|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
39-1136 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1794.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 39 KRKSPKKVPMV-SLPNLIEAQTDSYRWFL-------EKGFQELLDEINPITDFAGKdLEISISDYYLDEPKYDEITAKNK 110
Cdd:PRK00405 11 IRKSFGKIKEVlELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGN-LSLEFVSYELGEPKYDVEECKER 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 111 NISFEAPLRAKASLLIKRTGEIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFTMNYQK---GKKLFGAKI 187
Cdd:PRK00405 90 GLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtssGKLLYSARI 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 188 IPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYgSDEKLRKIFTDTDN-------------------------- 241
Cdd:PRK00405 170 IPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEKEEfgkeievpveyllgkvlaedivdeet 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 242 --------------GDTKYIEETISKDISKNQGEGYKEVYKRIRPGDFATEENAKQMIDSMFFNFERYDFGSVGRYRLNQ 307
Cdd:PRK00405 249 gevlaeandeiteeLDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNK 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 308 RLRVDRknNEESRVLNVEDLILIIKEVIKLNNDpLAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRMSTCDV 387
Cdd:PRK00405 329 KLGLDE--DEDVRVLTKEDIIATIKYLINLRNG-KGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 388 ITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRERAGFEVRDVHHSHYGRICPVQTP 467
Cdd:PRK00405 406 DTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 468 EGPNIGLVGHMATYARINKFGFLETPYRKieqeVENKVkmlinkilgenisgvakkgekidnvlaekivkskkdkvkvfp 547
Cdd:PRK00405 486 EGPNIGLINSLATYARVNEYGFIETPYRK----VVDGK------------------------------------------ 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 548 fITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVSAKQCISVATSMIPFLEHDDAN 627
Cdd:PRK00405 520 -VTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDAN 598
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 628 RALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAADSGQVVISYGDGTVIEVDARHIIVKEKTPVGSKKSsfNREYILQSFI 707
Cdd:PRK00405 599 RALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDG--VDIYNLIKFQ 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 708 KSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFS 787
Cdd:PRK00405 677 RSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYE 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 788 VEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAEERLLRAIFGEKSRDVKDSS 867
Cdd:PRK00405 757 IEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTS 836
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 868 LYLPHGEHGKVVDIKIFSR-EQGDKLSTGVIQKIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDI 946
Cdd:PRK00405 837 LRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDI 916
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 947 ILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIM 1026
Cdd:PRK00405 917 VLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYM 996
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1027 YIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIK 1106
Cdd:PRK00405 997 YMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVK 1076
|
1130 1140 1150
....*....|....*....|....*....|
gi 818367371 1107 GEPITSPNIPASFHVLVNELKGLCLNVQLL 1136
Cdd:PRK00405 1077 GENIPEPGIPESFNVLVKELQSLGLDVELL 1106
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
51-1136 |
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: 1659.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 51 LPNLIEAQTDSYRWFLEKGFQELLDEINPITDFAGkDLEISISDYYLDEPKYDEITAKNKNISFEAPLRAKASLLIKRTG 130
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTG-NLSLEFGDYRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKETG 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 131 EIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFTMNYQK-GKKLFGAKIIPNRGAWLEIDTDFDGVISVKI 209
Cdd:COG0085 92 EIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKsGKDLYSAKVIPSRGAWLEFETDKDGTIYVRI 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 210 DRKRKVPITALLRAFGYGSDEKLRKIFTDTDngDTKYIEETISKDISKNQGEGYKEVYKRIRPGDFATEENAKQMIDSMF 289
Cdd:COG0085 172 DRKRKIPVTVLLRALGLETDEEILEAFGDDP--IQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLF 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 290 FNFERYDFGSVGRYRLNQRLRVDrkNNEESRVLNVEDLILIIKEVIKLNNDPLaQADDIDHLGNRRVRGVGELVQNKLRV 369
Cdd:COG0085 250 FDPKRYDLAHVGRYKINKKLGLD--VPPEDRVLTAEDIVATIKYLLELHLGER-EPDDIDHLGNRRVRLVGELLQNQFRV 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 370 GMARMIRNIKDRMSTCDVITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRERAGFE 449
Cdd:COG0085 327 GLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFE 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 450 VRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKieqeVENKVkmlinkilgenisgvakkgekidn 529
Cdd:COG0085 407 VRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRK----VENGK------------------------ 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 530 vlaekivkskkdkvkvfpfITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVSAKQ 609
Cdd:COG0085 459 -------------------VTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQ 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 610 CISVATSMIPFLEHDDANRALMGSNMQRQAVSCVVPEAPVvgtgiedkaaadsgqvvisygdgtvievdarhiivkektp 689
Cdd:COG0085 520 IVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------------------------------------- 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 690 vgskkssfnREYILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNFEDAIIVS 769
Cdd:COG0085 560 ---------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIIS 630
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 770 ERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAEE 849
Cdd:COG0085 631 ERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEE 710
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 850 RLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSREQGDKLSTGVIQKIQVSVAQLRKISVGDKLAGRHGNKGVISRI 929
Cdd:COG0085 711 RLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRI 790
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 930 APVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLV 1009
Cdd:COG0085 791 LPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLY 870
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1010 NGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTI 1089
Cdd:COG0085 871 DGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTI 950
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|....*..
gi 818367371 1090 KSDDVMGRSKAYESIIKGEPITSPNIPASFHVLVNELKGLCLNVQLL 1136
Cdd:COG0085 951 KSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVL 997
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
39-1135 |
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: 1572.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 39 KRKSPKKVP-MVSLPNLIEAQTDSYRWFL----------EKGFQELLDEINPITDFAGkDLEISISDYYLDEPKYDEITA 107
Cdd:TIGR02013 4 IRIDFGKIPeVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTG-NIELEYLSYRLGEPKYSVEEC 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 108 KNKNISFEAPLRAKASLLIKR---TGEIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFF---TMNYQKGKK 181
Cdd:TIGR02013 83 KERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFsseKDTTKSGKV 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 182 LFGAKIIPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYGSDeklrKIFTDtDNGDTKYIEETISKDISKNQGE 261
Cdd:TIGR02013 163 LFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTID----TLILN-RLGSGEYIRNTLRKDPTNSEEE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 262 GYKEVYKRIRPGDFATEENAKQMIDSMFFNFERYDFGSVGRYRLNQRLRVDrkNNEESRVLNVEDLILIIKEVIKLNNDp 341
Cdd:TIGR02013 238 ALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLD--VPESIGVLTKEDIIATIKYLIKLRNG- 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 342 LAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRMSTCDVITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQV 421
Cdd:TIGR02013 315 KGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQT 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 422 NPLAELEHKRRLSAMGPGGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKIEqev 501
Cdd:TIGR02013 395 NPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVK--- 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 502 enkvkmlinkilgeniSGVAKKgekidnvlaekivkskkdkvkvfpfiTETIEYIDATVEDRKIIAHAGIEIDKDGNIME 581
Cdd:TIGR02013 472 ----------------DGKVVV--------------------------TDEIDYLTADEEDNYVIAQANAPLDENGRFVE 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 582 SMVEARVKGHPEMIEVDKLDYIDVSAKQCISVATSMIPFLEHDDANRALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAAD 661
Cdd:TIGR02013 510 DLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARD 589
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 662 SGQVVISYGDGTVIEVDARHIIVKEKTPVGSKKSSFNReYILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDH 741
Cdd:TIGR02013 590 SGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDI-YRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDL 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 742 GELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGII 821
Cdd:TIGR02013 669 GELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 822 RIGAEVSSGDIMVGKITPKGEGDLTAEERLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSREQGDKLSTGVIQKIQ 901
Cdd:TIGR02013 749 RIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVK 828
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 902 VSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGY---NI 978
Cdd:TIGR02013 829 VYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRkgvPI 908
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 979 ATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGK 1058
Cdd:TIGR02013 909 ATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGK 988
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818367371 1059 AQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIKGEPITSPNIPASFHVLVNELKGLCLNVQL 1135
Cdd:TIGR02013 989 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
54-1135 |
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: 837.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 54 LIEAQTDSYRWFLEKGFQELLDEINPITDFAGKD-LEISISDYYLDEPKYDEIT---------AKNKNISFEAPLRAKAS 123
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGrLKLKFGDIYLGKPKVEEGGvtrkltpneCRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 124 LLIKRTGEIREQEIYLGDFPIMTDrgtFVVNGVERVVVSQLIRS------PGVFFtmnyqkgkklfgakIIpnRGAwlei 197
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLR---SKLCNLNGLTPEELIKLgecpldPGGYF--------------II--NGT---- 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 198 dtdfDGVISVKIDRKRKVPITallrafgygSDEKLRKIFT-DTDNGDTKYIEETISKDISKNQGEGYKEVYKRIRpgdfa 276
Cdd:cd00653 138 ----EKVIINQEQRSPNVIIV---------EDSKGKRIYTkTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKRQ----- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 277 teENAKQMIDSMFfnferydfgsvgryrlnqrlrvdrknneesrvlnvEDLILIIKEVIKLNNDPLAQaDDIDHLGNRRV 356
Cdd:cd00653 200 --EEALKYIGKRF-----------------------------------EDLIYMIRKLILLVLGKGKL-DDIDHLGNKRV 241
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 357 RGVGELVQNKLRVGMARMIRNIKDRMSTCD--VITVVPGQLVNSRPIAAAIKEFFSSSQ------------LSQFMDQVN 422
Cdd:cd00653 242 RLAGELLQNLFRSGLKRLEREVKEKLQKQLskKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLN 321
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 423 PLAELEHKRRLSAmgpGGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINkfGFLETPYRKIEQEVe 502
Cdd:cd00653 322 PLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEKEV- 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 503 nkvkmlinkilgenisgvakkgekidnvlaekivkskkdkvkvfpfitetieyidatvedrkiiahagieidkdgnimes 582
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 583 mvearvkghpemievdklDYIDVSAKQCISVATSMIPFLEHDDANRALMGSNMQRQAV----------------SCVVPE 646
Cdd:cd00653 396 ------------------THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVgtpalnqqyrmdtklyLLLYPQ 457
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 647 APVVGTGIEDKAAADsgqvvisygdgtvievdarhiivkektpvgskkssfnreyilqsfiksnaftsmnqiprvkkgdd 726
Cdd:cd00653 458 KPLVGTGIEEYIAFG----------------------------------------------------------------- 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 727 vhkgqlladgastdhgELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTR-DIP 805
Cdd:cd00653 473 ----------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIP 536
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 806 NIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAeerllraIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFS 885
Cdd:cd00653 537 NVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFS 609
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 886 REqgdkLSTGVIQKIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILET 965
Cdd:cd00653 610 RE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLES 685
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 966 HLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIG 1045
Cdd:cd00653 686 LLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTG 765
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1046 PYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESII----------KGEPITSPNI 1115
Cdd:cd00653 766 PYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGI 845
|
1130 1140
....*....|....*....|
gi 818367371 1116 PASFHVLVNELKGLCLNVQL 1135
Cdd:cd00653 846 PYAFKLLFQELQSMNIDPRL 865
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
667-1060 |
1.69e-158 |
|
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: 475.87 E-value: 1.69e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 667 ISYGDGTVIEVDARHIIVKektpvgskkSSFNRE----YILQSFIKSNAFTSM---NQIPRVKKGDdVHKGQLladgast 739
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQ---------CAMGKQamgiYTLNKFYRSDQNTYVlcyPQKPLVKTGA-VEAGGF------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 740 dhGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEdfSVEVRDTKLGP-EVVTRDIPNIGEERLKNLDET 818
Cdd:pfam00562 64 --GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPiEEITRDIPNVSEEALKKLDED 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 819 GIIRIGAEVSSGDIMVGKITPkgegdlTAEERLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSreqgdkLSTGVIQ 898
Cdd:pfam00562 140 GIVRVGAEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIK 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 899 KIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNI 978
Cdd:pfam00562 208 MVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFV 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 979 ATPALDGVSE--DYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLG 1056
Cdd:pfam00562 288 DATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLG 367
|
....
gi 818367371 1057 GKAQ 1060
Cdd:pfam00562 368 GRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
39-1136 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1794.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 39 KRKSPKKVPMV-SLPNLIEAQTDSYRWFL-------EKGFQELLDEINPITDFAGKdLEISISDYYLDEPKYDEITAKNK 110
Cdd:PRK00405 11 IRKSFGKIKEVlELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGN-LSLEFVSYELGEPKYDVEECKER 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 111 NISFEAPLRAKASLLIKRTGEIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFTMNYQK---GKKLFGAKI 187
Cdd:PRK00405 90 GLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtssGKLLYSARI 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 188 IPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYgSDEKLRKIFTDTDN-------------------------- 241
Cdd:PRK00405 170 IPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEKEEfgkeievpveyllgkvlaedivdeet 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 242 --------------GDTKYIEETISKDISKNQGEGYKEVYKRIRPGDFATEENAKQMIDSMFFNFERYDFGSVGRYRLNQ 307
Cdd:PRK00405 249 gevlaeandeiteeLDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNK 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 308 RLRVDRknNEESRVLNVEDLILIIKEVIKLNNDpLAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRMSTCDV 387
Cdd:PRK00405 329 KLGLDE--DEDVRVLTKEDIIATIKYLINLRNG-KGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 388 ITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRERAGFEVRDVHHSHYGRICPVQTP 467
Cdd:PRK00405 406 DTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 468 EGPNIGLVGHMATYARINKFGFLETPYRKieqeVENKVkmlinkilgenisgvakkgekidnvlaekivkskkdkvkvfp 547
Cdd:PRK00405 486 EGPNIGLINSLATYARVNEYGFIETPYRK----VVDGK------------------------------------------ 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 548 fITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVSAKQCISVATSMIPFLEHDDAN 627
Cdd:PRK00405 520 -VTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDAN 598
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 628 RALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAADSGQVVISYGDGTVIEVDARHIIVKEKTPVGSKKSsfNREYILQSFI 707
Cdd:PRK00405 599 RALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRVEELDPGEDG--VDIYNLIKFQ 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 708 KSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFS 787
Cdd:PRK00405 677 RSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYE 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 788 VEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAEERLLRAIFGEKSRDVKDSS 867
Cdd:PRK00405 757 IEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTS 836
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 868 LYLPHGEHGKVVDIKIFSR-EQGDKLSTGVIQKIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDI 946
Cdd:PRK00405 837 LRVPHGEEGTVIDVKVFTRiEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDI 916
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 947 ILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIM 1026
Cdd:PRK00405 917 VLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYM 996
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1027 YIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIK 1106
Cdd:PRK00405 997 YMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVK 1076
|
1130 1140 1150
....*....|....*....|....*....|
gi 818367371 1107 GEPITSPNIPASFHVLVNELKGLCLNVQLL 1136
Cdd:PRK00405 1077 GENIPEPGIPESFNVLVKELQSLGLDVELL 1106
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
51-1136 |
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: 1659.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 51 LPNLIEAQTDSYRWFLEKGFQELLDEINPITDFAGkDLEISISDYYLDEPKYDEITAKNKNISFEAPLRAKASLLIKRTG 130
Cdd:COG0085 13 LPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTG-NLSLEFGDYRLGEPKYTPEECKERDLTYAAPLYVKVRLVNKETG 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 131 EIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFTMNYQK-GKKLFGAKIIPNRGAWLEIDTDFDGVISVKI 209
Cdd:COG0085 92 EIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKsGKDLYSAKVIPSRGAWLEFETDKDGTIYVRI 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 210 DRKRKVPITALLRAFGYGSDEKLRKIFTDTDngDTKYIEETISKDISKNQGEGYKEVYKRIRPGDFATEENAKQMIDSMF 289
Cdd:COG0085 172 DRKRKIPVTVLLRALGLETDEEILEAFGDDP--IQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLF 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 290 FNFERYDFGSVGRYRLNQRLRVDrkNNEESRVLNVEDLILIIKEVIKLNNDPLaQADDIDHLGNRRVRGVGELVQNKLRV 369
Cdd:COG0085 250 FDPKRYDLAHVGRYKINKKLGLD--VPPEDRVLTAEDIVATIKYLLELHLGER-EPDDIDHLGNRRVRLVGELLQNQFRV 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 370 GMARMIRNIKDRMSTCDVITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRERAGFE 449
Cdd:COG0085 327 GLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFE 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 450 VRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKieqeVENKVkmlinkilgenisgvakkgekidn 529
Cdd:COG0085 407 VRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRK----VENGK------------------------ 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 530 vlaekivkskkdkvkvfpfITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVSAKQ 609
Cdd:COG0085 459 -------------------VTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQ 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 610 CISVATSMIPFLEHDDANRALMGSNMQRQAVSCVVPEAPVvgtgiedkaaadsgqvvisygdgtvievdarhiivkektp 689
Cdd:COG0085 520 IVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------------------------------------- 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 690 vgskkssfnREYILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNFEDAIIVS 769
Cdd:COG0085 560 ---------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIIS 630
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 770 ERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAEE 849
Cdd:COG0085 631 ERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEE 710
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 850 RLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSREQGDKLSTGVIQKIQVSVAQLRKISVGDKLAGRHGNKGVISRI 929
Cdd:COG0085 711 RLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRI 790
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 930 APVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLV 1009
Cdd:COG0085 791 LPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLY 870
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1010 NGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTI 1089
Cdd:COG0085 871 DGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTI 950
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|....*..
gi 818367371 1090 KSDDVMGRSKAYESIIKGEPITSPNIPASFHVLVNELKGLCLNVQLL 1136
Cdd:COG0085 951 KSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVL 997
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
39-1135 |
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: 1572.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 39 KRKSPKKVP-MVSLPNLIEAQTDSYRWFL----------EKGFQELLDEINPITDFAGkDLEISISDYYLDEPKYDEITA 107
Cdd:TIGR02013 4 IRIDFGKIPeVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTG-NIELEYLSYRLGEPKYSVEEC 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 108 KNKNISFEAPLRAKASLLIKR---TGEIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFF---TMNYQKGKK 181
Cdd:TIGR02013 83 KERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFsseKDTTKSGKV 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 182 LFGAKIIPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYGSDeklrKIFTDtDNGDTKYIEETISKDISKNQGE 261
Cdd:TIGR02013 163 LFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTID----TLILN-RLGSGEYIRNTLRKDPTNSEEE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 262 GYKEVYKRIRPGDFATEENAKQMIDSMFFNFERYDFGSVGRYRLNQRLRVDrkNNEESRVLNVEDLILIIKEVIKLNNDp 341
Cdd:TIGR02013 238 ALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLD--VPESIGVLTKEDIIATIKYLIKLRNG- 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 342 LAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRMSTCDVITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQV 421
Cdd:TIGR02013 315 KGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQT 394
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 422 NPLAELEHKRRLSAMGPGGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKIEqev 501
Cdd:TIGR02013 395 NPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVK--- 471
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 502 enkvkmlinkilgeniSGVAKKgekidnvlaekivkskkdkvkvfpfiTETIEYIDATVEDRKIIAHAGIEIDKDGNIME 581
Cdd:TIGR02013 472 ----------------DGKVVV--------------------------TDEIDYLTADEEDNYVIAQANAPLDENGRFVE 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 582 SMVEARVKGHPEMIEVDKLDYIDVSAKQCISVATSMIPFLEHDDANRALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAAD 661
Cdd:TIGR02013 510 DLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARD 589
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 662 SGQVVISYGDGTVIEVDARHIIVKEKTPVGSKKSSFNReYILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDH 741
Cdd:TIGR02013 590 SGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDI-YRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDL 668
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 742 GELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGII 821
Cdd:TIGR02013 669 GELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIV 748
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 822 RIGAEVSSGDIMVGKITPKGEGDLTAEERLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSREQGDKLSTGVIQKIQ 901
Cdd:TIGR02013 749 RIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVK 828
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 902 VSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGY---NI 978
Cdd:TIGR02013 829 VYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRkgvPI 908
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 979 ATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGK 1058
Cdd:TIGR02013 909 ATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGK 988
|
1050 1060 1070 1080 1090 1100 1110
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 818367371 1059 AQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIKGEPITSPNIPASFHVLVNELKGLCLNVQL 1135
Cdd:TIGR02013 989 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
48-1133 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1060.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 48 MVSLPNLIEAQTDSYRWFLEKGFQELLDEINPITDFAGK-DLEISISDYYLDEPKYDEITAKNKNISFEAPLRAKASLLI 126
Cdd:CHL00207 4 NFALPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNlELLLFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFIN 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 127 KRTGEIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFTMNY-QKGKKLFGAKIIPNRGAWLEIDTDFDGVI 205
Cdd:CHL00207 84 LKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIkKNSNKIYSATLIPNRGSWIKFELDKNKEI 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 206 SVKIDRKRKVPITALLRAFGYGSDEklrkIFTDTDNGDTKYIEETISKDISK-NQGEGYKEVYKRIRPGDFATEENAKQM 284
Cdd:CHL00207 164 WIRIDKNRKKPLIIFLKALGLTDQD----IYSRLTKSEFLKKLKPILLNSNSyTNEEILLEIYKNLSPIEPATVNDANQN 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 285 IDSMFFNFERYDFGSVGRYRLNQRLrvDRKNNEESRVLNVEDLILIIKEVIKLNNDPLAQaDDIDHLGNRRVRGVGELVQ 364
Cdd:CHL00207 240 LFSRFFDPKNYDLGKVGRYKINNKL--NLNIPERVRNLTYEDILSIIDKLINLKINKGNF-DDIDHLKNRRVRSVGELLQ 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 365 NKLRVGMARMIRNIKDRMSTCDVITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRE 444
Cdd:CHL00207 317 NQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKD 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 445 RAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKIEQeveNKVKMLINKIlgenisgvakkg 524
Cdd:CHL00207 397 RISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVIN---GKVKKFGNPI------------ 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 525 ekidnvlaekivkskkdkvkvfpfitetieYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYID 604
Cdd:CHL00207 462 ------------------------------YLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIA 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 605 VSAKQCISVATSMIPFLEHDDANRALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAADSGQVVISYGDGTVIEVDARHIIV 684
Cdd:CHL00207 512 ISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIII 591
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 685 KEKtpvgskkssFNRE--YILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNF 762
Cdd:CHL00207 592 QDD---------NNRYihYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNF 662
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 763 EDAIIVSERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGE 842
Cdd:CHL00207 663 EDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGE 742
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 843 GDLTAEERLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSREQGDKLSTGVIQKIQVSVAQLRKISVGDKLAGRHGN 922
Cdd:CHL00207 743 SDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGN 822
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 923 KGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGV-----SEDYIKEELKK 997
Cdd:CHL00207 823 KGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMygseySRILINNKLNQ 902
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 998 AGLPED----------GKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFG 1067
Cdd:CHL00207 903 ASIKNNeywlfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFG 982
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 818367371 1068 EMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIKGEPITSPNIPASFHVLVNELKGLCLNV 1133
Cdd:CHL00207 983 EMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDI 1048
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
44-1132 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1041.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 44 KKVPMVSLPNLIEAQTDSYRWFLEKGFQELLDEINPITDfagKDLEISIS----DYYLDEPKYDEITAKNKNISFEAPLR 119
Cdd:CHL00001 5 GNEGMSTIPGFNQIQFEGFCRFIDQGLTEELSKFPKIED---TDQEIEFQlfveTYQLVEPLIKERDAVYESLTYSSELY 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 120 AKASLLIKRTGEIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFT-MNYQKGKKLFGAKIIPNRGAWLEID 198
Cdd:CHL00001 82 VPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRsELDHNGISVYTGTIISDWGGRLELE 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 199 TDFDGVISVKIDRKRKVPITALLRAFGYGSDEKLR-----KIFTDTDNGDTKYIEETISKDISknqgEGYKEVYkrIRPG 273
Cdd:CHL00001 162 IDRKARIWARVSRKQKISILVLLSAMGLNLREILDnvcypEIFLSFLNDKEKKKIGSKENAIL----EFYQQFA--CVGG 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 274 DFATEENAKQMIDSMFFNfERYDFGSVGRYRLNQRLRVDRKNNEesRVLNVEDLILIIKEVIKLNNDpLAQADDIDHLGN 353
Cdd:CHL00001 236 DPVFSESLCKELQKKFFQ-QRCELGRIGRRNMNRKLNLDIPENN--TFLLPQDVLAAADYLIGMKFG-MGTLDDIDHLKN 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 354 RRVRGVGELVQNKLRVGMARMIRNIKDRMstCDVI----TVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEH 429
Cdd:CHL00001 312 KRIRSVADLLQDQFGLALNRLENAVRGTI--CGAIrrklIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVH 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 430 KRRLSAMGPGGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKIEqEVENKVKMLi 509
Cdd:CHL00001 390 GRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEIS-ERSKEERMV- 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 510 nkilgenisgvakkgekidnvlaekivkskkdkvkvfpfitetieYIDATVEDRKIIAhAGIEIDKDGNIMES-MVEARV 588
Cdd:CHL00001 468 ---------------------------------------------YLSPSEDEYYMIA-AGNSLALNQGIQEEqVVPARY 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 589 KGHPEMIEVDKLDYIDVSAKQCISVATSMIPFLEHDDANRALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAADSGQVVIS 668
Cdd:CHL00001 502 RQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIA 581
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 669 YGDGTVIEVDARHIIVkektpvgskksSFNREYI---LQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELA 745
Cdd:CHL00001 582 EHEGKIIYTDTDKIIL-----------SGNGDTLsipLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELA 650
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 746 LGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGA 825
Cdd:CHL00001 651 LGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGS 730
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 826 EVSSGDIMVGKITPK--GEGDLTAEERLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKifsREQGDKLSTGVIQKIQVS 903
Cdd:CHL00001 731 WVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR---WIQKKGGSSYNPETIHVY 807
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 904 VAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPAL 983
Cdd:CHL00001 808 ILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPF 887
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 984 DgvsEDYIKE--------ELKKAGL---------PED-GKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIG 1045
Cdd:CHL00001 888 D---ERYEQEasrklvfsELYEASKqtanpwvfePEYpGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSG 964
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1046 PYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIKGEPITSPN-IPASFHVLVN 1124
Cdd:CHL00001 965 PYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPEdAPESFRLLVR 1044
|
....*...
gi 818367371 1125 ELKGLCLN 1132
Cdd:CHL00001 1045 ELRSLALE 1052
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
41-1137 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 934.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 41 KSPKKVpmvSLPNLIEAQTDSYRWFL------EKGFQELLDEINPITDfAGKDLEISISDYYLDEPKYDEITAKNKNISF 114
Cdd:PRK09603 17 KTPTDL---EVPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPIQD-EHNRITLEYAGCEFGKSKYTVREAMERGITY 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 115 EAPLRAKASLLI----KRTGE------IREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFT---MNYQKGKK 181
Cdd:PRK09603 93 SIPLKIKVRLILwekdTKSGEkngikdIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKeeeSSTSLNKL 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 182 LFGAKIIPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYgSDEKLRKIF------------------------- 236
Cdd:PRK09603 173 IYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDY-QKQDIIKMFyplvkvryendkylipfasldanqr 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 237 ---------------------------------------------------------------TDTDNGDTKYIEE---- 249
Cdd:PRK09603 252 mefdlkdpqgkiillagkkltsrkikelkenhlewveypmdillnrhlaepvmvgkevlldmlTQLDKNKLEKIHDlgvq 331
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 250 --TISKDISK--------------------NQGEGYKE--------VYKRIRPGDFATEENAKQMIDSMFFNFERYDFGS 299
Cdd:PRK09603 332 efVIINDLALghdasiihsfsadseslkllKQTEKIDDenalaairIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTM 411
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 300 VGRYRLNQRLRVDRKnnEESRVLNVEDLILIIKEVIKLNNDpLAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIK 379
Cdd:PRK09603 412 VGRMKMNHKLGLHVP--DYITTLTHEDIITTVKYLMKIKNN-QGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIK 488
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 380 DRMSTCDVI--TVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRERAGFEVRDVHHSH 457
Cdd:PRK09603 489 DKLTTMSGAfdSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTH 568
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 458 YGRICPVQTPEGPNIGLVGHMATYARINKFGFLETPYRKIEQEVenkvkmlinkilgenisgvakkgekidnvlaekivk 537
Cdd:PRK09603 569 YGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGK------------------------------------ 612
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 538 skkdkvkvfpfITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVSAKQCISVATSM 617
Cdd:PRK09603 613 -----------VVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASL 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 618 IPFLEHDDANRALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAADSGQVVISYGDGTVIEVDARHI-IVKEktpvgSKKSS 696
Cdd:PRK09603 682 IPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIyILGE-----GKEEA 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 697 FNREYILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQAD 776
Cdd:PRK09603 757 YIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDD 836
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 777 RYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAEERLLRAIF 856
Cdd:PRK09603 837 IFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIF 916
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 857 GEKSRDVKDSSLYLPHGEHGKVVDIKIFSR-------------------------------------------------- 886
Cdd:PRK09603 917 GDKAGHVVNKSLYCPPSLEGTVIDVKVFTKkgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqailee 996
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 887 --------------------------------------------------------------------EQGDKLSTGVIQ 898
Cdd:PRK09603 997 pfshngkdykegdqipkeeiasinrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheeklsilEKDDILPNGVIK 1076
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 899 KIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNI 978
Cdd:PRK09603 1077 KVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQI 1156
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 979 ----------------------------------------------------------ATPALDGVSEDYIKEELKKAGL 1000
Cdd:PRK09603 1157 asmledktkdfakelrakmleianainekdpltihalencsdeelleyakdwskgvkmAIPVFEGISQEKFYKLFELAKI 1236
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1001 PEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAA 1080
Cdd:PRK09603 1237 AMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAA 1316
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|....*..
gi 818367371 1081 HTLQEMLTIKSDDVMGRSKAYESIIKGEPITSPNIPASFHVLVNELKGLCLNVQLLG 1137
Cdd:PRK09603 1317 HTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFG 1373
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
50-1135 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 877.41 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 50 SLPNLIEAQTDSYRWFLEKG-----FQELLDEINPITDFAGKdLEISISDYYLDEPKYDEITAKNKNISFEAPLRAKASL 124
Cdd:PRK14844 28 SLLDLVKVQKESYDSFTPKNkgnerLEVIFHTIFPINDPLHR-ATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 125 LIKRTG-----------------------EIREQEIYLGDFPIMTDRGTFVVNGVERVVVSQLIRSPGVFFTMN----YQ 177
Cdd:PRK14844 107 VIMQDGisldeyksikesgdhsklatvikSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDkgktYN 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 178 KGKKLFGAKIIPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYGSDEKLRKIFTDT------------------ 239
Cdd:PRK14844 187 SGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIkyikhkdgwkvpfvpdkf 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 240 ---------------------------------DNGDTKYI----------------------------EETISKDISK- 257
Cdd:PRK14844 267 kgvrlpfdlmdvegnvllkanvritsrlakklyDNELKEYLvpfdsicglflaedlidsasstkilsagESIKLEDIKKl 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 258 ----------------------------NQGEGYK----EVYKRIRPGDFATEENAKQMIDSMFFNFERYDFGSVGRYRL 305
Cdd:PRK14844 347 ellsideisvlnidnlsvgpyilntlflDENMSYQdalyEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKL 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 306 NQRLRVDRknNEESRVLNVEDLILIIKEVIKLNnDPLAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRMSTC 385
Cdd:PRK14844 427 NSYLGLNY--DEDLTVLTHEDIIEIVRKIVLLR-DGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTS 503
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 386 DVITVVPGQLVNSRPIAAAIKEFFSSSQLSQFMDQVNPLAELEHKRRLSAMGPGGLTRERAGFEVRDVHHSHYGRICPVQ 465
Cdd:PRK14844 504 SLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIE 583
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 466 TPEGPNIGLVGHMATYARINKFGFLETPYRKIeqevenkvkmlINKIlgenisgvakkgekidnvlaekivkskkdkvkv 545
Cdd:PRK14844 584 TPEGQNIGLINSLAIYARINKYGFIESPYRKV-----------VNRV--------------------------------- 619
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 546 fpfITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVSAKQCISVATSMIPFLEHDD 625
Cdd:PRK14844 620 ---VTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDD 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 626 ANRALMGSNMQRQAVSCVVPEAPVVGTGIEDKAAADSGQVVISYGDGTVIEVDARHIIVKektpvgskksSFNRE----- 700
Cdd:PRK14844 697 ANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIR----------AFDKErvnyl 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 701 ----YILQSFIKSNAFTSMNQIPRVKKGDDVHKGQLLADGASTDHGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQAD 776
Cdd:PRK14844 767 dvdiYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKD 846
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 777 RYSSIHIEDFSVEVRDTKLGPEVVTRDIPNIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAEERLLRAIF 856
Cdd:PRK14844 847 LFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIF 926
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 857 GEKSRDVKDSSLYLPHGEHGKVVDIKIFSR-------------------------------------------------- 886
Cdd:PRK14844 927 GEKSFDCADSSLYTSPDVEGTVIDVQVFTRrgveenerallikqkeindfekerdyiinvtseyfydelkkllinsgsqd 1006
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 887 ---------------------------------------------------EQGDKLSTGVIQKIQVSVAQLRKISVGDK 915
Cdd:PRK14844 1007 rekfdsiereqwwgiglknqsiseqvkslkkdfdekvshaiaqfkrkveklHEGYDLPQGVSMSVKVFIAVKHSLQPGDK 1086
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 916 LAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYN------------------ 977
Cdd:PRK14844 1087 MAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKvgnildeinkiksafckg 1166
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 --------------------------------------------------------------------------------
Cdd:PRK14844 1167 irslnddnftkfaaayldnkkienidddeitasvlntpnknalndelnelvenylnscksaysnlrnflievyscgsnvs 1246
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 978 -------------------------IATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLN 1032
Cdd:PRK14844 1247 icnnirdisdnnliefarklrdgipVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLH 1326
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1033 HLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESIIKGEPITS 1112
Cdd:PRK14844 1327 HLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFE 1406
|
1450 1460
....*....|....*....|...
gi 818367371 1113 PNIPASFHVLVNELKGLCLNVQL 1135
Cdd:PRK14844 1407 CGIPESFNVMIKELRSLCLNVDL 1429
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
54-1135 |
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: 837.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 54 LIEAQTDSYRWFLEKGFQELLDEINPITDFAGKD-LEISISDYYLDEPKYDEIT---------AKNKNISFEAPLRAKAS 123
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDDDGrLKLKFGDIYLGKPKVEEGGvtrkltpneCRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 124 LLIKRTGEIREQEIYLGDFPIMTDrgtFVVNGVERVVVSQLIRS------PGVFFtmnyqkgkklfgakIIpnRGAwlei 197
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLR---SKLCNLNGLTPEELIKLgecpldPGGYF--------------II--NGT---- 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 198 dtdfDGVISVKIDRKRKVPITallrafgygSDEKLRKIFT-DTDNGDTKYIEETISKDISKNQGEGYKEVYKRIRpgdfa 276
Cdd:cd00653 138 ----EKVIINQEQRSPNVIIV---------EDSKGKRIYTkTSIPSYSPYRGSWLEVKSDKKKDRIYVRIDLKRQ----- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 277 teENAKQMIDSMFfnferydfgsvgryrlnqrlrvdrknneesrvlnvEDLILIIKEVIKLNNDPLAQaDDIDHLGNRRV 356
Cdd:cd00653 200 --EEALKYIGKRF-----------------------------------EDLIYMIRKLILLVLGKGKL-DDIDHLGNKRV 241
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 357 RGVGELVQNKLRVGMARMIRNIKDRMSTCD--VITVVPGQLVNSRPIAAAIKEFFSSSQ------------LSQFMDQVN 422
Cdd:cd00653 242 RLAGELLQNLFRSGLKRLEREVKEKLQKQLskKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLN 321
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 423 PLAELEHKRRLSAmgpGGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYARINkfGFLETPYRKIEQEVe 502
Cdd:cd00653 322 PLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEKEV- 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 503 nkvkmlinkilgenisgvakkgekidnvlaekivkskkdkvkvfpfitetieyidatvedrkiiahagieidkdgnimes 582
Cdd:cd00653 --------------------------------------------------------------------------------
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 583 mvearvkghpemievdklDYIDVSAKQCISVATSMIPFLEHDDANRALMGSNMQRQAV----------------SCVVPE 646
Cdd:cd00653 396 ------------------THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVgtpalnqqyrmdtklyLLLYPQ 457
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 647 APVVGTGIEDKAAADsgqvvisygdgtvievdarhiivkektpvgskkssfnreyilqsfiksnaftsmnqiprvkkgdd 726
Cdd:cd00653 458 KPLVGTGIEEYIAFG----------------------------------------------------------------- 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 727 vhkgqlladgastdhgELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEVRDTKLGPEVVTR-DIP 805
Cdd:cd00653 473 ----------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIP 536
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 806 NIGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKGEGDLTAeerllraIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFS 885
Cdd:cd00653 537 NVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFS 609
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 886 REqgdkLSTGVIQKIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILET 965
Cdd:cd00653 610 RE----LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLES 685
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 966 HLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIG 1045
Cdd:cd00653 686 LLGKAGALLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTG 765
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1046 PYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVMGRSKAYESII----------KGEPITSPNI 1115
Cdd:cd00653 766 PYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGI 845
|
1130 1140
....*....|....*....|
gi 818367371 1116 PASFHVLVNELKGLCLNVQL 1135
Cdd:cd00653 846 PYAFKLLFQELQSMNIDPRL 865
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
667-1060 |
1.69e-158 |
|
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: 475.87 E-value: 1.69e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 667 ISYGDGTVIEVDARHIIVKektpvgskkSSFNRE----YILQSFIKSNAFTSM---NQIPRVKKGDdVHKGQLladgast 739
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQ---------CAMGKQamgiYTLNKFYRSDQNTYVlcyPQKPLVKTGA-VEAGGF------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 740 dhGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEdfSVEVRDTKLGP-EVVTRDIPNIGEERLKNLDET 818
Cdd:pfam00562 64 --GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIK--EIEARKTKLGPiEEITRDIPNVSEEALKKLDED 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 819 GIIRIGAEVSSGDIMVGKITPkgegdlTAEERLLRAIFGEKSRDVKDSSLYLPHGEHGKVVDIKIFSreqgdkLSTGVIQ 898
Cdd:pfam00562 140 GIVRVGAEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------LPPGGIK 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 899 KIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNI 978
Cdd:pfam00562 208 MVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFV 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 979 ATPALDGVSE--DYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLG 1056
Cdd:pfam00562 288 DATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLG 367
|
....
gi 818367371 1057 GKAQ 1060
Cdd:pfam00562 368 GRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
53-1136 |
5.71e-105 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 356.19 E-value: 5.71e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 53 NLIEAQTDSYRWFLEKGFQELLDEINPITDFaGKDLEISISDYYLDEPKYDEIT----------AKNKNISFEAPLRAKA 122
Cdd:PRK08565 13 GLVRQHLDSYNDFIERGLQEIVDEFGEIKTE-IPGLKIVLGKIRVGEPEIKEADgserpitpmeARLRNLTYAAPLYLTM 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 123 SLLIKrTGEIREQEIYLGDFPIMTDRgtfVVNGVERVVVSQLI------RSPGVFFTMN------------------YQK 178
Cdd:PRK08565 92 IPVEN-GIEYEPEEVKIGDLPIMVKS---KICPLSGLSPDELIeigedpKDPGGYFIINgservivsqedlapnrvlVDK 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 179 GKK----LFGAKIIPNRG---AWLEIDTDFDGVISVKIDRKR-KVPITALLRAFGYGSDEKLRKIFTDTDNGDTKY---I 247
Cdd:PRK08565 168 GEAgssiTHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAVPgKIPFVILMRALGLETDRDIVYAVSLDPEIQQELlpsL 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 248 EEtiSKDISKNQGEGYKEVYKRIRPGDfATE---ENAKQMIDSMFFNferydfgSVGryrlnqrlrvdrkNNEESRVLNV 324
Cdd:PRK08565 248 EQ--ASSIAATVEDALDYIGKRVAIGQ-PREyriERAEQILDKYLLP-------HLG-------------TSPEDRIKKA 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 325 EDLILIIKEVIKLNNDpLAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRMSTcdviTVVPGQLVNSRPIAAA 404
Cdd:PRK08565 305 YFLGQMASKLLELYLG-RREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEK----SYARGRKLDLRAIVRP 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 405 ------IKEFFSSSQ-------LSQFMDQVNPLAELEHKRRLSAmgpgGLTRERAGFEVRDVHHSHYGRICPVQTPEGPN 471
Cdd:PRK08565 380 diiterIRHALATGNwvggrtgVSQLLDRTNYLSTLSHLRRVVS----PLSRGQPHFEARDLHGTQWGRICPFETPEGPN 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 472 IGLVGHMATYARINkFGFLETPYRK---------IEQEVENKVKMLINKILGENISGVAKKGEKIDNVLAEKIVKSKKDK 542
Cdd:PRK08565 456 CGLVKNLALMAQIS-VGVDEEEVEEilyelgvvpVEEAREEEYISWSRVYLNGRLIGYHPDGEELAEKIRELRRSGKISD 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 543 VKVFPFI-TETIE--YIDA----------TVEDRKI-IAHAGIEIDKDGNI-MESMVEarvKGHPEMIEVDKLD--YIDV 605
Cdd:PRK08565 535 EVNVAYIeTGEINevYVNCdsgrvrrpliVVENGKPkLTREHVEKLKKGELtFDDLVK---MGVIEYLDAEEEEnaYVAL 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 606 SAKQCIS--------------VATSMIPFLEHDDANRALMGSNMQRQAVscvvpeapvvgtGIedkaaadsgqvvisYGD 671
Cdd:PRK08565 612 DPEDLTPehthleiwppailgITASIIPYPEHNQSPRNTYQAAMAKQSL------------GL--------------YAA 665
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 672 GTVIEVDAR-HIIVKEKTPvgskkssfnreyILQSfiKSNAFTSMNQIPRvkkgddvhkgqlladgastdhgelalGQNV 750
Cdd:PRK08565 666 NFRIRTDTRgHLLHYPQRP------------LVQT--RALEIIGYNDRPA--------------------------GQNA 705
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 751 MVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEVR-------DTKLGPEvvtrdiPNI----GEERLKNLDETG 819
Cdd:PRK08565 706 VVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERkypggqeDKIEIPE------PNVrgyrGEEYYRKLDEDG 779
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 820 IIRIGAEVSSGDIMVGKITPKgegDLTAEERLLRAIFGEKsrdvKDSSLYLPHGEHGKVVDIKIFSREQGDKLstgviqk 899
Cdd:PRK08565 780 IVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----RDTSVTVRHGEKGIVDTVLITESPEGNKL------- 845
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 900 IQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIA 979
Cdd:PRK08565 846 VKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVD 925
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 980 TPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKA 1059
Cdd:PRK08565 926 ATPFYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRA 1005
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1060 QFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSD-------DVMG-------RSKAYESIIKGE-----PITspnIPASFH 1120
Cdd:PRK08565 1006 REGGLRFGEMERDCLIGHGAAMLLKERLLDSSDkttiyvcELCGhiawydrRKNKYVCPIHGDkgnisPVE---VSYAFK 1082
|
1210
....*....|....*.
gi 818367371 1121 VLVNELKGLCLNVQLL 1136
Cdd:PRK08565 1083 LLLQELMSMGISPRLK 1098
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
553-1140 |
9.12e-75 |
|
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: 259.57 E-value: 9.12e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 553 IEYIDATVEDRKIIAHAGIEIDKDGNIMESMvearvkghPEMIevdkldyidvsakqcISVATSMIPFLEHDDANRALMG 632
Cdd:TIGR03670 92 IEYLDAEEEENAYIALDPEELTPEHTHLEID--------PSAI---------------LGIIASTIPYPEHNQSPRNTMG 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 633 SNMQRQAVscvvpeapvvgtGIedkaaadsgqvvisYGDGTVIEVDAR-HIIvkeKTPvgskkssfnreyilqsfiksna 711
Cdd:TIGR03670 149 AAMAKQSL------------GL--------------YAANYRIRLDTRgHLL---HYP---------------------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 712 ftsmnQIPRVK-KGDDVhkgqlladgasTDHGELALGQNVMVAFIPWEGYNFEDAIIVSERVLQADRYSSIHIEDFSVEV 790
Cdd:TIGR03670 178 -----QKPLVKtRVLEL-----------IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 791 RDTKLG-------PEVVTRDIPniGEERLKNLDETGIIRIGAEVSSGDIMVGKITPKgegdltaeeRLL--RAIFGEKSR 861
Cdd:TIGR03670 242 RRYPGGqedrfeiPEPDVRGYR--GEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTE 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 862 DVKDSSLYLPHGEHGKVVDIKIFSREQGDKLstgviqkIQVSVAQLRKISVGDKLAGRHGNKGVISRIAPVEDMPYLPDG 941
Cdd:TIGR03670 311 RRRDTSVTVRHGEKGIVDKVIITETEEGNKL-------VKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDG 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 942 NPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGVSEDYIKEELKKAGLPEDGKVRLVNGKTGEYYDNPS 1021
Cdd:TIGR03670 384 IVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEI 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1022 TVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVWALEGYGAAHTLQEMLTIKSDDVM------ 1095
Cdd:TIGR03670 464 FIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVvyvcen 543
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*.
gi 818367371 1096 -GRSkAYESIIKGEP----------ITSPNIPASFHVLVNELKGLCLNVQLLGGHR 1140
Cdd:TIGR03670 544 cGHI-AWEDKRKGTAycpvcgetgdISPVEMSYAFKLLLDELKSLGISPRLELGDK 598
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
553-1135 |
5.66e-68 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 240.63 E-value: 5.66e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 553 IEYIDATVEDRKIIA---------HAGIEIDkdgnimesmvearvkghPEMIevdkldyidvsakqcISVATSMIPFLEH 623
Cdd:PRK07225 98 IEYLDAEEEENAYIAvyeedlteeHTHLEID-----------------PSLI---------------LGIGAGMIPYPEH 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 624 DDANRALMGSNMQRQAVScvVPEAPVvgtgiedKAAADSGQVVISYGdgtvievdarhiivkektpvgskkssfnreyil 703
Cdd:PRK07225 146 NASPRITMGAGMIKQSLG--LPAANY-------KLRPDTRGHLLHYP--------------------------------- 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 704 qsfiksnaftsmnQIPRVKkgddvhkgqlladgasTDHGEL------ALGQNVMVAFIPWEGYNFEDAIIVS----ERVL 773
Cdd:PRK07225 184 -------------QVPLVK----------------TQTQEIigfderPAGQNFVVAVMSYEGYNIEDALIMNkasiERGL 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 774 -----------QADRYSSIHIEDFSV---EVRDTKlgpevvtrdipniGEERLKNLDETGIIRIGAEVSSGDIMVGKITP 839
Cdd:PRK07225 235 grshffrtyegEERRYPGGQEDRFEIpdkDVRGYR-------------GEEAYRHLDEDGLVNPETEVKEGDVLIGKTSP 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 840 K---GEGD---LTAEERllraifgeksrdvKDSSLYLPHGEHGkVVDIKIFSR-EQGDKLStgviqkiQVSVAQLRKISV 912
Cdd:PRK07225 302 PrflEEPDdfgISPEKR-------------RETSVTMRSGEEG-IVDTVILTEtEEGSRLV-------KVRVRDLRIPEL 360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 913 GDKLAGRHGNKGVISRIAPVEDMPYLPDGNPVDIILNPLGVASRMNIGQILETHLGWAAKQLGYNIATPALDGVSEDYIK 992
Cdd:PRK07225 361 GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLR 440
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 993 EELKKAGLPEDGKVRLVNGKTGEYYDNPSTVGIMYIMKLNHLVDDKLHMRSIGPYSLITQQPLGGKAQFGGQRFGEMEVW 1072
Cdd:PRK07225 441 EALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERD 520
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 818367371 1073 ALEGYGAAHTLQEMLTIKSDDVM---------------GRSKAYESIIKGEP-ITSPNIPASFHVLVNELKGLCLNVQL 1135
Cdd:PRK07225 521 VLIGHGAAMLLKERLLDESDKVEiyvcakcgmiaiydkKRNRKYCPICGEETdIYPVEMSYAFKLLLDELKSLGIAPRL 599
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
416-483 |
1.06e-34 |
|
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: 126.49 E-value: 1.06e-34
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 818367371 416 QFMDQVNPLAELEHKRRLSAmGPGGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNIGLVGHMATYAR 483
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1062-1136 |
2.24e-29 |
|
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: 112.30 E-value: 2.24e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 1062 GGQRFGEMEVWALEGYGAAHTLQEMLTIKSD----DVMGRSKAYES-----IIKGEPITSP-NIPASFHVLVNELKGLCL 1131
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPgYIPESFKLLFQELQSLGI 80
|
....*
gi 818367371 1132 NVQLL 1136
Cdd:pfam04560 81 DPRLL 85
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
54-486 |
1.40e-27 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 118.13 E-value: 1.40e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 54 LIEAQTDSYRWFLEKGFQELLDEINPITDFAGKDLEISISDYYLDEPKYDEI----------TAKNKNISFEAPLRAKAS 123
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIETEIEDGVYVELGKIRVGKPVVKEAdgsereiypmEARLRNLTYSAPLYLEMS 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 124 LlIKRTGEIREQEIYLGDFPIMTDRgtfVVNGVERVVVSQLI------RSPGVFFTMNYQKGKKLFGAKIIPNRgAWLEI 197
Cdd:PRK09606 98 P-VEGGEEEEPEEVYIGELPVMVGS---KICNLYGLSEEELIevgedpLDPGGYFIVNGSERVLMTLEDLAPNK-ILVEK 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 198 DTDFDGVISVK--------------IDRKRK-------------VPITALLRAFGYGSDEKLRKIFTDtDNGDTKYIEET 250
Cdd:PRK09606 173 DERYGDRIEVAkvfsqrrgyralvtVERNRDgllevsfpsvpgsIPFVILMRALGLETDEEIVEAVSD-DPEIVKFMLEN 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 251 ISKDISKNQGEGYKEVYKRIRPGDfaTEEN----AKQMIDsmffnfeRYDFGSVGryrlnqrlrvdrkNNEESRVLNVED 326
Cdd:PRK09606 252 LEEAEVDTQEEALEYIGKRVAPGQ--TKEYrikrAEYVID-------RYLLPHLG-------------VEPEVRRAKAHY 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 327 LILIIKEVIKLNNDpLAQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIK-------DRMSTCDVITVVPGQLVNSR 399
Cdd:PRK09606 310 LGRMAEACFELALG-RREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqleranMRNRELSIKTAVRSDVLTER 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 400 piaaaIKEFFSSSQ-------LSQFMDQVNPLAELEHKRRLSAmgpgGLTRERAGFEVRDVHHSHYGRICPVQTPEGPNI 472
Cdd:PRK09606 389 -----LEHAMATGNwvggrtgVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNC 459
|
490
....*....|....
gi 818367371 473 GLVGHMATYARINK 486
Cdd:PRK09606 460 GLVKNFAQMVEIST 473
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
53-403 |
1.94e-27 |
|
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: 115.94 E-value: 1.94e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 53 NLIEAQTDSYRWFLEKGFQELLDEINPI--------TDFAGKDLEISISDYYLDEPKYDEIT----------AKNKNISF 114
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIesefeiqhPGENGDKLSLKFGQIRLGKPMFDETDgstreiypqeCRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 115 EAPLRAKASLLIKRTGEIREQEIYLGDFPIMTD------------------------RGTFVVNGVERVVVSQLIRS--- 167
Cdd:pfam04563 81 SAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRsnacilsgateselvklgecpldpGGYFIINGSEKVIVAQEHRSrnh 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 168 PGVFFTMnyQKGKKLFGAKI--------IPNRGAWLEI-DTDFDGVISVKID-RKRKVPITALLRAFGYGSDEKLRK--I 235
Cdd:pfam04563 161 PIVFKKA--DPKKRGSVASVrssaeisvRPDSTSWVNVlEYLSNGTIYFKFPyIKKEIPIVIILRALGFTSDREIFEliC 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 236 FtdtDNGDTKY-------IEETISKDISKNQ------GEGYKEVYKRIRPGDFATEENAKQMIDSMFFNFERYDFGSVGR 302
Cdd:pfam04563 239 Y---DVNDQQLqeellpsLEEGFKIRIQTQEqaldyiGGRGRAIFRMGRPREPRIKYAEEILQKEVLPHLGTYELDETKK 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 303 YRLnqrlrvdrknneesrvlnvedLILIIKEVIKLNNDPLaQADDIDHLGNRRVRGVGELVQNKLRVGMARMIRNIKDRM 382
Cdd:pfam04563 316 AYF---------------------IGYMIRRLLLLALGRR-EVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERL 373
|
410 420
....*....|....*....|...
gi 818367371 383 STC--DVITVVPGQLVNSRPIAA 403
Cdd:pfam04563 374 QKVlgSPDDLMLQLLVNAKPITS 396
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
549-606 |
1.95e-14 |
|
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pssm-ID: 463067 [Multi-domain] Cd Length: 66 Bit Score: 68.93 E-value: 1.95e-14
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 818367371 549 ITETIEYIDATVEDRKIIAHAGIEIDKDGNIMESMVEARVKGHPEMIEVDKLDYIDVS 606
Cdd:pfam10385 9 VTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
166-357 |
3.38e-14 |
|
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: 71.99 E-value: 3.38e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 166 RSPGVFFTMNYQKGK--KLFGAKIIPNRGAWLEIDTDFDGVISVKIDRKRKVPITALLRAFGYGSDEKLRKIFTDTDNGD 243
Cdd:pfam04561 1 RSNGIYVEKELDKNGiiATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCYDFNDP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 818367371 244 T---KYIEETISKDISKNQGEGYKEVYKRI--RPGDFATEENAKQMIDSMFfnferydfgsvGRYRLNQRLRVDrkNNEE 318
Cdd:pfam04561 81 QmleLLKPELEEAENIYTQEEALDYIGKGFalRRGEEPRLQRAREILYSRD-----------PKYNLNKHLGLN--EPFE 147
|
170 180 190
....*....|....*....|....*....|....*....
gi 818367371 319 SRVLNVEDLILIIKEVIKLNNDPLaQADDIDHLGNRRVR 357
Cdd:pfam04561 148 NERLKAQDILYMIDRLLNLKLGRR-KPDDIDHLGNKRVR 185
|
|
| |
