|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
11-1060 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1929.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 11 TKIPGAPKRYSFAKIDEPITVPGLLDVQLDSYSWLIGTPEWREREqelrgpdarvtsGLEDILNELSPIEDYSERMSLSL 90
Cdd:PRK00405 4 SYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDE------------GLEEVFRSIFPIEDFNGNLSLEF 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 91 SEPRFEPVKYTVDESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYF 170
Cdd:PRK00405 72 VSYELGEPKYDVEECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYF 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 171 DQTIDK-STERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFG------------- 236
Cdd:PRK00405 152 DHDKDKtSSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYekeefgkeievpv 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 237 --------------------------------FSELMMSTLEGDGVANTDEALLEIYRKQRPGEQPTRDLALAMLANSFF 284
Cdd:PRK00405 232 eyllgkvlaedivdeetgevlaeandeiteelDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFF 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 285 KAKRYDLARVGRYKINRKLGLGGDhDGLMTLTEEDIAVTLEYLVRLHAGEREmkapngqmiplnTDDIDHFGNRRLRTVG 364
Cdd:PRK00405 312 DPKRYDLSKVGRYKLNKKLGLDED-EDVRVLTKEDIIATIKYLINLRNGKGE------------VDDIDHLGNRRVRSVG 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 365 ELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGG 444
Cdd:PRK00405 379 ELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGG 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 445 LSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFIETPYRKVEDGRITDEVVYVTADEEDRYAIA 524
Cdd:PRK00405 459 LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIA 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 525 QAEVERDEQGYITDSRIEVRlKEGDIGVTDAKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSE 604
Cdd:PRK00405 539 QANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPE 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 605 APFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIM------DDSGQrDTYLLRKFERTNQGTNYNQTPLVSAGDRV 678
Cdd:PRK00405 618 APLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRveeldpGEDGV-DIYNLIKFQRSNQNTCINQRPIVKVGDRV 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 679 EAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARDTKLGAEEITREIPNV 758
Cdd:PRK00405 697 EKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNV 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 759 SEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSRD 838
Cdd:PRK00405 777 SEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRI 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 839 ED-DDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVH 917
Cdd:PRK00405 857 EQgDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETH 936
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 918 LGWLAHS-GWKIdvedpknaeilktlpeelydvpadsltATPVFDGATNEEISRLLASSRpnrdgdvlVDEHGKARLFDG 996
Cdd:PRK00405 937 LGWAAKGlGIKF---------------------------ATPVFDGAKEEEIKELLEEAG--------LPEDGKTTLYDG 981
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 46361012 997 RSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060
Cdd:PRK00405 982 RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
19-1060 |
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: 1791.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 19 RYSFAKIDEPITVPGLLDVQLDSYSWLIgtpewrereqelrgpdarvTSGLEDILNELSPIEDYSERMSLSLSEPRFEPV 98
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL-------------------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEP 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 99 KYTVDESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQTIDKSt 178
Cdd:COG0085 62 KYTPEECKERDLTYAAPLYVKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKS- 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 179 ERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGW-TEEQIRERFGF---SELMMSTLEGDGVANTD 254
Cdd:COG0085 141 GKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLeTDEEILEAFGDdpiQEYILATLEKDNTKTQE 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 255 EALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGGDHDGlMTLTEEDIAVTLEYLVRLHAGE 334
Cdd:COG0085 221 EALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLGLDVPPED-RVLTAEDIVATIKYLLELHLGE 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 335 REmkapngqmiplnTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFG 414
Cdd:COG0085 300 RE------------PDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFG 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 415 TSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFI 494
Cdd:COG0085 368 SSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFI 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 495 ETPYRKVEDGRITDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKeGDIGVTDAKGVDFIDVSPRQMVSVATA 574
Cdd:COG0085 448 ETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYR-GEEVLVPPEEVDYMDVSPKQIVSVATS 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 575 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPFvgtgmeqraaydagdliinakdgvveavsaqsitimddsgqrDTYLL 654
Cdd:COG0085 527 LIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------------------LHYPL 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 655 RKFERTNQGTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHI 734
Cdd:COG0085 565 QKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHI 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 735 EEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREV 814
Cdd:COG0085 645 EEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREV 724
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 815 RDTSMKVPHGETGKVIGVARFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTP 894
Cdd:COG0085 725 RDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTP 804
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 895 VDIILNTHGVPRRMNIGQVLEVHLGWLAHS-GWKIdvedpknaeilktlpeelydvpadsltATPVFDGATNEEISRLLA 973
Cdd:COG0085 805 VDIVLNPLGVPSRMNVGQVLETHLGWAAALlGRRV---------------------------ATPVFDGAPEEEIRELLE 857
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 974 SSRPNRDgdvlvdehGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 1053
Cdd:COG0085 858 KAGLPPD--------GKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGE 929
|
....*..
gi 46361012 1054 MEVWAMQ 1060
Cdd:COG0085 930 MEVWALE 936
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
16-1060 |
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: 1637.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 16 APKRYSFAKIDEPITVPGLLDVQLDSYSWLIGTPEWREREQElrgpdarvtSGLEDILNELSPIEDYSERMSLSLSEPRF 95
Cdd:TIGR02013 2 KRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKE---------EGLEEVFKSIFPIEDYTGNIELEYLSYRL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 96 EPVKYTVDESKEKDINYSAPLYVTAEFVNKD---TQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQ 172
Cdd:TIGR02013 73 GEPKYSVEECKERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSS 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 173 TIDKSTE-RPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIR-ERFGFSELMMSTLEGDGV 250
Cdd:TIGR02013 153 EKDTTKSgKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLIlNRLGSGEYIRNTLRKDPT 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 251 ANTDEALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGGDhDGLMTLTEEDIAVTLEYLVRL 330
Cdd:TIGR02013 233 NSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVP-ESIGVLTKEDIIATIKYLIKL 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 331 HAGEREmkapngqmiplnTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIR 410
Cdd:TIGR02013 312 RNGKGE------------IDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIK 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 411 EFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNP 490
Cdd:TIGR02013 380 EFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 491 FGFIETPYRKVEDGRI--TDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKeGDIGVTDAKGVDFIDVSPRQM 568
Cdd:TIGR02013 460 YGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYR-GEITLVSPDQVDYMDVSPKQV 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 569 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIMDDS-- 646
Cdd:TIGR02013 539 VSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEde 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 647 ----GQRDTYLLRKFERTNQGTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQ 722
Cdd:TIGR02013 619 eepdGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISER 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 723 IVEDDTLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERL 802
Cdd:TIGR02013 699 LVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKL 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 803 LRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILP 882
Cdd:TIGR02013 779 LRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILP 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 883 PEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHSGWKIDVEdpknaeilktlpeelydvpadslTATPVFDG 962
Cdd:TIGR02013 859 IEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVP-----------------------IATPVFDG 915
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 963 ATNEEISRLLASSRPNRDgdvlvdehGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGG 1042
Cdd:TIGR02013 916 ASEEEIKEYLEKAGLPRD--------GKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGG 987
|
1050
....*....|....*...
gi 46361012 1043 KAQFGGQRFGEMEVWAMQ 1060
Cdd:TIGR02013 988 KAQFGGQRFGEMEVWALE 1005
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
34-1059 |
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: 869.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 34 LLDVQLDSYSWLIgtpewrereqelrgpdarvTSGLEDILNELSPIEDYS--ERMSLSLSEPRFEP---------VKYTV 102
Cdd:cd00653 1 LVKQQIDSFNYFL-------------------NVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKpkveeggvtRKLTP 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 103 DESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTD------------------------RGTFIVNGTERVI 158
Cdd:cd00653 62 NECRLRDLTYSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 159 VSQLVRSPGVYFdqtIDKSTERPLHAVKVIPS----RGAWLEFDVDKR-DTVGVRIDRKRRqpvtvllkalgwteeqire 233
Cdd:cd00653 142 INQEQRSPNVII---VEDSKGKRIYTKTSIPSyspyRGSWLEVKSDKKkDRIYVRIDLKRQ------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 234 rfgfselmmstlegdgvantDEALLEIYRKqrpgeqptrdlalamlansfFkakrydlarvgrykinrklglggdhdglm 313
Cdd:cd00653 200 --------------------EEALKYIGKR--------------------F----------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 314 tlteEDIAVTLEYLVRLHAGEREMkapngqmiplntDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAES 393
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKL------------DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKK 274
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 394 --ITPTSLINVRPVSAAIREFFGTSQ------------LSQFMDQNNSLSGLTHKRRLSAlgpGGLSRERAGIEVRDVHP 459
Cdd:cd00653 275 kdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHP 351
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 460 SHYGRMCPIETPEGPNIGLIGSLASYARVNpfGFIETPYRKVEdgritdevvyvtadeedryaiaqaeverdeqgyitds 539
Cdd:cd00653 352 SHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------------------------------- 392
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 540 rievrlkegdigvtdaKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVP----------------LVRS 603
Cdd:cd00653 393 ----------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYP 456
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 604 EAPFVGTGMEQRAAYdagdliinakdgvveavsaqsitimddsgqrdtyllrkfertnqgtnynqtplvsagdrveagqv 683
Cdd:cd00653 457 QKPLVGTGIEEYIAF----------------------------------------------------------------- 471
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 684 ladgpgthnGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARDTKLGAEEITR-EIPNVSEDV 762
Cdd:cd00653 472 ---------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEK 542
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 763 LRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPeerllraIFGEKAREVRDTSMKVPHGETGKVIGVARFSRDEDDd 842
Cdd:cd00653 543 LKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELND- 614
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 843 lapGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWL- 921
Cdd:cd00653 615 ---GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAg 691
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 922 AHSGWKIDvedpknaeilktlpeelydvpadsltATPvFDGATNEEISRLLASSRPNRdgdvlvdeHGKARLFDGRSGEP 1001
Cdd:cd00653 692 ALLGKFGD--------------------------ATP-FDGAEEEDISELLGEAGLNY--------YGKEVLYDGRTGEP 736
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*...
gi 46361012 1002 YKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAM 1059
Cdd:cd00653 737 LEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDAL 794
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
629-1045 |
5.67e-174 |
|
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: 513.23 E-value: 5.67e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 629 DGVVEAVSAQSITIMDDSGQR--DTYLLRKFERTNQGT---NYNQTPLVSAGdRVEAGQvladgpgthNGEMSLGRNLLV 703
Cdd:pfam00562 5 IPFVDHNQSPRNTYQCAMGKQamGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGELPLGQNAIV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 704 AFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEheIDARDTKLGA-EEITREIPNVSEDVLRDLDDRGIIRIGADVRPGD 782
Cdd:pfam00562 75 AVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 783 ILVGKVtpkGETELTpeeRLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFsrdeddDLAPGVNEMIRVYVAQKRKIQ 862
Cdd:pfam00562 153 ILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------ELPPGGIKMVKVYIRQKRKPE 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 863 DGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHsgwkidvedpknaeilktl 942
Cdd:pfam00562 221 VGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAA------------------- 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 943 peeLYDVPADsltaTPVFDGATN--EEISRLLASSRPNRdgdvlvdeHGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLV 1020
Cdd:pfam00562 282 ---LLGVFVD----ATPFDGASTevEDIGELLEKAGYNY--------YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMV 346
|
410 420
....*....|....*....|....*
gi 46361012 1021 DEKIHARSTGPYSMITQQPLGGKAQ 1045
Cdd:pfam00562 347 DDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
11-1060 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1929.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 11 TKIPGAPKRYSFAKIDEPITVPGLLDVQLDSYSWLIGTPEWREREqelrgpdarvtsGLEDILNELSPIEDYSERMSLSL 90
Cdd:PRK00405 4 SYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDE------------GLEEVFRSIFPIEDFNGNLSLEF 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 91 SEPRFEPVKYTVDESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYF 170
Cdd:PRK00405 72 VSYELGEPKYDVEECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYF 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 171 DQTIDK-STERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFG------------- 236
Cdd:PRK00405 152 DHDKDKtSSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYekeefgkeievpv 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 237 --------------------------------FSELMMSTLEGDGVANTDEALLEIYRKQRPGEQPTRDLALAMLANSFF 284
Cdd:PRK00405 232 eyllgkvlaedivdeetgevlaeandeiteelDGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFF 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 285 KAKRYDLARVGRYKINRKLGLGGDhDGLMTLTEEDIAVTLEYLVRLHAGEREmkapngqmiplnTDDIDHFGNRRLRTVG 364
Cdd:PRK00405 312 DPKRYDLSKVGRYKLNKKLGLDED-EDVRVLTKEDIIATIKYLINLRNGKGE------------VDDIDHLGNRRVRSVG 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 365 ELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGG 444
Cdd:PRK00405 379 ELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGG 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 445 LSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFIETPYRKVEDGRITDEVVYVTADEEDRYAIA 524
Cdd:PRK00405 459 LTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIA 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 525 QAEVERDEQGYITDSRIEVRlKEGDIGVTDAKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSE 604
Cdd:PRK00405 539 QANAPLDEDGRFVDELVTAR-YKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPE 617
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 605 APFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIM------DDSGQrDTYLLRKFERTNQGTNYNQTPLVSAGDRV 678
Cdd:PRK00405 618 APLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRveeldpGEDGV-DIYNLIKFQRSNQNTCINQRPIVKVGDRV 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 679 EAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARDTKLGAEEITREIPNV 758
Cdd:PRK00405 697 EKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNV 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 759 SEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSRD 838
Cdd:PRK00405 777 SEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRI 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 839 ED-DDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVH 917
Cdd:PRK00405 857 EQgDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETH 936
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 918 LGWLAHS-GWKIdvedpknaeilktlpeelydvpadsltATPVFDGATNEEISRLLASSRpnrdgdvlVDEHGKARLFDG 996
Cdd:PRK00405 937 LGWAAKGlGIKF---------------------------ATPVFDGAKEEEIKELLEEAG--------LPEDGKTTLYDG 981
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 46361012 997 RSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060
Cdd:PRK00405 982 RTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
19-1060 |
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: 1791.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 19 RYSFAKIDEPITVPGLLDVQLDSYSWLIgtpewrereqelrgpdarvTSGLEDILNELSPIEDYSERMSLSLSEPRFEPV 98
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL-------------------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEP 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 99 KYTVDESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQTIDKSt 178
Cdd:COG0085 62 KYTPEECKERDLTYAAPLYVKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKS- 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 179 ERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGW-TEEQIRERFGF---SELMMSTLEGDGVANTD 254
Cdd:COG0085 141 GKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLeTDEEILEAFGDdpiQEYILATLEKDNTKTQE 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 255 EALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGGDHDGlMTLTEEDIAVTLEYLVRLHAGE 334
Cdd:COG0085 221 EALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLGLDVPPED-RVLTAEDIVATIKYLLELHLGE 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 335 REmkapngqmiplnTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFG 414
Cdd:COG0085 300 RE------------PDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFG 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 415 TSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFI 494
Cdd:COG0085 368 SSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFI 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 495 ETPYRKVEDGRITDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKeGDIGVTDAKGVDFIDVSPRQMVSVATA 574
Cdd:COG0085 448 ETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYR-GEEVLVPPEEVDYMDVSPKQIVSVATS 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 575 MIPFLEHDDANRALMGANMQRQAVPLVRSEAPFvgtgmeqraaydagdliinakdgvveavsaqsitimddsgqrDTYLL 654
Cdd:COG0085 527 LIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------------------LHYPL 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 655 RKFERTNQGTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHI 734
Cdd:COG0085 565 QKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHI 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 735 EEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREV 814
Cdd:COG0085 645 EEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREV 724
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 815 RDTSMKVPHGETGKVIGVARFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTP 894
Cdd:COG0085 725 RDTSLRVPHGEKGKVIDVKVFSREEGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTP 804
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 895 VDIILNTHGVPRRMNIGQVLEVHLGWLAHS-GWKIdvedpknaeilktlpeelydvpadsltATPVFDGATNEEISRLLA 973
Cdd:COG0085 805 VDIVLNPLGVPSRMNVGQVLETHLGWAAALlGRRV---------------------------ATPVFDGAPEEEIRELLE 857
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 974 SSRPNRDgdvlvdehGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGE 1053
Cdd:COG0085 858 KAGLPPD--------GKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGE 929
|
....*..
gi 46361012 1054 MEVWAMQ 1060
Cdd:COG0085 930 MEVWALE 936
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
16-1060 |
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: 1637.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 16 APKRYSFAKIDEPITVPGLLDVQLDSYSWLIGTPEWREREQElrgpdarvtSGLEDILNELSPIEDYSERMSLSLSEPRF 95
Cdd:TIGR02013 2 KRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKE---------EGLEEVFKSIFPIEDYTGNIELEYLSYRL 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 96 EPVKYTVDESKEKDINYSAPLYVTAEFVNKD---TQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQ 172
Cdd:TIGR02013 73 GEPKYSVEECKERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSS 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 173 TIDKSTE-RPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIR-ERFGFSELMMSTLEGDGV 250
Cdd:TIGR02013 153 EKDTTKSgKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLIlNRLGSGEYIRNTLRKDPT 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 251 ANTDEALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGGDhDGLMTLTEEDIAVTLEYLVRL 330
Cdd:TIGR02013 233 NSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVP-ESIGVLTKEDIIATIKYLIKL 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 331 HAGEREmkapngqmiplnTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIR 410
Cdd:TIGR02013 312 RNGKGE------------IDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIK 379
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 411 EFFGTSQLSQFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNP 490
Cdd:TIGR02013 380 EFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNE 459
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 491 FGFIETPYRKVEDGRI--TDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKeGDIGVTDAKGVDFIDVSPRQM 568
Cdd:TIGR02013 460 YGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYR-GEITLVSPDQVDYMDVSPKQV 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 569 VSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIMDDS-- 646
Cdd:TIGR02013 539 VSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEde 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 647 ----GQRDTYLLRKFERTNQGTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQ 722
Cdd:TIGR02013 619 eepdGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISER 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 723 IVEDDTLTSIHIEEHEIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERL 802
Cdd:TIGR02013 699 LVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKL 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 803 LRAIFGEKAREVRDTSMKVPHGETGKVIGVARFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILP 882
Cdd:TIGR02013 779 LRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILP 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 883 PEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHSGWKIDVEdpknaeilktlpeelydvpadslTATPVFDG 962
Cdd:TIGR02013 859 IEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRKGVP-----------------------IATPVFDG 915
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 963 ATNEEISRLLASSRPNRDgdvlvdehGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGG 1042
Cdd:TIGR02013 916 ASEEEIKEYLEKAGLPRD--------GKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGG 987
|
1050
....*....|....*...
gi 46361012 1043 KAQFGGQRFGEMEVWAMQ 1060
Cdd:TIGR02013 988 KAQFGGQRFGEMEVWALE 1005
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
30-1060 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1106.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 30 TVPGLLDVQLDSYSWLIgtpewrereqelrgpdarvTSGLEDILNELSPIEDYSERMSLSL--SEPRFEPVKYTVDESKE 107
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFL-------------------NEGLNEELNIFSKIFDYTGNLELLLfgKNYKLKYPKYNLLSAKS 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 108 KDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQTIDKSTERPLHAvKV 187
Cdd:CHL00207 67 YDSNYSIQIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSA-TL 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 188 IPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFGFS---ELMMSTLEGDGVANTDEALLEIYRKQ 264
Cdd:CHL00207 146 IPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSeflKKLKPILLNSNSYTNEEILLEIYKNL 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 265 RPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKINRKLGLGGDHDgLMTLTEEDIAVTLEYLVRLhageremkapngQM 344
Cdd:CHL00207 226 SPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPER-VRNLTYEDILSIIDKLINL------------KI 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 345 IPLNTDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQ 424
Cdd:CHL00207 293 NKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQ 372
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 425 NNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFIETPYRKVEDG 504
Cdd:CHL00207 373 TNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVING 452
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 505 RI--TDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKeGDIGVTDAKGVDFIDVSPRQMVSVATAMIPFLEHD 582
Cdd:CHL00207 453 KVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYK-QEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHN 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 583 DANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIMDDSGQRDTYLLRKFERTNQ 662
Cdd:CHL00207 532 DANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQ 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 663 GTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDAR 742
Cdd:CHL00207 612 NTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 743 DTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVP 822
Cdd:CHL00207 692 QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMP 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 823 HGETGKVIGVARFSRDEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTH 902
Cdd:CHL00207 772 NGGYGRVIKVEIFSRSKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPL 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 903 GVPRRMNIGQVLEVHLGWLAHSgwkidvedpKNAEIlKTLPeelydvpadsltatpvFDGATNEEISRLL-------ASS 975
Cdd:CHL00207 852 GVPSRMNVGQLFECLLGLAGDN---------LNKRF-KILP----------------FDEMYGSEYSRILinnklnqASI 905
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 976 RPNRDGDVLVDEHGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 1055
Cdd:CHL00207 906 KNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEME 985
|
....*
gi 46361012 1056 VWAMQ 1060
Cdd:CHL00207 986 VWALE 990
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
30-1060 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1050.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 30 TVPGLLDVQLDSYSWLIgtpewrerEQelrgpdarvtsGLEDILNELSPIEDYSERMSLSLSEPRF---EPvKYTVDESK 106
Cdd:CHL00001 11 TIPGFNQIQFEGFCRFI--------DQ-----------GLTEELSKFPKIEDTDQEIEFQLFVETYqlvEP-LIKERDAV 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 107 EKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGVYFDQTIDKStERPLHAVK 186
Cdd:CHL00001 71 YESLTYSSELYVPAGLIWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHN-GISVYTGT 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 187 VIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERFGFSELMMSTL---EGDGVANTDEALLEIYRK 263
Cdd:CHL00001 150 IISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLndkEKKKIGSKENAILEFYQQ 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 264 -QRPGEQPTRDLAL-AMLANSFFKaKRYDLARVGRYKINRKLGLGGDHDGLmTLTEEDIAVTLEYLVRLHAGEremkapn 341
Cdd:CHL00001 230 fACVGGDPVFSESLcKELQKKFFQ-QRCELGRIGRRNMNRKLNLDIPENNT-FLLPQDVLAAADYLIGMKFGM------- 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 342 GQMiplntDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERM--TTQDAESITPTSLINVRPVSAAIREFFGTSQLS 419
Cdd:CHL00001 301 GTL-----DDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTIcgAIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLS 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 420 QFMDQNNSLSGLTHKRRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFIETPYR 499
Cdd:CHL00001 376 QFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFY 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 500 KVEDGRITDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRLKEgDIGVTDAKGVDFIDVSPRQMVSVATAMIPFL 579
Cdd:CHL00001 456 EISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQ-EFLTIAWEQIHLRSIFPFQYFSIGASLIPFL 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 580 EHDDANRALMGANMQRQAVPLVRSEAPFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITImddSGQRDT--YLLRKF 657
Cdd:CHL00001 535 EHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIIL---SGNGDTlsIPLVMY 611
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 658 ERTNQGTNYNQTPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEH 737
Cdd:CHL00001 612 QRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKY 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 738 EIDARDTKLGAEEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPK--GETELTPEERLLRAIFGEKAREVR 815
Cdd:CHL00001 692 EIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSK 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 816 DTSMKVPHGETGKVIGVARFSRDEDDDlapGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPV 895
Cdd:CHL00001 772 ETCLKLPIGGRGRVIDVRWIQKKGGSS---YNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPV 848
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 896 DIILNTHGVPRRMNIGQVLEVHLGwLAHSgwkidvedpknaeilktLPEELYDVPAdsltatpvFDGATNEEISRLLASS 975
Cdd:CHL00001 849 DMVLNPLGVPSRMNVGQIFECLLG-LAGD-----------------LLNRHYRIAP--------FDERYEQEASRKLVFS 902
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 976 RPNRDGD------VLVDEH-GKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 1048
Cdd:CHL00001 903 ELYEASKqtanpwVFEPEYpGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGG 982
|
1050
....*....|..
gi 46361012 1049 QRFGEMEVWAMQ 1060
Cdd:CHL00001 983 QRVGEMEVWALE 994
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
19-1060 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 981.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 19 RYSFAKIDEPITVPGLLDVQLDSYSWLIGTPEWREreqelrgpdarvtSGLEDILNELSPIEDYSERMSLSLSEPRFEPV 98
Cdd:PRK09603 12 RADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKE-------------SGIEKVFKSIFPIQDEHNRITLEYAGCEFGKS 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 99 KYTVDESKEKDINYSAPLYVTAEFV--NKDTQ--------EIKSQTVFIGDFPMMTDRGTFIVNGTERVIVSQLVRSPGV 168
Cdd:PRK09603 79 KYTVREAMERGITYSIPLKIKVRLIlwEKDTKsgekngikDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGV 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 169 YF-DQTIDKSTERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIRERF------------ 235
Cdd:PRK09603 159 IFkEEESSTSLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFyplvkvryendk 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 --------------------------------------------------------------------------------
Cdd:PRK09603 239 ylipfasldanqrmefdlkdpqgkiillagkkltsrkikelkenhlewveypmdillnrhlaepvmvgkevlldmltqld 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 236 ----------GFSELMMSTLEGDGVANT-------------------------DEALLEIYRKQRPGEQPTRDLALAMLA 280
Cdd:PRK09603 319 knklekihdlGVQEFVIINDLALGHDASiihsfsadseslkllkqtekiddenALAAIRIHKVMKPGDPVTTEVAKQFVK 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 281 NSFFKAKRYDLARVGRYKINRKLGLGGDhDGLMTLTEEDIAVTLEYLvrlhagereMKAPNGQMiplNTDDIDHFGNRRL 360
Cdd:PRK09603 399 KLFFDPERYDLTMVGRMKMNHKLGLHVP-DYITTLTHEDIITTVKYL---------MKIKNNQG---KIDDRDHLGNRRI 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 361 RTVGELIQNQVRVGLSRMERVVRERMTTQDA--ESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHKRRLS 438
Cdd:PRK09603 466 RAVGELLANELHSGLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLS 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 439 ALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFIETPYRKVEDGRITDEVVYVTADEE 518
Cdd:PRK09603 546 ALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQE 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 519 DRYAIAQAEVERDEQGYITDSRIEVRlKEGDIGVTDAKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAV 598
Cdd:PRK09603 626 DSHIIAPASTPIDEEGNILGDLIETR-VEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAV 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 599 PLVRSEAPFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIM--DDSGQR-DTYLLRKFERTNQGTNYNQTPLVSAG 675
Cdd:PRK09603 705 PLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILgeGKEEAYiDAYSLQKNLRTNQNTSFNQVPIVKVG 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 676 DRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARDTKLGAEEITREI 755
Cdd:PRK09603 785 DKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADI 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 756 PNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARF 835
Cdd:PRK09603 865 PDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVF 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 836 SRD----------------------------------------------------------------------------- 838
Cdd:PRK09603 945 TKKgyekdarvlsayeeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftl 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 839 ----------------------------------------EDDDLAP-GVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVV 877
Cdd:PRK09603 1025 aslvkkyskevqnhyeitknnfleqkkvlgeeheeklsilEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIV 1104
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 878 GKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHS-GWKI-DVEDPKNAEILKTLPEELYDV-----P 950
Cdd:PRK09603 1105 SNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEfGKQIaSMLEDKTKDFAKELRAKMLEIanainE 1184
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 951 ADSLT-------------------------ATPVFDGATNEEISRLLASSRpnrdgdvlVDEHGKARLFDGRSGEPYKYP 1005
Cdd:PRK09603 1185 KDPLTihalencsdeelleyakdwskgvkmAIPVFEGISQEKFYKLFELAK--------IAMDGKMDLYDGRTGEKMRER 1256
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*
gi 46361012 1006 VSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060
Cdd:PRK09603 1257 VNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALE 1311
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
34-1059 |
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: 869.19 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 34 LLDVQLDSYSWLIgtpewrereqelrgpdarvTSGLEDILNELSPIEDYS--ERMSLSLSEPRFEP---------VKYTV 102
Cdd:cd00653 1 LVKQQIDSFNYFL-------------------NVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKpkveeggvtRKLTP 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 103 DESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTD------------------------RGTFIVNGTERVI 158
Cdd:cd00653 62 NECRLRDLTYSAPLYVDIRLTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 159 VSQLVRSPGVYFdqtIDKSTERPLHAVKVIPS----RGAWLEFDVDKR-DTVGVRIDRKRRqpvtvllkalgwteeqire 233
Cdd:cd00653 142 INQEQRSPNVII---VEDSKGKRIYTKTSIPSyspyRGSWLEVKSDKKkDRIYVRIDLKRQ------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 234 rfgfselmmstlegdgvantDEALLEIYRKqrpgeqptrdlalamlansfFkakrydlarvgrykinrklglggdhdglm 313
Cdd:cd00653 200 --------------------EEALKYIGKR--------------------F----------------------------- 210
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 314 tlteEDIAVTLEYLVRLHAGEREMkapngqmiplntDDIDHFGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAES 393
Cdd:cd00653 211 ----EDLIYMIRKLILLVLGKGKL------------DDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKK 274
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 394 --ITPTSLINVRPVSAAIREFFGTSQ------------LSQFMDQNNSLSGLTHKRRLSAlgpGGLSRERAGIEVRDVHP 459
Cdd:cd00653 275 kdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHP 351
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 460 SHYGRMCPIETPEGPNIGLIGSLASYARVNpfGFIETPYRKVEdgritdevvyvtadeedryaiaqaeverdeqgyitds 539
Cdd:cd00653 352 SHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------------------------------- 392
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 540 rievrlkegdigvtdaKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVP----------------LVRS 603
Cdd:cd00653 393 ----------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYP 456
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 604 EAPFVGTGMEQRAAYdagdliinakdgvveavsaqsitimddsgqrdtyllrkfertnqgtnynqtplvsagdrveagqv 683
Cdd:cd00653 457 QKPLVGTGIEEYIAF----------------------------------------------------------------- 471
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 684 ladgpgthnGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARDTKLGAEEITR-EIPNVSEDV 762
Cdd:cd00653 472 ---------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEK 542
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 763 LRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPeerllraIFGEKAREVRDTSMKVPHGETGKVIGVARFSRDEDDd 842
Cdd:cd00653 543 LKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRELND- 614
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 843 lapGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWL- 921
Cdd:cd00653 615 ---GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAg 691
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 922 AHSGWKIDvedpknaeilktlpeelydvpadsltATPvFDGATNEEISRLLASSRPNRdgdvlvdeHGKARLFDGRSGEP 1001
Cdd:cd00653 692 ALLGKFGD--------------------------ATP-FDGAEEEDISELLGEAGLNY--------YGKEVLYDGRTGEP 736
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*...
gi 46361012 1002 YKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEVWAM 1059
Cdd:cd00653 737 LEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDAL 794
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
19-1060 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 868.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 19 RYSFAK-IDEPITVPGLLDVQLDSYSWLIGTPEWREReqelrgpdarvtsgLEDILNELSPIEDYSERMSLSLSEPRFEP 97
Cdd:PRK14844 16 RVSYSRsIDLKDSLLDLVKVQKESYDSFTPKNKGNER--------------LEVIFHTIFPINDPLHRATIEFISCRVDD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 98 VKYTVDESKEKDINYSAPLYVTAEFVN-------KDTQEIK----------------SQTVFIGDFPMMTDRGTFIVNGT 154
Cdd:PRK14844 82 PKYDESECIKRGITFSAQVIASIRLVImqdgislDEYKSIKesgdhsklatviksieEQEVHFCELPMMTDKGTFIINGV 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 155 ERVIVSQLVRSPGVYFDQTIDKS--TERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALGWTEEQIR 232
Cdd:PRK14844 162 EKVIVSQMHRSPGVFFDSDKGKTynSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDIL 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 233 ERF---------------------------------------------------------GFSELM-------------- 241
Cdd:PRK14844 242 DRFyekikyikhkdgwkvpfvpdkfkgvrlpfdlmdvegnvllkanvritsrlakklydnELKEYLvpfdsicglflaed 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 242 --------------------------------MSTLEGDGVA------NT---------DEALLEIYRKQRPGEQPTRDL 274
Cdd:PRK14844 322 lidsasstkilsagesikledikklellsideISVLNIDNLSvgpyilNTlfldenmsyQDALYEIYKVLRPGEVPVLEI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 275 ALAMLANSFFKAKRYDLARVGRYKINRKLGLGGDHDgLMTLTEEDIAVTLEYLVRLHAGERemkapngqmiplNTDDIDH 354
Cdd:PRK14844 402 VEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDED-LTVLTHEDIIEIVRKIVLLRDGQG------------SVDDIDH 468
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 355 FGNRRLRTVGELIQNQVRVGLSRMERVVRERMTTQDAESITPTSLINVRPVSAAIREFFGTSQLSQFMDQNNSLSGLTHK 434
Cdd:PRK14844 469 LGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHK 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 435 RRLSALGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARVNPFGFIETPYRKVEDGRITDEVVYVT 514
Cdd:PRK14844 549 RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLS 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 515 ADEEDRYAIAQAEVERDEQGYITDSRIEVRLKeGDIGVTDAKGVDFIDVSPRQMVSVATAMIPFLEHDDANRALMGANMQ 594
Cdd:PRK14844 629 AIDEGLYYIADTSAKLDENNCFVDDMLYCRYA-GSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQ 707
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 595 RQAVPLVRSEAPFVGTGMEQRAAYDAGDLIINAKDGVVEAVSAQSITIMDDSGQR------DTYLLRKFERTNQGTNYNQ 668
Cdd:PRK14844 708 RQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERvnyldvDIYHLRKFQRSNHNTCINQ 787
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 669 TPLVSAGDRVEAGQVLADGPGTHNGEMSLGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARDTKLGA 748
Cdd:PRK14844 788 KPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGS 867
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 749 EEITREIPNVSEDVLRDLDDRGIIRIGADVRPGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSMKVPHGETGK 828
Cdd:PRK14844 868 EKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGT 947
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 829 VIGVARFSR----------------------------------------------------------------------- 837
Cdd:PRK14844 948 VIDVQVFTRrgveenerallikqkeindfekerdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqs 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 838 ------------------------------DEDDDLAPGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMP 887
Cdd:PRK14844 1028 iseqvkslkkdfdekvshaiaqfkrkveklHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMP 1107
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 888 FMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHS-GWKI-------------------------------------D 929
Cdd:PRK14844 1108 YLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKlGEKVgnildeinkiksafckgirslnddnftkfaaayldnkK 1187
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 930 VEDPKNAEI----------------LKTLPE------------------ELY-------------DVPADSL-------- 954
Cdd:PRK14844 1188 IENIDDDEItasvlntpnknalndeLNELVEnylnscksaysnlrnfliEVYscgsnvsicnnirDISDNNLiefarklr 1267
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 955 ----TATPVFDGATNEEISRLLASSRpnrdgdvlVDEHGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTG 1030
Cdd:PRK14844 1268 dgipVAAPVFEGPKDEQIAKLFELAG--------LDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVG 1339
|
1370 1380 1390
....*....|....*....|....*....|
gi 46361012 1031 PYSMITQQPLGGKAQFGGQRFGEMEVWAMQ 1060
Cdd:PRK14844 1340 PYSLVTQQPLGGKSHFGGQRFGEMECWALQ 1369
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
629-1045 |
5.67e-174 |
|
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: 513.23 E-value: 5.67e-174
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 629 DGVVEAVSAQSITIMDDSGQR--DTYLLRKFERTNQGT---NYNQTPLVSAGdRVEAGQvladgpgthNGEMSLGRNLLV 703
Cdd:pfam00562 5 IPFVDHNQSPRNTYQCAMGKQamGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGELPLGQNAIV 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 704 AFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEheIDARDTKLGA-EEITREIPNVSEDVLRDLDDRGIIRIGADVRPGD 782
Cdd:pfam00562 75 AVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 783 ILVGKVtpkGETELTpeeRLLRAIFGEKAREVRDTSMKVPHGETGKVIGVARFsrdeddDLAPGVNEMIRVYVAQKRKIQ 862
Cdd:pfam00562 153 ILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------ELPPGGIKMVKVYIRQKRKPE 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 863 DGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAHsgwkidvedpknaeilktl 942
Cdd:pfam00562 221 VGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAA------------------- 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 943 peeLYDVPADsltaTPVFDGATN--EEISRLLASSRPNRdgdvlvdeHGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLV 1020
Cdd:pfam00562 282 ---LLGVFVD----ATPFDGASTevEDIGELLEKAGYNY--------YGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMV 346
|
410 420
....*....|....*....|....*
gi 46361012 1021 DEKIHARSTGPYSMITQQPLGGKAQ 1045
Cdd:pfam00562 347 DDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
33-1056 |
3.52e-103 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 349.26 E-value: 3.52e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 33 GLLDVQLDSYswligtpewrereqelrgpDARVTSGLEDILNELSPIEDYSERMSLSLS-----EPRFE-----PVKYTV 102
Cdd:PRK08565 13 GLVRQHLDSY-------------------NDFIERGLQEIVDEFGEIKTEIPGLKIVLGkirvgEPEIKeadgsERPITP 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 103 DESKEKDINYSAPLYVTAEFVNkDTQEIKSQTVFIGDFPMM------------TDR------------GTFIVNGTERVI 158
Cdd:PRK08565 74 MEARLRNLTYAAPLYLTMIPVE-NGIEYEPEEVKIGDLPIMvkskicplsglsPDElieigedpkdpgGYFIINGSERVI 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 159 VSQLVRSPgvyfDQTI-DKSTERP--LHAVKVIPSRG---AWLEFDVDKRDTVGVRIDRKR-RQPVTVLLKALGW-TEEQ 230
Cdd:PRK08565 153 VSQEDLAP----NRVLvDKGEAGSsiTHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAVPgKIPFVILMRALGLeTDRD 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 231 IRERFGF-----SELMMSTLEGDGVANT-DEALLEIYRKQRPGeQPtRDL----ALAMLANSFF----------KAKRYD 290
Cdd:PRK08565 229 IVYAVSLdpeiqQELLPSLEQASSIAATvEDALDYIGKRVAIG-QP-REYrierAEQILDKYLLphlgtspedrIKKAYF 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 291 LARVgrykINRklglggdhdglmtlteediavtleyLVRLHAGEREmkapngqmiplnTDDIDHFGNRRLRTVGELIQNQ 370
Cdd:PRK08565 307 LGQM----ASK-------------------------LLELYLGRRE------------PDDKDHYANKRLRLAGDLLAEL 345
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 371 VRVGLSRMERVVRERMTTQDAESITPTSLINVRP--VSAAIREFFGTSQ-------LSQFMDQNNSLSGLTHKRRLsaLG 441
Cdd:PRK08565 346 FRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPdiITERIRHALATGNwvggrtgVSQLLDRTNYLSTLSHLRRV--VS 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 442 PggLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLA-----------------------------------SYA 486
Cdd:PRK08565 424 P--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLAlmaqisvgvdeeeveeilyelgvvpveeareeeyiSWS 501
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 487 RV----NPFGFIETPYRKVE-------DGRITDEV------------VYVTAD-----------EEDRYAIAQAEVERDE 532
Cdd:PRK08565 502 RVylngRLIGYHPDGEELAEkirelrrSGKISDEVnvayietgeineVYVNCDsgrvrrplivvENGKPKLTREHVEKLK 581
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 533 QGYITdsrIEVRLKEGDIGVTDAKGVD--FIDVSPRQ--------------MVSVATAMIPFLEHDDANRALMGANMQRQ 596
Cdd:PRK08565 582 KGELT---FDDLVKMGVIEYLDAEEEEnaYVALDPEDltpehthleiwppaILGITASIIPYPEHNQSPRNTYQAAMAKQ 658
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 597 AVPLVRSEapfvgtgMEQRaaydagdliinakdgvveavsaqsitiMDDSGqrdtYLLrkfertnqgtNYNQTPLVSAgd 676
Cdd:PRK08565 659 SLGLYAAN-------FRIR---------------------------TDTRG----HLL----------HYPQRPLVQT-- 688
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 677 RVEAGQVLADGPGthngemslGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARdTKLGAEEITREIP 756
Cdd:PRK08565 689 RALEIIGYNDRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEER-KYPGGQEDKIEIP 759
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 757 --NVS----EDVLRDLDDRGIIRIGADVRPGDILVGKVTPKgetELTPEERLLRAIFGEKarevRDTSMKVPHGETGKVi 830
Cdd:PRK08565 760 epNVRgyrgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----RDTSVTVRHGEKGIV- 831
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 831 gvarfsrdeDDDL---APGVNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRR 907
Cdd:PRK08565 832 ---------DTVLiteSPEGNKLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSR 902
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 908 MNIGQVLEVHLGWLAH-SGWKIDvedpknaeilktlpeelydvpadsltATPvFDGATNEEISRLLASS--RPNrdgdvl 984
Cdd:PRK08565 903 MTVGQLLESIAGKVAAlEGRFVD--------------------------ATP-FYGEPEEELRKELLKLgyKPD------ 949
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 46361012 985 vdehGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEMEV 1056
Cdd:PRK08565 950 ----GTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMER 1017
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
489-1055 |
5.69e-66 |
|
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: 233.77 E-value: 5.69e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 489 NPFGFIETPYRKVEDGRITDEV-VYVTADEEDRYAIAQA-EVERD----EQG--YITDSRIEvRLKEGDIGVTD--AKG- 557
Cdd:TIGR03670 13 DPEELVEEVRKLRRSGKLSQEVnVAYYEETNEVYINCDAgRIRRPlivvENGkpKLTREHVE-KLKEGELTWDDlvKQGv 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 558 VDFID------------------------VSPRQMVSVATAMIPFLEHDDANRALMGANMQRQAVPLVRSEAPFvgtGME 613
Cdd:TIGR03670 92 IEYLDaeeeenayialdpeeltpehthleIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRI---RLD 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 614 QRAaydagdliinakdgvveavsaqsitimddsgqrdtYLLrkfertnqgtNYNQTPLVSAgdRVEAGQVLADGPGthng 693
Cdd:TIGR03670 169 TRG-----------------------------------HLL----------HYPQKPLVKT--RVLELIGYDDRPA---- 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 694 emslGRNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDARdTKLGAEEITREIPNV------SEDVLRDLD 767
Cdd:TIGR03670 198 ----GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEER-RYPGGQEDRFEIPEPdvrgyrGEEAYKHLD 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 768 DRGIIRIGADVRPGDILVGKVTPKgeteltpeeRLL--RAIFGEKAREVRDTSMKVPHGETGKVIGVArFSRDEDDdlap 845
Cdd:TIGR03670 273 EDGIVYPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRRDTSVTVRHGEKGIVDKVI-ITETEEG---- 338
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 846 gvNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFMEDGTPVDIILNTHGVPRRMNIGQVLEVHLGWL-AHS 924
Cdd:TIGR03670 339 --NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVaALE 416
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 925 GWKIDvedpknaeilktlpeelydvpadsltATPvFDGATNEEISRLLAssrpnRDGdvlVDEHGKARLFDGRSGEPYKY 1004
Cdd:TIGR03670 417 GRRVD--------------------------GTP-FEGEPEEELRKELL-----KLG---FKPDGKEVMYDGITGEKLEA 461
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|.
gi 46361012 1005 PVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGGQRFGEME 1055
Cdd:TIGR03670 462 EIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEME 512
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
536-1055 |
5.52e-62 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 222.53 E-value: 5.52e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 536 ITDSRIEvRLKEGDIGVTD--AKG-VDFID------------------------VSPRQMVSVATAMIPFLEHDDANRAL 588
Cdd:PRK07225 74 LTEEHIE-KLKNGELTFDDlvKQGvIEYLDaeeeenayiavyeedlteehthleIDPSLILGIGAGMIPYPEHNASPRIT 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 589 MGANMQRQAVPLvrseapfvgtgmeqraaydagdliinakdgvveavSAQSITIMDDSGQrdtYLLrkfertnqgtNYNQ 668
Cdd:PRK07225 153 MGAGMIKQSLGL-----------------------------------PAANYKLRPDTRG---HLL----------HYPQ 184
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 669 TPLVSAG-------DRVEAGQvladgpgthngemslgrNLLVAFMPWEGHNYEDAIILNQQIVEDDTLTSIHIEEHEIDA 741
Cdd:PRK07225 185 VPLVKTQtqeiigfDERPAGQ-----------------NFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEE 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 742 RDTKLGAEEiTREIPNV------SEDVLRDLDDRGIIRIGADVRPGDILVGKVTP------KGETELTPEERllraifge 809
Cdd:PRK07225 248 RRYPGGQED-RFEIPDKdvrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfleePDDFGISPEKR-------- 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 810 karevRDTSMKVPHGETGKVIGVArFSRDEDDdlapgvNEMIRVYVAQKRKIQDGDKLAGRHGNKGVVGKILPPEDMPFM 889
Cdd:PRK07225 319 -----RETSVTMRSGEEGIVDTVI-LTETEEG------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFT 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 890 EDGTPVDIILNTHGVPRRMNIGQVLEVHLGWLAH-SGWKIDvedpknaeilktlpeelydvpadsltATPvFDGATNEEI 968
Cdd:PRK07225 387 ESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSlEGRRVD--------------------------GTA-FSGEDEEDL 439
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 969 SRLLAssrpnRDGdvlVDEHGKARLFDGRSGEPYKYPVSVGYMYMLKLHHLVDEKIHARSTGPYSMITQQPLGGKAQFGG 1048
Cdd:PRK07225 440 REALE-----KLG---FEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGG 511
|
....*..
gi 46361012 1049 QRFGEME 1055
Cdd:PRK07225 512 LRFGEME 518
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
33-407 |
8.37e-43 |
|
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: 161.39 E-value: 8.37e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 33 GLLDVQLDSYSWLIgtpewREREQELRGPDARVTSGledilnelSPIEDYSERM--------SLSLSEPRF-----EPVK 99
Cdd:pfam04563 1 GLVRQQLDSFNEFV-----DNDLQKIIDENALIESE--------FEIQHPGENGdklslkfgQIRLGKPMFdetdgSTRE 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 100 YTVDESKEKDINYSAPLYVTAEFVNKDTQEIKSQTVFIGDFPMMTDR------------------------GTFIVNGTE 155
Cdd:pfam04563 68 IYPQECRLRNLTYSAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSE 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 156 RVIVSQLVRS---PGVYFDqtidKSTERPLHAVKV--------IPSRGAWLEF-DVDKRDTVGVRID-RKRRQPVTVLLK 222
Cdd:pfam04563 148 KVIVAQEHRSrnhPIVFKK----ADPKKRGSVASVrssaeisvRPDSTSWVNVlEYLSNGTIYFKFPyIKKEIPIVIILR 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 223 ALGWT-EEQIRER--FGFSELMMstlegdgvantDEALLEIYRKQRPGEQPTRDLALAMLANSFFKAKRYDLARVGRYKI 299
Cdd:pfam04563 224 ALGFTsDREIFELicYDVNDQQL-----------QEELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKY 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 300 NRKLgLGGD---HDGLMTLTEEDIAVTLEYLVR----LHAGEREMkapngqmiplntDDIDHFGNRRLRTVGELIQNQVR 372
Cdd:pfam04563 293 AEEI-LQKEvlpHLGTYELDETKKAYFIGYMIRrlllLALGRREV------------DDRDHLGNKRLRLAGPLLASLFR 359
|
410 420 430
....*....|....*....|....*....|....*..
gi 46361012 373 VGLSRMERVVRERMTTQ--DAESITPTSLINVRPVSA 407
Cdd:pfam04563 360 VLFKKLVRDVRERLQKVlgSPDDLMLQLLVNAKPITS 396
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
33-488 |
3.17e-37 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 147.02 E-value: 3.17e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 33 GLLDVQLDSYSWLIgtpewrereqelrgpdarvTSGLEDILNELSPIE-DYSERMSLSLSEPRFE-PVKYTVDESKEK-- 108
Cdd:PRK09606 17 RLVRHHIDSYNDFV-------------------DNGLQKIIDEQGPIEtEIEDGVYVELGKIRVGkPVVKEADGSEREiy 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 109 -------DINYSAPLYVTAEFVnKDTQEIKSQTVFIGDFPMM-----------TDR-------------GTFIVNGTERV 157
Cdd:PRK09606 78 pmearlrNLTYSAPLYLEMSPV-EGGEEEEPEEVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERV 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 158 IVSQLVRSPGVYFDQTIDKSTERpLHAVKVIPSRGAWlefdvdkRDTVGVRIDRK-----------RRQPVTVLLKALGW 226
Cdd:PRK09606 157 LMTLEDLAPNKILVEKDERYGDR-IEVAKVFSQRRGY-------RALVTVERNRDgllevsfpsvpGSIPFVILMRALGL 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 227 -TEEQIRERFG----FSELMMSTLEGDGVANTDEALLEIYRKQRPGEqptrdlalamlansffkAKRYDLARvGRYKINR 301
Cdd:PRK09606 229 eTDEEIVEAVSddpeIVKFMLENLEEAEVDTQEEALEYIGKRVAPGQ-----------------TKEYRIKR-AEYVIDR 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 302 KL--GLGGDHDGLMTLTEEdIAVTLEYLVRLHAGEREmkapngqmiplnTDDIDHFGNRRLRTVGELIQNQVRVGLSRME 379
Cdd:PRK09606 291 YLlpHLGVEPEVRRAKAHY-LGRMAEACFELALGRRE------------EDDKDHYANKRLKLAGDLMEDLFRVAFNRLA 357
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 380 RVVRERMTTQDAESITPTSLINVRP--VSAAIREFFGTSQ-------LSQFMDQNNSLSGLTHKRRLSAlgpgGLSRERA 450
Cdd:PRK09606 358 RDVKYQLERANMRNRELSIKTAVRSdvLTERLEHAMATGNwvggrtgVSQLLDRTDYMATLSHLRRVVS----PLSRSQP 433
|
490 500 510
....*....|....*....|....*....|....*...
gi 46361012 451 GIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYARV 488
Cdd:PRK09606 434 HFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEI 471
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
420-487 |
6.33e-33 |
|
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: 121.48 E-value: 6.33e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 46361012 420 QFMDQNNSLSGLTHKRRLSAlGPGGLSRERAGIEVRDVHPSHYGRMCPIETPEGPNIGLIGSLASYAR 487
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
498-564 |
3.67e-25 |
|
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: 99.36 E-value: 3.67e-25
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 46361012 498 YRKVEDGRITDEVVYVTADEEDRYAIAQAEVERDEQGYITDSRIEVRlKEGDIGVTDAKGVDFIDVS 564
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSAR-YRGEFPLVPPEEVDYMDVS 66
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
164-361 |
1.21e-19 |
|
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: 87.79 E-value: 1.21e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 164 RSPGVYFDQTIDKSTERPLHAVKVIPSRGAWLEFDVDKRDTVGVRIDRKRRQPVTVLLKALG-WTEEQIRERFGFS---- 238
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIATYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGlVSDREILDRLCYDfndp 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 46361012 239 ----ELMMSTLEGDGVANTDEALLEIYR--KQRPGEQPTRDLALAMLANSFFKakrydlarvgrYKINRKLGLGGDHDGl 312
Cdd:pfam04561 81 qmleLLKPELEEAENIYTQEEALDYIGKgfALRRGEEPRLQRAREILYSRDPK-----------YNLNKHLGLNEPFEN- 148
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 46361012 313 MTLTEEDIAVTLEYLVRLHAGEREmkapngqmiplnTDDIDHFGNRRLR 361
Cdd:pfam04561 149 ERLKAQDILYMIDRLLNLKLGRRK------------PDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1047-1060 |
4.97e-04 |
|
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: 39.88 E-value: 4.97e-04
|
| |
