|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
39-1067 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 806.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 39 FSIITK-NNFIKFKLLPEYLKFKLSKLNdSTINAVEEKTPKIQVIVPLKIIFKTLNKYILIYCPLIELPYTDLQGNFILN 117
Cdd:CHL00207 33 FSKIFDyTGNLELLLFGKNYKLKYPKYN-LLSAKSYDSNYSIQIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIIN 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 118 GMKRGLVSKMVRQNGVYFNL-RRKYGEDIYSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNSTIS 194
Cdd:CHL00207 112 GLERVIVSQIIRSPGIYFKKeIKKNSNKIYSATLIPN-RGSWIKFELDKNKEIWIRIDKnrKKPLIIFLKALGLTDQDIY 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 195 SISRYgtteIFKNFYYFNSKEDIQELEKIKTLLNMLN---PELNLKY-LKNKLNFSRHLTSlKNSLISRTGNFL------ 264
Cdd:CHL00207 191 SRLTK----SEFLKKLKPILLNSNSYTNEEILLEIYKnlsPIEPATVnDANQNLFSRFFDP-KNYDLGKVGRYKinnkln 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 265 ----ESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLIS-------AHLEYILPNKLFKilnllFKSK 333
Cdd:CHL00207 266 lnipERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQnqfriglKRLERILRNRMTI-----CDID 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 334 FITSSLLIENlkesfNKNKISIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICI 413
Cdd:CHL00207 341 SLSKFNLINP-----KPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICP 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 414 LDTNEGPSSGLVVALASNARINKEGSIETLIHPNKKLRSYSK----FLNSFEQESFLVSFENLIPRKQSFLNKYSTSItF 489
Cdd:CHL00207 416 IETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFgnpiYLTADSEDLYRIAPNDINLNKNNYFKKNIIPV-R 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 490 EKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLR 569
Cdd:CHL00207 495 YKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTII 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 570 AYQEGVITKVTSYKIVLIDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLY 649
Cdd:CHL00207 575 SLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAY 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 650 GSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDIL 729
Cdd:CHL00207 655 MPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR-QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDIL 733
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 730 ISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYGQnYLTLRVFVAKQRMLQ 809
Cdd:CHL00207 734 VGKITPKG-ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGY-YLKIRVFIAQIRKIQ 811
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRlLINSLLNNNLNNN 889
Cdd:CHL00207 812 VGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKR-FKILPFDEMYGSE 890
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 890 YTKTYLYTSLQSLKYYTGNKSLLNPYIPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPI 969
Cdd:CHL00207 891 YSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPL 970
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 970 KGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLEG 1049
Cdd:CHL00207 971 GGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
|
1050
....*....|....*...
gi 1833819269 1050 FMVTDLLDGKLLPLNINY 1067
Cdd:CHL00207 1051 YKIENFLEGQRLEIEINL 1068
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
55-1048 |
2.83e-178 |
|
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: 549.27 E-value: 2.83e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 55 EYLKFKLSKLNDStinaVEE-----KTPKIQVIVPLKIIFK--TLNKYI---LIYcpLIELPYTDLQGNFILNGMKRGLV 124
Cdd:TIGR02013 66 EYLSYRLGEPKYS----VEEckergLTYSAPLKVKLRLINKeeDGTKEIkeqDVY--MGDIPLMTDRGTFIINGAERVVV 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 125 SKMVRQNGVYFN---LRRKYGEDIYSAQLILNERS-KYFIELFKEGIFIYNKFNKKINLINFLHFIGLNNSTISsISRYG 200
Cdd:TIGR02013 140 SQLHRSPGVFFSsekDTTKSGKVLFSARIIPYRGSwLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI-LNRLG 218
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 201 TTEifknfYYFNS----KEDIQElEKIKTLLNMLNP-----ELNLKYLKNKLNFS--RH-LTSLKNSLISRTGNFLESSF 268
Cdd:TIGR02013 219 SGE-----YIRNTlrkdPTNSEE-EALVEIYRKLRPgepptVEAARSLLENLFFDpkRYdLGRVGRYKLNKKLGLDVPES 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 269 AIL--GQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILpNKLFKI---------LNLLFKSKFITS 337
Cdd:TIGR02013 293 IGVltKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGL-ARMERIvrermstqdTDTLTPQDLINA 371
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 338 SLLIENLKESFNKNKISikelltvnpliQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTN 417
Cdd:TIGR02013 372 KPISAAIKEFFGSSQLS-----------QFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 440
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 418 EGPSSGLVVALASNARINKEGSIETlihPNKKLRS-------YSKFLNSFEQESFLVSF------ENLIPRKQSFLNKYs 484
Cdd:TIGR02013 441 EGPNIGLINSLSTYARVNEYGFIET---PYRKVKDgkvvvtdEIDYLTADEEDNYVIAQanapldENGRFVEDLVVARY- 516
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 485 tsitfeKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKT 564
Cdd:TIGR02013 517 ------RGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDS 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 565 SNLLRAYQEGVITKVTSYKIVL------IDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSE 638
Cdd:TIGR02013 591 GAVIVAKRGGVVEYVDAKRIVIrydedeEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 639 FNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkypiDT---PEYSTLDLPKRTSYQKRHLDKLG 715
Cdd:TIGR02013 671 LALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEAR----DTklgPEEITRDIPNVSEEALRNLDENG 746
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 716 IITEGSKVLDGDILISKI---SVSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYG 792
Cdd:TIGR02013 747 IVRIGAEVKAGDILVGKVtpkGETELTPEE----KLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPG 822
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 793 QNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLK 872
Cdd:TIGR02013 823 VNKL-VKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL 901
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 873 DKRLLINSllnnnlnnnyTKTYLYTSLQSLKYYTgNKSLLNPyiPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDK 952
Cdd:TIGR02013 902 GRKGVPIA----------TPVFDGASEEEIKEYL-EKAGLPR--DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDK 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 953 VHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEA 1032
Cdd:TIGR02013 969 MHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPES 1048
|
1050
....*....|....*.
gi 1833819269 1033 LKLLIRELHGLSLNLE 1048
Cdd:TIGR02013 1049 FNVLIKELQSLGLDIE 1064
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
112-1048 |
2.02e-153 |
|
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: 482.30 E-value: 2.02e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 112 GNFILNGMKRGLVSKMVRQNGVYFN-LRRKYGEDIYSAQLILNeRSKYF-IELFKEGIfIYNKFN--KKINLINFLHFIG 187
Cdd:COG0085 110 GTFIINGTERVIVSQLVRSPGVYFVeEEDKSGKDLYSAKVIPS-RGAWLeFETDKDGT-IYVRIDrkRKIPVTVLLRALG 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 188 L-NNSTIssISRYGTTEIFKNFYY------FNSKED-IQEL------------EKIKTLL-NML-NPE-----------L 234
Cdd:COG0085 188 LeTDEEI--LEAFGDDPIQEYILAtlekdnTKTQEEaLLEIyrklrpgepptiERAEQLLdNLFfDPKrydlahvgrykI 265
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 235 NLKYLKNKLNFSRHLTslknslisrtgnflessfailGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAH- 313
Cdd:COG0085 266 NKKLGLDVPPEDRVLT---------------------AEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQf 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 314 ------LEYILPNKLFKIlnllfKSKFITSSLLIenlkesfNKNKI--SIKELLTVNPLIQYLEEVNSVSELMHKVRISS 385
Cdd:COG0085 325 rvglsrMERVVRERMTTQ-----DVEAITPQSLI-------NIRPVvaAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 386 IGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihP-----NKKLRSYSKFLNSF 460
Cdd:COG0085 393 LGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIET---PyrkveNGKVTDEIEYLTAD 469
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 461 EQESFLVSFENL-IPRKQSFLNKYSTSITFEKGEIKSKTNIsdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQT 539
Cdd:COG0085 470 EEENYYIAQANApLDEDGNFLEERVLVRYRGEEVLVPPEEV--DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 540 QAVPLIYRNKPYIltgfesiiasktsnllrayqegvitkvtsykivlidlfnreiTYYLQKYKKTNQGTFIHQLPIVWPG 619
Cdd:COG0085 548 QAVPLLRPEAPLL------------------------------------------HYPLQKFQRSNQGTCINQRPIVRVG 585
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 620 ERVLSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDtPEYSTLD 699
Cdd:COG0085 586 DRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLG-PEEITRD 664
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 700 LPKRTSYQKRHLDKLGIITEGSKVLDGDILISKIS---VSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVI 776
Cdd:COG0085 665 IPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTpkgETELTPEE----RLLRAIFGEKAREVRDTSLRVPHGEKGKVI 740
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 777 KTELFAVTNKATSTYGQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYnvMSQ--YPDIITGPLGVPSR 854
Cdd:COG0085 741 DVKVFSREEGDELPPGVNKL-VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF--LEDgtPVDIVLNPLGVPSR 817
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 855 MNLGQLFESLFGYNCVLKDKRLLinsllnnnlnnnyTKTYLYTSLQSLKYYTGnKSLLNPyiPGKLLLRDGRTGYRLKGG 934
Cdd:COG0085 818 MNVGQVLETHLGWAAALLGRRVA-------------TPVFDGAPEEEIRELLE-KAGLPP--DGKEVLYDGRTGEPFDNP 881
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 935 AFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPikgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDDLISRNNL 1014
Cdd:COG0085 882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPlggkaqfggqrfgEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961
|
970 980 990
....*....|....*....|....*....|....*
gi 1833819269 1015 QEYLLNNTPL-EPNyLPEALKLLIRELHGLSLNLE 1048
Cdd:COG0085 962 YEAIVKGENIpEPG-IPESFKVLLKELQSLGLDVE 995
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
21-1048 |
7.68e-130 |
|
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: 415.81 E-value: 7.68e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 21 YDTLLKVSILQAIKSLVPFSIITKNNFIKFKllpeYLKFKLSKLNDSTINAVEEKTP----------------KIQVIVP 84
Cdd:cd00653 9 FNYFLNVGLQEIVKSIPPITDTDDDGRLKLK----FGDIYLGKPKVEEGGVTRKLTPnecrlrdltysaplyvDIRLTVN 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 85 LKIIFKTLNKYI--------LIYCPLIELPYTDL----------QGNFILNGMKRGLVSKMVRQNGVYFNLRRKyGEDIY 146
Cdd:cd00653 85 DKGKIKEQEVFIgeipimlrSKLCNLNGLTPEELiklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVEDSK-GKRIY 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 147 SAQLILNERSKYfielfkeGIFIYNKFNKKINLINFLHfiglnnstissisrygtteifknfYYFNSKEDIQELEKiktl 226
Cdd:cd00653 164 TKTSIPSYSPYR-------GSWLEVKSDKKKDRIYVRI------------------------DLKRQEEALKYIGK---- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 227 lnmlnpelnlkylknklnfsrhltslknslisrtgnflessfaiLGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESL 306
Cdd:cd00653 209 --------------------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLA 244
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 307 GHLIS-------AHLEYILPNKLFKIL---NLLFKSKFITSSLLIENLKESFNK-NKISIKELLTVNPLIQYLEEVNSVS 375
Cdd:cd00653 245 GELLQnlfrsglKRLEREVKEKLQKQLskkKDLTPQLLINSKPITSGIKEFLATgNWGSKRFLMQRSGLSQVLDRLNPLS 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 376 ELMHKVRISSigpGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINkeGSIEtlihpnkklRSYSK 455
Cdd:cd00653 325 ELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIE---------RPYRI 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 456 flnsfeqesflvsfenliprkqsflnkystsitfekgeIKSKTnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGA 535
Cdd:cd00653 391 --------------------------------------VEKEV----THIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 536 RMQTQAVPLIYRNKPYIltgfesiIASKTSNLLRAYQEGVITKvtsykivLIDLFNREityylqkykktnqgtfihQLPi 615
Cdd:cd00653 429 NMQKQAVGTPALNQQYR-------MDTKLYLLLYPQKPLVGTG-------IEEYIAFG------------------ELP- 475
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 616 vwpgervlSGQlltenqdisdsefNI--------GNNLNvlygsyygyeyeDSLIISQKVLYKNIFTSIHFDIYEIKYSK 687
Cdd:cd00653 476 --------LGQ-------------NAivavmsysGYNFE------------DAIIINKSSVDRGFFRSIHYKKYEIELRK 522
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 688 YPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKISVSNLTLEDSPFselifslfGTKLRQLQDKSISV 767
Cdd:cd00653 523 TKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIF--------GEKARDVRDTSLKY 594
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 768 PIGNSGRVIKTELFAVTNKAtstygQNYLTLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITG 847
Cdd:cd00653 595 PGGEKGIVDDVKIFSRELND-----GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILN 669
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 848 PLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnNLNNNYTKTYLYTSLQSLKyytgnKSLLNPYipGKLLLRDGRT 927
Cdd:cd00653 670 PHGFPSRMTIGQLLESLLGKAGALLGKF---------GDATPFDGAEEEDISELLG-----EAGLNYY--GKEVLYDGRT 733
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 928 GYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIkgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDD 1007
Cdd:cd00653 734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLkgrsrgggqrfgEMERDALIAHGAAYLLQERLTIKSDD 813
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|.
gi 1833819269 1008 LISRNNLQEYLL----------NNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:cd00653 814 VVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPR 864
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
570-969 |
2.21e-82 |
|
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: 272.48 E-value: 2.21e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 570 AYQEGVITKVTSYKIVLIDLFNREI--TYYLQKYKKTNQGTF---IHQLPIVWPGeRVLSGQLltenqdisdSEFNIGNN 644
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAmgIYTLNKFYRSDQNTYvlcYPQKPLVKTG-AVEAGGF---------GELPLGQN 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 645 LNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKysKYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVL 724
Cdd:pfam00562 72 AIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEAR--KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVK 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 725 DGDILISKISvsnltleDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKatstygqNYLTLRVFVAK 804
Cdd:pfam00562 150 PGDILVGKVG-------PTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFELPPG-------GIKMVKVYIRQ 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 805 QRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRLLINSLLNN 884
Cdd:pfam00562 216 KRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGA 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 885 NLNNNYTKTYLYtslqslkyytgnKSLLNPYipGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEI 964
Cdd:pfam00562 296 STEVEDIGELLE------------KAGYNYY--GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLL 361
|
....*
gi 1833819269 965 TQQPI 969
Cdd:pfam00562 362 TRQPL 366
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
39-1067 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 806.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 39 FSIITK-NNFIKFKLLPEYLKFKLSKLNdSTINAVEEKTPKIQVIVPLKIIFKTLNKYILIYCPLIELPYTDLQGNFILN 117
Cdd:CHL00207 33 FSKIFDyTGNLELLLFGKNYKLKYPKYN-LLSAKSYDSNYSIQIYLPLKFINLKTNKIKFINYLIGNLPKMTQRGTFIIN 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 118 GMKRGLVSKMVRQNGVYFNL-RRKYGEDIYSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNSTIS 194
Cdd:CHL00207 112 GLERVIVSQIIRSPGIYFKKeIKKNSNKIYSATLIPN-RGSWIKFELDKNKEIWIRIDKnrKKPLIIFLKALGLTDQDIY 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 195 SISRYgtteIFKNFYYFNSKEDIQELEKIKTLLNMLN---PELNLKY-LKNKLNFSRHLTSlKNSLISRTGNFL------ 264
Cdd:CHL00207 191 SRLTK----SEFLKKLKPILLNSNSYTNEEILLEIYKnlsPIEPATVnDANQNLFSRFFDP-KNYDLGKVGRYKinnkln 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 265 ----ESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLIS-------AHLEYILPNKLFKilnllFKSK 333
Cdd:CHL00207 266 lnipERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQnqfriglKRLERILRNRMTI-----CDID 340
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 334 FITSSLLIENlkesfNKNKISIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICI 413
Cdd:CHL00207 341 SLSKFNLINP-----KPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICP 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 414 LDTNEGPSSGLVVALASNARINKEGSIETLIHPNKKLRSYSK----FLNSFEQESFLVSFENLIPRKQSFLNKYSTSItF 489
Cdd:CHL00207 416 IETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFgnpiYLTADSEDLYRIAPNDINLNKNNYFKKNIIPV-R 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 490 EKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLR 569
Cdd:CHL00207 495 YKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTII 574
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 570 AYQEGVITKVTSYKIVLIDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLY 649
Cdd:CHL00207 575 SLTEGIVVSVSAYKIIIQDDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAY 654
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 650 GSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDIL 729
Cdd:CHL00207 655 MPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELR-QTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDIL 733
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 730 ISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYGQnYLTLRVFVAKQRMLQ 809
Cdd:CHL00207 734 VGKITPKG-ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDELKFGY-YLKIRVFIAQIRKIQ 811
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRlLINSLLNNNLNNN 889
Cdd:CHL00207 812 VGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKR-FKILPFDEMYGSE 890
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 890 YTKTYLYTSLQSLKYYTGNKSLLNPYIPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPI 969
Cdd:CHL00207 891 YSRILINNKLNQASIKNNEYWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPL 970
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 970 KGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLEG 1049
Cdd:CHL00207 971 GGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
|
1050
....*....|....*...
gi 1833819269 1050 FMVTDLLDGKLLPLNINY 1067
Cdd:CHL00207 1051 YKIENFLEGQRLEIEINL 1068
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
55-1048 |
2.83e-178 |
|
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: 549.27 E-value: 2.83e-178
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 55 EYLKFKLSKLNDStinaVEE-----KTPKIQVIVPLKIIFK--TLNKYI---LIYcpLIELPYTDLQGNFILNGMKRGLV 124
Cdd:TIGR02013 66 EYLSYRLGEPKYS----VEEckergLTYSAPLKVKLRLINKeeDGTKEIkeqDVY--MGDIPLMTDRGTFIINGAERVVV 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 125 SKMVRQNGVYFN---LRRKYGEDIYSAQLILNERS-KYFIELFKEGIFIYNKFNKKINLINFLHFIGLNNSTISsISRYG 200
Cdd:TIGR02013 140 SQLHRSPGVFFSsekDTTKSGKVLFSARIIPYRGSwLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI-LNRLG 218
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 201 TTEifknfYYFNS----KEDIQElEKIKTLLNMLNP-----ELNLKYLKNKLNFS--RH-LTSLKNSLISRTGNFLESSF 268
Cdd:TIGR02013 219 SGE-----YIRNTlrkdPTNSEE-EALVEIYRKLRPgepptVEAARSLLENLFFDpkRYdLGRVGRYKLNKKLGLDVPES 292
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 269 AIL--GQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILpNKLFKI---------LNLLFKSKFITS 337
Cdd:TIGR02013 293 IGVltKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGL-ARMERIvrermstqdTDTLTPQDLINA 371
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 338 SLLIENLKESFNKNKISikelltvnpliQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTN 417
Cdd:TIGR02013 372 KPISAAIKEFFGSSQLS-----------QFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETP 440
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 418 EGPSSGLVVALASNARINKEGSIETlihPNKKLRS-------YSKFLNSFEQESFLVSF------ENLIPRKQSFLNKYs 484
Cdd:TIGR02013 441 EGPNIGLINSLSTYARVNEYGFIET---PYRKVKDgkvvvtdEIDYLTADEEDNYVIAQanapldENGRFVEDLVVARY- 516
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 485 tsitfeKGEIKSKTNISDTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKT 564
Cdd:TIGR02013 517 ------RGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDS 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 565 SNLLRAYQEGVITKVTSYKIVL------IDLFNREITYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSE 638
Cdd:TIGR02013 591 GAVIVAKRGGVVEYVDAKRIVIrydedeEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGE 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 639 FNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSkypiDT---PEYSTLDLPKRTSYQKRHLDKLG 715
Cdd:TIGR02013 671 LALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEAR----DTklgPEEITRDIPNVSEEALRNLDENG 746
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 716 IITEGSKVLDGDILISKI---SVSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKATSTYG 792
Cdd:TIGR02013 747 IVRIGAEVKAGDILVGKVtpkGETELTPEE----KLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPG 822
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 793 QNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLK 872
Cdd:TIGR02013 823 VNKL-VKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRL 901
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 873 DKRLLINSllnnnlnnnyTKTYLYTSLQSLKYYTgNKSLLNPyiPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDK 952
Cdd:TIGR02013 902 GRKGVPIA----------TPVFDGASEEEIKEYL-EKAGLPR--DGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDK 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 953 VHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEA 1032
Cdd:TIGR02013 969 MHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPES 1048
|
1050
....*....|....*.
gi 1833819269 1033 LKLLIRELHGLSLNLE 1048
Cdd:TIGR02013 1049 FNVLIKELQSLGLDIE 1064
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
33-1052 |
3.05e-169 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 525.62 E-value: 3.05e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 33 IKSLVPFSIITK-NNFIKFKLLPEYLKFKLSKLNDStiNAVEEK-TPKIQVIVPLKIIFKTLN---KYILIYCpliELPY 107
Cdd:CHL00001 32 TEELSKFPKIEDtDQEIEFQLFVETYQLVEPLIKER--DAVYESlTYSSELYVPAGLIWKKSRdmqEQTVFIG---NIPL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 108 TDLQGNFILNGMKRGLVSKMVRQNGVYFNLRRKY-GEDIYSAQLILN--ERSKYFIELfKEGIFIYNKFNKKINLINFLH 184
Cdd:CHL00001 107 MNSLGTFIINGIYRVVINQILRSPGIYYRSELDHnGISVYTGTIISDwgGRLELEIDR-KARIWARVSRKQKISILVLLS 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 185 FIGLNNSTISSISRYgtTEIFKNFYYFNSKEDIQELEKIktllnMLNPELNLKYLKNKLNFSRHLTS-LKNSL------I 257
Cdd:CHL00001 186 AMGLNLREILDNVCY--PEIFLSFLNDKEKKKIGSKENA-----ILEFYQQFACVGGDPVFSESLCKeLQKKFfqqrceL 258
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 258 SRTG----------NFLESSFAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILpNKL----F 323
Cdd:CHL00001 259 GRIGrrnmnrklnlDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLAL-NRLenavR 337
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 324 KILNLLFKSKFI-------TSSLLIENLKESFNknkisikelltVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQA 396
Cdd:CHL00001 338 GTICGAIRRKLIptpqnlvTSTPLTTTYESFFG-----------SHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTA 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 397 GVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihPNKKLRSYSK-----FLNSFEQESFLVSFEN 471
Cdd:CHL00001 407 SFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLES---PFYEISERSKeermvYLSPSEDEYYMIAAGN 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 472 L------IPRKQSFLNKYS---TSITFEKGEIKSktnisdtyykINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAV 542
Cdd:CHL00001 484 SlalnqgIQEEQVVPARYRqefLTIAWEQIHLRS----------IFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAV 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 543 PLIYRNKPYILTGFESIIASKTSNLLRAYQEGVITKVTSYKIVLIDLFNrEITYYLQKYKKTNQGTFIHQLPIVWPGERV 622
Cdd:CHL00001 554 PLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGD-TLSIPLVMYQRSNKNTCMHQKPQVRRGKCV 632
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 623 LSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKySKYPIDTPEYSTLDLPK 702
Cdd:CHL00001 633 KKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQ-THVTSQGPERITKEIPH 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 703 RTSYQKRHLDKLGIITEGSKVLDGDILISKIsvSNLTLEDS---PFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIktE 779
Cdd:CHL00001 712 LEAHLLRNLDKNGIVMLGSWVETGDILVGKL--TPQEAEESsyaPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVI--D 787
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 780 LFAVTNKATSTYgqNYLTLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYnVMSQYP-DIITGPLGVPSRMNLG 858
Cdd:CHL00001 788 VRWIQKKGGSSY--NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPY-LQDGTPvDMVLNPLGVPSRMNVG 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 859 QLFESLFG---------YNCVLKDKRllinsllnnnlnnnYTK--------TYLY-TSLQslkyyTGNKSLLNPYIPGKL 920
Cdd:CHL00001 865 QIFECLLGlagdllnrhYRIAPFDER--------------YEQeasrklvfSELYeASKQ-----TANPWVFEPEYPGKS 925
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 921 LLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLREL 1000
Cdd:CHL00001 926 RLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEM 1005
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|...
gi 1833819269 1001 LTSKSDDLISRNNLQEYLLNNTPL-EPNYLPEALKLLIRELHGLSLNLEGFMV 1052
Cdd:CHL00001 1006 LTYKSDHIRARQEVLGAIITGGTIpKPEDAPESFRLLVRELRSLALELNHFLV 1058
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
83-1048 |
1.08e-155 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 491.15 E-value: 1.08e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 83 VPLKIIFKTLNKYI------LIYcpLIELPY-TDlQGNFILNGMKRGLVSKMVRQNGVYFNL---RRKYGEDIYSAQLIL 152
Cdd:PRK00405 95 APLRVKLRLINKETgeikeqEVY--MGDIPLmTE-NGTFIINGTERVIVSQLHRSPGVYFDHdkdKTSSGKLLYSARIIP 171
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 153 NERSkyFIELF---KEGIFIYNKFNKKINLINFLHFIGLNNSTIssISRYGTTEIFKNF-----------YYFNSKEDIQ 218
Cdd:PRK00405 172 YRGS--WLEFEfdpKDILYVRIDRRRKLPVTVLLRALGYSDEEI--LDLFYEKEEFGKEievpveyllgkVLAEDIVDEE 247
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 219 ELEKIKTLLNMLNPELNLKYLKNKLNfSRHLTSLKNSLIS-----RTG---------NFLESSF---------------- 268
Cdd:PRK00405 248 TGEVLAEANDEITEELDGPYIRNTLE-KDPTSSREEALVEiyrrlRPGepptveaarSLLENLFfdpkrydlskvgrykl 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 269 -------------AILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLI--------------------SAHLE 315
Cdd:PRK00405 327 nkklgldededvrVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLqnqfriglsrmeravrermsLQDLD 406
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 316 YILPNKLfkiLNllfkSKFITSSllienlkesfnknkisIKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQ 395
Cdd:PRK00405 407 TLTPQDL---IN----AKPVVAA----------------IKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRER 463
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 396 AGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihP-----NKKLRSYSKFLNSFEQESFLV--- 467
Cdd:PRK00405 464 AGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIET---PyrkvvDGKVTDEIVYLTADEEDNYVIaqa 540
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 468 --------SF-ENLIP--RKQSFlnkystsITFEKGEIksktnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGAR 536
Cdd:PRK00405 541 napldedgRFvDELVTarYKGEF-------VLVPPEEV--------DYMDVSPKQVVSVAASLIPFLEHDDANRALMGSN 605
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 537 MQTQAVPLIYRNKPYILTGFESIIASKTSNLLRAYQEGVITKVTSYKIV-----LIDLFNREITYYLQKYKKTNQGTFIH 611
Cdd:PRK00405 606 MQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVvrveeLDPGEDGVDIYNLIKFQRSNQNTCIN 685
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 612 QLPIVWPGERVLSGQLLTENQDISDSEFNIGNNL----------NvlygsyygyeYEDSLIISQKVLYKNIFTSIHFDIY 681
Cdd:PRK00405 686 QRPIVKVGDRVEKGDVLADGPSTDNGELALGQNVlvafmpwngyN----------FEDAILISERLVKEDVFTSIHIEEY 755
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 682 EIKYSkypiDT---PEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKIS---VSNLTLEDspfsELIFSLFGT 755
Cdd:PRK00405 756 EIEAR----DTklgPEEITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTpkgETELTPEE----KLLRAIFGE 827
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 756 KLRQLQDKSISVPIGNSGRVIKTELFA-VTNKATSTYGQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELP 834
Cdd:PRK00405 828 KARDVKDTSLRVPHGEEGTVIDVKVFTrIEQGDELPPGVNKL-VKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMP 906
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 835 Y-----NVmsqypDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnnlnnnyTKTYLY--TSLQSLKYYTg 907
Cdd:PRK00405 907 YledgtPV-----DIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK---------------FATPVFdgAKEEEIKELL- 965
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 908 NKSLLNPYipGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPikgrgkgggqrfgEMEVWA 987
Cdd:PRK00405 966 EEAGLPED--GKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPlggkaqfggqrfgEMEVWA 1043
|
1050 1060 1070 1080 1090 1100
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1833819269 988 LEAFGASYTLRELLTSKSDDLISRNNLQEYLL--NNTPlEPNyLPEALKLLIRELHGLSLNLE 1048
Cdd:PRK00405 1044 LEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVkgENIP-EPG-IPESFNVLVKELQSLGLDVE 1104
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
112-1048 |
2.02e-153 |
|
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: 482.30 E-value: 2.02e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 112 GNFILNGMKRGLVSKMVRQNGVYFN-LRRKYGEDIYSAQLILNeRSKYF-IELFKEGIfIYNKFN--KKINLINFLHFIG 187
Cdd:COG0085 110 GTFIINGTERVIVSQLVRSPGVYFVeEEDKSGKDLYSAKVIPS-RGAWLeFETDKDGT-IYVRIDrkRKIPVTVLLRALG 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 188 L-NNSTIssISRYGTTEIFKNFYY------FNSKED-IQEL------------EKIKTLL-NML-NPE-----------L 234
Cdd:COG0085 188 LeTDEEI--LEAFGDDPIQEYILAtlekdnTKTQEEaLLEIyrklrpgepptiERAEQLLdNLFfDPKrydlahvgrykI 265
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 235 NLKYLKNKLNFSRHLTslknslisrtgnflessfailGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAH- 313
Cdd:COG0085 266 NKKLGLDVPPEDRVLT---------------------AEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQf 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 314 ------LEYILPNKLFKIlnllfKSKFITSSLLIenlkesfNKNKI--SIKELLTVNPLIQYLEEVNSVSELMHKVRISS 385
Cdd:COG0085 325 rvglsrMERVVRERMTTQ-----DVEAITPQSLI-------NIRPVvaAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSA 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 386 IGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETlihP-----NKKLRSYSKFLNSF 460
Cdd:COG0085 393 LGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIET---PyrkveNGKVTDEIEYLTAD 469
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 461 EQESFLVSFENL-IPRKQSFLNKYSTSITFEKGEIKSKTNIsdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQT 539
Cdd:COG0085 470 EEENYYIAQANApLDEDGNFLEERVLVRYRGEEVLVPPEEV--DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQR 547
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 540 QAVPLIYRNKPYIltgfesiiasktsnllrayqegvitkvtsykivlidlfnreiTYYLQKYKKTNQGTFIHQLPIVWPG 619
Cdd:COG0085 548 QAVPLLRPEAPLL------------------------------------------HYPLQKFQRSNQGTCINQRPIVRVG 585
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 620 ERVLSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDtPEYSTLD 699
Cdd:COG0085 586 DRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLG-PEEITRD 664
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 700 LPKRTSYQKRHLDKLGIITEGSKVLDGDILISKIS---VSNLTLEDspfsELIFSLFGTKLRQLQDKSISVPIGNSGRVI 776
Cdd:COG0085 665 IPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTpkgETELTPEE----RLLRAIFGEKAREVRDTSLRVPHGEKGKVI 740
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 777 KTELFAVTNKATSTYGQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYnvMSQ--YPDIITGPLGVPSR 854
Cdd:COG0085 741 DVKVFSREEGDELPPGVNKL-VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPF--LEDgtPVDIVLNPLGVPSR 817
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 855 MNLGQLFESLFGYNCVLKDKRLLinsllnnnlnnnyTKTYLYTSLQSLKYYTGnKSLLNPyiPGKLLLRDGRTGYRLKGG 934
Cdd:COG0085 818 MNVGQVLETHLGWAAALLGRRVA-------------TPVFDGAPEEEIRELLE-KAGLPP--DGKEVLYDGRTGEPFDNP 881
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 935 AFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPikgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDDLISRNNL 1014
Cdd:COG0085 882 VTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPlggkaqfggqrfgEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKV 961
|
970 980 990
....*....|....*....|....*....|....*
gi 1833819269 1015 QEYLLNNTPL-EPNyLPEALKLLIRELHGLSLNLE 1048
Cdd:COG0085 962 YEAIVKGENIpEPG-IPESFKVLLKELQSLGLDVE 995
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
21-1048 |
7.68e-130 |
|
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: 415.81 E-value: 7.68e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 21 YDTLLKVSILQAIKSLVPFSIITKNNFIKFKllpeYLKFKLSKLNDSTINAVEEKTP----------------KIQVIVP 84
Cdd:cd00653 9 FNYFLNVGLQEIVKSIPPITDTDDDGRLKLK----FGDIYLGKPKVEEGGVTRKLTPnecrlrdltysaplyvDIRLTVN 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 85 LKIIFKTLNKYI--------LIYCPLIELPYTDL----------QGNFILNGMKRGLVSKMVRQNGVYFNLRRKyGEDIY 146
Cdd:cd00653 85 DKGKIKEQEVFIgeipimlrSKLCNLNGLTPEELiklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVEDSK-GKRIY 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 147 SAQLILNERSKYfielfkeGIFIYNKFNKKINLINFLHfiglnnstissisrygtteifknfYYFNSKEDIQELEKiktl 226
Cdd:cd00653 164 TKTSIPSYSPYR-------GSWLEVKSDKKKDRIYVRI------------------------DLKRQEEALKYIGK---- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 227 lnmlnpelnlkylknklnfsrhltslknslisrtgnflessfaiLGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVESL 306
Cdd:cd00653 209 --------------------------------------------RFEDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLA 244
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 307 GHLIS-------AHLEYILPNKLFKIL---NLLFKSKFITSSLLIENLKESFNK-NKISIKELLTVNPLIQYLEEVNSVS 375
Cdd:cd00653 245 GELLQnlfrsglKRLEREVKEKLQKQLskkKDLTPQLLINSKPITSGIKEFLATgNWGSKRFLMQRSGLSQVLDRLNPLS 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 376 ELMHKVRISSigpGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINkeGSIEtlihpnkklRSYSK 455
Cdd:cd00653 325 ELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIE---------RPYRI 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 456 flnsfeqesflvsfenliprkqsflnkystsitfekgeIKSKTnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGA 535
Cdd:cd00653 391 --------------------------------------VEKEV----THIEISPSQILSVAASLIPFPEHNQSPRNLYQS 428
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 536 RMQTQAVPLIYRNKPYIltgfesiIASKTSNLLRAYQEGVITKvtsykivLIDLFNREityylqkykktnqgtfihQLPi 615
Cdd:cd00653 429 NMQKQAVGTPALNQQYR-------MDTKLYLLLYPQKPLVGTG-------IEEYIAFG------------------ELP- 475
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 616 vwpgervlSGQlltenqdisdsefNI--------GNNLNvlygsyygyeyeDSLIISQKVLYKNIFTSIHFDIYEIKYSK 687
Cdd:cd00653 476 --------LGQ-------------NAivavmsysGYNFE------------DAIIINKSSVDRGFFRSIHYKKYEIELRK 522
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 688 YPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKISVSNLTLEDSPFselifslfGTKLRQLQDKSISV 767
Cdd:cd00653 523 TKNGPEEITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTPIF--------GEKARDVRDTSLKY 594
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 768 PIGNSGRVIKTELFAVTNKAtstygQNYLTLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITG 847
Cdd:cd00653 595 PGGEKGIVDDVKIFSRELND-----GGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILN 669
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 848 PLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnNLNNNYTKTYLYTSLQSLKyytgnKSLLNPYipGKLLLRDGRT 927
Cdd:cd00653 670 PHGFPSRMTIGQLLESLLGKAGALLGKF---------GDATPFDGAEEEDISELLG-----EAGLNYY--GKEVLYDGRT 733
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 928 GYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIkgrgkgggqrfgEMEVWALEAFGASYTLRELLTSKSDD 1007
Cdd:cd00653 734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLkgrsrgggqrfgEMERDALIAHGAAYLLQERLTIKSDD 813
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|.
gi 1833819269 1008 LISRNNLQEYLL----------NNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:cd00653 814 VVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPR 864
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
273-1065 |
2.56e-101 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 352.30 E-value: 2.56e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 273 QDLISILDFLLDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEYILPnKLFKILnllfKSKFITSSLLIENL--KESFNK 350
Cdd:PRK09603 435 EDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLV-KMQKTI----KDKLTTMSGAFDSLmpHDLVNS 509
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 351 NKIS--IKELLTVNPLIQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVAL 428
Cdd:PRK09603 510 KMITstIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTL 589
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 429 ASNARINKEGSIETlihPNKKL-----RSYSKFLNSFEQESFLVS------------FENLIPrkqsflnkystsiTFEK 491
Cdd:PRK09603 590 STFTRVNDLGFIEA---PYKKVvdgkvVGETIYLTAIQEDSHIIApastpideegniLGDLIE-------------TRVE 653
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 492 GEI----KSKTNISDtyykINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNL 567
Cdd:PRK09603 654 GEIvlneKSKVTLMD----LSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGA 729
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 568 LRAYQEGVITKVTSYKIVLIDLFNREI---TYYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNN 644
Cdd:PRK09603 730 IKANRAGVVEKIDSKNIYILGEGKEEAyidAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKN 809
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 645 LNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDTPEYsTLDLPKRTSYQKRHLDKLGIITEGSKVL 724
Cdd:PRK09603 810 VRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEF-TADIPDVKEEALAHLDESGIVKVGTYVS 888
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 725 DGDILISKISVSNlTLEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELF----------------------- 781
Cdd:PRK09603 889 AGMILVGKTSPKG-EIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFtkkgyekdarvlsayeeekakld 967
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 782 -------------------------------------------------AVTNKAT-------------STYGQ---NYL 796
Cdd:PRK09603 968 mehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiASINRFTlaslvkkyskevqNHYEItknNFL 1047
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 797 T-----------------------------LRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITG 847
Cdd:PRK09603 1048 EqkkvlgeeheeklsilekddilpngvikkVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLN 1127
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 848 PLGVPSRMNLGQLFESLFGY---------NCVLKDK--------RLLINSLLNNNLNNNYTKTYLYTSLQS---LKYYTG 907
Cdd:PRK09603 1128 PLGVPSRMNIGQILEMHLGLvgkefgkqiASMLEDKtkdfakelRAKMLEIANAINEKDPLTIHALENCSDeelLEYAKD 1207
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 908 NKSLLNPYIP----------------------GKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEIT 965
Cdd:PRK09603 1208 WSKGVKMAIPvfegisqekfyklfelakiamdGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVT 1287
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 966 QQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRNNLQEYLLNNTPLEPNYLPEALKLLIRELHGLSL 1045
Cdd:PRK09603 1288 HQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLAL 1367
|
970 980
....*....|....*....|
gi 1833819269 1046 NLEGFMVTDLLDGKLLPLNI 1065
Cdd:PRK09603 1368 DINIFGDDVDEDGAPKPIVI 1387
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
203-1048 |
9.45e-95 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 332.74 E-value: 9.45e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 203 EIFKNFYYFNSKEDIQELEKIKtllnmLNPELNLKYLKNklnfsrhLTSLKNslisrtgnflessfailgQDLISILDFL 282
Cdd:PRK14844 404 EFFRNLFFSPEYYDLSNIGRLK-----LNSYLGLNYDED-------LTVLTH------------------EDIIEIVRKI 453
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 283 LDLKFKKRTLNDLDHFGNRKVESLGHLISAHLEY--------ILPNKLFKILNLLFKSKFITSSLLIENLKESFNKNKIS 354
Cdd:PRK14844 454 VLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTgllkleraVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLS 533
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 355 ikelltvnpliQYLEEVNSVSELMHKVRISSIGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARI 434
Cdd:PRK14844 534 -----------QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARI 602
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 435 NKEGSIETLIHP--NKKLRSYSKFLNSFEQESFLVSFENL-IPRKQSFLN-----KYSTSITfekgeIKSKTNISdtYYK 506
Cdd:PRK14844 603 NKYGFIESPYRKvvNRVVTDQIEYLSAIDEGLYYIADTSAkLDENNCFVDdmlycRYAGSFV-----MVSSDQVS--YID 675
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 507 INPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNKPYILTGFESIIASKTSNLLRAYQEGVITKVTSYKIVl 586
Cdd:PRK14844 676 VSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIV- 754
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 587 IDLFNREIT-------YYLQKYKKTNQGTFIHQLPIVWPGERVLSGQLLTENQDISDSEFNIGNNLNVLYGSYYGYEYED 659
Cdd:PRK14844 755 IRAFDKERVnyldvdiYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFED 834
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 660 SLIISQKVLYKNIFTSIHFDIYEIKYSKYPIDTpEYSTLDLPKRTSYQKRHLDKLGIITEGSKVLDGDILISKISVSNlT 739
Cdd:PRK14844 835 SIIISSEVVKKDLFTSIHIEEFECVVHDTPLGS-EKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTPKP-S 912
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 740 LEDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELF-------------------------------------- 781
Cdd:PRK14844 913 LSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFtrrgveenerallikqkeindfekerdyiinvtseyfy 992
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 782 -----------------------------AVTNKATSTYGQNY---------------------------------LTLR 799
Cdd:PRK14844 993 delkkllinsgsqdrekfdsiereqwwgiGLKNQSISEQVKSLkkdfdekvshaiaqfkrkveklhegydlpqgvsMSVK 1072
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 800 VFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNC---------- 869
Cdd:PRK14844 1073 VFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACkklgekvgni 1152
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 870 -----------------------------VLKDKRLLINSLLNNNLNNNYT--------------KTYL------YTSLQ 900
Cdd:PRK14844 1153 ldeinkiksafckgirslnddnftkfaaaYLDNKKIENIDDDEITASVLNTpnknalndelnelvENYLnscksaYSNLR 1232
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 901 S----LKYYTGNKSLLNPY------------------IP--------------------------GKLLLRDGRTGYRLK 932
Cdd:PRK14844 1233 NflieVYSCGSNVSICNNIrdisdnnliefarklrdgIPvaapvfegpkdeqiaklfelagldnsGQAVLYDGCSGEKFD 1312
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 933 GGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSDDLISRN 1012
Cdd:PRK14844 1313 RKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRV 1392
|
1050 1060 1070
....*....|....*....|....*....|....*.
gi 1833819269 1013 NLQEYLLNNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:PRK14844 1393 KIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVD 1428
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
570-969 |
2.21e-82 |
|
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: 272.48 E-value: 2.21e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 570 AYQEGVITKVTSYKIVLIDLFNREI--TYYLQKYKKTNQGTF---IHQLPIVWPGeRVLSGQLltenqdisdSEFNIGNN 644
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAmgIYTLNKFYRSDQNTYvlcYPQKPLVKTG-AVEAGGF---------GELPLGQN 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 645 LNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKysKYPIDTPEYSTLDLPKRTSYQKRHLDKLGIITEGSKVL 724
Cdd:pfam00562 72 AIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIEAR--KTKLGPIEEITRDIPNVSEEALKKLDEDGIVRVGAEVK 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 725 DGDILISKISvsnltleDSPFSELIFSLFGTKLRQLQDKSISVPIGNSGRVIKTELFAVTNKatstygqNYLTLRVFVAK 804
Cdd:pfam00562 150 PGDILVGKVG-------PTELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFELPPG-------GIKMVKVYIRQ 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 805 QRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRLLINSLLNN 884
Cdd:pfam00562 216 KRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDGA 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 885 NLNNNYTKTYLYtslqslkyytgnKSLLNPYipGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEI 964
Cdd:pfam00562 296 STEVEDIGELLE------------KAGYNYY--GKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLL 361
|
....*
gi 1833819269 965 TQQPI 969
Cdd:pfam00562 362 TRQPL 366
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
659-1006 |
8.89e-41 |
|
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: 159.81 E-value: 8.89e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 659 DSLIISQKVLYKNIFTSIHFDIYEIKYSKYP------IDTPEYSTLDLPKRTSYqkRHLDKLGIITEGSKVLDGDILISK 732
Cdd:TIGR03670 215 DALIMNKASIERGLARSTFFRTYEAEERRYPggqedrFEIPEPDVRGYRGEEAY--KHLDEDGIVYPEVEVKGGDVLIGK 292
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 733 ISVSNLtLEDspfseliFSLFGTKLRQLQDKSISVPIGNSG---RVIKTElfavtnkatstYGQNYLTLRVFVAKQRMLQ 809
Cdd:TIGR03670 293 TSPPRF-LEE-------LREFGLVTERRRDTSVTVRHGEKGivdKVIITE-----------TEEGNKLVKVRVRDLRIPE 353
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 810 IGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRLLINSllnnnlnnn 889
Cdd:TIGR03670 354 LGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTP--------- 424
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 890 ytktYLYTSLQSLKyytgnKSLL-NPYIP-GKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQ 967
Cdd:TIGR03670 425 ----FEGEPEEELR-----KELLkLGFKPdGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQ 495
|
330 340 350
....*....|....*....|....*....|....*....
gi 1833819269 968 PIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSD 1006
Cdd:TIGR03670 496 PTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 534
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
282-1006 |
1.28e-39 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 159.74 E-value: 1.28e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 282 LLDLKFKKRTLNDLDHFGNRKVESLGHLISAhleyilpnklfkilnlLFKSKFITsslLIENLKESFNKNKISiKELLTV 361
Cdd:PRK08565 314 LLELYLGRREPDDKDHYANKRLRLAGDLLAE----------------LFRVAFKQ---LVKDLKYQLEKSYAR-GRKLDL 373
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 362 NPLI--------------------------QYLEEVNSVSELMHKVRISSigpgSLTQNQAGVAVREVRPSQLGKICILD 415
Cdd:PRK08565 374 RAIVrpdiiterirhalatgnwvggrtgvsQLLDRTNYLSTLSHLRRVVS----PLSRGQPHFEARDLHGTQWGRICPFE 449
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 416 TNEGPSSGLVVALASNARIN---KEGSIETLI-------------------------------HPN--------KKLRSY 453
Cdd:PRK08565 450 TPEGPNCGLVKNLALMAQISvgvDEEEVEEILyelgvvpveeareeeyiswsrvylngrligyHPDgeelaekiRELRRS 529
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 454 SK--------FLNSFEQESFLV----------------------------------SFENLIPR-KQSFL------NKYs 484
Cdd:PRK08565 530 GKisdevnvaYIETGEINEVYVncdsgrvrrplivvengkpkltrehveklkkgelTFDDLVKMgVIEYLdaeeeeNAY- 608
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 485 tsITFEKGEIKSKTnisdTYYKINPSQLLSYTENLIPFLFYNDPTRCLMGARMQTQAVPLIYRNkpyiltgfesiiaskt 564
Cdd:PRK08565 609 --VALDPEDLTPEH----THLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAAN---------------- 666
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 565 snllraYQegvitkvtsykivlidlfnreityylqkYKKTNQGTFIH--QLPIVwpGERVLSGqlltenqdISDSEFNIG 642
Cdd:PRK08565 667 ------FR----------------------------IRTDTRGHLLHypQRPLV--QTRALEI--------IGYNDRPAG 702
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 643 NNLNVLYGSYYGYEYEDSLIISQKVLYKNIFTSIHFDIYEIKYSKYP------IDTPEYSTLDLPKRTSYqkRHLDKLGI 716
Cdd:PRK08565 703 QNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEERKYPggqedkIEIPEPNVRGYRGEEYY--RKLDEDGI 780
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 717 ITEGSKVLDGDILISKISvsnltledsP--FSELiFSLFGTKLRQLQDKSISVPIGNSG---RVIKTElfavtnkatsTY 791
Cdd:PRK08565 781 VSPEVEVKGGDVLIGKTS---------PprFLEE-LEELSLGLQERRDTSVTVRHGEKGivdTVLITE----------SP 840
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 792 GQNYLtLRVFVAKQRMLQIGDKLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVL 871
Cdd:PRK08565 841 EGNKL-VKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAAL 919
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 872 KDKRLlinsllnnnlnnnyTKTYLY-TSLQSLKyytgnKSLL-NPYIP-GKLLLRDGRTGYRLKGGAFMGTLYYSKLIHM 948
Cdd:PRK08565 920 EGRFV--------------DATPFYgEPEEELR-----KELLkLGYKPdGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHM 980
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*...
gi 1833819269 949 VKDKVHYRTFGPYTEITQQPIKGRGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSD 1006
Cdd:PRK08565 981 VADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD 1038
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
659-1006 |
8.24e-32 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 132.39 E-value: 8.24e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 659 DSLIISQKVLYKNIFTSIHFDIYEIKYSKYP------IDTPEYSTLDLPKRTSYqkRHLDKLGIITEGSKVLDGDILISK 732
Cdd:PRK07225 221 DALIMNKASIERGLGRSHFFRTYEGEERRYPggqedrFEIPDKDVRGYRGEEAY--RHLDEDGLVNPETEVKEGDVLIGK 298
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 733 ISVSNLtLEDspfseliFSLFGTKLRQLQDKSISVPIGNSGRVIKTELfavtnkaTSTYGQNYLTlRVFVAKQRMLQIGD 812
Cdd:PRK07225 299 TSPPRF-LEE-------PDDFGISPEKRRETSVTMRSGEEGIVDTVIL-------TETEEGSRLV-KVRVRDLRIPELGD 362
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 813 KLCGRHGNKGVISNIAEEAELPYNVMSQYPDIITGPLGVPSRMNLGQLFESLFGYNCVLKDKRllinsllnnNLNNNYTK 892
Cdd:PRK07225 363 KFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRR---------VDGTAFSG 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 893 TyLYTSLQ-SLKYYtGNKSllnpyiPGKLLLRDGRTGYRLKGGAFMGTLYYSKLIHMVKDKVHYRTFGPYTEITQQPIKG 971
Cdd:PRK07225 434 E-DEEDLReALEKL-GFEH------TGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEG 505
|
330 340 350
....*....|....*....|....*....|....*
gi 1833819269 972 RGKGGGQRFGEMEVWALEAFGASYTLRELLTSKSD 1006
Cdd:PRK07225 506 RAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD 540
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
982-1048 |
6.49e-17 |
|
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: 76.47 E-value: 6.49e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1833819269 982 EMEVWALEAFGASYTLRELLTSKSD----DLISRNNLQEYLL------NNTPLEPNYLPEALKLLIRELHGLSLNLE 1048
Cdd:pfam04560 7 EMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAYNkcpickGETDISPGYIPESFKLLFQELQSLGIDPR 83
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
366-433 |
1.91e-14 |
|
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: 68.71 E-value: 1.91e-14
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1833819269 366 QYLEEVNSVSELMHKVRISSiGPGSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNAR 433
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
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|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
109-444 |
9.59e-07 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 52.64 E-value: 9.59e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 109 DLQGNFILNGMKRGLVS-KMVRQNGVYFNLRRKYGEDIYSAQlILNERSKY----FIELFKEGIFiYNKF---NKKINLI 180
Cdd:PRK09606 143 DPGGYFIVNGSERVLMTlEDLAPNKILVEKDERYGDRIEVAK-VFSQRRGYralvTVERNRDGLL-EVSFpsvPGSIPFV 220
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 181 NFLHFIGL--NNSTISSISRYgtTEIFKNFYyfnskEDIQELEkIKTllnmlnPELNLKYLKNKL--------NFSRHLT 250
Cdd:PRK09606 221 ILMRALGLetDEEIVEAVSDD--PEIVKFML-----ENLEEAE-VDT------QEEALEYIGKRVapgqtkeyRIKRAEY 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 251 SLKNSLISRTGNflESSfailgqDLISILDFL-------LDLKFKKRTLNDLDHFGNRKVESLGHLISAhleyilpnklf 323
Cdd:PRK09606 287 VIDRYLLPHLGV--EPE------VRRAKAHYLgrmaeacFELALGRREEDDKDHYANKRLKLAGDLMED----------- 347
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250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 324 kilnlLFKSKFitsSLLIENLKESFNKNKISIKEL----------LTVN---PLI------------QYLEEVNSVSELM 378
Cdd:PRK09606 348 -----LFRVAF---NRLARDVKYQLERANMRNRELsiktavrsdvLTERlehAMAtgnwvggrtgvsQLLDRTDYMATLS 419
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1833819269 379 HKVRISSigpgSLTQNQAGVAVREVRPSQLGKICILDTNEGPSSGLVVALASNARINKEGSIETLI 444
Cdd:PRK09606 420 HLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEISTGEDEEEVK 481
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| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
129-304 |
4.74e-05 |
|
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: 45.42 E-value: 4.74e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 129 RQNGVYFNlRRKYGEDI---YSAQLILNeRSKYFIELFKEGIFIYNKFNK--KINLINFLHFIGLNNST--ISSISRYGT 201
Cdd:pfam04561 1 RSNGIYVE-KELDKNGIiatYTSSLISN-RGSWLKLEIDGKTLIWSRPSKkrKIPIVIFLKALGLVSDReiLDRLCYDFN 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1833819269 202 T---------EIFKNFYYFNSKEDIQELEKIKTLLNMLNPEL----NLKYLKN-KLNFSRHLTSlknslisrtgNFLESS 267
Cdd:pfam04561 79 DpqmlellkpELEEAENIYTQEEALDYIGKGFALRRGEEPRLqrarEILYSRDpKYNLNKHLGL----------NEPFEN 148
|
170 180 190
....*....|....*....|....*....|....*..
gi 1833819269 268 FAILGQDLISILDFLLDLKFKKRTLNDLDHFGNRKVE 304
Cdd:pfam04561 149 ERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
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