|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
6-1151 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2218.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 6 VQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL-------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDL 78
Cdd:PRK00405 4 SYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDV 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 79 EESKNRDATYAAPLRVKVRLIIKETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDK--NGRV 156
Cdd:PRK00405 84 EECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 157 NYDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYsTDQEIIELIGD----------------------- 213
Cdd:PRK00405 164 LYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEkeefgkeievpveyllgkvlaed 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 214 ----------------------NEYLRNTLEKDSTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVG 271
Cdd:PRK00405 243 ivdeetgevlaeandeiteeldGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVG 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 272 RYKANKKLHLKhrlfnqklaepivntetgeivaeegtvldrrkldeimdvletnanaqvyelpnsiidepveiqsikvyv 351
Cdd:PRK00405 323 RYKLNKKLGLD--------------------------------------------------------------------- 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 352 pnddeertttvignafPDSEVKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVR 431
Cdd:PRK00405 334 ----------------EDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVR 397
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 432 ERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYG 511
Cdd:PRK00405 398 ERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 512 RMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEI 591
Cdd:PRK00405 478 RICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKV--VDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 592 VCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGMEHVAARDSGA 671
Cdd:PRK00405 556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 672 AVISKYRGRVEHVQSSEILVRrlVEENGQEVDGTlDRYPLAKFKRSNSGTCYNQRPIIAKGDIVEKGEILADGPSMELGE 751
Cdd:PRK00405 636 VVVAKRDGVVEYVDASRIVVR--VEELDPGEDGV-DIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGE 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 752 MALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYV 831
Cdd:PRK00405 713 LALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRI 792
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 832 GAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDSLSPGVNQLVRV 911
Cdd:PRK00405 793 GAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKV 872
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 912 YIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPV 991
Cdd:PRK00405 873 YIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPV 952
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 992 FDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFG 1071
Cdd:PRK00405 953 FDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1032
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1072 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNE 1151
Cdd:PRK00405 1033 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
14-1147 |
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: 1988.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 14 RRNYARISEVLELPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLR 93
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLTYAAPLY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 94 VKVRLIIKETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDKNGRVNYDATVIPNRGAWLEYE 173
Cdd:COG0085 81 VKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 174 TDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQEIIELIGDN---EYLRNTLEKDSTENTEQALLEIYERLRPGEPPTVEN 250
Cdd:COG0085 161 TDKDGTIYVRIDRKRKIPVTVLLRALGLETDEEILEAFGDDpiqEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIER 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 251 AKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivntetgeivaeegtvldrrkldeimdvletnanaqv 330
Cdd:COG0085 241 AEQLLDNLFFDPKRYDLAHVGRYKINKKLGLD------------------------------------------------ 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 331 yelpnsiidepveiqsikvyvpnddeertttvignafPDSEVKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRS 410
Cdd:COG0085 273 -------------------------------------VPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRL 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 411 VGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGP 490
Cdd:COG0085 316 VGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGP 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 491 GGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiETNTITDQIDYLTADEEDS 570
Cdd:COG0085 396 GGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKV--ENGKVTDEIEYLTADEEEN 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 571 YVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLL 650
Cdd:COG0085 474 YYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLL 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 651 NPESPfvgtgmehvaardsgaaviskyrgrvehvqsseilvrrlveengqevdgtLDRYPLAKFKRSNSGTCYNQRPIIA 730
Cdd:COG0085 554 RPEAP--------------------------------------------------LLHYPLQKFQRSNQGTCINQRPIVR 583
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 731 KGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR 810
Cdd:COG0085 584 VGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITR 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 811 DIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVK 890
Cdd:COG0085 664 DIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVK 743
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 891 VFNREEGDDsLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQ 970
Cdd:COG0085 744 VFSREEGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQ 822
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 971 VLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHA 1050
Cdd:COG0085 823 VLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHA 902
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1051 RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRV 1130
Cdd:COG0085 903 RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKV 982
|
1130
....*....|....*..
gi 504427648 1131 LMKELQSLGLDVKVMDE 1147
Cdd:COG0085 983 LLKELQSLGLDVEVLSE 999
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1144 |
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: 1917.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 10 RHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLE 79
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 80 ESKNRDATYAAPLRVKVRLIIKE---TGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLD--KNG 154
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 155 RVNYDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQEIIELIGDNEYLRNTLEKDSTENTEQALL 234
Cdd:TIGR02013 161 KVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNSEEEALV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 235 EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivntetgeiVAEEGTVLdrrk 314
Cdd:TIGR02013 241 EIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLD--------------------VPESIGVL---- 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 315 ldeimdvletnanaqvyelpnsiidepveiqsikvyvpnddeertttvignafpdsevkciTPADIVASMSYFFNLLHGI 394
Cdd:TIGR02013 297 -------------------------------------------------------------TKEDIIATIKYLIKLRNGK 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 395 GYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474
Cdd:TIGR02013 316 GEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTN 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIETN 554
Cdd:TIGR02013 396 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKV 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 555 TITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSN 634
Cdd:TIGR02013 476 VVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDAN 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 635 RALMGANMQRQAVPLLNPESPFVGTGMEHVAARDSGAAVISKYRGRVEHVQSSEILVRRlvEENGQEVDGTLDRYPLAKF 714
Cdd:TIGR02013 556 RALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY--DEDEEEPDGGIDIYRLLKY 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 715 KRSNSGTCYNQRPIIAKGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEY 794
Cdd:TIGR02013 634 QRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 795 ESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDT 874
Cdd:TIGR02013 714 EVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDT 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 875 SLRVPHGAGGIVLDVKVFNREEGDDsLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPID 954
Cdd:TIGR02013 794 SLRVPPGVEGTVIDVKVFSREQGDE-LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVD 872
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 955 IMLNPLGVPSRMNIGQVLELHLGMAAKNLG---IHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRIS 1031
Cdd:TIGR02013 873 IVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVT 952
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1032 VGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYE 1111
Cdd:TIGR02013 953 VGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYE 1032
|
1130 1140 1150
....*....|....*....|....*....|...
gi 504427648 1112 AIVKGENISRPSVPESFRVLMKELQSLGLDVKV 1144
Cdd:TIGR02013 1033 AIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
29-1145 |
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: 988.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 29 LIEIQTKSYDWFLKEGLLEMFRDISPIEDFT--GNLSLEFVDYRLGEPKYDL---------EESKNRDATYAAPLRVKVR 97
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 98 LIIKETGEVKDQEVFMGDFPLMTE------------------------TGTFVINGAERVIVSQLVRSPSVYFNEklDKN 153
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 154 GRVNYDATVIPN----RGAWLEYETDA-KDVVYVRIDRTRKlpltvllralgystdqeiieligdneylrntlekdsten 228
Cdd:cd00653 159 GKRIYTKTSIPSyspyRGSWLEVKSDKkKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 229 tEQALLEIYERLRpgepptvenaksllysrffdpkrydlasvgrykankklhlkhrlfnqklaepivntetgeivaeegt 308
Cdd:cd00653 200 -EEALKYIGKRFE------------------------------------------------------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 309 vldrrkldeimdvletnanaqvyelpnsiidepveiqsikvyvpnddeertttvignafpdsevkcitpaDIVASMSYFF 388
Cdd:cd00653 212 ----------------------------------------------------------------------DLIYMIRKLI 221
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 389 NLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS--ITPQQLINIRPVIASIKEFFGSSQ- 465
Cdd:cd00653 222 LLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNw 301
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 466 -----------LSQFMDQANPLAELTHKRRLSAlgpGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534
Cdd:cd00653 302 gskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMA 378
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 535 RVNefGFIETPYRKVDIETntitdqidyltadeedsyvvaqansrldengrfiddeivcrfrgnnttmakekmDYMDVSP 614
Cdd:cd00653 379 RIS--GRIERPYRIVEKEV------------------------------------------------------THIEISP 402
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 615 KQVVSAATACIPFLENDDSNRALMGANMQRQAVP----------------LLNPESPFVGTGMEHVAARDsgaaviskyr 678
Cdd:cd00653 403 SQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG---------- 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 679 grvehvqsseilvrrlveengqevdgtldryplakfkrsnsgtcynqrpiiakgdivekgeiladgpsmelgEMALGRNV 758
Cdd:cd00653 473 ------------------------------------------------------------------------ELPLGQNA 480
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 759 VVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR-DIPNVSENALKNLDDRGIVYVGAEVKD 837
Cdd:cd00653 481 IVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEP 560
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 838 GDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREegddsLSPGVNQLVRVYIVQKR 917
Cdd:cd00653 561 GDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE-----LNDGGNKLVKVYIRQKR 628
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 918 KIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGAND 997
Cdd:cd00653 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEE 708
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 998 DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1077
Cdd:cd00653 709 EDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504427648 1078 MEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIV----------KGENISRPSVPESFRVLMKELQSLGLDVKVM 1145
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
679-1069 |
0e+00 |
|
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: 565.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 679 GRVEHVQSSEILVRRlveengQEVDGTLDRYPLAKFKRSNSGT---CYNQRPIIAKGdIVEKGEiladgpsmeLGEMALG 755
Cdd:pfam00562 6 PFVDHNQSPRNTYQC------AMGKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGELPLG 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 756 RNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYEseARDTKLGP-EEITRDIPNVSENALKNLDDRGIVYVGAE 834
Cdd:pfam00562 70 QNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAE 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 835 VKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFnreegddSLSPGVNQLVRVYIV 914
Cdd:pfam00562 148 VKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF-------ELPPGGIKMVKVYIR 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 915 QKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDG 994
Cdd:pfam00562 215 QKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDG 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504427648 995 AND--DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQ 1069
Cdd:pfam00562 295 ASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
6-1151 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2218.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 6 VQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL-------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDL 78
Cdd:PRK00405 4 SYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPKYDV 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 79 EESKNRDATYAAPLRVKVRLIIKETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDK--NGRV 156
Cdd:PRK00405 84 EECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsSGKL 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 157 NYDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYsTDQEIIELIGD----------------------- 213
Cdd:PRK00405 164 LYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEkeefgkeievpveyllgkvlaed 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 214 ----------------------NEYLRNTLEKDSTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVG 271
Cdd:PRK00405 243 ivdeetgevlaeandeiteeldGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVG 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 272 RYKANKKLHLKhrlfnqklaepivntetgeivaeegtvldrrkldeimdvletnanaqvyelpnsiidepveiqsikvyv 351
Cdd:PRK00405 323 RYKLNKKLGLD--------------------------------------------------------------------- 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 352 pnddeertttvignafPDSEVKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVR 431
Cdd:PRK00405 334 ----------------EDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVR 397
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 432 ERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYG 511
Cdd:PRK00405 398 ERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYG 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 512 RMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiETNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEI 591
Cdd:PRK00405 478 RICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKV--VDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 592 VCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGMEHVAARDSGA 671
Cdd:PRK00405 556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 672 AVISKYRGRVEHVQSSEILVRrlVEENGQEVDGTlDRYPLAKFKRSNSGTCYNQRPIIAKGDIVEKGEILADGPSMELGE 751
Cdd:PRK00405 636 VVVAKRDGVVEYVDASRIVVR--VEELDPGEDGV-DIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGE 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 752 MALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYV 831
Cdd:PRK00405 713 LALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRI 792
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 832 GAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDSLSPGVNQLVRV 911
Cdd:PRK00405 793 GAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNKLVKV 872
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 912 YIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPV 991
Cdd:PRK00405 873 YIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKFATPV 952
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 992 FDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFG 1071
Cdd:PRK00405 953 FDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFG 1032
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1072 GQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNE 1151
Cdd:PRK00405 1033 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDEDGNE 1112
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
14-1147 |
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: 1988.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 14 RRNYARISEVLELPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLR 93
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLTYAAPLY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 94 VKVRLIIKETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDKNGRVNYDATVIPNRGAWLEYE 173
Cdd:COG0085 81 VKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 174 TDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQEIIELIGDN---EYLRNTLEKDSTENTEQALLEIYERLRPGEPPTVEN 250
Cdd:COG0085 161 TDKDGTIYVRIDRKRKIPVTVLLRALGLETDEEILEAFGDDpiqEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIER 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 251 AKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivntetgeivaeegtvldrrkldeimdvletnanaqv 330
Cdd:COG0085 241 AEQLLDNLFFDPKRYDLAHVGRYKINKKLGLD------------------------------------------------ 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 331 yelpnsiidepveiqsikvyvpnddeertttvignafPDSEVKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRS 410
Cdd:COG0085 273 -------------------------------------VPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRL 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 411 VGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGP 490
Cdd:COG0085 316 VGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGP 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 491 GGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiETNTITDQIDYLTADEEDS 570
Cdd:COG0085 396 GGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKV--ENGKVTDEIEYLTADEEEN 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 571 YVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLL 650
Cdd:COG0085 474 YYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLL 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 651 NPESPfvgtgmehvaardsgaaviskyrgrvehvqsseilvrrlveengqevdgtLDRYPLAKFKRSNSGTCYNQRPIIA 730
Cdd:COG0085 554 RPEAP--------------------------------------------------LLHYPLQKFQRSNQGTCINQRPIVR 583
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 731 KGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR 810
Cdd:COG0085 584 VGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITR 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 811 DIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVK 890
Cdd:COG0085 664 DIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVK 743
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 891 VFNREEGDDsLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQ 970
Cdd:COG0085 744 VFSREEGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQ 822
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 971 VLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHA 1050
Cdd:COG0085 823 VLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHA 902
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1051 RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRV 1130
Cdd:COG0085 903 RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKV 982
|
1130
....*....|....*..
gi 504427648 1131 LMKELQSLGLDVKVMDE 1147
Cdd:COG0085 983 LLKELQSLGLDVEVLSE 999
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1144 |
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: 1917.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 10 RHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLE 79
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 80 ESKNRDATYAAPLRVKVRLIIKE---TGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLD--KNG 154
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 155 RVNYDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQEIIELIGDNEYLRNTLEKDSTENTEQALL 234
Cdd:TIGR02013 161 KVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNSEEEALV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 235 EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivntetgeiVAEEGTVLdrrk 314
Cdd:TIGR02013 241 EIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLD--------------------VPESIGVL---- 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 315 ldeimdvletnanaqvyelpnsiidepveiqsikvyvpnddeertttvignafpdsevkciTPADIVASMSYFFNLLHGI 394
Cdd:TIGR02013 297 -------------------------------------------------------------TKEDIIATIKYLIKLRNGK 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 395 GYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474
Cdd:TIGR02013 316 GEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTN 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIETN 554
Cdd:TIGR02013 396 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKV 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 555 TITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSN 634
Cdd:TIGR02013 476 VVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDAN 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 635 RALMGANMQRQAVPLLNPESPFVGTGMEHVAARDSGAAVISKYRGRVEHVQSSEILVRRlvEENGQEVDGTLDRYPLAKF 714
Cdd:TIGR02013 556 RALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY--DEDEEEPDGGIDIYRLLKY 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 715 KRSNSGTCYNQRPIIAKGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEY 794
Cdd:TIGR02013 634 QRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 795 ESEARDTKLGPEEITRDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDT 874
Cdd:TIGR02013 714 EVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDT 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 875 SLRVPHGAGGIVLDVKVFNREEGDDsLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPID 954
Cdd:TIGR02013 794 SLRVPPGVEGTVIDVKVFSREQGDE-LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVD 872
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 955 IMLNPLGVPSRMNIGQVLELHLGMAAKNLG---IHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRIS 1031
Cdd:TIGR02013 873 IVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVT 952
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1032 VGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYE 1111
Cdd:TIGR02013 953 VGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYE 1032
|
1130 1140 1150
....*....|....*....|....*....|...
gi 504427648 1112 AIVKGENISRPSVPESFRVLMKELQSLGLDVKV 1144
Cdd:TIGR02013 1033 AIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
26-1144 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1251.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 26 LPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFV--DYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKET 103
Cdd:CHL00207 7 LPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFgkNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFINLKT 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 104 GEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDKNGRVNYDATVIPNRGAWLEYETDAKDVVYVR 183
Cdd:CHL00207 87 NKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIR 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 184 IDRTRKLPLTVLLRALGYsTDQEIIELIGDN---EYLRNTLEKDSTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFF 260
Cdd:CHL00207 167 IDKNRKKPLIIFLKALGL-TDQDIYSRLTKSeflKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFF 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 261 DPKRYDLASVGRYKANKKLHLKhrlfnqklaepivntetgeivaeegtvldrrkldeimdvletnanaqvyeLPNSIide 340
Cdd:CHL00207 246 DPKNYDLGKVGRYKINNKLNLN--------------------------------------------------IPERV--- 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 341 pveiqsikvyvpnddeertttvignafpdsevKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFR 420
Cdd:CHL00207 273 --------------------------------RNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFR 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 421 IGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQM 500
Cdd:CHL00207 321 IGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISF 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 501 EVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDIETNTITDQIDYLTADEEDSYVVAQANSRL 580
Cdd:CHL00207 401 AVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIAPNDINL 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 581 DENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTG 660
Cdd:CHL00207 481 NKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTG 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 661 MEHVAARDSGAAVISKYRGRVEHVQSSEILVRrlvEENGQEVDgtldrYPLAKFKRSNSGTCYNQRPIIAKGDIVEKGEI 740
Cdd:CHL00207 561 YEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ---DDNNRYIH-----YYLQKYQRSNQNTCINYRPIVWVGEKINIGQI 632
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 741 LADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENAL 820
Cdd:CHL00207 633 LADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSL 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 821 KNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGdDS 900
Cdd:CHL00207 713 KNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKG-DE 791
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 901 LSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAA 980
Cdd:CHL00207 792 LKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAG 871
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 981 KNLGIHVASPVFDGANDDD-----VWSTIEEAGMARD----------GKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVD 1045
Cdd:CHL00207 872 DNLNKRFKILPFDEMYGSEysrilINNKLNQASIKNNeywlfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVD 951
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1046 DKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVP 1125
Cdd:CHL00207 952 DKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTP 1031
|
1130
....*....|....*....
gi 504427648 1126 ESFRVLMKELQSLGLDVKV 1144
Cdd:CHL00207 1032 ESFKVLMRELQSLGLDIEA 1050
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
26-1143 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1198.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 26 LPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFV--DYRLGEPKYdleesKNRDA-----TYAAPLRVKVRL 98
Cdd:CHL00001 12 IPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFveTYQLVEPLI-----KERDAvyeslTYSSELYVPAGL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 99 IIKETGEVKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLDKNGRVNYDATVIPNRGAWLEYETDAKD 178
Cdd:CHL00001 87 IWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 179 VVYVRIDRTRKLPLTVLLRALGySTDQEIIELIGDNEYLRNTL---EKDSTENTEQALLEIYERL--RPGEPPTVENAKS 253
Cdd:CHL00001 167 RIWARVSRKQKISILVLLSAMG-LNLREILDNVCYPEIFLSFLndkEKKKIGSKENAILEFYQQFacVGGDPVFSESLCK 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 254 LLYSRFFDpKRYDLASVGRYKANKKLHLKhrlfnqklaepivntetgeiVAEEGTVLdrrkldeimdvletnanaqvyel 333
Cdd:CHL00001 246 ELQKKFFQ-QRCELGRIGRRNMNRKLNLD--------------------IPENNTFL----------------------- 281
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 334 pnsiidepveiqsikvyvpnddeertttvignafpdsevkciTPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGE 413
Cdd:CHL00001 282 ------------------------------------------LPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVAD 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 414 LLQNQFRIGLSRMERVVRERMS--IQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPG 491
Cdd:CHL00001 320 LLQDQFGLALNRLENAVRGTICgaIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPG 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 492 GLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKvdIETNTITDQIDYLTADEEDSY 571
Cdd:CHL00001 400 GLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYE--ISERSKEERMVYLSPSEDEYY 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 572 VVAQANSrLDENGRFIDDEIV-CRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLL 650
Cdd:CHL00001 478 MIAAGNS-LALNQGIQEEQVVpARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLS 556
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 651 NPESPFVGTGMEHVAARDSGAAVISKYRGRVEHVQSSEILVRrlveengqeVDGTLDRYPLAKFKRSNSGTCYNQRPIIA 730
Cdd:CHL00001 557 RSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILS---------GNGDTLSIPLVMYQRSNKNTCMHQKPQVR 627
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 731 KGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR 810
Cdd:CHL00001 628 RGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITK 707
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 811 DIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTEL--TAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLD 888
Cdd:CHL00001 708 EIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESsyAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVID 787
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 889 VKVFNREEGDDSlSPGVnqlVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNI 968
Cdd:CHL00001 788 VRWIQKKGGSSY-NPET---IHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNV 863
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 969 GQVLELHLGMAAKNLGIHVASPVFDGANDDD-----VWSTIEEAGMARD----------GKTVLYDGRTGEPFDNRISVG 1033
Cdd:CHL00001 864 GQIFECLLGLAGDLLNRHYRIAPFDERYEQEasrklVFSELYEASKQTAnpwvfepeypGKSRLFDGRTGDPFEQPVTIG 943
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1034 VMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAI 1113
Cdd:CHL00001 944 KAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAI 1023
|
1130 1140 1150
....*....|....*....|....*....|.
gi 504427648 1114 VKGENISRP-SVPESFRVLMKELQSLGLDVK 1143
Cdd:CHL00001 1024 ITGGTIPKPeDAPESFRLLVRELRSLALELN 1054
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
10-1151 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1096.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 10 RHRKRRNYARISEVLELPNLIEIQTKSYDWFL------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKN 83
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 84 RDATYAAPLRVKVRLIIKE----TGE------VKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSVYFNEKLD-- 151
Cdd:PRK09603 88 RGITYSIPLKIKVRLILWEkdtkSGEkngikdIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESst 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 152 KNGRVNYDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYSTdQEIIELIgdneylrNTLEKDSTENTEQ 231
Cdd:PRK09603 168 SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQK-QDIIKMF-------YPLVKVRYENDKY 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 232 ALleiyerlrpgePPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLH-LKHR-----------LFNQKLAEPIVNTEt 299
Cdd:PRK09603 240 LI-----------PFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKeLKENhlewveypmdiLLNRHLAEPVMVGK- 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 300 gEIVAEEGTVLDRRKLDEIMD--VLE-TNANAQVYELPNSIID------------------------------------E 340
Cdd:PRK09603 308 -EVLLDMLTQLDKNKLEKIHDlgVQEfVIINDLALGHDASIIHsfsadseslkllkqtekiddenalaairihkvmkpgD 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 341 PVEIQSIKVYVPN---DDEERTTTVIGNA---------FPDSeVKCITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRL 408
Cdd:PRK09603 387 PVTTEVAKQFVKKlffDPERYDLTMVGRMkmnhklglhVPDY-ITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRI 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 409 RSVGELLQNQFRIGLSRMERVVRERMSIQDT--DSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLS 486
Cdd:PRK09603 466 RAVGELLANELHSGLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLS 545
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 487 ALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiETNTITDQIDYLTAD 566
Cdd:PRK09603 546 ALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKV--VDGKVVGETIYLTAI 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 567 EEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQA 646
Cdd:PRK09603 624 QEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQA 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 647 VPLLNPESPFVGTGMEHVAARDSGAAVISKYRGRVEHVQSSEILVRrlveenGQEVDGT-LDRYPLAKFKRSNSGTCYNQ 725
Cdd:PRK09603 704 VPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYIL------GEGKEEAyIDAYSLQKNLRTNQNTSFNQ 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 726 RPIIAKGDIVEKGEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGP 805
Cdd:PRK09603 778 VPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGV 857
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 806 EEITRDIPNVSENALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGI 885
Cdd:PRK09603 858 EEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGT 937
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 886 VLDVKVF---------------------------------NRE------------------------------------- 895
Cdd:PRK09603 938 VIDVKVFtkkgyekdarvlsayeeekakldmehfdrltmlNREellrvssllsqaileepfshngkdykegdqipkeeia 1017
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 896 -----------------------------------------------EGDDSLSPGVNQLVRVYIVQKRKIHVGDKMCGR 928
Cdd:PRK09603 1018 sinrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGR 1097
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 929 HGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNL------------------------- 983
Cdd:PRK09603 1098 HGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFgkqiasmledktkdfakelrakmle 1177
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 984 ---------------------------------GIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRI 1030
Cdd:PRK09603 1178 ianainekdpltihalencsdeelleyakdwskGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERV 1257
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1031 SVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTY 1110
Cdd:PRK09603 1258 NVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAY 1337
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|.
gi 504427648 1111 EAIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDEQDNE 1151
Cdd:PRK09603 1338 RAIAKGEQVGESEIPETFYVLTKELQSLALDINIFGDDVDE 1378
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
14-1182 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 988.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 14 RRNYARISEVLE-LPNLIEIQTKSYDWFL-----KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDAT 87
Cdd:PRK14844 16 RVSYSRSIDLKDsLLDLVKVQKESYDSFTpknkgNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGIT 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 88 YAAPLRVKVRLI-------------IKETGE----------VKDQEVFMGDFPLMTETGTFVINGAERVIVSQLVRSPSV 144
Cdd:PRK14844 96 FSAQVIASIRLVimqdgisldeyksIKESGDhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGV 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 145 YFNEKLDK---NGRVNYDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQ------EIIELIG--- 212
Cdd:PRK14844 176 FFDSDKGKtynSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDildrfyEKIKYIKhkd 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 213 --------------------------------------------DNE--------------------------------- 215
Cdd:PRK14844 256 gwkvpfvpdkfkgvrlpfdlmdvegnvllkanvritsrlakklyDNElkeylvpfdsicglflaedlidsasstkilsag 335
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 216 -------------------------------YLRNTLEKDSTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKR 264
Cdd:PRK14844 336 esikledikklellsideisvlnidnlsvgpYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEY 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 265 YDLASVGRYKANKKLHLkhrlfnqklaepivntetgeivaeegtvldrrkldeimdvletnanaqvyelpnsiidepvei 344
Cdd:PRK14844 416 YDLSNIGRLKLNSYLGL--------------------------------------------------------------- 432
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 345 qsikvyvpNDDEERTTtvignafpdsevkcITPADIVASMSYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLS 424
Cdd:PRK14844 433 --------NYDEDLTV--------------LTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLL 490
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 425 RMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRD 504
Cdd:PRK14844 491 KLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRD 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 505 VHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdiETNTITDQIDYLTADEEDSYVVAQANSRLDENG 584
Cdd:PRK14844 571 VHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKV--VNRVVTDQIEYLSAIDEGLYYIADTSAKLDENN 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 585 RFIDDEIVCRFRGNNTTMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLLNPESPFVGTGMEHV 664
Cdd:PRK14844 649 CFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESF 728
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 665 AARDSGAAVISKYRGRVEHVQSSEILVRRLVEENGQEVDgtLDRYPLAKFKRSNSGTCYNQRPIIAKGDIVEKGEILADG 744
Cdd:PRK14844 729 VASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLD--VDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADG 806
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 745 PSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSENALKNLD 824
Cdd:PRK14844 807 PAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLD 886
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 825 DRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR---------- 894
Cdd:PRK14844 887 DSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRrgveeneral 966
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 --------------------------------------------------------------------------------
Cdd:PRK14844 967 likqkeindfekerdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvsha 1046
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 895 -----------EEGDDsLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963
Cdd:PRK14844 1047 iaqfkrkveklHEGYD-LPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVP 1125
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 964 SRMNIGQVLELHLGMAAKNL------------------------------------------------------------ 983
Cdd:PRK14844 1126 SRMNVGQILETHVGWACKKLgekvgnildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpn 1205
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 984 ---------------------------------------------------------------GIHVASPVFDGANDDDV 1000
Cdd:PRK14844 1206 knalndelnelvenylnscksaysnlrnflievyscgsnvsicnnirdisdnnliefarklrdGIPVAAPVFEGPKDEQI 1285
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1001 WSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1080
Cdd:PRK14844 1286 AKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMEC 1365
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1081 WALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIVKGENISRPSVPESFRVLMKELQSLGLDVKvMDEQDNEIEMRDLDDD 1160
Cdd:PRK14844 1366 WALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVD-LKQNDVVIEDISHTNI 1444
|
1530 1540
....*....|....*....|..
gi 504427648 1161 DIPDRKVNMQPSSvPESQKEFN 1182
Cdd:PRK14844 1445 AQSFNEVSISIAS-PESIKRMS 1465
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
29-1145 |
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: 988.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 29 LIEIQTKSYDWFLKEGLLEMFRDISPIEDFT--GNLSLEFVDYRLGEPKYDL---------EESKNRDATYAAPLRVKVR 97
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 98 LIIKETGEVKDQEVFMGDFPLMTE------------------------TGTFVINGAERVIVSQLVRSPSVYFNEklDKN 153
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 154 GRVNYDATVIPN----RGAWLEYETDA-KDVVYVRIDRTRKlpltvllralgystdqeiieligdneylrntlekdsten 228
Cdd:cd00653 159 GKRIYTKTSIPSyspyRGSWLEVKSDKkKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 229 tEQALLEIYERLRpgepptvenaksllysrffdpkrydlasvgrykankklhlkhrlfnqklaepivntetgeivaeegt 308
Cdd:cd00653 200 -EEALKYIGKRFE------------------------------------------------------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 309 vldrrkldeimdvletnanaqvyelpnsiidepveiqsikvyvpnddeertttvignafpdsevkcitpaDIVASMSYFF 388
Cdd:cd00653 212 ----------------------------------------------------------------------DLIYMIRKLI 221
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 389 NLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS--ITPQQLINIRPVIASIKEFFGSSQ- 465
Cdd:cd00653 222 LLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNw 301
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 466 -----------LSQFMDQANPLAELTHKRRLSAlgpGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534
Cdd:cd00653 302 gskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMA 378
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 535 RVNefGFIETPYRKVDIETntitdqidyltadeedsyvvaqansrldengrfiddeivcrfrgnnttmakekmDYMDVSP 614
Cdd:cd00653 379 RIS--GRIERPYRIVEKEV------------------------------------------------------THIEISP 402
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 615 KQVVSAATACIPFLENDDSNRALMGANMQRQAVP----------------LLNPESPFVGTGMEHVAARDsgaaviskyr 678
Cdd:cd00653 403 SQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG---------- 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 679 grvehvqsseilvrrlveengqevdgtldryplakfkrsnsgtcynqrpiiakgdivekgeiladgpsmelgEMALGRNV 758
Cdd:cd00653 473 ------------------------------------------------------------------------ELPLGQNA 480
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 759 VVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR-DIPNVSENALKNLDDRGIVYVGAEVKD 837
Cdd:cd00653 481 IVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEP 560
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 838 GDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREegddsLSPGVNQLVRVYIVQKR 917
Cdd:cd00653 561 GDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE-----LNDGGNKLVKVYIRQKR 628
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 918 KIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGAND 997
Cdd:cd00653 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEE 708
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 998 DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1077
Cdd:cd00653 709 EDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504427648 1078 MEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYEAIV----------KGENISRPSVPESFRVLMKELQSLGLDVKVM 1145
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
679-1069 |
0e+00 |
|
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: 565.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 679 GRVEHVQSSEILVRRlveengQEVDGTLDRYPLAKFKRSNSGT---CYNQRPIIAKGdIVEKGEiladgpsmeLGEMALG 755
Cdd:pfam00562 6 PFVDHNQSPRNTYQC------AMGKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGELPLG 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 756 RNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYEseARDTKLGP-EEITRDIPNVSENALKNLDDRGIVYVGAE 834
Cdd:pfam00562 70 QNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVGAE 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 835 VKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFnreegddSLSPGVNQLVRVYIV 914
Cdd:pfam00562 148 VKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF-------ELPPGGIKMVKVYIR 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 915 QKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDG 994
Cdd:pfam00562 215 QKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFDG 294
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 504427648 995 AND--DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQ 1069
Cdd:pfam00562 295 ASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
28-1145 |
1.19e-126 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 416.28 E-value: 1.19e-126
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 28 NLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYD-LEESKN---------RDATYAAPLRVKVR 97
Cdd:PRK08565 13 GLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKeADGSERpitpmearlRNLTYAAPLYLTMI 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 98 LIIkETGEVKDQEVFMGDFPLMTET------------------------GTFVINGAERVIVSQLVRSPSVYFNEKLDKN 153
Cdd:PRK08565 93 PVE-NGIEYEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNRVLVDKGEAG 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 154 GRVNYDATVIPNRGAW-----LEYETDAkdVVYVRIDRTR-KLPLTVLLRALGYSTDQEIIELIGDNEYLRNTLEkDSTE 227
Cdd:PRK08565 172 SSITHTAKVISSRAGYraqvtVERRKDG--TIYVSFPAVPgKIPFVILMRALGLETDRDIVYAVSLDPEIQQELL-PSLE 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 228 NTEQALleiyerlrpgepPTVENAKSLLYSRFfdpkrydlaSVGRYKANkklhlkhRLfnqKLAEpivntetgeivaeeg 307
Cdd:PRK08565 249 QASSIA------------ATVEDALDYIGKRV---------AIGQPREY-------RI---ERAE--------------- 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 308 TVLDRrkldeimdvletnanaqvYELPNsiidepveiqsikvyvpnddeertttvIGNAFPDSEVKCITPADIVASMsyf 387
Cdd:PRK08565 283 QILDK------------------YLLPH---------------------------LGTSPEDRIKKAYFLGQMASKL--- 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 388 FNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRiglSRMERVVRErMSIQDTDSITPQQLINIRPVIAS--IKEFF---- 461
Cdd:PRK08565 315 LELYLGRREPDDKDHYANKRLRLAGDLLAELFR---VAFKQLVKD-LKYQLEKSYARGRKLDLRAIVRPdiITERIrhal 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 462 -------GSSQLSQFMDQANPLAELTHKRRLsaLGPggLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534
Cdd:PRK08565 391 atgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 535 R----VNEFGFIETPYRK--VDIETNTITDQID----YLTAD----EEDSYVVAQANSRLDENGRfIDDEIVCRFRGNNT 600
Cdd:PRK08565 467 QisvgVDEEEVEEILYELgvVPVEEAREEEYISwsrvYLNGRligyHPDGEELAEKIRELRRSGK-ISDEVNVAYIETGE 545
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 601 T-------------------------MAKE----------------KM---DYMD----------VSPKQVVS------- 619
Cdd:PRK08565 546 InevyvncdsgrvrrplivvengkpkLTREhveklkkgeltfddlvKMgviEYLDaeeeenayvaLDPEDLTPehthlei 625
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 620 -------AATACIPFLENDDSNRALMGANMQRQAVpllnpespfvGTGMEHVAAR-DSgaaviskyRGRVEHVQSseilv 691
Cdd:PRK08565 626 wppailgITASIIPYPEHNQSPRNTYQAAMAKQSL----------GLYAANFRIRtDT--------RGHLLHYPQ----- 682
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 692 RRLVEENGQEVDGtldryplakfkrsnsgtcYNQRPIiakgdivekgeiladgpsmelgemalGRNVVVGFMTWDGYNYE 771
Cdd:PRK08565 683 RPLVQTRALEIIG------------------YNDRPA--------------------------GQNAVVAVLSYTGYNIE 718
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 772 DAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPE-EITRDIPNVS----ENALKNLDDRGIVYVGAEVKDGDILVGKVT 846
Cdd:PRK08565 719 DAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVRgyrgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTS 798
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 847 PKGVTELTAEERLlhaifGEKARevRDTSLRVPHGAGGIVLDVKVFNREEGddslspgvNQLVRVYIVQKRKIHVGDKMC 926
Cdd:PRK08565 799 PPRFLEELEELSL-----GLQER--RDTSVTVRHGEKGIVDTVLITESPEG--------NKLVKVRVRDLRIPELGDKFA 863
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 927 GRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEE 1006
Cdd:PRK08565 864 SRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLK 943
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1007 AGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1086
Cdd:PRK08565 944 LGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGH 1023
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 504427648 1087 GAAYTLQEILTYKSDDTV--------------GRVKTYEAIVKGE--NISRPSVPESFRVLMKELQSLGLDVKVM 1145
Cdd:PRK08565 1024 GAAMLLKERLLDSSDKTTiyvcelcghiawydRRKNKYVCPIHGDkgNISPVEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
560-1143 |
8.51e-90 |
|
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: 301.95 E-value: 8.51e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 560 IDYLTADEEDSYVVAQANSRLdengrfiddeivcrfrgnnttmaKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMG 639
Cdd:TIGR03670 92 IEYLDAEEEENAYIALDPEEL-----------------------TPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMG 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 640 ANMQRQAVPLlnpespfvgtgmehvaardsgaaVISKYRGRVEhvqsseilvrrlveengqeVDGTLDRYPlakfkrsns 719
Cdd:TIGR03670 149 AAMAKQSLGL-----------------------YAANYRIRLD-------------------TRGHLLHYP--------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 720 gtcynQRPIIaKGDIVEkgeiladgpSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEAR 799
Cdd:TIGR03670 178 -----QKPLV-KTRVLE---------LIGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEER 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 800 DTKLGPE-EITRDIPNV----SENALKNLDDRGIVYVGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKAREVR 872
Cdd:TIGR03670 243 RYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTERRR 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 873 DTSLRVPHGAGGIVLDVKVFNREEGddslspgvNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRP 952
Cdd:TIGR03670 314 DTSVTVRHGEKGIVDKVIITETEEG--------NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIV 385
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 953 IDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISV 1032
Cdd:TIGR03670 386 PDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFI 465
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1033 GVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTV-------G 1105
Cdd:TIGR03670 466 GVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVvyvcencG 545
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 504427648 1106 RVKTYEAI-------VKGE--NISRPSVPESFRVLMKELQSLGLDVK 1143
Cdd:TIGR03670 546 HIAWEDKRkgtaycpVCGEtgDISPVEMSYAFKLLLDELKSLGISPR 592
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
560-1141 |
1.59e-82 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 281.85 E-value: 1.59e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 560 IDYLTADEEDSYVVAQANSRLDENgrfiddeivcrfrgnNTtmakekmdYMDVSPKQVVSAATACIPFLENDDSNRALMG 639
Cdd:PRK07225 98 IEYLDAEEEENAYIAVYEEDLTEE---------------HT--------HLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 640 ANMQRQAVpllnpespfvGTGMEHVAAR-DSgaaviskyRGRVEH-VQSSeilvrrLVEENGQEVDGtldryplakfkrs 717
Cdd:PRK07225 155 AGMIKQSL----------GLPAANYKLRpDT--------RGHLLHyPQVP------LVKTQTQEIIG------------- 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 718 nsgtcYNQRPIiakgdivekgeiladgpsmelgemalGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESE 797
Cdd:PRK07225 198 -----FDERPA--------------------------GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 798 ARDTKLGPE-EITRDIPNV----SENALKNLDDRGIVYVGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKARE 870
Cdd:PRK07225 247 ERRYPGGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEK 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 871 VRDTSLRVPHGAGGIVLDVKVFNREEGddslspgvNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950
Cdd:PRK07225 318 RRETSVTMRSGEEGIVDTVILTETEEG--------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESG 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 951 RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRI 1030
Cdd:PRK07225 390 VVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEI 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1031 SVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTV------ 1104
Cdd:PRK07225 470 FVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEiyvcak 549
|
570 580 590 600
....*....|....*....|....*....|....*....|....*..
gi 504427648 1105 -GRVKTYEAI-------VKGE--NISRPSVPESFRVLMKELQSLGLD 1141
Cdd:PRK07225 550 cGMIAIYDKKrnrkycpICGEetDIYPVEMSYAFKLLLDELKSLGIA 596
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
28-453 |
3.80e-44 |
|
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: 165.25 E-value: 3.80e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 28 NLIEIQTKSYDWFLKEGLLEMFRDISPIE---------DFTGNLSLEFVDYRLGEPKYD----------LEESKNRDATY 88
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIEsefeiqhpgENGDKLSLKFGQIRLGKPMFDetdgstreiyPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 89 AAPLRVKVRLIIKETGEVKDQEVFMGDFPLMTET------------------------GTFVINGAERVIVSQLVRS--- 141
Cdd:pfam04563 81 SAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQEHRSrnh 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 142 PSVYFNEKLDK---NGRVNYDA--TVIPNRGAWLE-YETDAKDVVYVRIDRTRK-LPLTVLLRALGYSTDQEIIELI--- 211
Cdd:pfam04563 161 PIVFKKADPKKrgsVASVRSSAeiSVRPDSTSWVNvLEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREIFELIcyd 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 212 -GDNEY---LRNTLEKDSTENTeqalleiyerlrpgepPTVENAKSLLYSRFFDPKRYDLASVGRYKankklhlkhrlfn 287
Cdd:pfam04563 241 vNDQQLqeeLLPSLEEGFKIRI----------------QTQEQALDYIGGRGRAIFRMGRPREPRIK------------- 291
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 288 qklaepivntetgeiVAEEgtVLDRRKLdeimdvletnANAQVYELpnsiidepveiqsikvyvpndDEERTTTVIGNAf 367
Cdd:pfam04563 292 ---------------YAEE--ILQKEVL----------PHLGTYEL---------------------DETKKAYFIGYM- 322
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 368 pdsevkcitpadivasMSYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERM--SIQDTDSITPQ 445
Cdd:pfam04563 323 ----------------IRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQ 386
|
....*...
gi 504427648 446 QLINIRPV 453
Cdd:pfam04563 387 LLVNAKPI 394
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
29-538 |
1.12e-40 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 157.80 E-value: 1.12e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 29 LIEIQTKSYDWFLKEGLLEMFRDISPIE-DFTGNLSLEFVDYRLGEP----------KYDLEESKNRDATYAAPLRVKVR 97
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIEtEIEDGVYVELGKIRVGKPvvkeadgserEIYPMEARLRNLTYSAPLYLEMS 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 98 lIIKETGEVKDQEVFMGDFPLMTET------------------------GTFVINGAERVIVSQLVRSPSVYFNEKLDKN 153
Cdd:PRK09606 98 -PVEGGEEEEPEEVYIGELPVMVGSkicnlyglseeelievgedpldpgGYFIVNGSERVLMTLEDLAPNKILVEKDERY 176
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 154 GRVNYDATVIPNRG---AWLEYETDAKDVVYVRIDR-TRKLPLTVLLRALGYSTDQEIIELIGDNE----YLRNTLEKDS 225
Cdd:PRK09606 177 GDRIEVAKVFSQRRgyrALVTVERNRDGLLEVSFPSvPGSIPFVILMRALGLETDEEIVEAVSDDPeivkFMLENLEEAE 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 226 TENTEQALLEIYERLRPGEpptvenaksllysrffdPKRYDLasvgrykankklhlkhrlfnqKLAEpivntetgeivae 305
Cdd:PRK09606 257 VDTQEEALEYIGKRVAPGQ-----------------TKEYRI---------------------KRAE------------- 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 306 egTVLDRrkldeimdvletnanaqvYELPNsiidepveiqsikvyvpnddeertttvIGNafpDSEVKcITPADIVASM- 384
Cdd:PRK09606 286 --YVIDR------------------YLLPH---------------------------LGV---EPEVR-RAKAHYLGRMa 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 385 SYFFNLLHGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVR---ERMSIQDTD-SItpQQLI-------NIRPV 453
Cdd:PRK09606 315 EACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqlERANMRNRElSI--KTAVrsdvlteRLEHA 392
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 454 IASIKEFFGSSQLSQFMDQANPLAELTHKRRLSAlgpgGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSY 533
Cdd:PRK09606 393 MATGNWVGGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQM 468
|
....*
gi 504427648 534 ARVNE 538
Cdd:PRK09606 469 VEIST 473
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
468-535 |
1.93e-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: 123.02 E-value: 1.93e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504427648 468 QFMDQANPLAELTHKRRLSAlGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYAR 535
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1071-1147 |
3.98e-33 |
|
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: 123.08 E-value: 3.98e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 1071 GGQRFGEMEVWALEAYGAAYTLQEILTYKSD----DTVGRVKTYEA-----IVKGENISRP-SVPESFRVLMKELQSLGL 1140
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPgYIPESFKLLFQELQSLGI 80
|
....*..
gi 504427648 1141 DVKVMDE 1147
Cdd:pfam04560 81 DPRLLLE 87
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
546-613 |
4.95e-28 |
|
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: 107.45 E-value: 4.95e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 504427648 546 YRKVDieTNTITDQIDYLTADEEDSYVVAQANSRLDENGRFIDDEIVCRFRGNNTTMAKEKMDYMDVS 613
Cdd:pfam10385 1 YRKVE--DGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
140-409 |
2.54e-24 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 101.27 E-value: 2.54e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 140 RSPSVYFNEKLDKNGRVN-YDATVIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGYSTDQEIIELI--GDNEY 216
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIAtYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLcyDFNDP 80
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 217 LRNTLEKDSTE------NTEQALLEIYE--RLRPGEPPTVENAKSLLYSRFfdpkrydlasvGRYKANKKLHLkhrlfnq 288
Cdd:pfam04561 81 QMLELLKPELEeaeniyTQEEALDYIGKgfALRRGEEPRLQRAREILYSRD-----------PKYNLNKHLGL------- 142
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170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 504427648 289 klaepivntetgeivaeegtvldrrkldeimdvletnanaqvyelpnsiiDEPVEIQSIKVYvpnddeertttvignafp 368
Cdd:pfam04561 143 --------------------------------------------------NEPFENERLKAQ------------------ 154
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250 260 270 280
....*....|....*....|....*....|....*....|.
gi 504427648 369 dsevkcitpaDIVASMSYFFNLLHGIGYTDDIDHLGNRRLR 409
Cdd:pfam04561 155 ----------DILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
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