|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
5-1374 |
0e+00 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 2777.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 5 MAERANLVFHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSL 84
Cdd:CHL00117 1 MAERANLVFHNKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 85 ILEKHHHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQM 164
Cdd:CHL00117 81 ILEKHYHYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 165 IDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSPRNGMMPERIF 244
Cdd:CHL00117 161 IDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGMMIERIL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 245 IQTLIGRVLADDIYMGPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGI 324
Cdd:CHL00117 241 IQTLIGRVLADDIYIGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGI 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 325 IAGQSIGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDLVHPTRTRHGHPAFLCYIDLYVTIESEDILHNVNI 404
Cdd:CHL00117 321 IAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRAPFNGKIKFNEDLVHPTRTRHGHPAFLCKIDLYVTIESEDIIHNVNI 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 405 PPKSFLLVQNDQYVESEQVIAEIRAGTSTLNFKERVRKHIYSDSEGEMHWSTDVYHAPEFTYGNVHLLPKTSHLWILSGG 484
Cdd:CHL00117 401 PPKSLLLVQNDQYVESEQVIAEIRAGTSTLNFKEKVRKHIYSDSEGEMHWSTDVYHAPEFTYGNVHLLPKTSHLWILSGG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 485 PCRSSVAPFSLHKDQDQMNVHsLSVERRYISNLSVTN---DQVRHKFFSSYFsgKKEGRIPDYSELNRIIGTSRCNLIYP 561
Cdd:CHL00117 481 VYRSSLVSFSLHKDQDQINIH-LSVERRYISRLSVINtnnGQVRHKLFSSDG--KKEKRILDYSELNRIISNGHCNFIYP 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 562 AILYENSDLLAKRRKNRFIIPFQSIQEREKELMPRsGISIEIPINGIFRRNSILAYFDDPRYRRKSSGITKYGTIEVHSI 641
Cdd:CHL00117 558 AILHENSDLLAKRRRNRFLIPFQSIQEREKELMPC-GISIEIPINGILRRNSIFAYFDDPRYRTKSSGITKYGTIEVDSI 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 642 VKKEDLIEYRGVKEFRPKYQMKVDRFFFIPEEVHILPGSSSIMVRNNSIIGVNTQITLNTRSRVGGLVRVERKKKRIELK 721
Cdd:CHL00117 637 VKKEDLIEYRGVKEFKPKYQMKVDRFFFIPEEVHILPESSSILVRNNSIIGVDTQITLNIRSKVGGLVRIEKKKKRIELK 716
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 722 IFSGDIHFPGETDKISRHSGILIPPGTGKANSKESKKLKSWIYVQRITPTKKKYFVLVRPVVTYEIADGINLATLFPQDL 801
Cdd:CHL00117 717 IFSGDIHFPGETDKISRHSGILIPPGTGKKNSKESKKIKNWIYVQRITPTKKKYFVLVRPVVTYEIADGINLATLFPQDL 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 802 LQERDNVQLRVVNYILYGNSKPIRRISdtSIQLVRTCLVLNWDQDKKSSSIEEAHASFVEVKTNGLIRDFLRIDLVKSPI 881
Cdd:CHL00117 797 LQEKDNLQLRVVNYILYGNGKPIRGIS--SIQLVRTCLVLNWDQDKKSSSIEEARASFVEVRTNGLIRDFLRINLVKSPI 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 882 SYTGKRNDPSGSGLI--SDSGSDRTNinpfysIYSKARIQ-QSLSQNQGTIRTLLNRNKECQSLIILSSSNCSRMGPF-- 956
Cdd:CHL00117 875 SYIRKRNDPSSSGLLvqSNNFLDSTN------IYSKAEIQsQSLSQNQGTIRTLLNRNKESQSLLILSSSDCFRIGPFng 948
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 957 NSVKYHNvIKESikkDPLIPIRNLLGPLGTALQIANFYSFYHLITHNQILVTNYLQLDNLK---QAQVLKYYLMDENGRI 1033
Cdd:CHL00117 949 KKSKYHN-IKES---NPLIPIRNSLGPLGTVLQIANFSSSYHLLTHNQILVTKYLQLDNLKqtfQVKVLKYYLIDENGKI 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1034 YNPDPCSNILLNPFNLNWYFLHHNYCEETSTKMSLGQFICENVCIAKNGPHlKSGQVLIVQVDYVVIRLAKPYLATPGAT 1113
Cdd:CHL00117 1025 YNPDPCSNIILNPFNLNWYFLHHNYCEETSTIISLGQFICENVCISKNGPH-KSGQIIIVQVDSLVIRSAKPYLATPGAT 1103
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1114 VHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVRSIDSISMNLEKRVKGWNEHITRILGIPWGFLIGAELTI 1193
Cdd:CHL00117 1104 VHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARSIDSISMNLEKRLEGWNERITRILGIPWGFLIGAELSI 1183
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1194 VQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNVFSPGELIGLLRAERTGRALEEAICYRAILLGI 1273
Cdd:CHL00117 1184 AQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPILLGI 1263
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1274 TRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKGLVHRSRQHNNILLETKKKNLFEGE 1353
Cdd:CHL00117 1264 TKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSKQHKNKNLEIKKKNLFEGE 1343
|
1370 1380
....*....|....*....|.
gi 1573382102 1354 MRDILFHHRELFDSCVSKNFH 1374
Cdd:CHL00117 1344 MRDILFHHRELFDSCISKNFH 1364
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
12-1329 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 703.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 12 VFHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKHHH 91
Cdd:PRK02597 2 IFRNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 92 YGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQS 171
Cdd:PRK02597 82 RGEITEVERFQKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 172 NLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSPRNGMMPERI-FIQTLIG 250
Cdd:PRK02597 162 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIpLGDRLLG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 251 RVLADDIyMGPR--CIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQ 328
Cdd:PRK02597 242 RVLAEDV-VDPEgeVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 329 SIGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDL-VHPTRTRHGHPAFLCYIDLYVTIESEDILHN--VNIP 405
Cdd:PRK02597 321 SIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFAGTVEFGKKLrTRPYRTRHGVEALQAEVDFDLVLKPSGKGKPqkIEIT 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 406 PKSFLLVQNDQYVESEQVIAEIRAG---TSTlnfkERVRKHIYSDSEGEMHWSTDVyhAPEFT--YGNV-HLLPKTSHLW 479
Cdd:PRK02597 401 QGSLLFVDDGQTVEADQLLAEVAAGavkKST----EKATKDVICDLAGEVRFADLI--PEEKTdrQGNTtRKAQRGGLLW 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 480 ILSGG-----PCRSSVApfslhKDQDQMNVHSLSVERRYISNlsvtndqvrhkffssyFSGkkEGRIPDYSELNR---II 551
Cdd:PRK02597 475 VLSGDvynlpPGAEPVV-----SNGDRVEEGDVLAETKLVSE----------------HGG--VVRLRESSGDSReveII 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 552 GTSrcnliypaILYENSDLLAkrrknrfiipfQSIQEREKELmprsgisIEIPINGIFRRNS----------ILAYFDDP 621
Cdd:PRK02597 532 TAS--------VLLDQAKVLE-----------ESTHGREQYN-------LETKDGQRFRLNAtpgtkvqngeVVAELIDD 585
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 622 RYRRKSSGITKYGTIEvhsiVKKEdlieyRGVKEfrpKYQM-KVDRFFFIPEEVH-ILPGSSSIMVRNNSIIGVNTQITL 699
Cdd:PRK02597 586 RYRTKTGGLVKYAGLE----VKKA-----GSAKN---GYEVsKGGTLLWIPEETHeVNKDISLLMVEDGQYVEAGTEVVK 653
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 700 NTRSRVGGLVRVERKKKRI-ELKIFSGDIHFPGETDKISRH--SGILIPPGTGKANSKESKKLKswiYVQRITPTKKKYf 776
Cdd:PRK02597 654 DIFCQTSGVVEVTQKNDILrEIIIKPGELHLCDDPEALERFtgDGQLVNPGEEVLPGVVTDELR---YVEWVETPEGPG- 729
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 777 VLVRPVVTYEIADGinlATLFPQDLLQERD--NVQLRVVNYILYGNSKPIRriSDTSIQLVRTCLVLNWDQDkksssiee 854
Cdd:PRK02597 730 LLLRPVEEFTIPDE---PQVPSQGSVKQEKgrSIGLRAVQRLPYKDGERVK--SVEGVELLRTQLVLEIFDT-------- 796
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 855 ahasfvevkTNGLIRDflrIDLVKSPisytgkrndpsgsglisdsgsdrtninpfysiyskariqqslsqnqgtirtlln 934
Cdd:PRK02597 797 ---------TPQLTAD---IELIPDE------------------------------------------------------ 810
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 935 RNKECQ--SLIILSSSncsrmgpfnsvkyhnVIKESIKKDPLipirnllgplgtalqianfysfyHLITHNQILVTNYLQ 1012
Cdd:PRK02597 811 KDKEIQrlQLVILESL---------------LVRRDTASDSS-----------------------HGSTHTELLVKDGQQ 852
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1013 LD----------NLKQAQVLKYYLM-DENGR---IYNPDPCSNILLNpfnlnwyflhhnyceeTSTKMSLGQFICENVCI 1078
Cdd:PRK02597 853 IKpgdvvartqiLCKEAGEVRGIRVgGEAVRrllVERDEDTITIPLS----------------GKPTVKVGDLVVAGDEL 916
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1079 AKNGPHLKSGQVLIVQVDYVVIRLAKPYLATPGATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVR--- 1155
Cdd:PRK02597 917 APGVPAPESGEVEAVSGGSVTLRLGRPYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARkpk 996
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1156 -----------------SIDSISMN-LEK---------------------RVKGwNEHIT-------RILGIPWGFLI-- 1187
Cdd:PRK02597 997 escilakkpgtvqikygDDESVDVKvIESdgtiteypilpgqnvmvsdgqQVDA-GEPLTdgpinphELLEIFFEDLRdr 1075
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1188 -----GAELTI--VQSRisLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVsEDGMSNVFSPGELIGLLRAERTGRAL 1260
Cdd:PRK02597 1076 kglyeAALEALqkLQRF--LVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRI-DDGGDTTMLPGELIELRQVEQVNEAM 1152
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1573382102 1261 eeAIC------YRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKG 1329
Cdd:PRK02597 1153 --AITggapaeYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSG 1225
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
12-1331 |
0e+00 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 680.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 12 VFHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKHHH 91
Cdd:TIGR02388 1 IFKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 92 YGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQS 171
Cdd:TIGR02388 81 RGEITEVERFQKVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 172 NLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSPRNGMMPERIFIQTLIGR 251
Cdd:TIGR02388 161 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKISLGDRLLGR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 252 VLADDIyMGPR--CIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQS 329
Cdd:TIGR02388 241 LVAEDV-LHPEgeVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQS 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 330 IGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDL-VHPTRTRHGHPAFLCYIDLYVTIESE----DILHNVNI 404
Cdd:TIGR02388 320 IGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKLrTRGYRTRHGEDAKQVEVAGLLIIKPTgsitNKAQEIEV 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 405 PPKSFLLVQNDQYVESEQVIAEIRAGTSTLNfKERVRKHIYSDSEGEMHWSTDVYHAPEFTYGNVHLL-PKTSHLWILSG 483
Cdd:TIGR02388 400 TQGSLLFVEDGQTVDAGQLLAEIALGAVRKS-TEKATKDVASDLAGEVKFDKVVPEEKTDRQGNTTRIaQRGGLIWVLSG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 484 G-----PCRSSVApfslhKDQDQMNVHSLSVERRYISNlsvtndqvrhkffssyFSGkkEGRIPDYSELNRIIgtsrcNL 558
Cdd:TIGR02388 479 EvynlpPGAEPVV-----KNGDRVEQGTVLAETKLSTE----------------HGG--VVRLPESVGDSREV-----EI 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 559 IYPAILYENSDLLAKRRKNR--FIIPFQSIQEREKELMPRSGISieipiNGifrrnSILAYFDDPRYRRKSSGITKYGTI 636
Cdd:TIGR02388 531 ITASVLLDQAKVIEESSQGRelYHIETADGQRFRLKAAPGTKVQ-----NG-----QVVAELIDDRYRTTTGGLLKYAGV 600
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 637 EVHSIVKKEDLIEYrgvkefrpkyqMKVDRFFFIPEEVH-ILPGSSSIMVRNNSIIGVNTQITLNTRSRVGGLVRVERKK 715
Cdd:TIGR02388 601 EVAKKGKAKQGYEV-----------SQGGTLLWIPEETHeINKDISLLMVEDGQYVEAGTEVVKDIFCQNSGIVEVTQKN 669
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 716 KRI-ELKIFSGDIHFPGETDKISRHSGILIPPG----TGKANSKESkklkswiYVQRITPTKKKYfVLVRPVVTYEIADG 790
Cdd:TIGR02388 670 DILrEIIVKPGEFHEVDDPEAVSTEEGTLLQPGeevlPGVVVDELS-------QVQYLETPEGPG-LLLRPVEEYTVPDE 741
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 791 INLATLFPQDllQER-DNVQLRVVNYILYGNSKPIRRISdtSIQLVRTCLVLNWDQDKKSSSIEeahasfVEVKTNGLIR 869
Cdd:TIGR02388 742 PEVPSQSSVS--QEKgRSIALRAVQRLPYKDGERVKSVE--GVELLRTQLVLEIFDEGPQLAAD------IELIQDEEDK 811
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 870 DFLRIDLV--KSPISYTGKRNDPS-GSGLISDSGSDRTNINPFYSIyskARiQQSLSQNQGTIRtLLNRNKEcqsliils 946
Cdd:TIGR02388 812 DIQRLQLVilESLVLRRDIASDSTqGSTHTSLLVKDGDLIKPGAVI---AR-TQILCKEAGVVQ-GIDSGGE-------- 878
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 947 ssncsrmgpfnsvkyhnvikesikkdpliPIRNLLgplgtalqianfysfyhLITHNQILVTnylqldNLKQAQVLKyyl 1026
Cdd:TIGR02388 879 -----------------------------SIRRLL-----------------VERNSDRLKV------NIKAKPVVK--- 903
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1027 mdengriynpdpcsnillnpfnlnwyflhhnyceetstkmsLGQFICENVCIAKNGPHLKSGQVLIVQVDYVVIRLAKPY 1106
Cdd:TIGR02388 904 -----------------------------------------TGDLVVAGDELAKGVKAEESGEIEEVASDYVILRIGRPY 942
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1107 LATPGATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVR-----SI----------------DSISMNLE 1165
Cdd:TIGR02388 943 RVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARkpkeaCIlakrpgvvqvkygtddESVSIKVI 1022
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1166 KR---------VKGWNEHIT-------------------RILGIPW-------GFLIGAELTIVQSRISLVNKIQKVYRS 1210
Cdd:TIGR02388 1023 ERdgtiseyplLPGQNIMVSdgqqvtggepltdgpinphDILDVFFsyykdqdGLYEAAQESLQKVQRFLVNEVQNVYQS 1102
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1211 QGVQIHNRHIEIIVRQITSKVLVsEDGMSNVFSPGELIGLLRAERTGRALeeAIC------YRAILLGITRASLNTQSFI 1284
Cdd:TIGR02388 1103 QGVDISDKHIEVIVRQMTSKVRI-DDAGDTTLLPGELVELRQVEQVNEAM--AITggapaqYTPVLLGITKASLNTDSFI 1179
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|....*..
gi 1573382102 1285 SEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKGLV 1331
Cdd:TIGR02388 1180 SAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYE 1226
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
12-426 |
7.99e-116 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 391.74 E-value: 7.99e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 12 VFHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKHHH 91
Cdd:PRK00566 568 INVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYR 647
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 92 YGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMT-DPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQ 170
Cdd:PRK00566 648 RGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDqESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIK 727
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 171 SNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSP--RNGMMPERIFiQTL 248
Cdd:PRK00566 728 SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAiiEGGEVIEPLE-ERI 806
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 249 IGRVLADDIYmGPRC---IAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGII 325
Cdd:PRK00566 807 LGRVLAEDVV-DPETgevIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVI 885
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 326 AGQSIGEPGTQLTLRTFHTGGV-FTGG---TAE--HVRAPSN--------GKIKFNEDlvhpTRTRHghpaflcyiDLYV 391
Cdd:PRK00566 886 AAQSIGEPGTQLTMRTFHTGGVdITGGlprVAElfEARKPKGpaiiaeidGTVSFGKE----TKGKR---------RIVI 952
|
410 420 430
....*....|....*....|....*....|....*
gi 1573382102 392 TIESEDIlHNVNIPPKSFLLVQNDQYVESEQVIAE 426
Cdd:PRK00566 953 TPDDGEE-REYLIPKGKHLLVQEGDHVEAGDKLTD 986
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
15-426 |
1.81e-98 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 342.41 E-value: 1.81e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 15 NKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKHHHYGN 94
Cdd:TIGR02386 562 NEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGL 641
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 95 VHAVEKLRQSIEIWYATSEYLRQEMNPNFRM-TDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSNL 173
Cdd:TIGR02386 642 ITDEERYRKVVSIWSETKDKVTDAMMKLLKKdTYKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSF 721
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 174 REGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSP-RNG------MMPERIFiq 246
Cdd:TIGR02386 722 REGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAiVEGkdeiieSLKDRIV-- 799
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 247 tliGRVLADDIY--MGPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGI 324
Cdd:TIGR02386 800 ---GRYSAEDVYdpDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGV 876
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 325 IAGQSIGEPGTQLTLRTFHTGGV------FTGG---TAE--HVRAPSN--------GKIKFNEDLVHPTRTrhghpaflc 385
Cdd:TIGR02386 877 IAAQSIGEPGTQLTMRTFHTGGVagasgdITQGlprVKElfEARTPKDkaviaevdGTVEIIEDIVKNKRV--------- 947
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 1573382102 386 yidLYVTIESEDIlHNVNIPPKSFLLVQNDQYVESEQVIAE 426
Cdd:TIGR02386 948 ---VVIKDENDEE-KKYTIPFGAQLRVKDGDSVSAGDKLTE 984
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
10-223 |
3.85e-94 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 318.31 E-value: 3.85e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 10 NLVFHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKH 89
Cdd:cd01609 447 GLPFINKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQ 526
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 90 HHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPI 169
Cdd:cd01609 527 YEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDK-DPFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPI 605
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1573382102 170 QSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTD 223
Cdd:cd01609 606 KSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
10-427 |
6.72e-90 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 317.87 E-value: 6.72e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 10 NLVFHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKH 89
Cdd:COG0086 569 EVPFYNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQ 648
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 90 HHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFrmtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPI 169
Cdd:COG0086 649 YAEGLITEPERYNKVIDGWTKASLETESFLMAAF---SSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPI 725
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 170 QSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSP--RNGMMPERIFiQT 247
Cdd:COG0086 726 GSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDRGITVTAikEGGEVIEPLK-ER 804
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 248 LIGRVLADDIYM--GPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGII 325
Cdd:COG0086 805 ILGRVAAEDVVDpgTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVI 884
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 326 AGQSIGEPGTQLTLRTFHTGGV-FTGGTAEHVRAPSNGKIKFNEDLVHPTRTRHGHPAFlCYIDLYVTIESEDILHNVNI 404
Cdd:COG0086 885 AAQSIGEPGTQLTMRTFHIGGAaSRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVS-RNSELVIVDDGGRREEEYKV 963
|
410 420
....*....|....*....|...
gi 1573382102 405 PPKSFLLVQNDQYVESEQVIAEI 427
Cdd:COG0086 964 PYGGVLVVVGGGVVVGGGIVAEW 986
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
13-347 |
5.61e-81 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 293.70 E-value: 5.61e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 13 FHNKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKHHHY 92
Cdd:PRK14906 672 YLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYED 751
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 93 GNVHAVEKLRQSIEIWYATSEYLRQEMNPNFrmtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSN 172
Cdd:PRK14906 752 GFLSERERHKQVVDIWTEATEEVGEAMLAGF---DEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKAN 828
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 173 LREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSPRNgmmPERIFIQTLIGRV 252
Cdd:PRK14906 829 FREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVK---PKGDVDTNLIGRC 905
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 253 LADDIY--MGPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQSI 330
Cdd:PRK14906 906 LLEDVCdpNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSI 985
|
330
....*....|....*..
gi 1573382102 331 GEPGTQLTLRTFHTGGV 347
Cdd:PRK14906 986 GEPGTQLTMRTFHSGGV 1002
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1139-1327 |
3.65e-71 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 236.66 E-value: 3.65e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1139 GDITQGLPKVEQVLEVRsidsismnlekrvKGWNEHITRILGIpwgfligaelTIVQSRISLVNKIQKVYRSQGVQIHNR 1218
Cdd:cd02655 36 TDITQGLPRVEELFEAR-------------KINPHDLLRIKFL----------GPEAVQKYLVEEIQKVYRSQGVNINDK 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1219 HIEIIVRQITSKVLVSEDGMSNvFSPGELIGLLRAERTGRAL----EEAICYRAILLGITRASLNTQSFISEASFQETAR 1294
Cdd:cd02655 93 HIEIIVRQMTSKVKIIDPGDSG-FLPGELVDLNEFEEENKRLlllgKKPAKYEPVLLGITKASLNTESFISAASFQETTK 171
|
170 180 190
....*....|....*....|....*....|...
gi 1573382102 1295 VLAKAALRGRIDWLKGLKENVVLGGMIPVGTGF 1327
Cdd:cd02655 172 VLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
21-366 |
3.36e-70 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 261.40 E-value: 3.36e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 21 TAMKRLISRLIDHF----GMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILEKHHHYGNVH 96
Cdd:PRK09603 1971 PMKKKDIGVLVDYVhkvgGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLT 2050
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 97 AVEKLRQSIEIWYATSEYLRQEMNPNFRM-TDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSNLRE 175
Cdd:PRK09603 2051 DQERYNKIIDTWTEVNDKMSKEMMTAIAKdKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKE 2130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 176 GLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISV------SPRNGMMPERIFiqtli 249
Cdd:PRK09603 2131 GLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEItdiavgSELIEPLEERIF----- 2205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 250 GRVLADDIY--MGPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAG 327
Cdd:PRK09603 2206 GRVLLEDVIdpITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAA 2285
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 1573382102 328 QSIGEPGTQLTLRTFHTGGVFTGGTAE-HVRAPSNGKIKF 366
Cdd:PRK09603 2286 QSIGEPGTQLTLRTFHVGGTASRSQDErEIVASKEGFVRF 2325
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
10-426 |
4.48e-64 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 241.45 E-value: 4.48e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 10 NLVFH--NKVIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLAQDAEQQSLILE 87
Cdd:PRK14844 2016 NLGFDliNQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFS 2095
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 88 KHHHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTD---PFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQM 164
Cdd:PRK14844 2096 MQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIYDgnsKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEI 2175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 165 IDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISV-SPRNGMMPERI 243
Cdd:PRK14844 2176 IETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVrATVEGSTIVAS 2255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 244 FIQTLIGRVLADDIY--MGPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEA 321
Cdd:PRK14844 2256 LESVVLGRTAANDIYnpVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEA 2335
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 322 VGIIAGQSIGEPGTQLTLRTFHTGGVFTGGT-AEHVRAPSNGKIKFNEDLVhpTRTRHGHPAFL---CYIDLYVTIESED 397
Cdd:PRK14844 2336 VGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVeSSNIIASINAKIKLNNSNI--IIDKNGNKIVIsrsCEVVLIDSLGSEK 2413
|
410 420
....*....|....*....|....*....
gi 1573382102 398 ILHNVniPPKSFLLVQNDQYVESEQVIAE 426
Cdd:PRK14844 2414 LKHSV--PYGAKLYVDEGGSVKIGDKVAE 2440
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1140-1336 |
1.80e-50 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 195.67 E-value: 1.80e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1140 DITQGLPKVEQVLEVRS-------------IDSISMNLEKRVKgwneHITRILGIPWGFLI----------------GAE 1190
Cdd:PRK00566 908 DITGGLPRVAELFEARKpkgpaiiaeidgtVSFGKETKGKRRI----VITPDDGEEREYLIpkgkhllvqegdhveaGDK 983
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1191 LT--------------IVQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNvFSPGELIGLLRAERT 1256
Cdd:PRK00566 984 LTdgsidphdilrvlgVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTD-FLPGELVDRSEFEEE 1062
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1257 GRALEEA----ICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKglVH 1332
Cdd:PRK00566 1063 NRKLIAEgkepATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLA--RY 1140
|
....
gi 1573382102 1333 RSRQ 1336
Cdd:PRK00566 1141 RNIK 1144
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1136-1329 |
4.20e-47 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 184.87 E-value: 4.20e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1136 SRSGDITQGLPKVEQVLEVRS---------IDSISMNLEKRVKG-------WNEHITRILGIPWGFLI----------GA 1189
Cdd:TIGR02386 901 GASGDITQGLPRVKELFEARTpkdkaviaeVDGTVEIIEDIVKNkrvvvikDENDEEKKYTIPFGAQLrvkdgdsvsaGD 980
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1190 ELT--------------IVQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNVFsPGELIGLLRAER 1255
Cdd:TIGR02386 981 KLTegsidphdllrikgIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLL-PGELIDIHEFNE 1059
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1573382102 1256 TGRALEEA----ICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKG 1329
Cdd:TIGR02386 1060 ENRKLLEQgkkpASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKT 1137
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
176-426 |
5.37e-40 |
|
RNA polymerase Rpb1, domain 5; 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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 156.36 E-value: 5.37e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 176 GLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTIRGISVSP----RNGMMPERIFIQTLI-- 249
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQflygEDGLDPLKIEKQGRFti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 250 ------------------------------GRVLADDIYMGPRCIAARNQDIGIGLVNRFITFRAQPISIRTPFTCRSTS 299
Cdd:pfam04998 81 efsdlkledkfkndllddllllsefslsykKEILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 300 WICRLCYGRSPTHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGGTAEhvrapsnGKIKFNE------DLVHP 373
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTL-------GVPRLKEiinvskNIKSP 233
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|...
gi 1573382102 374 TRTRHGHPaflcyidlyvtiESEDILHNVNIPPKSFLLVQNDQYVESEQVIAE 426
Cdd:pfam04998 234 SLTVYLFD------------EVGRELEKAKKVYGAIEKVTLGSVVESGEILYD 274
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1106-1327 |
6.29e-31 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 133.21 E-value: 6.29e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1106 YLATPGATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVR---------SIDSISMNLEKRVKGWNEHIT 1176
Cdd:PRK14844 2518 YFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARrpkehaivsEIDGYVAFSEKDRRGKRSILI 2597
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1177 RILG---IPWGFLIGAELTIVQSRISLVNK------------------------------IQKVYRSQGVQIHNRHIEII 1223
Cdd:PRK14844 2598 KPVDeqiSPVEYLVSRSKHVIVNEGDFVRKgdllmdgdpdlhdilrvlglealahymiseIQQVYRLQGVRIDNKHLEVI 2677
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1224 VRQITSKVLVSEDGmSNVFSPGELIGLLRAERTGRALEEA----ICYRAILLGITRASLNTQSFISEASFQETARVLAKA 1299
Cdd:PRK14844 2678 LKQMLQKVEITDPG-DTMYLVGESIDKLEVDRENDAMSNSgkrpAHYLPILQGITRASLETSSFISAASFQETTKVLTEA 2756
|
250 260
....*....|....*....|....*...
gi 1573382102 1300 ALRGRIDWLKGLKENVVLGGMIPVGTGF 1327
Cdd:PRK14844 2757 AFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1137-1326 |
7.51e-29 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 126.58 E-value: 7.51e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1137 RSGDITQGLPKVEQVLEVRS-----------IDSIsMNLEKRVKGwNEHIT-----------------RILGIPWGFL-I 1187
Cdd:PRK09603 2639 KSRDITGGLPRVSELFEARKpkpkdvailseVDGI-VSFGKPIRN-KEHIIvtskdgrsmdyfvdkgkQILVHADEFVhA 2716
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1188 GAELT--IVQS----RIS--------LVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNvFSPGELIG-LLR 1252
Cdd:PRK09603 2717 GEAMTdgVVSShdilRISgekelykyIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSK-FIEGDLVSkKLF 2795
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1573382102 1253 AERTGRAL----EEAICyRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:PRK09603 2796 KEENARVIalkgEPAIA-EPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
1140-1328 |
2.65e-28 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 124.21 E-value: 2.65e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1140 DITQGLPKVEQVLEVRS------IDSISMNL----EKRVK---------GWNEHIT--RILGIPwGFLIGAELTIVQS-- 1196
Cdd:PRK14906 1006 DITQGLPRVAELFEARKpkgeavLAEISGTLqitgDKTEKtltihdqdgNSREYVVsaRVQFMP-GVEDGVEVRVGQQit 1084
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1197 ----------RIS--------LVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNvFSPGELIGLLRAERTGR 1258
Cdd:PRK14906 1085 rgsvnphdllRLTdpnttlryIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSD-YLPGRQVNRYEFEDTAN 1163
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1573382102 1259 AL----EEAICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFK 1328
Cdd:PRK14906 1164 NLilegKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLS 1237
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
26-220 |
1.14e-27 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 119.46 E-value: 1.14e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 26 LISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLL----TIPSKGWLAQDAEQQSLILEKHHHYGNVHAVEKL 101
Cdd:cd00399 301 LLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIddgvIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGM 380
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 102 -------RQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDP-------------- 160
Cdd:cd00399 381 tleesleDNILDFLNEARDKAGSAASVNLDLVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEgkriprgfsdrtlp 460
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1573382102 161 ------QGQMIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVR 220
Cdd:cd00399 461 hfskddYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVH 526
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1127-1326 |
3.57e-24 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 100.18 E-value: 3.57e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1127 TLVTFIYEKSRSGDITQGLPKVEQVLEVRSIdsismnlekrvkgwnEHITRILGIPWGfligaeltivqsRISLVNKIQK 1206
Cdd:cd00630 20 TLRTFHFAGVASMNVTLGLPRLKEILNAASI---------------HEMLEALGIEAA------------RETIIREIQK 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1207 VYRSQGVQIHNRHIEIIVRQITskvlvsedgmsnvfspgeligllraertgraleeaicYRAILLGITRASLN--TQSFI 1284
Cdd:cd00630 73 VLASQGVSVDRRHIELIADVMT-------------------------------------YSGGLRGVTRSGFRasKTSPL 115
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1573382102 1285 SEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:cd00630 116 MRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
314-349 |
1.94e-20 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 91.05 E-value: 1.94e-20
10 20 30
....*....|....*....|....*....|....*.
gi 1573382102 314 DLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFT 349
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT 36
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
15-347 |
4.56e-19 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 93.94 E-value: 4.56e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 15 NKVIDGTAMK---RLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLtIPSKgwlaqdAEQQslILEKhhh 91
Cdd:PRK14977 618 DDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLI-IPDE------AKQE--IEDD--- 685
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 92 YGNVHAV-------EKLRQSIEIWYATSEYLR-------------QEMNpNFR---------MTDPFNPVHIMSFSGARG 142
Cdd:PRK14977 686 IQGMKDEvsdlidqRKITRKITIYKGKEELLRgmkeeealeadivNELD-KARdkagssandCIDADNAGKIMAKTGARG 764
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 143 NASQVHQLVGMRGLMSDPQGQMIDLP----------------------------IQSNLREGLSLTEYIISCYGARKGVV 194
Cdd:PRK14977 765 SMANLAQIAGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGLI 844
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 195 DTAVRTSDAGYLTRRLVEVVQHIVVRRTdcGTIR------------GISVSPRNGMMPERIFIQTLIGRVLADDiymgpR 262
Cdd:PRK14977 845 DKARRTEDSGYFQRRLANALEDIRLEYD--ETVRdphghiiqfkfgEDGIDPQKLDHGEAFNLERIIEKQKIED-----R 917
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 263 CIAARNQDIGIGLVNRFITFRAQ-PISIRTPFTCRSTS-----WICR---LCYGRSPthgdlVELGEAVGIIAGQSIGEP 333
Cdd:PRK14977 918 GKGASKDEIEELAKEYTKTFNANlPKLLADAIHGAELKedeleAICAegkEGFEKAK-----VEPGQAIGIISAQSIAEP 992
|
410
....*....|....
gi 1573382102 334 GTQLTLRTFHTGGV 347
Cdd:PRK14977 993 GTQMTLRTFHAAGI 1006
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
26-228 |
5.10e-16 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 83.84 E-value: 5.10e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 26 LISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLlTIPSKGW-----LAQDAEQ--QSLIleKHHHYGNVHAV 98
Cdd:cd02582 608 LLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDE-DIPEEARkeieeIIKEAEKkvYELI--EQYKNGELEPL 684
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 99 --EKLRQSIEI---------WYATSEYLRQEMnpnfrmtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSdPQGQMID- 166
Cdd:cd02582 685 pgRTLEETLEMkimqvlgkaRDEAGKVASKYL-------DPFNNAVIMARTGARGSMLNLTQMAACLGQQS-VRGERINr 756
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 167 ------LP--------------IQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVrrTDCGT 226
Cdd:cd02582 757 gyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYV--EYDGT 834
|
..
gi 1573382102 227 IR 228
Cdd:cd02582 835 VR 836
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
127-228 |
7.77e-14 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 76.82 E-value: 7.77e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 127 DPFNPVHIMSFSGARG---NASQVHQLVG---------MRGLMSDPqgqmidLP--------------IQSNLREGLSLT 180
Cdd:PRK08566 721 GLDNPAVIMARTGARGsmlNLTQMAACVGqqsvrgeriRRGYRDRT------LPhfkpgdlgaeargfVRSSYKSGLTPT 794
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 1573382102 181 EYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVrRTDcGTIR 228
Cdd:PRK08566 795 EFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKV-EYD-GTVR 840
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
95-160 |
2.68e-12 |
|
RNA polymerase Rpb1, domain 4; 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, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 64.69 E-value: 2.68e-12
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1573382102 95 VHAVEKLRQSIEIWYATSEYLRQEMNPNFRM-------------TDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDP 160
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNkardpagniasksLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
315-347 |
4.52e-12 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 69.49 E-value: 4.52e-12
10 20 30
....*....|....*....|....*....|...
gi 1573382102 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:PRK04309 55 LVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGV 87
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
315-347 |
7.58e-12 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 68.82 E-value: 7.58e-12
10 20 30
....*....|....*....|....*....|...
gi 1573382102 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:cd06528 36 LIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGV 68
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
306-347 |
2.69e-11 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 67.00 E-value: 2.69e-11
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1573382102 306 YGRSpthgdLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:TIGR02389 36 YLRS-----LIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGV 72
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
319-347 |
1.16e-10 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 61.28 E-value: 1.16e-10
10 20
....*....|....*....|....*....
gi 1573382102 319 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGV 29
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
315-346 |
1.21e-10 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 64.52 E-value: 1.21e-10
10 20 30
....*....|....*....|....*....|..
gi 1573382102 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGG 346
Cdd:cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
315-347 |
2.15e-10 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 64.83 E-value: 2.15e-10
10 20 30
....*....|....*....|....*....|...
gi 1573382102 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:PRK14897 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGV 210
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
315-347 |
2.16e-10 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 63.39 E-value: 2.16e-10
10 20 30
....*....|....*....|....*....|...
gi 1573382102 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGV 38
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1264-1327 |
4.94e-09 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 60.30 E-value: 4.94e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1573382102 1264 ICYRAILLGITRASLNTQSF--ISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGF 1327
Cdd:cd02584 339 MTQRGHLMAITRHGINRQDTgpLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1191-1326 |
5.70e-09 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 59.57 E-value: 5.70e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1191 LTIVQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSNvfsPGEL--IGllraeRTGRALEEAicyra 1268
Cdd:cd06528 255 LGIEAARNAIINEIKRTLEEQGLDVDIRHI----------MLVA-DIMTY---DGEVrqIG-----RHGIAGEKP----- 310
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1573382102 1269 illgitraslntqSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:cd06528 311 -------------SVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
300-347 |
3.46e-08 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 57.60 E-value: 3.46e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1573382102 300 WIC---RLCYGRSpthgdLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:cd02584 10 WILgeiETRFNRS-----LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGV 55
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1121-1326 |
6.75e-08 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 56.39 E-value: 6.75e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1121 ILYEGDTLVtfIYeksrsgdiTQGLPkVEQVLEVRSIDSismnleKRVKGWNEH-ITRILGIPWGfligaeltivqsRIS 1199
Cdd:PRK04309 230 IRKEGDEYV--IY--------TEGSN-LKEVLKVEGVDA------TRTTTNNIHeIEEVLGIEAA------------RNA 280
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1200 LVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSNvfsPGEL--IGllraeRTGRALEEAicyraillgitras 1277
Cdd:PRK04309 281 IIEEIKNTLEEQGLDVDIRHI----------MLVA-DMMTW---DGEVrqIG-----RHGVSGEKA-------------- 327
|
170 180 190 200
....*....|....*....|....*....|....*....|....*....
gi 1573382102 1278 lntqSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:PRK04309 328 ----SVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
1112-1326 |
1.51e-07 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 56.19 E-value: 1.51e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1112 ATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVE-QVLE-----VRSIDSISMNLEKRvKGWNEHITRILGIPWG- 1184
Cdd:PRK14977 1101 ALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIAIRnKILDkpvkgVPDIERAWVELVEK-DGRDEWIIQTSGSNLAa 1179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1185 -----------------FLIGAELTIVQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVsedgmsnvfspgEL 1247
Cdd:PRK14977 1180 vlemkcidiantitndcFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTI------------EA 1247
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1248 IGLLRAE-RTGRALEEaicyraillgitraslntQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:PRK14977 1248 IGLQAAGvRHGFAGEK------------------DSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1191-1326 |
3.86e-07 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 53.38 E-value: 3.86e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1191 LTIVQSRISLVNKIQKVYRSQGVQIHNRHIEIivrqitskvlvsedgmsnvfspgeligllraertgraLEEAICYRAIL 1270
Cdd:cd02736 198 LGIEAARSTIINEIQYTMKSHGMSIDPRHIML-------------------------------------LADLMTFKGEV 240
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1573382102 1271 LGITRASL--NTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:cd02736 241 LGITRFGIakMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1187-1335 |
7.49e-06 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 50.19 E-value: 7.49e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1187 IGAELTIVQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSnvFSpgeliGLLRA-ERTGRALEEAic 1265
Cdd:PRK14897 392 IATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHI----------MLVA-DMMT--FD-----GSVKAiGRHGISGEKS-- 451
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1266 yraillgitraslntqSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKGLVHRSR 1335
Cdd:PRK14897 452 ----------------SVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGR 505
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1187-1326 |
1.04e-05 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 50.28 E-value: 1.04e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1187 IGAELTIVQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSNvfsPGELigllraERTGRAleeaicy 1266
Cdd:PRK14898 738 IQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHL----------MLVA-DIMTA---DGEV------KPIGRH------- 790
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1267 raillGItraSLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1326
Cdd:PRK14898 791 -----GV---AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
127-220 |
2.91e-05 |
|
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two largest subunits of RNA polymerase II (RNAP II), Rpb1 and Rpb2, form the active site, DNA entry channel and RNA exit channel. RNAP II is a large multi-subunit complex responsible for the synthesis of mRNA in eukaryotes. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, each makes up one clamp, one jaw, and part of the cleft. Rpb1_N contains part of the active site, forms the head and core of the one clamp, and makes up the pore and funnel regions of RNAP II.
Pssm-ID: 259848 [Multi-domain] Cd Length: 751 Bit Score: 48.69 E-value: 2.91e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 127 DPFNPVHIMSFSGARG---NASQVHQLVG--------------MRGLmsdPQGQMIDLPIQS------NLREGLSLTEYI 183
Cdd:cd02733 636 SEDNNFKAMVTAGSKGsfiNISQIIACVGqqnvegkripfgfrRRTL---PHFIKDDYGPESrgfvenSYLRGLTPQEFF 712
|
90 100 110
....*....|....*....|....*....|....*..
gi 1573382102 184 ISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVR 220
Cdd:cd02733 713 FHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVK 749
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
1134-1233 |
4.81e-05 |
|
RNA polymerase Rpb1, domain 5; 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, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound.
Pssm-ID: 398596 [Multi-domain] Cd Length: 516 Bit Score: 47.73 E-value: 4.81e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 1134 EKSRSGDIT-QGLPKVEQVLEVRSIDsismnlEKRVKGWNEHI-----TRILGIPwGFLIGAELT------------IVQ 1195
Cdd:pfam04998 390 VASLLGNITlRGIPGIKRILVNEDDK------GKVEPDWVLETegvnlLRVLLVP-GFVDAGRILsndiheileilgIEA 462
|
90 100 110
....*....|....*....|....*....|....*...
gi 1573382102 1196 SRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLV 1233
Cdd:pfam04998 463 ARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYI 500
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1266-1320 |
6.53e-05 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 47.46 E-value: 6.53e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1573382102 1266 YRAILLGITRASLNTQSFISEA-SFQETARVLAKAALRGRIDWLKGlkenvvLGGM 1320
Cdd:COG0086 660 YNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQ------LAGM 709
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
127-211 |
6.92e-05 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 47.54 E-value: 6.92e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1573382102 127 DPFNPVHIMSFSGARG---NASQVHQLVG------MRglmsdPQGQMID--LP--------------IQSNLREGLSLTE 181
Cdd:cd02583 697 HKSNSPLIMALCGSKGsniNISQMIACVGqqiisgKR-----IPNGFEDrtLPhfprnsktpaakgfVANSFYSGLTPTE 771
|
90 100 110
....*....|....*....|....*....|
gi 1573382102 182 YIISCYGARKGVVDTAVRTSDAGYLTRRLV 211
Cdd:cd02583 772 FFFHTMSGREGLVDTAVKTAETGYMQRRLM 801
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
315-339 |
4.79e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 44.88 E-value: 4.79e-04
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
12-66 |
2.00e-03 |
|
RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 40.30 E-value: 2.00e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*
gi 1573382102 12 VFHNKVIDGTAMKrLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDL 66
Cdd:pfam04983 105 VIDKKTVGKSLGS-LIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| |
