|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
3-1086 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1654.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 3 LFRQN----SALPNFLDSQRDSFRYFLETGIREELDFFSPIVGqslgssskrpTDRFISVSFHSKDFYFKKPHYTPQEAV 78
Cdd:CHL00001 1 MLRDGnegmSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIED----------TDQEIEFQLFVETYQLVEPLIKERDAV 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 79 QKLGTYKSSLIVPVHVYSKYLNLNATFPVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSF 158
Cdd:CHL00001 71 YESLTYSSELYVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTI 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 159 LSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDTIVGALKYPEALDPTL-KEVDWKLTTDEAILLLMSRLF 237
Cdd:CHL00001 151 ISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLnDKEKKKIGSKENAILEFYQQF 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 238 PNR---PATVLRGRKFLFNQFFNPRrYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEfLDDIDH 314
Cdd:CHL00001 231 ACVggdPVFSESLCKELQKKFFQQR-CELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGT-LDDIDH 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 315 LKNRRARLAGELIQTQFRLGLNRLERVIYNRISDenILRKTPgaLGSLNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPL 394
Cdd:CHL00001 309 LKNKRIRSVADLLQDQFGLALNRLENAVRGTICG--AIRRKL--IPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPL 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 395 AEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKlISESNtP 474
Cdd:CHL00001 385 TEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYE-ISERS-K 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 475 DRNGFFLLSAFYEEDTVVAQGDVDLSN-----FRIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRA 549
Cdd:CHL00001 463 EERMVYLSPSEDEYYMIAAGNSLALNQgiqeeQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRA 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 550 LMGSNMQRQAVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIDYFTpvigdtnlidyqnltaedvfasn 629
Cdd:CHL00001 543 LMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSG----------------------- 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 630 QFKHNTIWLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVY 709
Cdd:CHL00001 600 NGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVY 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 710 DDVFTSIHISRYEVSTARLREGQEYFTNQVDRN-----QYLDEFGVVKIGTWVEAGDVLVGKISPQ--PDSDNDPESRLL 782
Cdd:CHL00001 680 EDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLeahllRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYAPEGRLL 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 783 RAIFGGVARNTKTTSYCLSSGVSGRILDVRCEFKrqtkniEDESIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNI 862
Cdd:CHL00001 760 RAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQK------KGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKI 833
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 863 LPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSRGFVYHYLYKSRLLTQQ 942
Cdd:CHL00001 834 LPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTAN 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 943 KWLFKPNSPGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWAL 1022
Cdd:CHL00001 914 PWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWAL 993
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113170437 1023 EGFGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPK-SGIPESFKVLVSELRGLCLDMSIARI 1086
Cdd:CHL00001 994 EGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKpEDAPESFRLLVRELRSLALELNHFLV 1058
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1083 |
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: 1240.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 10 LPNFLDSQRDSFRYFLET----------GIREELDFFSPIvgqslgssskrpTDRFISVSFHSKDFYFKKPHYTPQEAVQ 79
Cdd:TIGR02013 17 VPNLLEIQLDSYDWFLQQdtppekrkeeGLEEVFKSIFPI------------EDYTGNIELEYLSYRLGEPKYSVEECKE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 80 KLGTYKSSLIVPVHVYSKYLNLNATF---PVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFD--KQGNRTH 154
Cdd:TIGR02013 85 RGLTYSAPLKVKLRLINKEEDGTKEIkeqDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLF 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 155 LVSFLSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDT-IVGALKYPEALDPTLkEVDWKLTTDEAILLLM 233
Cdd:TIGR02013 165 SARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTlILNRLGSGEYIRNTL-RKDPTNSEEEALVEIY 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 234 SRLFPNRPATVLRGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEfLDDID 313
Cdd:TIGR02013 244 RKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGE-IDDID 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 314 HLKNRRARLAGELIQTQFRLGLNRLERVIYNRISDENILRKTPGalgslnSLIRTQVLASVFQEFFGSNQLSQFMDQTNP 393
Cdd:TIGR02013 323 HLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQ------DLINAKPISAAIKEFFGSSQLSQFMDQTNP 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 394 LAEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLISESNT 473
Cdd:TIGR02013 397 LAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVV 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 474 PDRNGFFLlSAFYEEDTVVAQGDVDL---SNF---RIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDAN 547
Cdd:TIGR02013 477 VTDEIDYL-TADEEDNYVIAQANAPLdenGRFvedLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDAN 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 548 RALMGSNMQRQAVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIdyftpVIGDTNLIDYQNlTAEDVFA 627
Cdd:TIGR02013 556 RALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRI-----VIRYDEDEEEPD-GGIDIYR 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 628 snqfkhntiwLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERL 707
Cdd:TIGR02013 630 ----------LLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERL 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 708 VYDDVFTSIHISRYEVSTARLREGQEYFTNQVD-------RNqyLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESR 780
Cdd:TIGR02013 700 VKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPnvseealRN--LDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEK 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 781 LLRAIFGGVARNTKTTSYCLSSGVSGRILDVRcEFKRQTKNIEDESIEStgSVYVYLVEKRRLQVGDKVAGRHGNKGIVS 860
Cdd:TIGR02013 778 LLRAIFGEKARDVRDTSLRVPPGVEGTVIDVK-VFSREQGDELPPGVNK--LVKVYIAQKRKIQVGDKMAGRHGNKGVVS 854
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 861 NILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLkqnfkvlpfdEMHGAEVSRGFVYHYLYKSRLLT 940
Cdd:TIGR02013 855 KILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL----------GRKGVPIATPVFDGASEEEIKEY 924
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 941 QQKWLFKPNspGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVW 1020
Cdd:TIGR02013 925 LEKAGLPRD--GKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1002
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 113170437 1021 ALEGFGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:TIGR02013 1003 ALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
10-1083 |
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: 1218.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 10 LPNFLDSQRDSFRYFLETGIREELDFFSPIvgqslgssskRPTDRFISVSFhsKDFYFKKPHYTPQEAVQKLGTYKSSLI 89
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPI----------EDFTGNLSLEF--GDYRLGEPKYTPEECKERDLTYAAPLY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 90 VPVHVYSKYLNLNATFPVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSFLSAYGSWLRFE 169
Cdd:COG0085 81 VKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 170 TDKKGVVFAHIDNLRKVPVTVFLQALGFSMD----TIVGALKYPEALDPTLKEvDWKLTTDEAILLLMSRLFPNRPATVL 245
Cdd:COG0085 161 TDKDGTIYVRIDRKRKIPVTVLLRALGLETDeeilEAFGDDPIQEYILATLEK-DNTKTQEEALLEIYRKLRPGEPPTIE 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 246 RGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGEtEFLDDIDHLKNRRARLAGE 325
Cdd:COG0085 240 RAEQLLDNLFFDPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGE-REPDDIDHLGNRRVRLVGE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 326 LIQTQFRLGLNRLERVIYNRISDENILRKTPgalgslNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPLAEITHKRRLSS 405
Cdd:COG0085 319 LLQNQFRVGLSRMERVVRERMTTQDVEAITP------QSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 406 LGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLIsesntpdrNGFF----- 480
Cdd:COG0085 393 LGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVE--------NGKVtdeie 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 481 LLSAFYEEDTVVAQGDVDLSNF------RIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSN 554
Cdd:COG0085 465 YLTADEEENYYIAQANAPLDEDgnfleeRVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 555 MQRQAVSLLRSERPFVgtgleahvtrdigativakqnsyisyvdaqridyftpvigdtnlidyqnltaedvfasnqfkhn 634
Cdd:COG0085 545 MQRQAVPLLRPEAPLL---------------------------------------------------------------- 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 635 TIWLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFT 714
Cdd:COG0085 561 HYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLT 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 715 SIHISRYEVSTARLREGQEYFTN-------QVDRNqyLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESRLLRAIFG 787
Cdd:COG0085 641 SIHIEEYEIEARDTKLGPEEITRdipnvseEALRN--LDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 788 GVARNTKTTSYCLSSGVSGRILDVRcEFKRqtkniEDESIESTGS---VYVYLVEKRRLQVGDKVAGRHGNKGIVSNILP 864
Cdd:COG0085 719 EKAREVRDTSLRVPHGEKGKVIDVK-VFSR-----EEGDELPPGVnklVRVYVAQKRKIEVGDKLAGRHGNKGVISRILP 792
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 865 RVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSRgfvyhYLYKSRLltqqkw 944
Cdd:COG0085 793 QEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRE-----LLEKAGL------ 861
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 945 lfkpNSPGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEG 1024
Cdd:COG0085 862 ----PPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 937
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*....
gi 113170437 1025 FGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:COG0085 938 YGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
13-1083 |
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: 769.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 13 FLDSQRDSFRYFLETGIREELDFFSPIVgqslgssskrPTDRFISVSFHSKDFYFKKP---------HYTPQEAVQKLGT 83
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPIT----------DTDDDGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 84 YKSSLIVPVHVYSKYLNLNATFPVAFCDLPLMTEH------------------------GTFILNGSPRVIVHQIVRCPG 139
Cdd:cd00653 71 YSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRSklcnlngltpeeliklgecpldpgGYFIINGTEKVIINQEQRSPN 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 140 VYLKpqFDKQGNRTHLVSFLSAY----GSWLRFETD-KKGVVFAHIDNLRKvpvtvflqalgfsmdtivgalkypealdp 214
Cdd:cd00653 151 VIIV--EDSKGKRIYTKTSIPSYspyrGSWLEVKSDkKKDRIYVRIDLKRQ----------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 215 tlkevdwklttDEAilllmsrlfpnrpatvlrgRKFLFNQFFnprryslsdvgrkrvnqkfrmrsktkhltltpqDALAA 294
Cdd:cd00653 200 -----------EEA-------------------LKYIGKRFE---------------------------------DLIYM 216
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 295 LDYLLRCENGETEfLDDIDHLKNRRARLAGELIQTQFRLGLNRLERVIYNRISDENILRKTPgalgSLNSLIRTQVLASV 374
Cdd:cd00653 217 IRKLILLVLGKGK-LDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL----TPQLLINSKPITSG 291
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 375 FQEFFGSNQ------------LSQFMDQTNPLAEITHKRRLSSlgpGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNA 442
Cdd:cd00653 292 IKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENC 368
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 443 GLVGSIATFTQINknGFLESPYYKLISESntpdrngffllsafyeedtvvaqgdvdlsnfriptrnksqftenTVQEInf 522
Cdd:cd00653 369 GLVKNLALMARIS--GRIERPYRIVEKEV--------------------------------------------THIEI-- 400
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 523 lglCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQAV----------------SLLRSERPFVGTGLEAHVtrdigati 586
Cdd:cd00653 401 ---SPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVgtpalnqqyrmdtklyLLLYPQKPLVGTGIEEYI-------- 469
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 587 vakqnsyisyvdaqridyftpvigdtnlidyqnltaedvfasnqfkhntiwltsyqrsnqdtclnhkplveantwveagd 666
Cdd:cd00653 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 667 cladnaatAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVSTARLREGQEYFTNQVDRN---- 742
Cdd:cd00653 470 --------AFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNvsee 541
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 743 --QYLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPesrllraIFGGVARNTKTTSYCLSSGVSGRILDVRCeFKRQTK 820
Cdd:cd00653 542 klKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKI-FSRELN 613
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 821 NIEDESIEstgsvyVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLL 900
Cdd:cd00653 614 DGGNKLVK------VYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 901 GLAANTLKQNFKVLPFDEMHGAEVSRGFVYHYLyksrlltqqkwlfkpNSPGKSIVFDGRTGLNFDQPVTVGYPYILKLV 980
Cdd:cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGEAGL---------------NYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLK 752
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 981 HLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDDMIGRNRAFMSMI------- 1053
Cdd:cd00653 753 HMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcr 832
|
1130 1140 1150
....*....|....*....|....*....|...
gi 113170437 1054 ---RGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:cd00653 833 lckKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
587-1008 |
7.08e-146 |
|
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: 441.20 E-value: 7.08e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 587 VAKQNSYISYVDAQRIDYftpvigdtnlidyQNLTAEDvfasnqfKHNTIWLTSYQRSNQDT---CLNHKPLVEANTwVE 663
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTY-------------QCAMGKQ-------AMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VE 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 664 AGDcladnaataKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVSTARLrEGQEYFTNQVDRN- 742
Cdd:pfam00562 60 AGG---------FGELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKL-GPIEEITRDIPNVs 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 743 ----QYLDEFGVVKIGTWVEAGDVLVGKISPqpdsdnDPESRLLRAIFGGVARNTKTTSYCLSSGVSGRILDVRcefkrq 818
Cdd:pfam00562 130 eealKKLDEDGIVRVGAEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVI------ 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 819 tknIEDESIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFEC 898
Cdd:pfam00562 198 ---VFELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLET 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 899 LLGLAANTLKQNFKVLPFDemhGAEVSRGFVYHYLYKSRLltqqkwlfkpNSPGKSIVFDGRTGLNFDQPVTVGYPYILK 978
Cdd:pfam00562 275 HLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAGY----------NYYGKEVLYDGRTGEPFEAPIFVGPIYYQK 341
|
410 420 430
....*....|....*....|....*....|
gi 113170437 979 LVHLVDDKIHARSTGPYSLVTQQPLGGRSK 1008
Cdd:pfam00562 342 LKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
3-1086 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1654.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 3 LFRQN----SALPNFLDSQRDSFRYFLETGIREELDFFSPIVGqslgssskrpTDRFISVSFHSKDFYFKKPHYTPQEAV 78
Cdd:CHL00001 1 MLRDGnegmSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIED----------TDQEIEFQLFVETYQLVEPLIKERDAV 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 79 QKLGTYKSSLIVPVHVYSKYLNLNATFPVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSF 158
Cdd:CHL00001 71 YESLTYSSELYVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTI 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 159 LSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDTIVGALKYPEALDPTL-KEVDWKLTTDEAILLLMSRLF 237
Cdd:CHL00001 151 ISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLnDKEKKKIGSKENAILEFYQQF 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 238 PNR---PATVLRGRKFLFNQFFNPRrYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEfLDDIDH 314
Cdd:CHL00001 231 ACVggdPVFSESLCKELQKKFFQQR-CELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGT-LDDIDH 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 315 LKNRRARLAGELIQTQFRLGLNRLERVIYNRISDenILRKTPgaLGSLNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPL 394
Cdd:CHL00001 309 LKNKRIRSVADLLQDQFGLALNRLENAVRGTICG--AIRRKL--IPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPL 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 395 AEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKlISESNtP 474
Cdd:CHL00001 385 TEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYE-ISERS-K 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 475 DRNGFFLLSAFYEEDTVVAQGDVDLSN-----FRIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRA 549
Cdd:CHL00001 463 EERMVYLSPSEDEYYMIAAGNSLALNQgiqeeQVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRA 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 550 LMGSNMQRQAVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIDYFTpvigdtnlidyqnltaedvfasn 629
Cdd:CHL00001 543 LMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSG----------------------- 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 630 QFKHNTIWLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVY 709
Cdd:CHL00001 600 NGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVY 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 710 DDVFTSIHISRYEVSTARLREGQEYFTNQVDRN-----QYLDEFGVVKIGTWVEAGDVLVGKISPQ--PDSDNDPESRLL 782
Cdd:CHL00001 680 EDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLeahllRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYAPEGRLL 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 783 RAIFGGVARNTKTTSYCLSSGVSGRILDVRCEFKrqtkniEDESIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNI 862
Cdd:CHL00001 760 RAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQK------KGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKI 833
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 863 LPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSRGFVYHYLYKSRLLTQQ 942
Cdd:CHL00001 834 LPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTAN 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 943 KWLFKPNSPGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWAL 1022
Cdd:CHL00001 914 PWVFEPEYPGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWAL 993
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 113170437 1023 EGFGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPK-SGIPESFKVLVSELRGLCLDMSIARI 1086
Cdd:CHL00001 994 EGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKpEDAPESFRLLVRELRSLALELNHFLV 1058
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
10-1083 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1324.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 10 LPNFLDSQRDSFRYFL-------ETGIREELDFFSPIVgqslgSSSKRptdrfISVSFhsKDFYFKKPHYTPQEAVQKLG 82
Cdd:PRK00405 24 LPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIE-----DFNGN-----LSLEF--VSYELGEPKYDVEECKERGL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 83 TYKSSLIVPVHVYSKylnlnATF-----PVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQ--GNRTHL 155
Cdd:PRK00405 92 TYSAPLRVKLRLINK-----ETGeikeqEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKTssGKLLYS 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 156 VSFLSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFS---------------------MDTIVGALKYPEALDP 214
Cdd:PRK00405 167 ARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSdeeildlfyekeefgkeievpVEYLLGKVLAEDIVDE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 215 TLKEV-----------------------DWKLTTDEAILLLMSRLFPNRPATVLRGRKFLFNQFFNPRRYSLSDVGRKRV 271
Cdd:PRK00405 247 ETGEVlaeandeiteeldgpyirntlekDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKL 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 272 NQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEfLDDIDHLKNRRARLAGELIQTQFRLGLNRLERVIYNRIS---D 348
Cdd:PRK00405 327 NKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGE-VDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSlqdL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 349 ENIlrkTPgalgslNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPLAEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYY 428
Cdd:PRK00405 406 DTL---TP------QDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHY 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 429 GRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLIsesntpdrNGFFL-----LSAFYEEDTVVAQGDVDLS--- 500
Cdd:PRK00405 477 GRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVV--------DGKVTdeivyLTADEEDNYVIAQANAPLDedg 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 501 NF---RIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQAVSLLRSERPFVGTGLEAH 577
Cdd:PRK00405 549 RFvdeLVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERR 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 578 VTRDIGATIVAKQNSYISYVDAQRIdyftpvigdtnLIDYQNLTAEDvfasnqfKHNTIW-LTSYQRSNQDTCLNHKPLV 656
Cdd:PRK00405 629 VARDSGAVVVAKRDGVVEYVDASRI-----------VVRVEELDPGE-------DGVDIYnLIKFQRSNQNTCINQRPIV 690
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 657 EANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVsTAR-LREGQEYF 735
Cdd:PRK00405 691 KVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEI-EARdTKLGPEEI 769
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 736 TNQVD-------RNqyLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESRLLRAIFGGVARNTKTTSYCLSSGVSGRI 808
Cdd:PRK00405 770 TRDIPnvseealRN--LDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTV 847
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 809 LDVRcEFKRQTKNIEDES--IEStgsVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGV 886
Cdd:PRK00405 848 IDVK-VFTRIEQGDELPPgvNKL---VKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGV 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 887 PSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSRgfvyhYLYKSRLltqqkwlfkpNSPGKSIVFDGRTGLNFD 966
Cdd:PRK00405 924 PSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKE-----LLEEAGL----------PEDGKTTLYDGRTGEPFD 988
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 967 QPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDDMIGRN 1046
Cdd:PRK00405 989 RPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRT 1068
|
1130 1140 1150
....*....|....*....|....*....|....*..
gi 113170437 1047 RAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:PRK00405 1069 KVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVEL 1105
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1083 |
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: 1240.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 10 LPNFLDSQRDSFRYFLET----------GIREELDFFSPIvgqslgssskrpTDRFISVSFHSKDFYFKKPHYTPQEAVQ 79
Cdd:TIGR02013 17 VPNLLEIQLDSYDWFLQQdtppekrkeeGLEEVFKSIFPI------------EDYTGNIELEYLSYRLGEPKYSVEECKE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 80 KLGTYKSSLIVPVHVYSKYLNLNATF---PVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFD--KQGNRTH 154
Cdd:TIGR02013 85 RGLTYSAPLKVKLRLINKEEDGTKEIkeqDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSGKVLF 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 155 LVSFLSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDT-IVGALKYPEALDPTLkEVDWKLTTDEAILLLM 233
Cdd:TIGR02013 165 SARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTlILNRLGSGEYIRNTL-RKDPTNSEEEALVEIY 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 234 SRLFPNRPATVLRGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEfLDDID 313
Cdd:TIGR02013 244 RKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGE-IDDID 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 314 HLKNRRARLAGELIQTQFRLGLNRLERVIYNRISDENILRKTPGalgslnSLIRTQVLASVFQEFFGSNQLSQFMDQTNP 393
Cdd:TIGR02013 323 HLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQ------DLINAKPISAAIKEFFGSSQLSQFMDQTNP 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 394 LAEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLISESNT 473
Cdd:TIGR02013 397 LAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVV 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 474 PDRNGFFLlSAFYEEDTVVAQGDVDL---SNF---RIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDAN 547
Cdd:TIGR02013 477 VTDEIDYL-TADEEDNYVIAQANAPLdenGRFvedLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDAN 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 548 RALMGSNMQRQAVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIdyftpVIGDTNLIDYQNlTAEDVFA 627
Cdd:TIGR02013 556 RALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRI-----VIRYDEDEEEPD-GGIDIYR 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 628 snqfkhntiwLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERL 707
Cdd:TIGR02013 630 ----------LLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERL 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 708 VYDDVFTSIHISRYEVSTARLREGQEYFTNQVD-------RNqyLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESR 780
Cdd:TIGR02013 700 VKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPnvseealRN--LDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEK 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 781 LLRAIFGGVARNTKTTSYCLSSGVSGRILDVRcEFKRQTKNIEDESIEStgSVYVYLVEKRRLQVGDKVAGRHGNKGIVS 860
Cdd:TIGR02013 778 LLRAIFGEKARDVRDTSLRVPPGVEGTVIDVK-VFSREQGDELPPGVNK--LVKVYIAQKRKIQVGDKMAGRHGNKGVVS 854
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 861 NILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLkqnfkvlpfdEMHGAEVSRGFVYHYLYKSRLLT 940
Cdd:TIGR02013 855 KILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL----------GRKGVPIATPVFDGASEEEIKEY 924
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 941 QQKWLFKPNspGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVW 1020
Cdd:TIGR02013 925 LEKAGLPRD--GKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1002
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 113170437 1021 ALEGFGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:TIGR02013 1003 ALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
10-1083 |
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: 1218.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 10 LPNFLDSQRDSFRYFLETGIREELDFFSPIvgqslgssskRPTDRFISVSFhsKDFYFKKPHYTPQEAVQKLGTYKSSLI 89
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPI----------EDFTGNLSLEF--GDYRLGEPKYTPEECKERDLTYAAPLY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 90 VPVHVYSKYLNLNATFPVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSFLSAYGSWLRFE 169
Cdd:COG0085 81 VKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 170 TDKKGVVFAHIDNLRKVPVTVFLQALGFSMD----TIVGALKYPEALDPTLKEvDWKLTTDEAILLLMSRLFPNRPATVL 245
Cdd:COG0085 161 TDKDGTIYVRIDRKRKIPVTVLLRALGLETDeeilEAFGDDPIQEYILATLEK-DNTKTQEEALLEIYRKLRPGEPPTIE 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 246 RGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGEtEFLDDIDHLKNRRARLAGE 325
Cdd:COG0085 240 RAEQLLDNLFFDPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGE-REPDDIDHLGNRRVRLVGE 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 326 LIQTQFRLGLNRLERVIYNRISDENILRKTPgalgslNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPLAEITHKRRLSS 405
Cdd:COG0085 319 LLQNQFRVGLSRMERVVRERMTTQDVEAITP------QSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 406 LGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLIsesntpdrNGFF----- 480
Cdd:COG0085 393 LGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVE--------NGKVtdeie 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 481 LLSAFYEEDTVVAQGDVDLSNF------RIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSN 554
Cdd:COG0085 465 YLTADEEENYYIAQANAPLDEDgnfleeRVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGAN 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 555 MQRQAVSLLRSERPFVgtgleahvtrdigativakqnsyisyvdaqridyftpvigdtnlidyqnltaedvfasnqfkhn 634
Cdd:COG0085 545 MQRQAVPLLRPEAPLL---------------------------------------------------------------- 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 635 TIWLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFT 714
Cdd:COG0085 561 HYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLT 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 715 SIHISRYEVSTARLREGQEYFTN-------QVDRNqyLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESRLLRAIFG 787
Cdd:COG0085 641 SIHIEEYEIEARDTKLGPEEITRdipnvseEALRN--LDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFG 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 788 GVARNTKTTSYCLSSGVSGRILDVRcEFKRqtkniEDESIESTGS---VYVYLVEKRRLQVGDKVAGRHGNKGIVSNILP 864
Cdd:COG0085 719 EKAREVRDTSLRVPHGEKGKVIDVK-VFSR-----EEGDELPPGVnklVRVYVAQKRKIEVGDKLAGRHGNKGVISRILP 792
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 865 RVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSRgfvyhYLYKSRLltqqkw 944
Cdd:COG0085 793 QEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRE-----LLEKAGL------ 861
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 945 lfkpNSPGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEG 1024
Cdd:COG0085 862 ----PPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 937
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*....
gi 113170437 1025 FGAAYVLQELLTIKSDDMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:COG0085 938 YGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
7-1087 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1139.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 7 NSALPNFLDSQRDSFRYFLETGIREELDFFSPIVGQSlgssskrptdRFISVSFHSKDFYFKKPHYTPQEAVQKLGTYKS 86
Cdd:CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYT----------GNLELLLFGKNYKLKYPKYNLLSAKSYDSNYSI 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 87 SLIVPVHVYSKYLNLNATFPVAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSFLSAYGSWL 166
Cdd:CHL00207 74 QIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWI 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 167 RFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDTIVGALKYP--EALDPTLKEVDWKLTTDEAILLLMSRLFPNRPATV 244
Cdd:CHL00207 154 KFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSefLKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATV 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 245 LRGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEFlDDIDHLKNRRARLAG 324
Cdd:CHL00207 234 NDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNF-DDIDHLKNRRVRSVG 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 325 ELIQTQFRLGLNRLERVIYNRISDENILRKTPgalgslNSLIRTQVLASVFQEFFGSNQLSQFMDQTNPLAEITHKRRLS 404
Cdd:CHL00207 313 ELLQNQFRIGLKRLERILRNRMTICDIDSLSK------FNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRIS 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 405 SLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLISESNTPDRNGFFLlSA 484
Cdd:CHL00207 387 ILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGNPIYL-TA 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 485 FYEEDTVVAQGDVDL------SNFRIPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQ 558
Cdd:CHL00207 466 DSEDLYRIAPNDINLnknnyfKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQ 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 559 AVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIdyftpVIGDTN--LIDYqnltaedvfasnqfkhnti 636
Cdd:CHL00207 546 AVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKI-----IIQDDNnrYIHY------------------- 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 637 WLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSI 716
Cdd:CHL00207 602 YLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSI 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 717 HISRYEVSTARLREGQEYFTNQVDRNQY-----LDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESRLLRAIFGGVAR 791
Cdd:CHL00207 682 HIEKYEIELRQTKLGSEEITRNIPNVSEyslknLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAK 761
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 792 NTKTTSYCLSSGVSGRILDVRCeFKRQTKnieDESIESTG-SVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPY 870
Cdd:CHL00207 762 DVKDTSLRMPNGGYGRVIKVEI-FSRSKG---DELKFGYYlKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPY 837
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 871 LQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPFDEMHGAEVSRGFVYHYLYKSRLLTQQKWLFKPNS 950
Cdd:CHL00207 838 LPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYH 917
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 951 PGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYV 1030
Cdd:CHL00207 918 PGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYT 997
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*..
gi 113170437 1031 LQELLTIKSDDMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSIARIN 1087
Cdd:CHL00207 998 LKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYKIE 1054
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
13-1083 |
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: 769.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 13 FLDSQRDSFRYFLETGIREELDFFSPIVgqslgssskrPTDRFISVSFHSKDFYFKKP---------HYTPQEAVQKLGT 83
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPIT----------DTDDDGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 84 YKSSLIVPVHVYSKYLNLNATFPVAFCDLPLMTEH------------------------GTFILNGSPRVIVHQIVRCPG 139
Cdd:cd00653 71 YSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRSklcnlngltpeeliklgecpldpgGYFIINGTEKVIINQEQRSPN 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 140 VYLKpqFDKQGNRTHLVSFLSAY----GSWLRFETD-KKGVVFAHIDNLRKvpvtvflqalgfsmdtivgalkypealdp 214
Cdd:cd00653 151 VIIV--EDSKGKRIYTKTSIPSYspyrGSWLEVKSDkKKDRIYVRIDLKRQ----------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 215 tlkevdwklttDEAilllmsrlfpnrpatvlrgRKFLFNQFFnprryslsdvgrkrvnqkfrmrsktkhltltpqDALAA 294
Cdd:cd00653 200 -----------EEA-------------------LKYIGKRFE---------------------------------DLIYM 216
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 295 LDYLLRCENGETEfLDDIDHLKNRRARLAGELIQTQFRLGLNRLERVIYNRISDENILRKTPgalgSLNSLIRTQVLASV 374
Cdd:cd00653 217 IRKLILLVLGKGK-LDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKKDL----TPQLLINSKPITSG 291
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 375 FQEFFGSNQ------------LSQFMDQTNPLAEITHKRRLSSlgpGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNA 442
Cdd:cd00653 292 IKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENC 368
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 443 GLVGSIATFTQINknGFLESPYYKLISESntpdrngffllsafyeedtvvaqgdvdlsnfriptrnksqftenTVQEInf 522
Cdd:cd00653 369 GLVKNLALMARIS--GRIERPYRIVEKEV--------------------------------------------THIEI-- 400
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 523 lglCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQAV----------------SLLRSERPFVGTGLEAHVtrdigati 586
Cdd:cd00653 401 ---SPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVgtpalnqqyrmdtklyLLLYPQKPLVGTGIEEYI-------- 469
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 587 vakqnsyisyvdaqridyftpvigdtnlidyqnltaedvfasnqfkhntiwltsyqrsnqdtclnhkplveantwveagd 666
Cdd:cd00653 --------------------------------------------------------------------------------
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 667 cladnaatAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVSTARLREGQEYFTNQVDRN---- 742
Cdd:cd00653 470 --------AFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRGDIPNvsee 541
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 743 --QYLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPesrllraIFGGVARNTKTTSYCLSSGVSGRILDVRCeFKRQTK 820
Cdd:cd00653 542 klKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKI-FSRELN 613
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 821 NIEDESIEstgsvyVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLL 900
Cdd:cd00653 614 DGGNKLVK------VYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLL 687
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 901 GLAANTLKQNFKVLPFDEMHGAEVSRGFVYHYLyksrlltqqkwlfkpNSPGKSIVFDGRTGLNFDQPVTVGYPYILKLV 980
Cdd:cd00653 688 GKAGALLGKFGDATPFDGAEEEDISELLGEAGL---------------NYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLK 752
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 981 HLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDDMIGRNRAFMSMI------- 1053
Cdd:cd00653 753 HMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcr 832
|
1130 1140 1150
....*....|....*....|....*....|...
gi 113170437 1054 ---RGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:cd00653 833 lckKGTNISKVGIPYAFKLLFQELQSMNIDPRL 865
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
6-1083 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 769.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 6 QNSALPNFLDSQRDSFRYFL------ETGIREELDFFSPIvgqslGSSSKRPTDRFISVSFhskdfyfKKPHYTPQEAVQ 79
Cdd:PRK09603 20 TDLEVPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPI-----QDEHNRITLEYAGCEF-------GKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 80 KLGTYKSSLIVPVHVY-------------SKYLNLNATFpvaFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQf 146
Cdd:PRK09603 88 RGITYSIPLKIKVRLIlwekdtksgekngIKDIKEQSIF---IREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEE- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 147 DKQGNRTHLV---SFLSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDTIV-------------------- 203
Cdd:PRK09603 164 ESSTSLNKLIytgQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIkmfyplvkvryendkylipf 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 204 -----------------------------------------GALKYP-----------------EALDPTLKEVD----- 220
Cdd:PRK09603 244 asldanqrmefdlkdpqgkiillagkkltsrkikelkenhlEWVEYPmdillnrhlaepvmvgkEVLLDMLTQLDknkle 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 221 ---------------WKLTTDEAIL------------------------LLMSRLF----PNRPATVLRGRKFLFNQFFN 257
Cdd:PRK09603 324 kihdlgvqefviindLALGHDASIIhsfsadseslkllkqtekiddenaLAAIRIHkvmkPGDPVTTEVAKQFVKKLFFD 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 258 PRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGETEfLDDIDHLKNRRARLAGELIQTQFRLGLNR 337
Cdd:PRK09603 404 PERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGK-IDDRDHLGNRRIRAVGELLANELHSGLVK 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 338 LERVIYNRISDENilrktpGALGSL--NSLIRTQVLASVFQEFFGSNQLSQFMDQTNPLAEITHKRRLSSLGPGGLNRDR 415
Cdd:PRK09603 483 MQKTIKDKLTTMS------GAFDSLmpHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDR 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 416 AGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYKLISESNTPDrngFFLLSAFYEEDTVVAQG 495
Cdd:PRK09603 557 VGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGE---TIYLTAIQEDSHIIAPA 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 496 DVDLSNFR------IPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQAVSLLRSERPF 569
Cdd:PRK09603 634 STPIDEEGnilgdlIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 570 VGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIdyftpvigdtnlidyqNLTAEDvfasnqfkHNTIWLTSYQ-----RS 644
Cdd:PRK09603 714 VGTGIEKIIARDSWGAIKANRAGVVEKIDSKNI----------------YILGEG--------KEEAYIDAYSlqknlRT 769
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 645 NQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVS 724
Cdd:PRK09603 770 NQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVD 849
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 725 TARLREGQEYFTNQV-----DRNQYLDEFGVVKIGTWVEAGDVLVGKISPQPDSDNDPESRLLRAIFGGVARNTKTTS-Y 798
Cdd:PRK09603 850 ARELKHGVEEFTADIpdvkeEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSlY 929
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 799 CLSSgVSGRILDVRCEFKR------------------------------------------------------------- 817
Cdd:PRK09603 930 CPPS-LEGTVIDVKVFTKKgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykeg 1008
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 818 --------------------------------QTKN-------------------IEDESIESTG---SVYVYLVEKRRL 843
Cdd:PRK09603 1009 dqipkeeiasinrftlaslvkkyskevqnhyeITKNnfleqkkvlgeeheeklsiLEKDDILPNGvikKVKLYIATKRKL 1088
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 844 QVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTL------------KQNF 911
Cdd:PRK09603 1089 KVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFgkqiasmledktKDFA 1168
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 912 KVLPFDEMHGAEVSRG-------FVYHYLYKSRL-------------------LTQQKW-----LFKPNSPGKSIVFDGR 960
Cdd:PRK09603 1169 KELRAKMLEIANAINEkdpltihALENCSDEELLeyakdwskgvkmaipvfegISQEKFyklfeLAKIAMDGKMDLYDGR 1248
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 961 TGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSD 1040
Cdd:PRK09603 1249 TGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSD 1328
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|...
gi 113170437 1041 DMIGRNRAFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:PRK09603 1329 DIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINI 1371
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
107-1087 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 709.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 107 VAFCDLPLMTEHGTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLV---SFLSAYGSWLRFETDKKGVVFAHIDNL 183
Cdd:PRK14844 142 VHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKLIysaRVIPYRGSWLDIEFDVKDHLYFRIDRK 221
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 184 RKVPVTVFLQALGFS----MDTIVGALKY------------PEAL---------------------------------DP 214
Cdd:PRK14844 222 RKLPISVLLKALGLSnndiLDRFYEKIKYikhkdgwkvpfvPDKFkgvrlpfdlmdvegnvllkanvritsrlakklyDN 301
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 215 TLKEV-----------------------------------DWK----LTTDEAILL----------LMSRLFPNRPAT-- 243
Cdd:PRK14844 302 ELKEYlvpfdsicglflaedlidsasstkilsagesikleDIKklelLSIDEISVLnidnlsvgpyILNTLFLDENMSyq 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 244 --------VLRG---------RKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLTPQDALAALDYLLRCENGET 306
Cdd:PRK14844 382 dalyeiykVLRPgevpvleivEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQG 461
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 307 EfLDDIDHLKNRRARLAGELIQTQFRLGLNRLERVIYNRISDENILRKTPgalgslNSLIRTQVLASVFQEFFGSNQLSQ 386
Cdd:PRK14844 462 S-VDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSP------SDFINPKVLTNVLRDFFNSSQLSQ 534
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 387 FMDQTNPLAEITHKRRLSSLGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKNGFLESPYYK 466
Cdd:PRK14844 535 FMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRK 614
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 467 LISESNTpdrNGFFLLSAFYEEDTVVAQGDVDLSNFR------IPTRNKSQFTENTVQEINFLGLCPIQFMSIATSLIPF 540
Cdd:PRK14844 615 VVNRVVT---DQIEYLSAIDEGLYYIADTSAKLDENNcfvddmLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPF 691
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 541 LEHDDANRALMGSNMQRQAVSLLRSERPFVGTGLEAHVTRDIGATIVAKQNSYISYVDAQRIdyftpVIG--DTNLIDYQ 618
Cdd:PRK14844 692 LENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSI-----VIRafDKERVNYL 766
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 619 NLtaeDVFAsnqfkhntiwLTSYQRSNQDTCLNHKPLVEANTWVEAGDCLADNAATAKGELALGRNILIGYMPWEGYNFE 698
Cdd:PRK14844 767 DV---DIYH----------LRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFE 833
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 699 DAVLVSERLVYDDVFTSIHISRYEVSTARLREGQEYFTNQV----DRNQY-LDEFGVVKIGTWVEAGDVLVGKISPQPDS 773
Cdd:PRK14844 834 DSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIpgvnEENLYhLDDSGIVKIGTRVGPGYILVGKVTPKPSL 913
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 774 DNDPESRLLRAIFGGVARNTKTTSYCLSSGVSGRILDVRCEFKR------------------------------------ 817
Cdd:PRK14844 914 SLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRgveenerallikqkeindfekerdyiinvtseyfyd 993
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 818 -------------------------------------QTKNIE---DESIEST----------------------GSVYV 835
Cdd:PRK14844 994 elkkllinsgsqdrekfdsiereqwwgiglknqsiseQVKSLKkdfDEKVSHAiaqfkrkveklhegydlpqgvsMSVKV 1073
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 836 YLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQ------ 909
Cdd:PRK14844 1074 FIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEkvgnil 1153
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 910 -----------------------NFKVLPFDEMHGAEVS---------------------------------------RG 927
Cdd:PRK14844 1154 deinkiksafckgirslnddnftKFAAAYLDNKKIENIDddeitasvlntpnknalndelnelvenylnscksaysnlRN 1233
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 928 FVYH-YLYKSRL-------------LTQQKWLFKPNSP--------------------------GKSIVFDGRTGLNFDQ 967
Cdd:PRK14844 1234 FLIEvYSCGSNVsicnnirdisdnnLIEFARKLRDGIPvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFDR 1313
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 968 PVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDDMIGRNR 1047
Cdd:PRK14844 1314 KVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVK 1393
|
1290 1300 1310 1320
....*....|....*....|....*....|....*....|
gi 113170437 1048 AFMSMIRGTLLPKSGIPESFKVLVSELRGLCLDMSIARIN 1087
Cdd:PRK14844 1394 IYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQND 1433
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
587-1008 |
7.08e-146 |
|
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: 441.20 E-value: 7.08e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 587 VAKQNSYISYVDAQRIDYftpvigdtnlidyQNLTAEDvfasnqfKHNTIWLTSYQRSNQDT---CLNHKPLVEANTwVE 663
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTY-------------QCAMGKQ-------AMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VE 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 664 AGDcladnaataKGELALGRNILIGYMPWEGYNFEDAVLVSERLVYDDVFTSIHISRYEVSTARLrEGQEYFTNQVDRN- 742
Cdd:pfam00562 60 AGG---------FGELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEARKTKL-GPIEEITRDIPNVs 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 743 ----QYLDEFGVVKIGTWVEAGDVLVGKISPqpdsdnDPESRLLRAIFGGVARNTKTTSYCLSSGVSGRILDVRcefkrq 818
Cdd:pfam00562 130 eealKKLDEDGIVRVGAEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVI------ 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 819 tknIEDESIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFEC 898
Cdd:pfam00562 198 ---VFELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLET 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 899 LLGLAANTLKQNFKVLPFDemhGAEVSRGFVYHYLYKSRLltqqkwlfkpNSPGKSIVFDGRTGLNFDQPVTVGYPYILK 978
Cdd:pfam00562 275 HLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAGY----------NYYGKEVLYDGRTGEPFEAPIFVGPIYYQK 341
|
410 420 430
....*....|....*....|....*....|
gi 113170437 979 LVHLVDDKIHARSTGPYSLVTQQPLGGRSK 1008
Cdd:pfam00562 342 LKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
119-1083 |
2.51e-82 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 291.09 E-value: 2.51e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 119 GTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSFLSA---YGSWLRFETDKKGVVFAHIDNLR-KVPVTVFLQA 194
Cdd:PRK08565 141 GYFIINGSERVIVSQEDLAPNRVLVDKGEAGSSITHTAKVISSragYRAQVTVERRKDGTIYVSFPAVPgKIPFVILMRA 220
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 195 LGFSMDT-IVGALKY-PE---ALDPTLKEV-DWKLTTDEAILLLMSRLFPNRPATV--LRGRKFLFNQFFnPrryslsdv 266
Cdd:PRK08565 221 LGLETDRdIVYAVSLdPEiqqELLPSLEQAsSIAATVEDALDYIGKRVAIGQPREYriERAEQILDKYLL-P-------- 291
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 267 grkrvnqkfrmrsktkHLTLTPQDALAALDYLLRCENGETEFL------DDIDHLKNRRARLAGELIQTQFRLGLNRLER 340
Cdd:PRK08565 292 ----------------HLGTSPEDRIKKAYFLGQMASKLLELYlgrrepDDKDHYANKRLRLAGDLLAELFRVAFKQLVK 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 341 VIYNRIsdENILRKTPGAlgSLNSLIRTQVLASVFQEFF-------GSNQLSQFMDQTNPLAEITHKRRLSSlgpgGLNR 413
Cdd:PRK08565 356 DLKYQL--EKSYARGRKL--DLRAIVRPDIITERIRHALatgnwvgGRTGVSQLLDRTNYLSTLSHLRRVVS----PLSR 427
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 414 DRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINkNGFLESPYYKLI-----------SESNTPDR-----N 477
Cdd:PRK08565 428 GQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIS-VGVDEEEVEEILyelgvvpveeaREEEYISWsrvylN 506
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 478 GFFL---------------------LS-----AFYEEDT------------------VVAQGDVDLSNFRIPTRNKSQFT 513
Cdd:PRK08565 507 GRLIgyhpdgeelaekirelrrsgkISdevnvAYIETGEinevyvncdsgrvrrpliVVENGKPKLTREHVEKLKKGELT 586
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 514 ------------------ENTV---------QEINFLGLCPIQFMSIATSLIPFLEHDDANRALMGSNMQRQAVSL---- 562
Cdd:PRK08565 587 fddlvkmgvieyldaeeeENAYvaldpedltPEHTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLyaan 666
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 563 --LRS----------ERPFVGT-GLEahvtrdigativakqnsyisyvdaqridyftpvigdtnLIDYQNLTAedvfasn 629
Cdd:PRK08565 667 frIRTdtrghllhypQRPLVQTrALE--------------------------------------IIGYNDRPA------- 701
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 630 qfkhntiwltsyqrsnqdtclnhkplveantwveagdcladnaatakgelalGRNILIGYMPWEGYNFEDAVLVS----E 705
Cdd:PRK08565 702 ----------------------------------------------------GQNAVVAVLSYTGYNIEDAIIMNkasiE 729
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 706 RLVYDDVFTSIHIS-----------RYEVSTARLR--EGQEYFTNqvdrnqyLDEFGVVKIGTWVEAGDVLVGKISPqpd 772
Cdd:PRK08565 730 RGLARSTFFRTYETeerkypggqedKIEIPEPNVRgyRGEEYYRK-------LDEDGIVSPEVEVKGGDVLIGKTSP--- 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 773 sdndPesRLL--RAIFGGVARNTKTTSYCLSSGVSGRILDVrcefkrqtknIEDESIESTGSVYVYLVEKRRLQVGDKVA 850
Cdd:PRK08565 800 ----P--RFLeeLEELSLGLQERRDTSVTVRHGEKGIVDTV----------LITESPEGNKLVKVRVRDLRIPELGDKFA 863
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 851 GRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGLAANTLKQNFKVLPF-----DEMHGAEVS 925
Cdd:PRK08565 864 SRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFygepeEELRKELLK 943
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 926 RGFvyhylyksrlltqqkwlfKPNspGKSIVFDGRTGLNFDQPVTVGYPYILKLVHLVDDKIHARSTGPYSLVTQQPLGG 1005
Cdd:PRK08565 944 LGY------------------KPD--GTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEG 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 1006 RSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDD----------MIG----RNRAFMSMIRG--TLLPKSGIPESFKV 1069
Cdd:PRK08565 1004 RAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDKttiyvcelcgHIAwydrRKNKYVCPIHGdkGNISPVEVSYAFKL 1083
|
1130
....*....|....
gi 113170437 1070 LVSELRGLCLDMSI 1083
Cdd:PRK08565 1084 LLQELMSMGISPRL 1097
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
682-1083 |
1.64e-60 |
|
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: 218.36 E-value: 1.64e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 682 GRNILIGYMPWEGYNFEDAVLVSE--------RLVYDDVFTSIHI-------SRYEVSTARLR--EGQEYFTNqvdrnqy 744
Cdd:TIGR03670 198 GQNFVVAVMSYEGYNIEDALIMNKasierglaRSTFFRTYEAEERrypggqeDRFEIPEPDVRgyRGEEAYKH------- 270
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 745 LDEFGVVKIGTWVEAGDVLVGKISPqpdsdndpeSRLL--RAIFGGVARNTKTTSYCLSSGVSGrILDvrcefkrqtKNI 822
Cdd:TIGR03670 271 LDEDGIVYPEVEVKGGDVLIGKTSP---------PRFLeeLREFGLVTERRRDTSVTVRHGEKG-IVD---------KVI 331
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 823 EDESIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLGL 902
Cdd:TIGR03670 332 ITETEEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGK 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 903 AANTLKQNFKVLPFDEMHGAEVsrgfvyhylyKSRLLtqqKWLFKPNspGKSIVFDGRTGLNFDQPVTVGYPYILKLVHL 982
Cdd:TIGR03670 412 VAALEGRRVDGTPFEGEPEEEL----------RKELL---KLGFKPD--GKEVMYDGITGEKLEAEIFIGVIYYQKLHHM 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 983 VDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDD----------MIG-----RNR 1047
Cdd:TIGR03670 477 VADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKyvvyvcencgHIAwedkrKGT 556
|
410 420 430
....*....|....*....|....*....|....*...
gi 113170437 1048 AFMSmIRG--TLLPKSGIPESFKVLVSELRGLCLDMSI 1083
Cdd:TIGR03670 557 AYCP-VCGetGDISPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
682-1080 |
2.38e-56 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 206.35 E-value: 2.38e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 682 GRNILIGYMPWEGYNFEDAVLVS----ERLVYDDVF----------------TSIHISRYEVSTARlreGQEYFTNqvdr 741
Cdd:PRK07225 204 GQNFVVAVMSYEGYNIEDALIMNkasiERGLGRSHFfrtyegeerrypggqeDRFEIPDKDVRGYR---GEEAYRH---- 276
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 742 nqyLDEFGVVKIGTWVEAGDVLVGKISPqPDSDNDPEsrllraIFGGVARNTKTTSYCLSSGVSGrILDvrcefkrqtKN 821
Cdd:PRK07225 277 ---LDEDGLVNPETEVKEGDVLIGKTSP-PRFLEEPD------DFGISPEKRRETSVTMRSGEEG-IVD---------TV 336
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 822 IEDESIESTGSVYVYLVEKRRLQVGDKVAGRHGNKGIVSNILPRVDMPYLQSGKALDMVLNPLGVPSRMNVGQIFECLLG 901
Cdd:PRK07225 337 ILTETEEGSRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGG 416
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 902 LAANTLKQNFKVLPF-----DEMHGAEVSRGFVYHylyksrlltqqkwlfkpnspGKSIVFDGRTGLNFDQPVTVGYPYI 976
Cdd:PRK07225 417 KVGSLEGRRVDGTAFsgedeEDLREALEKLGFEHT--------------------GKEVMYDGITGEKIEAEIFVGVIYY 476
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 977 LKLVHLVDDKIHARSTGPYSLVTQQPLGGRSKKGGQRLGEMEVWALEGFGAAYVLQELLTIKSDD----------MIG-- 1044
Cdd:PRK07225 477 QKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKveiyvcakcgMIAiy 556
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 113170437 1045 ---RNRAFMSmIRG--TLLPKSGIPESFKVLVSELRGLCLD 1080
Cdd:PRK07225 557 dkkRNRKYCP-ICGeeTDIYPVEMSYAFKLLLDELKSLGIA 596
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
386-453 |
3.36e-30 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 113.78 E-value: 3.36e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 113170437 386 QFMDQTNPLAEITHKRRLSSlGPGGLNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQ 453
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
17-346 |
4.51e-28 |
|
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: 117.87 E-value: 4.51e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 17 QRDSFRYFLETGIREELDFFSPIVGQSLGSSSKRPTDRFiSVSFhsKDFYFKKPHYT----------PQEAVQKLGTYKS 86
Cdd:pfam04563 6 QLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGDKL-SLKF--GQIRLGKPMFDetdgstreiyPQECRLRNLTYSA 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 87 SLIVPVHvYSKYLNLNATFPVAFC-DLPLMTEH------------------------GTFILNGSPRVIVHQIVR---CP 138
Cdd:pfam04563 83 PLYVDLE-LSVYNGEDIKPIEVFIgRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQEHRsrnHP 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 139 GVYLKPQFdkqGNRTHLVSFLSAY--------GSWLRF-ETDKKGVVFAHIDNLRK-VPVTVFLQALGFSMDT-IVGALK 207
Cdd:pfam04563 162 IVFKKADP---KKRGSVASVRSSAeisvrpdsTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDReIFELIC 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 208 YpealdptlKEVDWKLttDEAILLLMSRLFPNRPATVLRGRKFLFNQFFNPRRYSLSDVGRKRVNQKFRMRSKTKHLTLT 287
Cdd:pfam04563 239 Y--------DVNDQQL--QEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTY 308
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 113170437 288 PQDA-------LAALDYLLRCENGETEfLDDIDHLKNRRARLAGELIQTQFRLGLNRLERVIYNRI 346
Cdd:pfam04563 309 ELDEtkkayfiGYMIRRLLLLALGRRE-VDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERL 373
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1010-1083 |
1.04e-25 |
|
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: 101.51 E-value: 1.04e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 1010 GGQRLGEMEVWALEGFGAAYVLQELLTIKSD----DMIGRNRAFMSM-----IRGTLLPKSG-IPESFKVLVSELRGLCL 1079
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAYnkcpiCKGETDISPGyIPESFKLLFQELQSLGI 80
|
....
gi 113170437 1080 DMSI 1083
Cdd:pfam04560 81 DPRL 84
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
136-321 |
3.68e-24 |
|
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: 100.88 E-value: 3.68e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 136 RCPGVYLKPQFDKQG-NRTHLVSFLSAYGSWLRFETDKKGVVFAHIDNLRKVPVTVFLQALGFSMDT-IVGALKYP---- 209
Cdd:pfam04561 1 RSNGIYVEKELDKNGiIATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDReILDRLCYDfndp 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 210 ---EALDPTLKEVDWKLTTDEAILLLMSRLF--PNRPATVLRGRKFLfnQFFNPRRyslsdvgrkRVNQKFRMRSKTKHL 284
Cdd:pfam04561 81 qmlELLKPELEEAENIYTQEEALDYIGKGFAlrRGEEPRLQRAREIL--YSRDPKY---------NLNKHLGLNEPFENE 149
|
170 180 190
....*....|....*....|....*....|....*..
gi 113170437 285 TLTPQDALAALDYLLRCENGETEfLDDIDHLKNRRAR 321
Cdd:pfam04561 150 RLKAQDILYMIDRLLNLKLGRRK-PDDIDHLGNKRVR 185
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
119-457 |
5.08e-23 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 104.26 E-value: 5.08e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 119 GTFILNGSPRVIVHQIVRCPGVYLKPQFDKQGNRTHLVSFLS---AYGSWLRFETDKKG---VVFAHIDnlRKVPVTVFL 192
Cdd:PRK09606 146 GYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSqrrGYRALVTVERNRDGlleVSFPSVP--GSIPFVILM 223
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 193 QALGFSMDT-IVGAL-KYPEALDPTLK-----EVDwklTTDEAILLLMSRLFPNRPATVLRGR-KFLFNQFFNPrrysls 264
Cdd:PRK09606 224 RALGLETDEeIVEAVsDDPEIVKFMLEnleeaEVD---TQEEALEYIGKRVAPGQTKEYRIKRaEYVIDRYLLP------ 294
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 265 dvgrkrvnqkfrmrsktkHLTLTPQDALAALDYLLR-----CE--NGETEfLDDIDHLKNRRARLAGELIQTQFRLGLNR 337
Cdd:PRK09606 295 ------------------HLGVEPEVRRAKAHYLGRmaeacFElaLGRRE-EDDKDHYANKRLKLAGDLMEDLFRVAFNR 355
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 113170437 338 LERVIYNRISDENILRKTPgalgSLNSLIRTQVLASVFQEFF-------GSNQLSQFMDQTNPLAEITHKRRLSSlgPgg 410
Cdd:PRK09606 356 LARDVKYQLERANMRNREL----SIKTAVRSDVLTERLEHAMatgnwvgGRTGVSQLLDRTDYMATLSHLRRVVS--P-- 427
|
330 340 350 360
....*....|....*....|....*....|....*....|....*..
gi 113170437 411 LNRDRAGLIVRGIHPSYYGRICPIETPEGKNAGLVGSIATFTQINKN 457
Cdd:PRK09606 428 LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTG 474
|
|
| |
