR02013 480 EIDYLTADEEDNyVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALM 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 534 GSNMQRQAVPLLKLERPIVGTGIESQVALDSGTVITAVQECKIHNVDATQI------AYVPKDSFELLYiNLLNYERSNN 607
Cdd:TIGR02013 560 GSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIvirydeDEEEPDGGIDIY-RLLKYQRSNQ 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 608 ATCLHQRPIVECGETVQKGQLIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEAR 687
Cdd:TIGR02013 639 DTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEAR 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 688 ETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKqSEGLLhTPESKLLQDILGVQAFGTQDTCLK 767
Cdd:TIGR02013 719 DTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPK-GETEL-TPEEKLLRAIFGEKARDVRDTSLR 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 768 VPTRGEGRVIDVRWITR---DNHLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLS 844
Cdd:TIGR02013 797 VPPGVEGTVIDVKVFSReqgDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLN 876
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 845 PLGVPSRMNVGQVFECLLGLAGGYLNQHyrimpfderyGRESSRKLVFSELYKASQTTNYPWIFEPDspGKSRLFDGRTG 924
Cdd:TIGR02013 877 PLGVPSRMNIGQILETHLGWAGKRLGRK----------GVPIATPVFDGASEEEIKEYLEKAGLPRD--GKVRLYDGRTG 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 925 EVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHA 1004
Cdd:TIGR02013 945 EQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1024
|
1050 1060 1070
....*....|....*....|....*....|....*...
gi 108796736 1005 TARAEAPNAIVTGNLVPKPiGTSDCLGVLIRELQCLGI 1042
Cdd:TIGR02013 1025 VGRTKAYEAIVKGENVPEP-GIPESFNVLIKELQSLGL 1061
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
13-1042 |
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: 1000.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 13 LPDFKQIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGelYRLEIPKFNEREAVYQSATYSSNLYAPAYLVDKKR 92
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGD--YRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKET 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 93 GIIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYT----LSVQGVYTATIICNSGKSFKLELDRQGCLWVR 168
Cdd:COG0085 91 GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVeeedKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVR 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 169 VGRNSKAPLL--------------LLLIALGLEMRYIPPMIVQRTKKLnqlllcVEDAKIDLCKRLKLKQKTTqIELGVT 234
Cdd:COG0085 171 IDRKRKIPVTvllralgletdeeiLEAFGDDPIQEYILATLEKDNTKT------QEEALLEIYRKLRPGEPPT-IERAEQ 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 235 DpIYSLFLKP--YELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCV 312
Cdd:COG0085 244 L-LDNLFFDPkrYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQN 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 313 QLNMALKKLNVAVHTNLNKMEARisRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGPGGLTP 392
Cdd:COG0085 323 QFRVGLSRMERVVRERMTTQDVE--AITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSR 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 393 RTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVCTnsmqGHV---IDML-PGEDEYSTI 468
Cdd:COG0085 401 ERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVEN----GKVtdeIEYLtADEEENYYI 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 469 ATESCLVVANSSNQFQSIPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLE 548
Cdd:COG0085 477 AQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 549 RPivgtgiesqvaldsgtvitavqeckihnvdatqiayvpkdsfeLLYINLLNYERSNNATCLHQRPIVECGETVQKGQL 628
Cdd:COG0085 557 AP-------------------------------------------LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDV 593
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 629 IADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQIPHLNAHVL 708
Cdd:COG0085 594 LADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEAL 673
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 709 RHLDETGVVSLGAWVETGDVLVGKLTAKqSEGLLhTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITRDN-- 786
Cdd:COG0085 674 RNLDEDGIIRIGAEVKGGDILVGKVTPK-GETEL-TPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEgd 751
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 787 -HLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLA 865
Cdd:COG0085 752 eLPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWA 831
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 866 GGYLNQHYRIMPFDERYGREssrklVFSELYKAsqttnypwIFEPDspGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQV 945
Cdd:COG0085 832 AALLGRRVATPVFDGAPEEE-----IRELLEKA--------GLPPD--GKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMV 896
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 946 DDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGNLVPKPiG 1025
Cdd:COG0085 897 DDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEP-G 975
|
1050
....*....|....*..
gi 108796736 1026 TSDCLGVLIRELQCLGI 1042
Cdd:COG0085 976 IPESFKVLLKELQSLGL 992
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
18-1042 |
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: 763.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 18 QIQIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLLGELYRLEIPKFNE---------REAVYQSATYSSNLYAPAYLV 88
Cdd:cd00653 3 KQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIRLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 89 DKKRGIIQKQTVFLGSIPLM------------------------SARGTFVIRGVSRCIVSQLLRSPGIYYTLSVQG--V 142
Cdd:cd00653 83 VNDKGKIKEQEVFIGEIPIMlrsklcnlngltpeeliklgecplDPGGYFIINGTEKVIINQEQRSPNVIIVEDSKGkrI 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 143 YTATIICNSGKSFKLELDrqgclwvrvgrnskaplllllialglemryippmivqrtkklnqlllcvedakidlckrLKL 222
Cdd:cd00653 163 YTKTSIPSYSPYRGSWLE-----------------------------------------------------------VKS 183
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 223 KQKTTQIELgvtdpiyslflkpyelgrmgRLNLNKRLNLRvseFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKR 302
Cdd:cd00653 184 DKKKDRIYV--------------------RIDLKRQEEAL---KYIGKRFEDLIYMIRKLILLVLGKGKLDDIDHLGNKR 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 303 VKWVSDLFCVQLNMALKKLNVAVHTNLNKMEARISRMSLKSVVSSNAIATTFFRFVASYQ------------LSQFLDQT 370
Cdd:cd00653 241 VRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRL 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 371 NPLSEIVHKRKLSllgPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIgdNGAIKTSLYKVctns 450
Cdd:cd00653 321 NPLSELSHKRRIS---SLGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARI--SGRIERPYRIV---- 391
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 451 mqghvidmlpgedeystiatesclvvanssnqfqsipaqhrREFVTLRwdEIGfrntlPVHSFSVGVVLIPFLEHDDATR 530
Cdd:cd00653 392 -----------------------------------------EKEVTHI--EIS-----PSQILSVAASLIPFPEHNQSPR 423
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 531 ALMGSNMQRQAVP----------------LLKLERPIVGTGIESQVALDsgtvitavqeckihnvdatqiayvpkdsfel 594
Cdd:cd00653 424 NLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG------------------------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 595 lyinllnyersnnatclhqrpivecgetvqkgqliadgsatvdgELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVY 674
Cdd:cd00653 473 --------------------------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFF 508
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 675 TSLHIERYEAEARETNQAIETITK-QIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAKQSEGLLHtpeskllqdI 753
Cdd:cd00653 509 RSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP---------I 579
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 754 LGVQAFGTQDTCLKVPTRGEGRVIDVRWITRDNhLLGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYL 833
Cdd:cd00653 580 FGEKARDVRDTSLKYPGGEKGIVDDVKIFSREL-NDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFT 658
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 834 QDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDERYGRESSRKLVFSELykasqttNYPwifepdsp 913
Cdd:cd00653 659 EDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGL-------NYY-------- 723
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 914 GKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVL 993
Cdd:cd00653 724 GKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLL 803
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*...
gi 108796736 994 QELLTTKSDHATARAEAPNAIV-TGNLVPKPIGTSDC--------LGVLIRELQCLGI 1042
Cdd:cd00653 804 QERLTIKSDDVVARVCVKCGIIlSANLCRLCKKGTNIskvgipyaFKLLFQELQSMNI 861
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
63-1045 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 677.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 63 PKFNEREAVYQSATYSSNLYAPAYLV----DKKRG------IIQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPG 132
Cdd:PRK09603 78 SKYTVREAMERGITYSIPLKIKVRLIlwekDTKSGekngikDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPG 157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 133 IYY------TLSVQGVYTATIICNSGKSFKLELDRQGCLWVRVGRNSKAPLLLL------------------LIALGLEM 188
Cdd:PRK09603 158 VIFkeeessTSLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILframdyqkqdiikmfyplVKVRYEND 237
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 189 RYIPP--------------------MIVQRTKKLNQ---------------------------------------LLLCV 209
Cdd:PRK09603 238 KYLIPfasldanqrmefdlkdpqgkIILLAGKKLTSrkikelkenhlewveypmdillnrhlaepvmvgkevlldMLTQL 317
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 210 EDAKI---------------DLC---------------KRLKLKQKTTQIE-------------LGVTDPIYS------- 239
Cdd:PRK09603 318 DKNKLekihdlgvqefviinDLAlghdasiihsfsadsESLKLLKQTEKIDdenalaairihkvMKPGDPVTTevakqfv 397
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 240 --LFLKP--YELGRMGRLNLNKRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQLN 315
Cdd:PRK09603 398 kkLFFDPerYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 316 MALKKLNVAVHTNLNKMEARISRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGPGGLTPRTA 395
Cdd:PRK09603 478 SGLVKMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRV 557
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 396 RFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAHIGDNGAIKTSLYKVctnsMQGHVIDmlpgEDEYSTIATESCLV 475
Cdd:PRK09603 558 GFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKV----VDGKVVG----ETIYLTAIQEDSHI 629
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 476 VANSSNQFQS--------IPAQHRREFVTLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKL 547
Cdd:PRK09603 630 IAPASTPIDEegnilgdlIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRS 709
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 548 ERPIVGTGIESQVALDSGTVITAVQECKIHNVDATQIaYVPKDSFELLYIN---LLNYERSNNATCLHQRPIVECGETVQ 624
Cdd:PRK09603 710 DAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNI-YILGEGKEEAYIDaysLQKNLRTNQNTSFNQVPIVKVGDKVE 788
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 625 KGQLIADGSATVDGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQIPHLN 704
Cdd:PRK09603 789 AGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVK 868
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 705 AHVLRHLDETGVVSLGAWVETGDVLVGKLTAKQSegLLHTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITR 784
Cdd:PRK09603 869 EEALAHLDESGIVKVGTYVSAGMILVGKTSPKGE--IKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTK 946
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 --------------------------------------------------------------------------------
Cdd:PRK09603 947 kgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlas 1026
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 785 ----------------DNHLLGHRKV-------------------------IHVYILQERKIQVGDKVAGRHGNKGVVSR 823
Cdd:PRK09603 1027 lvkkyskevqnhyeitKNNFLEQKKVlgeeheeklsilekddilpngvikkVKLYIATKRKLKVGDKMAGRHGNKGIVSN 1106
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 824 ILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDER---------------------- 881
Cdd:PRK09603 1107 IVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTkdfakelrakmleianainekd 1186
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 882 -----------------YGRESSRKLVFS-ELYKASQTTNYPWIFE---PDSPGKSRLFDGRTGEVFNQPVTVGRAYMFK 940
Cdd:PRK09603 1187 pltihalencsdeelleYAKDWSKGVKMAiPVFEGISQEKFYKLFElakIAMDGKMDLYDGRTGEKMRERVNVGYMYMIK 1266
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 941 LIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLTTKSDHATARAEAPNAIVTGnlv 1020
Cdd:PRK09603 1267 LHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKG--- 1343
|
1290 1300
....*....|....*....|....*...
gi 108796736 1021 pKPIGTS---DCLGVLIRELQCLGIQLD 1045
Cdd:PRK09603 1344 -EQVGESeipETFYVLTKELQSLALDIN 1370
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
28-1055 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 615.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 28 LTDLLRLELQRFGTI---KHANQQLE------FKLLGELYRLEI---------PKFNEREAVYQSATYSSNLYAPAYLVD 89
Cdd:PRK14844 29 LLDLVKVQKESYDSFtpkNKGNERLEvifhtiFPINDPLHRATIefiscrvddPKYDESECIKRGITFSAQVIASIRLVI 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 90 KKRGI-----------------------IQKQTVFLGSIPLMSARGTFVIRGVSRCIVSQLLRSPGIYYTlSVQG----- 141
Cdd:PRK14844 109 MQDGIsldeyksikesgdhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFD-SDKGktyns 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 142 ---VYTATIICNSGKSFKLELDRQGCLWVRVGRNSKAPLLLLLIAL-----------GLEMRYIP-------PMI----- 195
Cdd:PRK14844 188 gklIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALglsnndildrfYEKIKYIKhkdgwkvPFVpdkfk 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 196 --------------------VQRTKKL----------------------------------NQLLLCVEDAKIDLCKRLK 221
Cdd:PRK14844 268 gvrlpfdlmdvegnvllkanVRITSRLakklydnelkeylvpfdsicglflaedlidsassTKILSAGESIKLEDIKKLE 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 222 L----KQKTTQIE-----------------LGVTDPIYSLF--LKP----------------------YELGRMGRLNLN 256
Cdd:PRK14844 348 LlsidEISVLNIDnlsvgpyilntlfldenMSYQDALYEIYkvLRPgevpvleiveeffrnlffspeyYDLSNIGRLKLN 427
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 257 KRLNLRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQLNMALKKLNVAVHTNLNKmeARI 336
Cdd:PRK14844 428 SYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMST--SSL 505
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 337 SRMSLKSVVSSNAIATTFFRFVASYQLSQFLDQTNPLSEIVHKRKLSLLGPGGLTPRTARFRVRDIHPSQYGRICPVQTA 416
Cdd:PRK14844 506 DKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 585
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 417 EGQNAGVVNSFTICAHIGDNGAIKtSLYKVCTNSMQGHVIDMLPGEDEYST-IATESCLVVANSSNQFQSIPAQHRREFV 495
Cdd:PRK14844 586 EGQNIGLINSLAIYARINKYGFIE-SPYRKVVNRVVTDQIEYLSAIDEGLYyIADTSAKLDENNCFVDDMLYCRYAGSFV 664
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 496 TLRWDEIGFRNTLPVHSFSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLERPIVGTGIESQVALDSGTVITAVQECK 575
Cdd:PRK14844 665 MVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGI 744
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 576 IHNVDATQIAYVPKDSFELLYIN-----LLNYERSNNATCLHQRPIVECGETVQKGQLIADGSATVDGELALGKNVLVAY 650
Cdd:PRK14844 745 VDSSDSNSIVIRAFDKERVNYLDvdiyhLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAF 824
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 651 MPWEGYNFEDAVLINERLIYEDVYTSLHIERYEAEARETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGDVLV 730
Cdd:PRK14844 825 MSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILV 904
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 731 GKLTAKQSegLLHTPESKLLQDILGVQAFGTQDTCLKVPTRGEGRVIDVRWITR-----------------------DNH 787
Cdd:PRK14844 905 GKVTPKPS--LSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRrgveenerallikqkeindfekeRDY 982
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 788 LLG-----------------------------------------------------------------HRKV-------- 794
Cdd:PRK14844 983 IINvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfKRKVeklhegyd 1062
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 795 --------IHVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLA- 865
Cdd:PRK14844 1063 lpqgvsmsVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWAc 1142
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 866 -------GGYLNQ---------------------HYRIMPFDER------------------------------------ 881
Cdd:PRK14844 1143 kklgekvGNILDEinkiksafckgirslnddnftKFAAAYLDNKkienidddeitasvlntpnknalndelnelvenyln 1222
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 882 ------------------YGR-----------------ESSRKL-----VFSELYKASQTTNYPWIFE---PDSPGKSRL 918
Cdd:PRK14844 1223 scksaysnlrnflievysCGSnvsicnnirdisdnnliEFARKLrdgipVAAPVFEGPKDEQIAKLFElagLDNSGQAVL 1302
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 919 FDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAFQGFGAACVLQELLT 998
Cdd:PRK14844 1303 YDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLT 1382
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|....*..
gi 108796736 999 TKSDHATARAEAPNAIVTGNlVPKPIGTSDCLGVLIRELQCLGIQLDhtmLSQHNMI 1055
Cdd:PRK14844 1383 VKSDDINGRVKIYESIIKGD-SNFECGIPESFNVMIKELRSLCLNVD---LKQNDVV 1435
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
519-970 |
1.40e-134 |
|
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: 411.15 E-value: 1.40e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 519 LIPFLEHDDATRALMGSNMQRQAVpllklerpivgtGIesqvaldsgtvitavqeckihnvdatqiayvpkdsfellyIN 598
Cdd:pfam00562 4 LIPFVDHNQSPRNTYQCAMGKQAM------------GI----------------------------------------YT 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 599 LLNYERSNNAT---CLHQRPIVECGeTVQKGQLiadgsatvdGELALGKNVLVAYMPWEGYNFEDAVLINERLIYEDVYT 675
Cdd:pfam00562 32 LNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFT 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 676 SLHIERYEAEaRETNQAIETITKQIPHLNAHVLRHLDETGVVSLGAWVETGDVLVGKLTAkqsegllhTPESKLLQDILG 755
Cdd:pfam00562 102 SIHIKEIEAR-KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGP--------TELTKLLRAIFG 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 756 VQAFGTQDTCLKVPTRGEGRVIDVRWITRDNHllGHRKVIhVYILQERKIQVGDKVAGRHGNKGVVSRILPRQDMPYLQD 835
Cdd:pfam00562 173 EKARDVKDTSLKVPPGEEGVVDDVIVFELPPG--GIKMVK-VYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTED 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 836 GTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDeryGRESSRKLVFSELYKASqttnypwiFEPDspGK 915
Cdd:pfam00562 250 GIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAG--------YNYY--GK 316
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 108796736 916 SRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSR 970
Cdd:pfam00562 317 EVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
20-1042 |
2.69e-76 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 272.99 E-value: 2.69e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 20 QIDSFRHFLTDLLRLELQRFGTIKHANQQLEFKLlgELYRLEIPKFNE----------REAVYQSATYSSNLYAPAYLVD 89
Cdd:PRK08565 18 HLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVL--GKIRVGEPEIKEadgserpitpMEARLRNLTYAAPLYLTMIPVE 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 90 KkrGIIQK-QTVFLGSIPLM--SAR----------------------GTFVIRGVSRCIVSQL-LRSPGIYYTLSVQG-- 141
Cdd:PRK08565 96 N--GIEYEpEEVKIGDLPIMvkSKIcplsglspdelieigedpkdpgGYFIINGSERVIVSQEdLAPNRVLVDKGEAGss 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 142 -VYTATIICNS-GKSFKLELDRQ--GCLWVRVGR-NSKAPLLLLlialgleMRY------------------IPPMIVQR 198
Cdd:PRK08565 174 iTHTAKVISSRaGYRAQVTVERRkdGTIYVSFPAvPGKIPFVIL-------MRAlgletdrdivyavsldpeIQQELLPS 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 199 TKKLNQLLLCVEDAKIDLCKRLKLKQ-KTTQIE-------------LGVT--DPIYslflKPYELGRMGRlnlnkrlnlr 262
Cdd:PRK08565 247 LEQASSIAATVEDALDYIGKRVAIGQpREYRIEraeqildkyllphLGTSpeDRIK----KAYFLGQMAS---------- 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 263 vsefeillrsqdlivasdYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQLNMALKKLNVAVHTNLNKMEARISRMSLK 342
Cdd:PRK08565 313 ------------------KLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLR 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 343 SVVSSNAIATTFFRFVASYQ-------LSQFLDQTNPLSEIVH-KRKLSLLgpggltPRT-ARFRVRDIHPSQYGRICPV 413
Cdd:PRK08565 375 AIVRPDIITERIRHALATGNwvggrtgVSQLLDRTNYLSTLSHlRRVVSPL------SRGqPHFEARDLHGTQWGRICPF 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 414 QTAEGQNAGVVNSFTICAHIG---DNGAIKTSLYKvctnsmqghvIDMLPGEDEYSTIATESCLVVANSSnqfqsIPAQH 490
Cdd:PRK08565 449 ETPEGPNCGLVKNLALMAQISvgvDEEEVEEILYE----------LGVVPVEEAREEEYISWSRVYLNGR-----LIGYH 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 491 R--REFV-TLRwdeiGFRNTLPVHSfsvgVVLIPFLEHDDATRALMGSNMQRQAVPLL-------KLERPIV-----GT- 554
Cdd:PRK08565 514 PdgEELAeKIR----ELRRSGKISD----EVNVAYIETGEINEVYVNCDSGRVRRPLIvvengkpKLTREHVeklkkGEl 585
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 555 --------GI----------ESQVALDSGTVITAVQECK-----IHNVDATQIAYV-----PKDSFEL------LYINLL 600
Cdd:PRK08565 586 tfddlvkmGVieyldaeeeeNAYVALDPEDLTPEHTHLEiwppaILGITASIIPYPehnqsPRNTYQAamakqsLGLYAA 665
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 601 NYERS--NNATCLH--QRPIVEcgetvqkgqliadgSATVD----GELALGKNVLVAYMPWEGYNFEDAVLINERLIYED 672
Cdd:PRK08565 666 NFRIRtdTRGHLLHypQRPLVQ--------------TRALEiigyNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERG 731
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 673 VYTSLHIERYEAEARE----TNQAIETITKQIP-HLNAHVLRHLDETGVVSLGAWVETGDVLVGKltakqsegllhTPES 747
Cdd:PRK08565 732 LARSTFFRTYETEERKypggQEDKIEIPEPNVRgYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGK-----------TSPP 800
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 748 KLLQDI--LGVQAFGTQDTclKVPTR-GEGRVIDVRWITRDNhllGHRKVIHVYILQERKIQVGDKVAGRHGNKGVVSRI 824
Cdd:PRK08565 801 RFLEELeeLSLGLQERRDT--SVTVRhGEKGIVDTVLITESP---EGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGML 875
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 825 LPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDERyGRESSRKlvfsELYKASqttny 904
Cdd:PRK08565 876 VPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGE-PEEELRK----ELLKLG----- 945
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 905 pwiFEPDspGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAF 984
Cdd:PRK08565 946 ---YKPD--GTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCL 1020
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 108796736 985 QGFGAACVLQELLTTKSDHAT--------------ARAEAPNAIV---TGNLvpKPIGTSDCLGVLIRELQCLGI 1042
Cdd:PRK08565 1021 IGHGAAMLLKERLLDSSDKTTiyvcelcghiawydRRKNKYVCPIhgdKGNI--SPVEVSYAFKLLLQELMSMGI 1093
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
513-1042 |
2.94e-65 |
|
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: 231.84 E-value: 2.94e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 513 FSVGVVLIPFLEHDDATRALMGSNMQRQAVPLLKLERPIvgtgiesqvALDSgtvitavqecKIHnvdatqiayvpkdsf 592
Cdd:TIGR03670 127 LGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRI---------RLDT----------RGH--------------- 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 593 ellyinLLNYErsnnatclhQRPIVECGETVQKGQliadgsatvdGELALGKNVLVAYMPWEGYNFEDAVLINERLIYED 672
Cdd:TIGR03670 173 ------LLHYP---------QKPLVKTRVLELIGY----------DDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERG 227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 673 VYTSLHIERYEAEARE----TNQAIETITKQIP-HLNAHVLRHLDETGVVSLGAWVETGDVLVGKltakqsegllhTPES 747
Cdd:TIGR03670 228 LARSTFFRTYEAEERRypggQEDRFEIPEPDVRgYRGEEAYKHLDEDGIVYPEVEVKGGDVLIGK-----------TSPP 296
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 748 KLLQ--DILGVQAFGTQDTclKVPTR-GEGRVIDVRWITRDNHllGHRKViHVYILQERKIQVGDKVAGRHGNKGVVSRI 824
Cdd:TIGR03670 297 RFLEelREFGLVTERRRDT--SVTVRhGEKGIVDKVIITETEE--GNKLV-KVRVRDLRIPELGDKFASRHGQKGVIGMI 371
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 825 LPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGYLNQHYRIMPFDERyGRESSRKlvfsELYKASqttny 904
Cdd:TIGR03670 372 VPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGE-PEEELRK----ELLKLG----- 441
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 905 pwiFEPDspGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSRQGGQRVGEMEVWAF 984
Cdd:TIGR03670 442 ---FKPD--GKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVL 516
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 108796736 985 QGFGAACVLQELLTTKSDHATA-----------------RAEAPNAIVTGNLvpKPIGTSDCLGVLIRELQCLGI 1042
Cdd:TIGR03670 517 IGHGAAMLLKERLLDESDKYVVyvcencghiawedkrkgTAYCPVCGETGDI--SPVEMSYAFKLLLDELKSLGI 589
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
513-1002 |
6.68e-61 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 219.45 E-value: 6.68e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 513 FSVGVVLIPFLEHDDATRALMGSNMQRQAVPL----LKLeRPivgtgiesqvaldsgtvitavqECKIHnvdatqiayvp 588
Cdd:PRK07225 133 LGIGAGMIPYPEHNASPRITMGAGMIKQSLGLpaanYKL-RP----------------------DTRGH----------- 178
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 589 kdsfellyinLLNYErsnnatclhQRPIVECGETVQKGqliadgsatVDGELAlGKNVLVAYMPWEGYNFEDAVLINERL 668
Cdd:PRK07225 179 ----------LLHYP---------QVPLVKTQTQEIIG---------FDERPA-GQNFVVAVMSYEGYNIEDALIMNKAS 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 669 IYEDVYTSLHIERYEAEARE----TNQAIEtitkqIPHLN------AHVLRHLDETGVVSLGAWVETGDVLVGKltakqs 738
Cdd:PRK07225 230 IERGLGRSHFFRTYEGEERRypggQEDRFE-----IPDKDvrgyrgEEAYRHLDEDGLVNPETEVKEGDVLIGK------ 298
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 739 egllhTPESKLL--QDILGVQAFGTQDTclKVPTR-GEGRVIDVRWITRDNHllGHRKViHVYILQERKIQVGDKVAGRH 815
Cdd:PRK07225 299 -----TSPPRFLeePDDFGISPEKRRET--SVTMRsGEEGIVDTVILTETEE--GSRLV-KVRVRDLRIPELGDKFASRH 368
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 816 GNKGVVSRILPRQDMPYLQDGTPVDMVLSPLGVPSRMNVGQVFECLLGLAGGyLNQHyRI--MPF---DERYGRESSRKL 890
Cdd:PRK07225 369 GQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGS-LEGR-RVdgTAFsgeDEEDLREALEKL 446
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 891 VFSelykasqttnypwifepdSPGKSRLFDGRTGEVFNQPVTVGRAYMFKLIHQVDDKIHARSTGPYALVTQQPVRGRSR 970
Cdd:PRK07225 447 GFE------------------HTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAR 508
|
490 500 510
....*....|....*....|....*....|..
gi 108796736 971 QGGQRVGEMEVWAFQGFGAACVLQELLTTKSD 1002
Cdd:PRK07225 509 EGGLRFGEMERDVLIGHGAAMLLKERLLDESD 540
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
365-432 |
2.15e-27 |
|
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: 105.69 E-value: 2.15e-27
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 108796736 365 QFLDQTNPLSEIVHKRKLSLlGPGGLTPRTARFRVRDIHPSQYGRICPVQTAEGQNAGVVNSFTICAH 432
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
972-1042 |
1.64e-15 |
|
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: 72.62 E-value: 1.64e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 972 GGQRVGEMEVWAFQGFGAACVLQELLTTKSD----HATARAEAPNA-----IVTGNLVPKPIGTSDCLGVLIRELQCLGI 1042
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGYIPESFKLLFQELQSLGI 80
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
129-304 |
5.85e-15 |
|
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: 74.31 E-value: 5.85e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 129 RSPGIYYTL-----SVQGVYTATIICNSGKSFKLELDRQGCLWVRVGRNSKaplllllialglemryIPPMIVQR----- 198
Cdd:pfam04561 1 RSNGIYVEKeldknGIIATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRK----------------IPIVIFLKalglv 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 199 TKK--LNQLLLCVEDAKIDLCKRLKLKQK----TTQIELgvtDPIYSLFL----KPYELG--------RMGRLNLNKRLN 260
Cdd:pfam04561 65 SDReiLDRLCYDFNDPQMLELLKPELEEAeniyTQEEAL---DYIGKGFAlrrgEEPRLQrareilysRDPKYNLNKHLG 141
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 108796736 261 LRVSEFEILLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVK 304
Cdd:pfam04561 142 LNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
18-350 |
8.53e-11 |
|
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: 65.09 E-value: 8.53e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 18 QIQIDSFRHFLTDLLRLELQRFGTI------KHANQQLE-FKLLGELYRLEIPKFNER----------EAVYQSATYSSN 80
Cdd:pfam04563 4 RQQLDSFNEFVDNDLQKIIDENALIesefeiQHPGENGDkLSLKFGQIRLGKPMFDETdgstreiypqECRLRNLTYSAP 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 81 LYAPAYLVDKKRGIIQKQTVFLGSIPLM--SAR----------------------GTFVIRGVSRCIVSQLLRS---PGI 133
Cdd:pfam04563 84 LYVDLELSVYNGEDIKPIEVFIGRLPIMlrSNAcilsgateselvklgecpldpgGYFIINGSEKVIVAQEHRSrnhPIV 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 134 YY------TLSVQGVYTATIICNSGKSfkleldrqgCLWVRVGRNSKAPLLLLLIALGLemRYIPPMIVQR-------TK 200
Cdd:pfam04563 164 FKkadpkkRGSVASVRSSAEISVRPDS---------TSWVNVLEYLSNGTIYFKFPYIK--KEIPIVIILRalgftsdRE 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 201 KLNQLLLCVEDAKIDLCKRLKLKQ---KTTQIELGVTDPIYSLFLKPYELG--RMGRLN-----LNKRL--NLRVSEFEI 268
Cdd:pfam04563 233 IFELICYDVNDQQLQEELLPSLEEgfkIRIQTQEQALDYIGGRGRAIFRMGrpREPRIKyaeeiLQKEVlpHLGTYELDE 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 108796736 269 LLRSQDLIVASDYLVQVSNGIGSLDDIDDLKHKRVKWVSDLFCVQLNMALKKLNVAVHTNLNKMEARISRMSLKSVVSSN 348
Cdd:pfam04563 313 TKKAYFIGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAK 392
|
..
gi 108796736 349 AI 350
Cdd:pfam04563 393 PI 394
|
|
| |
