|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
3-1151 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2219.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 3 GQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL-------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPK 75
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 76 YDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK--N 153
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsS 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFsTDQEIVDLLGD-------------------- 213
Cdd:PRK00405 161 GKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEkeefgkeievpveyllgkvl 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 214 -------------------------SEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLA 268
Cdd:PRK00405 240 aedivdeetgevlaeandeiteeldGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLS 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 269 SVGRYKANKKLHLKhrlfnqklaepivnsetgeivvdegtvldrrkldeimdvletnansevfelegsvidepveiqsik 348
Cdd:PRK00405 320 KVGRYKLNKKLGLD------------------------------------------------------------------ 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 349 vyvpndeegrtttvignalPDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMER 428
Cdd:PRK00405 334 -------------------EDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMER 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 429 VVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYS 508
Cdd:PRK00405 395 AVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 509 HYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDldtNS-ITDQIDYLTADEEDSYVVAQANSRLDENGRFL 587
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVV---DGkVTDEIVYLTADEEDNYVIAQANAPLDEDGRFV 551
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 588 DDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAAR 667
Cdd:PRK00405 552 DELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVAR 631
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 668 DSGAAITAKHRGRVEHVESNEILVRRlveENGTEHEGELDRYPLAKFKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSM 747
Cdd:PRK00405 632 DSGAVVVAKRDGVVEYVDASRIVVRV---EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPST 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 748 ELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRG 827
Cdd:PRK00405 709 DNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESG 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 828 IVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQ 907
Cdd:PRK00405 789 IVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNK 868
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 908 LVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHV 987
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKF 948
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 988 ASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGK 1067
Cdd:PRK00405 949 ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1028
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1068 AQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147
Cdd:PRK00405 1029 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
|
....
gi 394298807 1148 HDNE 1151
Cdd:PRK00405 1109 DGNE 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: 1986.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 14 RRNYARISEVLELPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLR 93
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLTYAAPLY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 94 VKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYE 173
Cdd:COG0085 81 VKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 174 TDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGD---SEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVEN 250
Cdd:COG0085 161 TDKDGTIYVRIDRKRKIPVTVLLRALGLETDEEILEAFGDdpiQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIER 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 251 AKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivnsetgeivvdegtvldrrkldeimdvletnansev 330
Cdd:COG0085 241 AEQLLDNLFFDPKRYDLAHVGRYKINKKLGLD------------------------------------------------ 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 331 felegsvidepveiqsikvyvpndeegrtttvignalPDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRS 410
Cdd:COG0085 273 -------------------------------------VPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRL 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 411 VGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGP 490
Cdd:COG0085 316 VGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGP 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 491 GGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDldTNSITDQIDYLTADEEDS 570
Cdd:COG0085 396 GGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVE--NGKVTDEIEYLTADEEEN 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 571 YVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLM 650
Cdd:COG0085 474 YYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLL 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 651 NPEAPfvgtgmehvaardsgaaitakhrgrvehvesneilvrrlveengtehegeLDRYPLAKFKRSNSGTCYNQRPIVS 730
Cdd:COG0085 554 RPEAP--------------------------------------------------LLHYPLQKFQRSNQGTCINQRPIVR 583
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 731 IGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR 810
Cdd:COG0085 584 VGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITR 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 811 DIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVK 890
Cdd:COG0085 664 DIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVK 743
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 891 VFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQ 970
Cdd:COG0085 744 VFSREEGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQ 822
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 971 VLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHA 1050
Cdd:COG0085 823 VLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHA 902
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1051 RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRV 1130
Cdd:COG0085 903 RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKV 982
|
1130
....*....|....*..
gi 394298807 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: 1917.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 10 RHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLE 79
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 80 ESKNRDATYAAPLRVKVRLIIKE---TGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKID--KNG 154
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 155 RENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGDSEYLRNTLEKDGTENTEQALL 234
Cdd:TIGR02013 161 KVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNSEEEALV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 235 EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivnsetgeiVVDEGTVLdrrk 314
Cdd:TIGR02013 241 EIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLD--------------------VPESIGVL---- 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 315 ldeimdvletnansevfelegsvidepveiqsikvyvpndeegrtttvignalpdsevkciTPADIVASMSYFFNLLNGI 394
Cdd:TIGR02013 297 -------------------------------------------------------------TKEDIIATIKYLIKLRNGK 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 395 GYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474
Cdd:TIGR02013 316 GEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTN 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTN 554
Cdd:TIGR02013 396 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKV 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 555 SITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSN 634
Cdd:TIGR02013 476 VVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDAN 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 635 RALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRlvEENGTEHEGELDRYPLAKF 714
Cdd:TIGR02013 556 RALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY--DEDEEEPDGGIDIYRLLKY 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 715 KRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEY 794
Cdd:TIGR02013 634 QRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 795 ESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDT 874
Cdd:TIGR02013 714 EVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDT 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 875 SLRVPHGAGGIVLDVKVFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPID 954
Cdd:TIGR02013 794 SLRVPPGVEGTVIDVKVFSREQGDE-LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVD 872
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 955 IMLNPLGVPSRMNIGQVLELHLGMAAKNLG---IHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRIS 1031
Cdd:TIGR02013 873 IVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVT 952
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1032 VGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYE 1111
Cdd:TIGR02013 953 VGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYE 1032
|
1130 1140 1150
....*....|....*....|....*....|...
gi 394298807 1112 SIVKGENISRPSVPESFRVLMKELQSLGLDVKV 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: 997.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 29 LIEIQTKSYDWFLKEGLLEMFRDISPIEDFT--GNLSLEFVDYRLGEPKYDL---------EESKNRDATYAAPLRVKVR 97
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 98 LIIKETGEVKEQEVFMGDFPLMTD------------------------TGTFVINGAERVIVSQLVRSPSVYFNEkiDKN 153
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GRENYDATIIPN----RGAWLEYETDA-KDVVYVRIDRTRKlpltvllralgfstdqeivdllgdseylrntlekdgten 228
Cdd:cd00653 159 GKRIYTKTSIPSyspyRGSWLEVKSDKkKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 229 tEQALLEIYERLRpgepptvenaksllysrffdpkrydlasvgrykankklhlkhrlfnqklaepivnsetgeivvdegt 308
Cdd:cd00653 200 -EEALKYIGKRFE------------------------------------------------------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 309 vldrrkldeimdvletnansevfelegsvidepveiqsikvyvpndeegrtttvignalpdsevkcitpaDIVASMSYFF 388
Cdd:cd00653 212 ----------------------------------------------------------------------DLIYMIRKLI 221
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 389 NLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS--ITPQQLINIRPVIASIKEFFGSSQ- 465
Cdd:cd00653 222 LLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNw 301
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 466 -----------LSQFMDQANPLAELTHKRRLSAlgpGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534
Cdd:cd00653 302 gskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMA 378
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 535 RVNefGFIETPYRKVDLDTnsitdqidyltadeedsyvvaqansrldengrflddevvcrfrgnntvmakekmDYMDVSP 614
Cdd:cd00653 379 RIS--GRIERPYRIVEKEV------------------------------------------------------THIEISP 402
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 615 KQVVSAATACIPFLENDDSNRALMGANMQRQAVP----------------LMNPEAPFVGTGMEHVAARDsgaaitakhr 678
Cdd:cd00653 403 SQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG---------- 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 679 grvehvesneilvrrlveengtehegeldryplakfkrsnsgtcynqrpivsigdvveyneiladgpsmelgEMALGRNV 758
Cdd:cd00653 473 ------------------------------------------------------------------------ELPLGQNA 480
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 759 VVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR-DIPNVSESALKNLDDRGIVYVGAEVKD 837
Cdd:cd00653 481 IVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEP 560
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 838 GDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREegddtLSPGVNQLVRVYIVQKR 917
Cdd:cd00653 561 GDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE-----LNDGGNKLVKVYIRQKR 628
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 918 KIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGAND 997
Cdd:cd00653 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEE 708
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 998 DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1077
Cdd:cd00653 709 EDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 394298807 1078 MEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIV----------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 ... |
674-1069 |
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: 562.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 674 TAKHRGRVEHVESNEILVRRLVEEngteheGELDRYPLAKFKRSNSGT---CYNQRPIVSIGDVVEYNeiladgpsmeLG 750
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGK------QAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEAGG----------FG 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 751 EMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYEseARDTKLGP-EEITRDIPNVSESALKNLDDRGIV 829
Cdd:pfam00562 65 ELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIV 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 830 YVGAEVKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFnreegddTLSPGVNQLV 909
Cdd:pfam00562 143 RVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF-------ELPPGGIKMV 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 910 RVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVAS 989
Cdd:pfam00562 210 KVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDA 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 990 PVFDGAND--DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGK 1067
Cdd:pfam00562 290 TPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
..
gi 394298807 1068 AQ 1069
Cdd:pfam00562 370 AR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
3-1151 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2219.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 3 GQVVQYGRHRKRRNYARISEVLELPNLIEIQTKSYDWFL-------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPK 75
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLqldvppeDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 76 YDLEESKNRDATYAAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDK--N 153
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDHDKDKtsS 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFsTDQEIVDLLGD-------------------- 213
Cdd:PRK00405 161 GKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGY-SDEEILDLFYEkeefgkeievpveyllgkvl 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 214 -------------------------SEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLA 268
Cdd:PRK00405 240 aedivdeetgevlaeandeiteeldGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLS 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 269 SVGRYKANKKLHLKhrlfnqklaepivnsetgeivvdegtvldrrkldeimdvletnansevfelegsvidepveiqsik 348
Cdd:PRK00405 320 KVGRYKLNKKLGLD------------------------------------------------------------------ 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 349 vyvpndeegrtttvignalPDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMER 428
Cdd:PRK00405 334 -------------------EDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMER 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 429 VVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRDVHYS 508
Cdd:PRK00405 395 AVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 509 HYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDldtNS-ITDQIDYLTADEEDSYVVAQANSRLDENGRFL 587
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVV---DGkVTDEIVYLTADEEDNYVIAQANAPLDEDGRFV 551
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 588 DDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHVAAR 667
Cdd:PRK00405 552 DELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVAR 631
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 668 DSGAAITAKHRGRVEHVESNEILVRRlveENGTEHEGELDRYPLAKFKRSNSGTCYNQRPIVSIGDVVEYNEILADGPSM 747
Cdd:PRK00405 632 DSGAVVVAKRDGVVEYVDASRIVVRV---EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPST 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 748 ELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLDDRG 827
Cdd:PRK00405 709 DNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESG 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 828 IVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGDDTLSPGVNQ 907
Cdd:PRK00405 789 IVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTRIEQGDELPPGVNK 868
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 908 LVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHV 987
Cdd:PRK00405 869 LVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIKF 948
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 988 ASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGK 1067
Cdd:PRK00405 949 ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1028
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1068 AQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVKVMDE 1147
Cdd:PRK00405 1029 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
|
....
gi 394298807 1148 HDNE 1151
Cdd:PRK00405 1109 DGNE 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: 1986.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 14 RRNYARISEVLELPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDATYAAPLR 93
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLTYAAPLY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 94 VKVRLIIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYE 173
Cdd:COG0085 81 VKVRLVNKETGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 174 TDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGD---SEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVEN 250
Cdd:COG0085 161 TDKDGTIYVRIDRKRKIPVTVLLRALGLETDEEILEAFGDdpiQEYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIER 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 251 AKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivnsetgeivvdegtvldrrkldeimdvletnansev 330
Cdd:COG0085 241 AEQLLDNLFFDPKRYDLAHVGRYKINKKLGLD------------------------------------------------ 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 331 felegsvidepveiqsikvyvpndeegrtttvignalPDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRS 410
Cdd:COG0085 273 -------------------------------------VPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRL 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 411 VGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGP 490
Cdd:COG0085 316 VGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGP 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 491 GGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDldTNSITDQIDYLTADEEDS 570
Cdd:COG0085 396 GGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVE--NGKVTDEIEYLTADEEEN 473
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 571 YVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLM 650
Cdd:COG0085 474 YYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLL 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 651 NPEAPfvgtgmehvaardsgaaitakhrgrvehvesneilvrrlveengtehegeLDRYPLAKFKRSNSGTCYNQRPIVS 730
Cdd:COG0085 554 RPEAP--------------------------------------------------LLHYPLQKFQRSNQGTCINQRPIVR 583
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 731 IGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR 810
Cdd:COG0085 584 VGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITR 663
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 811 DIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVK 890
Cdd:COG0085 664 DIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVK 743
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 891 VFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQ 970
Cdd:COG0085 744 VFSREEGDE-LPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQ 822
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 971 VLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHA 1050
Cdd:COG0085 823 VLETHLGWAAALLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHA 902
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1051 RSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRV 1130
Cdd:COG0085 903 RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKV 982
|
1130
....*....|....*..
gi 394298807 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: 1917.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 10 RHRKRRNYARISEVLELPNLIEIQTKSYDWFL----------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLE 79
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLqqdtppekrkEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 80 ESKNRDATYAAPLRVKVRLIIKE---TGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKID--KNG 154
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEedgTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKDttKSG 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 155 RENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGDSEYLRNTLEKDGTENTEQALL 234
Cdd:TIGR02013 161 KVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLGSGEYIRNTLRKDPTNSEEEALV 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 235 EIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLHLKhrlfnqklaepivnsetgeiVVDEGTVLdrrk 314
Cdd:TIGR02013 241 EIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLD--------------------VPESIGVL---- 296
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 315 ldeimdvletnansevfelegsvidepveiqsikvyvpndeegrtttvignalpdsevkciTPADIVASMSYFFNLLNGI 394
Cdd:TIGR02013 297 -------------------------------------------------------------TKEDIIATIKYLIKLRNGK 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 395 GYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQAN 474
Cdd:TIGR02013 316 GEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTN 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 475 PLAELTHKRRLSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTN 554
Cdd:TIGR02013 396 PLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKV 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 555 SITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSN 634
Cdd:TIGR02013 476 VVTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDAN 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 635 RALMGANMQRQAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRlvEENGTEHEGELDRYPLAKF 714
Cdd:TIGR02013 556 RALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY--DEDEEEPDGGIDIYRLLKY 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 715 KRSNSGTCYNQRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEY 794
Cdd:TIGR02013 634 QRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEY 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 795 ESEARDTKLGPEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDT 874
Cdd:TIGR02013 714 EVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDT 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 875 SLRVPHGAGGIVLDVKVFNREEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPID 954
Cdd:TIGR02013 794 SLRVPPGVEGTVIDVKVFSREQGDE-LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVD 872
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 955 IMLNPLGVPSRMNIGQVLELHLGMAAKNLG---IHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRIS 1031
Cdd:TIGR02013 873 IVLNPLGVPSRMNIGQILETHLGWAGKRLGrkgVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVT 952
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1032 VGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYE 1111
Cdd:TIGR02013 953 VGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYE 1032
|
1130 1140 1150
....*....|....*....|....*....|...
gi 394298807 1112 SIVKGENISRPSVPESFRVLMKELQSLGLDVKV 1144
Cdd:TIGR02013 1033 AIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
26-1178 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1254.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 26 LPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFV--DYRLGEPKYDLEESKNRDATYAAPLRVKVRLIIKET 103
Cdd:CHL00207 7 LPDFLEIQRTSFCWFLNEGLNEELNIFSKIFDYTGNLELLLFgkNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFINLKT 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 104 GEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVR 183
Cdd:CHL00207 87 NKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIR 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 184 IDRTRKLPLTVLLRALGFsTDQEIVDLLGDS---EYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFF 260
Cdd:CHL00207 167 IDKNRKKPLIIFLKALGL-TDQDIYSRLTKSeflKKLKPILLNSNSYTNEEILLEIYKNLSPIEPATVNDANQNLFSRFF 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 261 DPKRYDLASVGRYKANKKLHLKHRLFnqklaepivnsetgeivvdegtvldrrkldeimdvletnansevfelegsvide 340
Cdd:CHL00207 246 DPKNYDLGKVGRYKINNKLNLNIPER------------------------------------------------------ 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 341 pveiqsikvyvpndeegrtttvignalpdseVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFR 420
Cdd:CHL00207 272 -------------------------------VRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFR 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 421 IGLSRMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQM 500
Cdd:CHL00207 321 IGLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISF 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 501 EVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDLDTNSITDQIDYLTADEEDSYVVAQANSRL 580
Cdd:CHL00207 401 AVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGKVKKFGNPIYLTADSEDLYRIAPNDINL 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 581 DENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTG 660
Cdd:CHL00207 481 NKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTG 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 661 MEHVAARDSGAAITAKHRGRVEHVESNEILVRrlveengtEHEGELDRYPLAKFKRSNSGTCYNQRPIVSIGDVVEYNEI 740
Cdd:CHL00207 561 YEKQIALDSGMTIISLTEGIVVSVSAYKIIIQ--------DDNNRYIHYYLQKYQRSNQNTCINYRPIVWVGEKINIGQI 632
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 741 LADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESAL 820
Cdd:CHL00207 633 LADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSL 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 821 KNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREEGdDT 900
Cdd:CHL00207 713 KNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKG-DE 791
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 901 LSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAA 980
Cdd:CHL00207 792 LKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAG 871
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 981 KNLGIHVASPVFDGANDDD-----VWSTIEEAGMARD----------GKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVD 1045
Cdd:CHL00207 872 DNLNKRFKILPFDEMYGSEysrilINNKLNQASIKNNeywlfnsyhpGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVD 951
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1046 DKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVP 1125
Cdd:CHL00207 952 DKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTP 1031
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|...
gi 394298807 1126 ESFRVLMKELQSLGLDVKVmdehdNEIEmaDVDDEDAAERKVDLQQKSAPESQ 1178
Cdd:CHL00207 1032 ESFKVLMRELQSLGLDIEA-----YKIE--NFLEGQRLEIEINLMENYKYFRK 1077
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
26-1157 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1203.96 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 26 LPNLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFV--DYRLGEPKYdleesKNRDA-----TYAAPLRVKVRL 98
Cdd:CHL00001 12 IPGFNQIQFEGFCRFIDQGLTEELSKFPKIEDTDQEIEFQLFveTYQLVEPLI-----KERDAvyeslTYSSELYVPAGL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 99 IIKETGEVKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKIDKNGRENYDATIIPNRGAWLEYETDAKD 178
Cdd:CHL00001 87 IWKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKA 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 179 VVYVRIDRTRKLPLTVLLRALGFSTDqEIVDLLGDSEYLRNTL---EKDGTENTEQALLEIYERL--RPGEPPTVENAKS 253
Cdd:CHL00001 167 RIWARVSRKQKISILVLLSAMGLNLR-EILDNVCYPEIFLSFLndkEKKKIGSKENAILEFYQQFacVGGDPVFSESLCK 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 254 LLYSRFFDpKRYDLASVGRYKANKKLHLkhrlfnqklaepivnsetgeivvdegtvldrrkldeimDVLETNanseVFel 333
Cdd:CHL00001 246 ELQKKFFQ-QRCELGRIGRRNMNRKLNL--------------------------------------DIPENN----TF-- 280
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 334 egsvidepveiqsikvyvpndeegrtttvignalpdsevkcITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGE 413
Cdd:CHL00001 281 -----------------------------------------LLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVAD 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 414 LLQNQFRIGLSRMERVVRERMS--IQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPG 491
Cdd:CHL00001 320 LLQDQFGLALNRLENAVRGTICgaIRRKLIPTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPG 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 492 GLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDldTNSITDQIDYLTADEEDSY 571
Cdd:CHL00001 400 GLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEIS--ERSKEERMVYLSPSEDEYY 477
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 572 VVAQANSrLDENGRFLDDEVV-CRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLM 650
Cdd:CHL00001 478 MIAAGNS-LALNQGIQEEQVVpARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLS 556
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 651 NPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVRRlveengtehEGELDRYPLAKFKRSNSGTCYNQRPIVS 730
Cdd:CHL00001 557 RSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSG---------NGDTLSIPLVMYQRSNKNTCMHQKPQVR 627
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 731 IGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR 810
Cdd:CHL00001 628 RGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITK 707
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 811 DIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTEL--TAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLD 888
Cdd:CHL00001 708 EIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESsyAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVID 787
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 889 VKVFNREEGddtlSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNI 968
Cdd:CHL00001 788 VRWIQKKGG----SSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNV 863
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 969 GQVLELHLGMAAKNLGIHVASPVFDGANDDD-----VWSTIEEAGMARD----------GKTVLYDGRTGEPFDNRISVG 1033
Cdd:CHL00001 864 GQIFECLLGLAGDLLNRHYRIAPFDERYEQEasrklVFSELYEASKQTAnpwvfepeypGKSRLFDGRTGDPFEQPVTIG 943
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1034 VMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESI 1113
Cdd:CHL00001 944 KAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAI 1023
|
1130 1140 1150 1160
....*....|....*....|....*....|....*....|....*..
gi 394298807 1114 VKGENISRP-SVPESFRVLMKELQSLGLDVK--VMDEHDNEIEMADV 1157
Cdd:CHL00001 1024 ITGGTIPKPeDAPESFRLLVRELRSLALELNhfLVSEKNFQINRKEV 1070
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
10-1161 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1103.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 10 RHRKRRNYARISEVLELPNLIEIQTKSYDWFL------KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKN 83
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLyskdgkESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 84 RDATYAAPLRVKVRLIIKE----TGE------VKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSVYFNEKiDKN 153
Cdd:PRK09603 88 RGITYSIPLKIKVRLILWEkdtkSGEkngikdIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEE-ESS 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GREN---YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTdQEIVDLLgdseylrntlekdgtente 230
Cdd:PRK09603 167 TSLNkliYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQK-QDIIKMF------------------- 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 231 QALLEI-YERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLH-LKHR-----------LFNQKLAEPIVNS 297
Cdd:PRK09603 227 YPLVKVrYENDKYLIPFASLDANQRMEFDLKDPQGKIILLAGKKLTSRKIKeLKENhlewveypmdiLLNRHLAEPVMVG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 298 EtgEIVVDEGTVLDRRKLDEIMD--VLE-TNANSEVFELEGSVID----------------------------------- 339
Cdd:PRK09603 307 K--EVLLDMLTQLDKNKLEKIHDlgVQEfVIINDLALGHDASIIHsfsadseslkllkqtekiddenalaairihkvmkp 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 340 -EPVEIQSIKVYVPN---DEEGRTTTVIGNA---------LPDSeVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNR 406
Cdd:PRK09603 385 gDPVTTEVAKQFVKKlffDPERYDLTMVGRMkmnhklglhVPDY-ITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNR 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 407 RLRSVGELLQNQFRIGLSRMERVVRERMSIQDT--DSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRR 484
Cdd:PRK09603 464 RIRAVGELLANELHSGLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRR 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 485 LSALGPGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVDldTNSITDQIDYLT 564
Cdd:PRK09603 544 LSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVV--DGKVVGETIYLT 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 565 ADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQR 644
Cdd:PRK09603 622 AIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQR 701
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 645 QAVPLMNPEAPFVGTGMEHVAARDSGAAITAKHRGRVEHVESNEILVrrLVEEngtEHEGELDRYPLAKFKRSNSGTCYN 724
Cdd:PRK09603 702 QAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI--LGEG---KEEAYIDAYSLQKNLRTNQNTSFN 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 725 QRPIVSIGDVVEYNEILADGPSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLG 804
Cdd:PRK09603 777 QVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHG 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 805 PEEITRDIPNVSESALKNLDDRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGG 884
Cdd:PRK09603 857 VEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEG 936
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 885 IVLDVKVF---------------------------------NRE------------------------------------ 895
Cdd:PRK09603 937 TVIDVKVFtkkgyekdarvlsayeeekakldmehfdrltmlNREellrvssllsqaileepfshngkdykegdqipkeei 1016
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 896 ------------------------------------------------EGDDTLSPGVNQLVRVYIVQKRKIHVGDKMCG 927
Cdd:PRK09603 1017 asinrftlaslvkkyskevqnhyeitknnfleqkkvlgeeheeklsilEKDDILPNGVIKKVKLYIATKRKLKVGDKMAG 1096
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 928 RHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNL------------------------ 983
Cdd:PRK09603 1097 RHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFgkqiasmledktkdfakelrakml 1176
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 984 ----------------------------------GIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNR 1029
Cdd:PRK09603 1177 eianainekdpltihalencsdeelleyakdwskGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRER 1256
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1030 ISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRVKT 1109
Cdd:PRK09603 1257 VNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENA 1336
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|....
gi 394298807 1110 YESIVKGENISRPSVPESFRVLMKELQSLGLDVKVM--DEHDNEIEMADVDDED 1161
Cdd:PRK09603 1337 YRAIAKGEQVGESEIPETFYVLTKELQSLALDINIFgdDVDEDGAPKPIVIKED 1390
|
|
| 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: 997.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 29 LIEIQTKSYDWFLKEGLLEMFRDISPIEDFT--GNLSLEFVDYRLGEPKYDL---------EESKNRDATYAAPLRVKVR 97
Cdd:cd00653 1 LVKQQIDSFNYFLNVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 98 LIIKETGEVKEQEVFMGDFPLMTD------------------------TGTFVINGAERVIVSQLVRSPSVYFNEkiDKN 153
Cdd:cd00653 81 LTVNDKGKIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQRSPNVIIVE--DSK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GRENYDATIIPN----RGAWLEYETDA-KDVVYVRIDRTRKlpltvllralgfstdqeivdllgdseylrntlekdgten 228
Cdd:cd00653 159 GKRIYTKTSIPSyspyRGSWLEVKSDKkKDRIYVRIDLKRQ--------------------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 229 tEQALLEIYERLRpgepptvenaksllysrffdpkrydlasvgrykankklhlkhrlfnqklaepivnsetgeivvdegt 308
Cdd:cd00653 200 -EEALKYIGKRFE------------------------------------------------------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 309 vldrrkldeimdvletnansevfelegsvidepveiqsikvyvpndeegrtttvignalpdsevkcitpaDIVASMSYFF 388
Cdd:cd00653 212 ----------------------------------------------------------------------DLIYMIRKLI 221
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 389 NLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERMSIQDTDS--ITPQQLINIRPVIASIKEFFGSSQ- 465
Cdd:cd00653 222 LLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNw 301
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 466 -----------LSQFMDQANPLAELTHKRRLSAlgpGGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534
Cdd:cd00653 302 gskrflmqrsgLSQVLDRLNPLSELSHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMA 378
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 535 RVNefGFIETPYRKVDLDTnsitdqidyltadeedsyvvaqansrldengrflddevvcrfrgnntvmakekmDYMDVSP 614
Cdd:cd00653 379 RIS--GRIERPYRIVEKEV------------------------------------------------------THIEISP 402
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 615 KQVVSAATACIPFLENDDSNRALMGANMQRQAVP----------------LMNPEAPFVGTGMEHVAARDsgaaitakhr 678
Cdd:cd00653 403 SQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpalnqqyrmdtklylLLYPQKPLVGTGIEEYIAFG---------- 472
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 679 grvehvesneilvrrlveengtehegeldryplakfkrsnsgtcynqrpivsigdvveyneiladgpsmelgEMALGRNV 758
Cdd:cd00653 473 ------------------------------------------------------------------------ELPLGQNA 480
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 759 VVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITR-DIPNVSESALKNLDDRGIVYVGAEVKD 837
Cdd:cd00653 481 IVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEP 560
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 838 GDILVGKVTPKGVTELTAeerllhaIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNREegddtLSPGVNQLVRVYIVQKR 917
Cdd:cd00653 561 GDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVDDVKIFSRE-----LNDGGNKLVKVYIRQKR 628
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 918 KIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGAND 997
Cdd:cd00653 629 KPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFGDATPFDGAEE 708
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 998 DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGE 1077
Cdd:cd00653 709 EDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGE 788
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 394298807 1078 MEVWALEAYGAAYTLQEILTYKSDDTVGRVKTYESIV----------KGENISRPSVPESFRVLMKELQSLGLDVKVM 1145
Cdd:cd00653 789 MERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| 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: 990.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 14 RRNYARISEVLE-LPNLIEIQTKSYDWFL-----KEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYDLEESKNRDAT 87
Cdd:PRK14844 16 RVSYSRSIDLKDsLLDLVKVQKESYDSFTpknkgNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGIT 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 88 YAAPLRVKVRLI-------------IKETGE----------VKEQEVFMGDFPLMTDTGTFVINGAERVIVSQLVRSPSV 144
Cdd:PRK14844 96 FSAQVIASIRLVimqdgisldeyksIKESGDhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGV 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 145 YFNE---KIDKNGRENYDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFST------------------ 203
Cdd:PRK14844 176 FFDSdkgKTYNSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNndildrfyekikyikhkd 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 204 --------------------------------------------DQEI-------------------------------- 207
Cdd:PRK14844 256 gwkvpfvpdkfkgvrlpfdlmdvegnvllkanvritsrlakklyDNELkeylvpfdsicglflaedlidsasstkilsag 335
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 208 -----------------------VDLLGDSEYLRNTLEKDGTENTEQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKR 264
Cdd:PRK14844 336 esikledikklellsideisvlnIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEY 415
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 265 YDLASVGRYKANKKLHLKHrlfnqklaepivnsetgeivvdegtvldrrkldeimdvletnansevfelegsvidepvei 344
Cdd:PRK14844 416 YDLSNIGRLKLNSYLGLNY------------------------------------------------------------- 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 345 qsikvyvpndeegrtttvignalpDSEVKCITPADIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLS 424
Cdd:PRK14844 435 ------------------------DEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLL 490
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 425 RMERVVRERMSIQDTDSITPQQLINIRPVIASIKEFFGSSQLSQFMDQANPLAELTHKRRLSALGPGGLTRERAQMEVRD 504
Cdd:PRK14844 491 KLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRD 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 505 VHYSHYGRMCPIETPEGPNIGLINSLSSYARVNEFGFIETPYRKVdlDTNSITDQIDYLTADEEDSYVVAQANSRLDENG 584
Cdd:PRK14844 571 VHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKV--VNRVVTDQIEYLSAIDEGLYYIADTSAKLDENN 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 585 RFLDDEVVCRFRGNNTVMAKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLMNPEAPFVGTGMEHV 664
Cdd:PRK14844 649 CFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESF 728
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 665 AARDSGAAITAKHRGRVEHVESNEILVRRLvEENGTEHEGeLDRYPLAKFKRSNSGTCYNQRPIVSIGDVVEYNEILADG 744
Cdd:PRK14844 729 VASGSGAVVLAKRDGIVDSSDSNSIVIRAF-DKERVNYLD-VDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADG 806
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 745 PSMELGEMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPEEITRDIPNVSESALKNLD 824
Cdd:PRK14844 807 PAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLD 886
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 825 DRGIVYVGAEVKDGDILVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFNR---------- 894
Cdd:PRK14844 887 DSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRrgveeneral 966
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 --------------------------------------------------------------------------------
Cdd:PRK14844 967 likqkeindfekerdyiinvtseyfydelkkllinsgsqdrekfdsiereqwwgiglknqsiseqvkslkkdfdekvsha 1046
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 895 -----------EEGDDtLSPGVNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVP 963
Cdd:PRK14844 1047 iaqfkrkveklHEGYD-LPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVP 1125
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 964 SRMNIGQVLELHLGMAAKNL------------------------------------------------------------ 983
Cdd:PRK14844 1126 SRMNVGQILETHVGWACKKLgekvgnildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpn 1205
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 984 ---------------------------------------------------------------GIHVASPVFDGANDDDV 1000
Cdd:PRK14844 1206 knalndelnelvenylnscksaysnlrnflievyscgsnvsicnnirdisdnnliefarklrdGIPVAAPVFEGPKDEQI 1285
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1001 WSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEV 1080
Cdd:PRK14844 1286 AKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMEC 1365
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1081 WALEAYGAAYTLQEILTYKSDDTVGRVKTYESIVKGENISRPSVPESFRVLMKELQSLGLDVkvmDEHDNEIEMADVDDE 1160
Cdd:PRK14844 1366 WALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNV---DLKQNDVVIEDISHT 1442
|
1530 1540
....*....|....*....|....
gi 394298807 1161 DAAE--RKVDLQQKSaPESQKETT 1182
Cdd:PRK14844 1443 NIAQsfNEVSISIAS-PESIKRMS 1465
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
674-1069 |
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: 562.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 674 TAKHRGRVEHVESNEILVRRLVEEngteheGELDRYPLAKFKRSNSGT---CYNQRPIVSIGDVVEYNeiladgpsmeLG 750
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGK------QAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGAVEAGG----------FG 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 751 EMALGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYEseARDTKLGP-EEITRDIPNVSESALKNLDDRGIV 829
Cdd:pfam00562 65 ELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIV 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 830 YVGAEVKDGDILVGKVTPkgvTELTaeeRLLHAIFGEKAREVRDTSLRVPHGAGGIVLDVKVFnreegddTLSPGVNQLV 909
Cdd:pfam00562 143 RVGAEVKPGDILVGKVGP---TELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF-------ELPPGGIKMV 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 910 RVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVAS 989
Cdd:pfam00562 210 KVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDA 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 990 PVFDGAND--DDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGK 1067
Cdd:pfam00562 290 TPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGR 369
|
..
gi 394298807 1068 AQ 1069
Cdd:pfam00562 370 AR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
28-1145 |
2.22e-127 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 418.21 E-value: 2.22e-127
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 28 NLIEIQTKSYDWFLKEGLLEMFRDISPIEDFTGNLSLEFVDYRLGEPKYD-LEESKN---------RDATYAAPLRVKVR 97
Cdd:PRK08565 13 GLVRQHLDSYNDFIERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKeADGSERpitpmearlRNLTYAAPLYLTMI 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 98 LIIkETGEVKEQEVFMGDFPLMTDT------------------------GTFVINGAERVIVSQLVRSPSVYFNEKIDKN 153
Cdd:PRK08565 93 PVE-NGIEYEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNRVLVDKGEAG 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GRENYDATIIPNRGAW-----LEYETDAkdVVYVRIDRTR-KLPLTVLLRALGFSTDQEIVDLLGDSEYLRNTLEkdgtE 227
Cdd:PRK08565 172 SSITHTAKVISSRAGYraqvtVERRKDG--TIYVSFPAVPgKIPFVILMRALGLETDRDIVYAVSLDPEIQQELL----P 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 228 NTEQALlEIYerlrpgepPTVENAKSLLYSRFfdpkrydlaSVGRYKANkklhlkhRLfnqklaepivnsetgeivvdeg 307
Cdd:PRK08565 246 SLEQAS-SIA--------ATVEDALDYIGKRV---------AIGQPREY-------RI---------------------- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 308 tvldrRKLDEIMDvletnansevfelegsvidepveiqsiKVYVPNdeegrtttvIGNALPDSEVKCITPADIVASMsyf 387
Cdd:PRK08565 279 -----ERAEQILD---------------------------KYLLPH---------LGTSPEDRIKKAYFLGQMASKL--- 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 388 FNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRiglSRMERVVRErMSIQDTDSITPQQLINIRPVIAS--IKEFF---- 461
Cdd:PRK08565 315 LELYLGRREPDDKDHYANKRLRLAGDLLAELFR---VAFKQLVKD-LKYQLEKSYARGRKLDLRAIVRPdiITERIrhal 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 462 -------GSSQLSQFMDQANPLAELTHKRRLsaLGPggLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSYA 534
Cdd:PRK08565 391 atgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 535 R----VNEFGFIETPYR------------------KVDLDTN----------------------SITDQID--YLTADEE 568
Cdd:PRK08565 467 QisvgVDEEEVEEILYElgvvpveeareeeyiswsRVYLNGRligyhpdgeelaekirelrrsgKISDEVNvaYIETGEI 546
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 569 DSYVVAQANSRLD------ENGRF-LDDEVVCRFRG----------------------NNTVMAKEKMD------YMDVS 613
Cdd:PRK08565 547 NEVYVNCDSGRVRrplivvENGKPkLTREHVEKLKKgeltfddlvkmgvieyldaeeeENAYVALDPEDltpehtHLEIW 626
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 614 PKQVVSAATACIPFLENDDSNRALMGANMQRQAVPLmnPEAPFvgtgmehvaardsgaaitakhRGRVEhvesneilVRr 693
Cdd:PRK08565 627 PPAILGITASIIPYPEHNQSPRNTYQAAMAKQSLGL--YAANF---------------------RIRTD--------TR- 674
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 694 lveengteheGELDRYPlakfkrsnsgtcynQRPIVS--IGDVVEYNeilaDGPSmelgemalGRNVVVGFMTWDGYNYE 771
Cdd:PRK08565 675 ----------GHLLHYP--------------QRPLVQtrALEIIGYN----DRPA--------GQNAVVAVLSYTGYNIE 718
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 772 DAVIMSERLVKDDVYTSIHIEEYESEARDTKLGPE-EITRDIPNVS----ESALKNLDDRGIVYVGAEVKDGDILVGKVT 846
Cdd:PRK08565 719 DAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVRgyrgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTS 798
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 847 PKGVTELTAEERLlhaifGEKARevRDTSLRVPHGAGGIVLDVKVfnreegddTLSPGVNQLVRVYIVQKRKIHVGDKMC 926
Cdd:PRK08565 799 PPRFLEELEELSL-----GLQER--RDTSVTVRHGEKGIVDTVLI--------TESPEGNKLVKVRVRDLRIPELGDKFA 863
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 927 GRHGNKGVISKIVPEEDMPYLPDGRPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEE 1006
Cdd:PRK08565 864 SRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEELRKELLK 943
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1007 AGMARDGKTVLYDGRTGEPFDNRISVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1086
Cdd:PRK08565 944 LGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGH 1023
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 394298807 1087 GAAYTLQEILTYKSDDTV--------------GRVKTYESIVKGE--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 |
3.52e-91 |
|
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: 305.80 E-value: 3.52e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 560 IDYLTADEEDSYVVAQANSRLdengrflddevvcrfrgnntvmaKEKMDYMDVSPKQVVSAATACIPFLENDDSNRALMG 639
Cdd:TIGR03670 92 IEYLDAEEEENAYIALDPEEL-----------------------TPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMG 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 640 ANMQRQAVPLMnpeapfvgtgmehvaardsgaaiTAKHRGRVEHvesneilvrrlveengtehEGELDRYPlakfkrsns 719
Cdd:TIGR03670 149 AAMAKQSLGLY-----------------------AANYRIRLDT-------------------RGHLLHYP--------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 720 gtcynQRPIVS--IGDVVEYNEILAdgpsmelgemalGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESE 797
Cdd:TIGR03670 178 -----QKPLVKtrVLELIGYDDRPA------------GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAE 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 798 ARDTKLGPE-EITRDIPNV----SESALKNLDDRGIVYVGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKARE 870
Cdd:TIGR03670 241 ERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSPP---------RFLeeLREFGLVTER 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 871 VRDTSLRVPHGAGGIVLDVKVFNREEGddtlspgvNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950
Cdd:TIGR03670 312 RRDTSVTVRHGEKGIVDKVIITETEEG--------NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDG 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 951 RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRI 1030
Cdd:TIGR03670 384 IVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEI 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1031 SVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTVGRV--- 1107
Cdd:TIGR03670 464 FIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVVYVcen 543
|
570 580 590 600
....*....|....*....|....*....|....*....|....*....
gi 394298807 1108 -----------KTYESIVKGE--NISRPSVPESFRVLMKELQSLGLDVK 1143
Cdd:TIGR03670 544 cghiawedkrkGTAYCPVCGEtgDISPVEMSYAFKLLLDELKSLGISPR 592
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
560-1148 |
1.59e-83 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 284.93 E-value: 1.59e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 560 IDYLTADEEDSYVVAQANSRLDENgrflddevvcrfrgnNTvmakekmdYMDVSPKQVVSAATACIPFLENDDSNRALMG 639
Cdd:PRK07225 98 IEYLDAEEEENAYIAVYEEDLTEE---------------HT--------HLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 640 ANMQRQAVPLMnpeapfvgtgmehvaardsgaaiTAKHRGRvehvesneilvrrlveengTEHEGELDRYPlakfkrsns 719
Cdd:PRK07225 155 AGMIKQSLGLP-----------------------AANYKLR-------------------PDTRGHLLHYP--------- 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 720 gtcynQRPIVS--IGDVVEYNEILAdgpsmelgemalGRNVVVGFMTWDGYNYEDAVIMSERLVKDDVYTSIHIEEYESE 797
Cdd:PRK07225 184 -----QVPLVKtqTQEIIGFDERPA------------GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 798 ARDTKLGPE-EITRDIPNV----SESALKNLDDRGIVYVGAEVKDGDILVGKVTPKgvteltaeeRLL--HAIFGEKARE 870
Cdd:PRK07225 247 ERRYPGGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPP---------RFLeePDDFGISPEK 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 871 VRDTSLRVPHGAGGIVLDVKVFNREEGddtlspgvNQLVRVYIVQKRKIHVGDKMCGRHGNKGVISKIVPEEDMPYLPDG 950
Cdd:PRK07225 318 RRETSVTMRSGEEGIVDTVILTETEEG--------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESG 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 951 RPIDIMLNPLGVPSRMNIGQVLELHLGMAAKNLGIHVASPVFDGANDDDVWSTIEEAGMARDGKTVLYDGRTGEPFDNRI 1030
Cdd:PRK07225 390 VVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEI 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1031 SVGVMYMLKLAHMVDDKLHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEILTYKSDDTV------ 1104
Cdd:PRK07225 470 FVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEiyvcak 549
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 394298807 1105 -GRVKTYESI-------VKGE--NISRPSVPESFRVLMKELQSLGLDVKVMDEH 1148
Cdd:PRK07225 550 cGMIAIYDKKrnrkycpICGEetDIYPVEMSYAFKLLLDELKSLGIAPRLELED 603
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
28-453 |
1.25e-43 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 164.09 E-value: 1.25e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 28 NLIEIQTKSYDWFLKEGLLEMFRDISPIE---------DFTGNLSLEFVDYRLGEPKYD----------LEESKNRDATY 88
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIEsefeiqhpgENGDKLSLKFGQIRLGKPMFDetdgstreiyPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 89 AAPLRVKVRLIIKETGEVKEQEVFMGDFPLMTDT------------------------GTFVINGAERVIVSQLVRS--- 141
Cdd:pfam04563 81 SAPLYVDLELSVYNGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQEHRSrnh 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 142 PSVYFNEKIDKNG-----RENYDATIIPNRGAWLE-YETDAKDVVYVRIDRTRK-LPLTVLLRALGFSTDQEIVDLL--- 211
Cdd:pfam04563 161 PIVFKKADPKKRGsvasvRSSAEISVRPDSTSWVNvLEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREIFELIcyd 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 212 -GDSEYLrntlekdgtenteQALLEIYERLRPGEPPTVENAKSLLYSRFFDPKRYDLASVGRYKANKKLhLKHRLFnqkl 290
Cdd:pfam04563 241 vNDQQLQ-------------EELLPSLEEGFKIRIQTQEQALDYIGGRGRAIFRMGRPREPRIKYAEEI-LQKEVL---- 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 291 aepiVNSETGEivvdegtvLDRRKldeimdvletnanSEVFelegsvidepveiqsikvyvpndeegrtttvignalpds 370
Cdd:pfam04563 303 ----PHLGTYE--------LDETK-------------KAYF--------------------------------------- 318
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 371 evkcitpadIVASMSYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVRERM--SIQDTDSITPQQLI 448
Cdd:pfam04563 319 ---------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLV 389
|
....*
gi 394298807 449 NIRPV 453
Cdd:pfam04563 390 NAKPI 394
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
29-538 |
2.93e-38 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 150.49 E-value: 2.93e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 29 LIEIQTKSYDWFLKEGLLEMFRDISPIE-DFTGNLSLEFVDYRLGEP----------KYDLEESKNRDATYAAPLRVKVR 97
Cdd:PRK09606 18 LVRHHIDSYNDFVDNGLQKIIDEQGPIEtEIEDGVYVELGKIRVGKPvvkeadgserEIYPMEARLRNLTYSAPLYLEMS 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 98 lIIKETGEVKEQEVFMGDFPLMTDT------------------------GTFVINGAERVIVSQLVRSPSVYFNEKIDKN 153
Cdd:PRK09606 98 -PVEGGEEEEPEEVYIGELPVMVGSkicnlyglseeelievgedpldpgGYFIVNGSERVLMTLEDLAPNKILVEKDERY 176
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 154 GRENYDATIIPNRG---AWLEYETDAKDVVYVRIDR-TRKLPLTVLLRALGFSTDQEIVDLLGDSE----YLRNTLEKDG 225
Cdd:PRK09606 177 GDRIEVAKVFSQRRgyrALVTVERNRDGLLEVSFPSvPGSIPFVILMRALGLETDEEIVEAVSDDPeivkFMLENLEEAE 256
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 226 TENTEQALLEIYERLRPGEpptvenaksllysrffdPKRYDLasvgrykankklhlkhrlfnqKLAEpivnsetgeivvd 305
Cdd:PRK09606 257 VDTQEEALEYIGKRVAPGQ-----------------TKEYRI---------------------KRAE------------- 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 306 egTVLDRRKLDEImdvletnansevfelegsvidepveiqsikvyvPNDEEGRtttvignalpdsevkcITPADIVASM- 384
Cdd:PRK09606 286 --YVIDRYLLPHL---------------------------------GVEPEVR----------------RAKAHYLGRMa 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 385 SYFFNLLNGIGYTDDIDHLGNRRLRSVGELLQNQFRIGLSRMERVVR---ERMSIQDTD-SItpQQLI-------NIRPV 453
Cdd:PRK09606 315 EACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqlERANMRNRElSI--KTAVrsdvlteRLEHA 392
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 454 IASIKEFFGSSQLSQFMDQANPLAELTHKRRLSAlgpgGLTRERAQMEVRDVHYSHYGRMCPIETPEGPNIGLINSLSSY 533
Cdd:PRK09606 393 MATGNWVGGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQM 468
|
....*
gi 394298807 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 |
1.92e-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: 1.92e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 394298807 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 |
9.62e-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: 121.93 E-value: 9.62e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 1071 GGQRFGEMEVWALEAYGAAYTLQEILTYKSD----DTVGRVKTYES-----IVKGENISRP-SVPESFRVLMKELQSLGL 1140
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPgYIPESFKLLFQELQSLGI 80
|
....*..
gi 394298807 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 |
7.51e-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: 107.07 E-value: 7.51e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 394298807 546 YRKVDLDTnsITDQIDYLTADEEDSYVVAQANSRLDENGRFLDDEVVCRFRGNNTVMAKEKMDYMDVS 613
Cdd:pfam10385 1 YRKVEDGK--VTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
140-409 |
1.37e-24 |
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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: 102.04 E-value: 1.37e-24
10 20 30 40 50 60 70 80
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gi 394298807 140 RSPSVYFNEKIDKNGREN-YDATIIPNRGAWLEYETDAKDVVYVRIDRTRKLPLTVLLRALGFSTDQEIVDLLGDS---- 214
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIAtYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDREILDRLCYDfndp 80
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 215 ----EYLRNTLEKDGTENTEQALLEIYE--RLRPGEPPTVENAKSLLYSRFfdpkrydlasvGRYKANKKLHLkhrlfnq 288
Cdd:pfam04561 81 qmleLLKPELEEAENIYTQEEALDYIGKgfALRRGEEPRLQRAREILYSRD-----------PKYNLNKHLGL------- 142
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170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 394298807 289 klaepivnsetgeivvdegtvldrrkldeimdvletnansevfelegsviDEPVEIQSIKVYvpndeegrtttvignalp 368
Cdd:pfam04561 143 --------------------------------------------------NEPFENERLKAQ------------------ 154
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250 260 270 280
....*....|....*....|....*....|....*....|.
gi 394298807 369 dsevkcitpaDIVASMSYFFNLLNGIGYTDDIDHLGNRRLR 409
Cdd:pfam04561 155 ----------DILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
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