|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
5-1375 |
0e+00 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 2772.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 5 MAERANLVYHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSL 84
Cdd:CHL00117 1 MAERANLVFHNKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 85 ILEKHHHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQM 164
Cdd:CHL00117 81 ILEKHYHYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 165 IDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSPRNGMMPERIF 244
Cdd:CHL00117 161 IDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGMMIERIL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 245 IQTLIGRVLADDIYMGPRCIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGI 324
Cdd:CHL00117 241 IQTLIGRVLADDIYIGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGI 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 325 IAGQSIGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDLVHPTRTRHGHPAFLCSIDLYVTIESEDIIHNVNI 404
Cdd:CHL00117 321 IAGQSIGEPGTQLTLRTFHTGGVFTGGTAEQVRAPFNGKIKFNEDLVHPTRTRHGHPAFLCKIDLYVTIESEDIIHNVNI 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 405 PPQSFLLVQNDQYVESEQVIAEIRAGTSTLNFKERVRKHIYSDSEGEMHWSTDVYHAPEFTYGNVQLLPKTSHLWILSGG 484
Cdd:CHL00117 401 PPKSLLLVQNDQYVESEQVIAEIRAGTSTLNFKEKVRKHIYSDSEGEMHWSTDVYHAPEFTYGNVHLLPKTSHLWILSGG 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 485 PCRSSLASLSLHKDQDQMNARsLSVKRRYISNLSVTN---DQVRHKFFSSDFsgKQEDGIPDYSERNRIICTGHCNLTYP 561
Cdd:CHL00117 481 VYRSSLVSFSLHKDQDQINIH-LSVERRYISRLSVINtnnGQVRHKLFSSDG--KKEKRILDYSELNRIISNGHCNFIYP 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 562 AILHGNSDLLAKRRRNRFIIPLQSIQEREKELIPRsGISIEIPINGIFRRNSILAYFDDPRYRRKSSGITKYGTIEVHSI 641
Cdd:CHL00117 558 AILHENSDLLAKRRRNRFLIPFQSIQEREKELMPC-GISIEIPINGILRRNSIFAYFDDPRYRTKSSGITKYGTIEVDSI 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 642 VKKEDLIEYRGVKEFRPKYQMKVDRFFFIPEDVHILPGSSSIMVRNNSIIGVDTQITFNTRSRVGGLVRVERKKKRIELK 721
Cdd:CHL00117 637 VKKEDLIEYRGVKEFKPKYQMKVDRFFFIPEEVHILPESSSILVRNNSIIGVDTQITLNIRSKVGGLVRIEKKKKRIELK 716
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 722 IFSGDIHFPGETDKISRHSGILIPPGTGKTNSKESKKLKNWIYVQRITPTKKKYFVLVRPVVTYEITDGINLATLFPPDL 801
Cdd:CHL00117 717 IFSGDIHFPGETDKISRHSGILIPPGTGKKNSKESKKIKNWIYVQRITPTKKKYFVLVRPVVTYEIADGINLATLFPQDL 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 802 LQEGDNVQLRVVNYILYGNGKPIRGISdtSIQLVRTCLVLNWGQDKKSSSIEEAHASFVEIRKNGLIRDFLRIDLVKSPI 881
Cdd:CHL00117 797 LQEKDNLQLRVVNYILYGNGKPIRGIS--SIQLVRTCLVLNWDQDKKSSSIEEARASFVEVRTNGLIRDFLRINLVKSPI 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 882 SYTGKRNDPSGSGLI--SENGSDRTNinpfssIYSKAKIQ-QSLNQNQGTIHTLLNRNKECQSLIILSSSNCSQMGPF-- 956
Cdd:CHL00117 875 SYIRKRNDPSSSGLLvqSNNFLDSTN------IYSKAEIQsQSLSQNQGTIRTLLNRNKESQSLLILSSSDCFRIGPFng 948
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 957 NDVKYHNvIKESikkDPLIPIRNSLGPLGTALQISNFYSFYHLITHNQLLVTNYLQLDNLKQTFQV--LKYYLMDENGKI 1034
Cdd:CHL00117 949 KKSKYHN-IKES---NPLIPIRNSLGPLGTVLQIANFSSSYHLLTHNQILVTKYLQLDNLKQTFQVkvLKYYLIDENGKI 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1035 YNPDPCSNIFLNPFNLNWYFLHHNYCEETSTIISLGQFICENVCIAKNGPHlKSGQVLIVQIDSLVIRSAKPYLATPGAT 1114
Cdd:CHL00117 1025 YNPDPCSNIILNPFNLNWYFLHHNYCEETSTIISLGQFICENVCISKNGPH-KSGQIIIVQVDSLVIRSAKPYLATPGAT 1103
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1115 VHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVRSIDSISMNLEKRVEGWNECITRILGIPWGFLIGAELTI 1194
Cdd:CHL00117 1104 VHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARSIDSISMNLEKRLEGWNERITRILGIPWGFLIGAELSI 1183
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1195 AQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNVFSPGELIGLLRAERMGRALEEAICYRAILLGI 1274
Cdd:CHL00117 1184 AQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVFLPGELIGLLRAERINRALEEAICYRPILLGI 1263
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1275 TRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKGLVHPSRQHNNIPLETKKKNLFEGE 1354
Cdd:CHL00117 1264 TKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSKQHKNKNLEIKKKNLFEGE 1343
|
1370 1380
....*....|....*....|.
gi 1732474081 1355 IRDILFHHRKLFDSCLSKNFH 1375
Cdd:CHL00117 1344 MRDILFHHRELFDSCISKNFH 1364
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
12-1336 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 691.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 12 VYHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHH 91
Cdd:PRK02597 2 IFRNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 92 YGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQS 171
Cdd:PRK02597 82 RGEITEVERFQKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 172 NLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSPRNGMMPERI-FIQTLIG 250
Cdd:PRK02597 162 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIpLGDRLLG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 251 RVLADDIyMGPR--CIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQ 328
Cdd:PRK02597 242 RVLAEDV-VDPEgeVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 329 SIGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDL-VHPTRTRHGHPAFLCSIDLYVTIESEDIIHN--VNIP 405
Cdd:PRK02597 321 SIGEPGTQLTMRTFHTGGVFTGEVARQVRSPFAGTVEFGKKLrTRPYRTRHGVEALQAEVDFDLVLKPSGKGKPqkIEIT 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 406 PQSFLLVQNDQYVESEQVIAEIRAG---TSTlnfkERVRKHIYSDSEGEMHWSTDVyhAPEFT--YGNVQLL-PKTSHLW 479
Cdd:PRK02597 401 QGSLLFVDDGQTVEADQLLAEVAAGavkKST----EKATKDVICDLAGEVRFADLI--PEEKTdrQGNTTRKaQRGGLLW 474
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 480 ILSGG-----PcrsslaslslhkdqdqmNARsLSVKRryisnlsvtNDQVRHKFFSSDFSGKQEDG----IPDYSERNR- 549
Cdd:PRK02597 475 VLSGDvynlpP-----------------GAE-PVVSN---------GDRVEEGDVLAETKLVSEHGgvvrLRESSGDSRe 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 550 --IICTghcnltypailhgnSDLLakrrrNRFIIPLQSIQEREKELiprsgisIEIPINGIFRRNS----------ILAY 617
Cdd:PRK02597 528 veIITA--------------SVLL-----DQAKVLEESTHGREQYN-------LETKDGQRFRLNAtpgtkvqngeVVAE 581
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 618 FDDPRYRRKSSGITKYGTIEvhsiVKKEdlieyRGVKEfrpKYQM-KVDRFFFIPEDVH-ILPGSSSIMVRNNSIIGVDT 695
Cdd:PRK02597 582 LIDDRYRTKTGGLVKYAGLE----VKKA-----GSAKN---GYEVsKGGTLLWIPEETHeVNKDISLLMVEDGQYVEAGT 649
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 696 QITFNTRSRVGGLVRVERKKKRI-ELKIFSGDIHFPGETDKISRH--SGILIPPGTGKTNSKESKKLKnwiYVQRITPTK 772
Cdd:PRK02597 650 EVVKDIFCQTSGVVEVTQKNDILrEIIIKPGELHLCDDPEALERFtgDGQLVNPGEEVLPGVVTDELR---YVEWVETPE 726
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 773 KKYfVLVRPVVTYEITDGINLatlfpPDL----LQEGDNVQLRVVNYILYGNGKPIRgiSDTSIQLVRTCLVLNWGQDkk 848
Cdd:PRK02597 727 GPG-LLLRPVEEFTIPDEPQV-----PSQgsvkQEKGRSIGLRAVQRLPYKDGERVK--SVEGVELLRTQLVLEIFDT-- 796
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 849 sssiEEAHASFVEIRKNGLIRDFLRIDLVkspI--SYTGKR---NDPS-GSGLISENGSDRTNINPfSSIYSKAKIQqsl 922
Cdd:PRK02597 797 ----TPQLTADIELIPDEKDKEIQRLQLV---IleSLLVRRdtaSDSShGSTHTELLVKDGQQIKP-GDVVARTQIL--- 865
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 923 nqnqgtihtllnrnkecqsliilsssnCSQMGpfndvkyhnvIKESIKKDpLIPIRnslgplgtalqisnfysfyhlith 1002
Cdd:PRK02597 866 ---------------------------CKEAG----------EVRGIRVG-GEAVR------------------------ 883
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1003 nQLLVTnylqldnlkqtfqvlkyylmdengkiyNPDPCSNIFLNpfnlnwyflhhnyceeTSTIISLGQFICENVCIAKN 1082
Cdd:PRK02597 884 -RLLVE---------------------------RDEDTITIPLS----------------GKPTVKVGDLVVAGDELAPG 919
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1083 GPHLKSGQVLIVQIDSLVIRSAKPYLATPGATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVR------ 1156
Cdd:PRK02597 920 VPAPESGEVEAVSGGSVTLRLGRPYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARkpkesc 999
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1157 --------------SIDSISMnleKRVE------------GWN--------------------------ECITRILGIPW 1184
Cdd:PRK02597 1000 ilakkpgtvqikygDDESVDV---KVIEsdgtiteypilpGQNvmvsdgqqvdagepltdgpinphellEIFFEDLRDRK 1076
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1185 GFLIGAELTIAQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVsEDGMSNVFSPGELIGLLRAERMGRALeeA 1264
Cdd:PRK02597 1077 GLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRI-DDGGDTTMLPGELIELRQVEQVNEAM--A 1153
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1732474081 1265 IC------YRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKGLVHPSR 1336
Cdd:PRK02597 1154 ITggapaeYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELS 1231
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
12-1332 |
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: 667.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 12 VYHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHH 91
Cdd:TIGR02388 1 IFKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 92 YGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQS 171
Cdd:TIGR02388 81 RGEITEVERFQKVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 172 NLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSPRNGMMPERIFIQTLIGR 251
Cdd:TIGR02388 161 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKISLGDRLLGR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 252 VLADDIyMGPR--CIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQS 329
Cdd:TIGR02388 241 LVAEDV-LHPEgeVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQS 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 330 IGEPGTQLTLRTFHTGGVFTGGTAEHVRAPSNGKIKFNEDL-VHPTRTRHGHPAFLCSIDLYVTIESEDIIHN----VNI 404
Cdd:TIGR02388 320 IGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKLrTRGYRTRHGEDAKQVEVAGLLIIKPTGSITNkaqeIEV 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 405 PPQSFLLVQNDQYVESEQVIAEIRAGTSTLNfKERVRKHIYSDSEGEMHWSTDVYHAPEFTYGNVQLL-PKTSHLWILSG 483
Cdd:TIGR02388 400 TQGSLLFVEDGQTVDAGQLLAEIALGAVRKS-TEKATKDVASDLAGEVKFDKVVPEEKTDRQGNTTRIaQRGGLIWVLSG 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 484 GPCRSSLASLSLHKDQDQMNARSLsvkrryisnLSVTNdqvrhkfFSSDFSG--KQEDGIPDYSERnRIICTghcnltyp 561
Cdd:TIGR02388 479 EVYNLPPGAEPVVKNGDRVEQGTV---------LAETK-------LSTEHGGvvRLPESVGDSREV-EIITA-------- 533
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 562 ailhgnSDLLAKrrrnrFIIPLQSIQEREKELiprsgisIEIPINGIFRRN----------SILAYFDDPRYRRKSSGIT 631
Cdd:TIGR02388 534 ------SVLLDQ-----AKVIEESSQGRELYH-------IETADGQRFRLKaapgtkvqngQVVAELIDDRYRTTTGGLL 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 632 KYGTIEVHSIVKKEDLIEYrgvkefrpkyqMKVDRFFFIPEDVH-ILPGSSSIMVRNNSIIGVDTQITFNTRSRVGGLVR 710
Cdd:TIGR02388 596 KYAGVEVAKKGKAKQGYEV-----------SQGGTLLWIPEETHeINKDISLLMVEDGQYVEAGTEVVKDIFCQNSGIVE 664
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 711 VERKKKRI-ELKIFSGDIHFPGETDKISRHSGILIPPG----TGKTNSKESkklknwiYVQRITPTKKKYfVLVRPVVTY 785
Cdd:TIGR02388 665 VTQKNDILrEIIVKPGEFHEVDDPEAVSTEEGTLLQPGeevlPGVVVDELS-------QVQYLETPEGPG-LLLRPVEEY 736
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 786 EITDGINLATLFPPDlLQEGDNVQLRVVNYILYGNGKPIRGISdtSIQLVRTCLVLNWGQDKKSSSIEeahasfVEIRKN 865
Cdd:TIGR02388 737 TVPDEPEVPSQSSVS-QEKGRSIALRAVQRLPYKDGERVKSVE--GVELLRTQLVLEIFDEGPQLAAD------IELIQD 807
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 866 GLIRDFLRIDLVkspisytgkrndpsgsglISENGSDRTNInpfssiyskakiqqSLNQNQGTIHTLLNRNKECQ----S 941
Cdd:TIGR02388 808 EEDKDIQRLQLV------------------ILESLVLRRDI--------------ASDSTQGSTHTSLLVKDGDLikpgA 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 942 LIILSSSNCSQMGPFNDVKYhnvIKESIKKdpLIPIRNSlgplgtalqisnfysfyhlithnqllvtnylqlDNLKqtfq 1021
Cdd:TIGR02388 856 VIARTQILCKEAGVVQGIDS---GGESIRR--LLVERNS---------------------------------DRLK---- 893
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1022 vlkyylmdengkiynpdpcsniflnpFNLNwyflhhnyceeTSTIISLGQFICENVCIAKNGPHLKSGQVLIVQIDSLVI 1101
Cdd:TIGR02388 894 --------------------------VNIK-----------AKPVVKTGDLVVAGDELAKGVKAEESGEIEEVASDYVIL 936
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1102 RSAKPYLATPGATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVR-----SI----------------DS 1160
Cdd:TIGR02388 937 RIGRPYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARkpkeaCIlakrpgvvqvkygtddES 1016
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1161 ISMNLEKR---------VEGWNECIT-------------------RILGIPW-------GFLIGAELTIAQSRISLVNKI 1205
Cdd:TIGR02388 1017 VSIKVIERdgtiseyplLPGQNIMVSdgqqvtggepltdgpinphDILDVFFsyykdqdGLYEAAQESLQKVQRFLVNEV 1096
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1206 QKVYRSQGVQIHNRHIEIIVRQITSKVLVsEDGMSNVFSPGELIGLLRAERMGRALeeAIC------YRAILLGITRASL 1279
Cdd:TIGR02388 1097 QNVYQSQGVDISDKHIEVIVRQMTSKVRI-DDAGDTTLLPGELVELRQVEQVNEAM--AITggapaqYTPVLLGITKASL 1173
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|...
gi 1732474081 1280 NTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKGLV 1332
Cdd:TIGR02388 1174 NTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYE 1226
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
12-426 |
2.77e-116 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 393.28 E-value: 2.77e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 12 VYHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHH 91
Cdd:PRK00566 568 INVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYR 647
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 92 YGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMT-DPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQ 170
Cdd:PRK00566 648 RGLITDGERYNKVIDIWSKATDEVAKAMMKNLSKDqESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIK 727
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 171 SNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSP--RNGMMPERIFiQTL 248
Cdd:PRK00566 728 SNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAiiEGGEVIEPLE-ERI 806
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 249 IGRVLADDIYmGPRC---IATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGII 325
Cdd:PRK00566 807 LGRVLAEDVV-DPETgevIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVI 885
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 326 AGQSIGEPGTQLTLRTFHTGGV-FTGG---TAE--HVRAPSN--------GKIKFNEDlvhpTRTRHGhpaflcsidlyV 391
Cdd:PRK00566 886 AAQSIGEPGTQLTMRTFHTGGVdITGGlprVAElfEARKPKGpaiiaeidGTVSFGKE----TKGKRR-----------I 950
|
410 420 430
....*....|....*....|....*....|....*.
gi 1732474081 392 TIESED-IIHNVNIPPQSFLLVQNDQYVESEQVIAE 426
Cdd:PRK00566 951 VITPDDgEEREYLIPKGKHLLVQEGDHVEAGDKLTD 986
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
15-426 |
4.76e-99 |
|
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: 343.95 E-value: 4.76e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 15 NKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHHYGN 94
Cdd:TIGR02386 562 NEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGL 641
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 95 VHAVEKLRQSIEIWYATSEYLRQEMNPNFRM-TDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSNL 173
Cdd:TIGR02386 642 ITDEERYRKVVSIWSETKDKVTDAMMKLLKKdTYKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSF 721
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 174 REGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSP-RNG------MMPERIFiq 246
Cdd:TIGR02386 722 REGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAiVEGkdeiieSLKDRIV-- 799
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 247 tliGRVLADDIY--MGPRCIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGI 324
Cdd:TIGR02386 800 ---GRYSAEDVYdpDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGV 876
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 325 IAGQSIGEPGTQLTLRTFHTGGV------FTGG---TAE--HVRAPSN--------GKIKFNEDLVHPTRTrhghpaflc 385
Cdd:TIGR02386 877 IAAQSIGEPGTQLTMRTFHTGGVagasgdITQGlprVKElfEARTPKDkaviaevdGTVEIIEDIVKNKRV--------- 947
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 1732474081 386 sidLYVTIESEDiIHNVNIPPQSFLLVQNDQYVESEQVIAE 426
Cdd:TIGR02386 948 ---VVIKDENDE-EKKYTIPFGAQLRVKDGDSVSAGDKLTE 984
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
10-223 |
6.85e-95 |
|
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: 320.23 E-value: 6.85e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 10 NLVYHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKH 89
Cdd:cd01609 447 GLPFINKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQ 526
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 90 HHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFRMtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPI 169
Cdd:cd01609 527 YEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDK-DPFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPI 605
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....
gi 1732474081 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 |
7.15e-91 |
|
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: 320.57 E-value: 7.15e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 10 NLVYHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKH 89
Cdd:COG0086 569 EVPFYNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQ 648
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 90 HHYGNVHAVEKLRQSIEIWYATSEYLRQEMNPNFrmtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPI 169
Cdd:COG0086 649 YAEGLITEPERYNKVIDGWTKASLETESFLMAAF---SSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPI 725
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 170 QSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSP--RNGMMPERIFiQT 247
Cdd:COG0086 726 GSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDRGITVTAikEGGEVIEPLK-ER 804
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 248 LIGRVLADDIYM--GPRCIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGII 325
Cdd:COG0086 805 ILGRVAAEDVVDpgTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVI 884
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 326 AGQSIGEPGTQLTLRTFHTGGV-FTGGTAEHVRAPSNGKIKFNEDLVHPTRTRHGHPAFLCSIDLyVTIESEDIIHNVNI 404
Cdd:COG0086 885 AAQSIGEPGTQLTMRTFHIGGAaSRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELV-IVDDGGRREEEYKV 963
|
410 420
....*....|....*....|...
gi 1732474081 405 PPQSFLLVQNDQYVESEQVIAEI 427
Cdd:COG0086 964 PYGGVLVVVGGGVVVGGGIVAEW 986
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
13-347 |
9.76e-81 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 292.93 E-value: 9.76e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 13 YHNKAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHHY 92
Cdd:PRK14906 672 YLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYED 751
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 93 GNVHAVEKLRQSIEIWYATSEYLRQEMNPNFrmtDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSN 172
Cdd:PRK14906 752 GFLSERERHKQVVDIWTEATEEVGEAMLAGF---DEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKAN 828
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 173 LREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSPRNgmmPERIFIQTLIGRV 252
Cdd:PRK14906 829 FREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVK---PKGDVDTNLIGRC 905
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 253 LADDIY--MGPRCIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQSI 330
Cdd:PRK14906 906 LLEDVCdpNGEVLLSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSI 985
|
330
....*....|....*..
gi 1732474081 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; ... |
1140-1328 |
9.26e-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: 235.50 E-value: 9.26e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1140 GDITQGLPKVEQVLEVRSIdsismnlekrvegWNECITRILGIpwgfligaelTIAQSRISLVNKIQKVYRSQGVQIHNR 1219
Cdd:cd02655 36 TDITQGLPRVEELFEARKI-------------NPHDLLRIKFL----------GPEAVQKYLVEEIQKVYRSQGVNINDK 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1220 HIEIIVRQITSKVLVSEDGMSNvFSPGELIGLLRAERMGRAL----EEAICYRAILLGITRASLNTQSFISEASFQETAR 1295
Cdd:cd02655 93 HIEIIVRQMTSKVKIIDPGDSG-FLPGELVDLNEFEEENKRLlllgKKPAKYEPVLLGITKASLNTESFISAASFQETTK 171
|
170 180 190
....*....|....*....|....*....|...
gi 1732474081 1296 VLAKAALRGRIDWLKGLKENVVLGGMIPVGTGF 1328
Cdd:cd02655 172 VLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
21-366 |
9.50e-71 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 262.94 E-value: 9.50e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 21 TAMKRLISRLIDHF----GMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHHYGNVH 96
Cdd:PRK09603 1971 PMKKKDIGVLVDYVhkvgGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLT 2050
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 97 AVEKLRQSIEIWYATSEYLRQEMNPNFRM-TDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSNLRE 175
Cdd:PRK09603 2051 DQERYNKIIDTWTEVNDKMSKEMMTAIAKdKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKE 2130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 176 GLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISV------SPRNGMMPERIFiqtli 249
Cdd:PRK09603 2131 GLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEItdiavgSELIEPLEERIF----- 2205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 250 GRVLADDIY--MGPRCIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAG 327
Cdd:PRK09603 2206 GRVLLEDVIdpITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAA 2285
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 1732474081 328 QSIGEPGTQLTLRTFHTGGVFTGGTAE-HVRAPSNGKIKF 366
Cdd:PRK09603 2286 QSIGEPGTQLTLRTFHVGGTASRSQDErEIVASKEGFVRF 2325
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
35-426 |
2.22e-64 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 242.61 E-value: 2.22e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 35 GMAYTSHILDQVKTLGFQQATATSISLGIDDLLTIPSKGWLVQDAEQQSLILEKHHHYGNVHAVEKLRQSIEIWYATSEY 114
Cdd:PRK14844 2043 GQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDM 2122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 115 LRQEMNPNFRMTD---PFNPVHIMSFSGARGNASQVHQLVGMRGLMSDPQGQMIDLPIQSNLREGLSLTEYIISCYGARK 191
Cdd:PRK14844 2123 IANDMLKAISIYDgnsKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARK 2202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 192 GVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISV-SPRNGMMPERIFIQTLIGRVLADDIY--MGPRCIATRN 268
Cdd:PRK14844 2203 GLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVrATVEGSTIVASLESVVLGRTAANDIYnpVTKELLVKAG 2282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 269 QDIGIGLINRFITFRAQPISIRTPFTCRSTSWICRLCYGRSPTHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVF 348
Cdd:PRK14844 2283 ELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVM 2362
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 349 TGGT-AEHVRAPSNGKIKFNEDLVhpTRTRHGHPAFL---CSIDLYVTIESEDIIHNVniPPQSFLLVQNDQYVESEQVI 424
Cdd:PRK14844 2363 TRGVeSSNIIASINAKIKLNNSNI--IIDKNGNKIVIsrsCEVVLIDSLGSEKLKHSV--PYGAKLYVDEGGSVKIGDKV 2438
|
..
gi 1732474081 425 AE 426
Cdd:PRK14844 2439 AE 2440
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1141-1329 |
3.87e-49 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 191.43 E-value: 3.87e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1141 DITQGLPKVEQVLEVR---------------SIDSISMNlEKRVEgwnecITRILGIPWGFLI----------------G 1189
Cdd:PRK00566 908 DITGGLPRVAELFEARkpkgpaiiaeidgtvSFGKETKG-KRRIV-----ITPDDGEEREYLIpkgkhllvqegdhveaG 981
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1190 AELT--------------IAQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNvFSPGELIGLLRAE 1255
Cdd:PRK00566 982 DKLTdgsidphdilrvlgVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTD-FLPGELVDRSEFE 1060
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1732474081 1256 RMGRALEEA----ICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFK 1329
Cdd:PRK00566 1061 EENRKLIAEgkepATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLA 1138
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1137-1330 |
3.98e-46 |
|
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: 181.79 E-value: 3.98e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1137 SRSGDITQGLPKVEQVLEVRS---------IDSISMNLEKRVEG-------WNECITRILGIPWGFLI----------GA 1190
Cdd:TIGR02386 901 GASGDITQGLPRVKELFEARTpkdkaviaeVDGTVEIIEDIVKNkrvvvikDENDEEKKYTIPFGAQLrvkdgdsvsaGD 980
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1191 ELT--------------IAQSRISLVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNVFsPGELIGLLRAER 1256
Cdd:TIGR02386 981 KLTegsidphdllrikgIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLL-PGELIDIHEFNE 1059
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1732474081 1257 MGRALEEA----ICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFKG 1330
Cdd:TIGR02386 1060 ENRKLLEQgkkpASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKT 1137
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
176-347 |
2.36e-39 |
|
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: 154.43 E-value: 2.36e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 176 GLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVRRTDCGTVRGISVSP----RNGMMPERIFIQTLI-- 249
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQflygEDGLDPLKIEKQGRFti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 250 ------------------------------GRVLADDIYMGPRCIATRNQDIGIGLINRFITFRAQPISIRTPFTCRSTS 299
Cdd:pfam04998 81 efsdlkledkfkndllddllllsefslsykKEILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 1732474081 300 WICRLCYGRSPTHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGV 208
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
1107-1328 |
2.33e-30 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 131.67 E-value: 2.33e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1107 YLATPGATVHGHYGEILYEGDTLVTFIYEKSRSGDITQGLPKVEQVLEVR---------SIDSISMNLEKRVEGWNECIT 1177
Cdd:PRK14844 2518 YFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEARrpkehaivsEIDGYVAFSEKDRRGKRSILI 2597
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1178 RILG---IPWGFLIGAELTIAQSRISLVNK------------------------------IQKVYRSQGVQIHNRHIEII 1224
Cdd:PRK14844 2598 KPVDeqiSPVEYLVSRSKHVIVNEGDFVRKgdllmdgdpdlhdilrvlglealahymiseIQQVYRLQGVRIDNKHLEVI 2677
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1225 VRQITSKVLVSEDGmSNVFSPGELIGLLRAER----MGRALEEAICYRAILLGITRASLNTQSFISEASFQETARVLAKA 1300
Cdd:PRK14844 2678 LKQMLQKVEITDPG-DTMYLVGESIDKLEVDRendaMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEA 2756
|
250 260
....*....|....*....|....*...
gi 1732474081 1301 ALRGRIDWLKGLKENVVLGGMIPVGTGF 1328
Cdd:PRK14844 2757 AFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
1141-1329 |
2.03e-28 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 124.60 E-value: 2.03e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1141 DITQGLPKVEQVLEVRS------IDSISMNLEKRVEGWNECIT---------------RILGIPwGFLIGAELTIAQS-- 1197
Cdd:PRK14906 1006 DITQGLPRVAELFEARKpkgeavLAEISGTLQITGDKTEKTLTihdqdgnsreyvvsaRVQFMP-GVEDGVEVRVGQQit 1084
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1198 ----------RIS--------LVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNvFSPGELIGLLRAERMGR 1259
Cdd:PRK14906 1085 rgsvnphdllRLTdpnttlryIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSD-YLPGRQVNRYEFEDTAN 1163
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1732474081 1260 AL----EEAICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGFK 1329
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 |
5.85e-28 |
|
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: 120.23 E-value: 5.85e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 26 LISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLL----TIPSKGWLVQDAEQQSLILEKHHHYGNVHAVEKL 101
Cdd:cd00399 301 LLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIddgvIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGM 380
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 102 -------RQSIEIWYATSEYLRQEMNPNFRMTDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDP-------------- 160
Cdd:cd00399 381 tleesleDNILDFLNEARDKAGSAASVNLDLVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEgkriprgfsdrtlp 460
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1732474081 161 ------QGQMIDLPIQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVR 220
Cdd:cd00399 461 hfskddYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVH 526
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1138-1327 |
2.35e-27 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 121.57 E-value: 2.35e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1138 RSGDITQGLPKVEQVLEVRS-----------IDSIsMNLEKRVEGWNECIT----------------RILGIPWGFL-IG 1189
Cdd:PRK09603 2639 KSRDITGGLPRVSELFEARKpkpkdvailseVDGI-VSFGKPIRNKEHIIVtskdgrsmdyfvdkgkQILVHADEFVhAG 2717
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1190 AELT--IAQS----RIS--------LVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLVSEDGMSNvFSPGELIG--LLR 1253
Cdd:PRK09603 2718 EAMTdgVVSShdilRISgekelykyIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSK-FIEGDLVSkkLFK 2796
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1732474081 1254 AE--RMGRALEEAICYRAILLGITRASLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:PRK09603 2797 EEnaRVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1128-1327 |
4.77e-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: 99.80 E-value: 4.77e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1128 TLVTFIYEKSRSGDITQGLPKVEQVLEVRSIDSIsmnlekrvegwneciTRILGIPWGfligaeltiaqsRISLVNKIQK 1207
Cdd:cd00630 20 TLRTFHFAGVASMNVTLGLPRLKEILNAASIHEM---------------LEALGIEAA------------RETIIREIQK 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1208 VYRSQGVQIHNRHIEIIVRQITskvlvsedgmsnvfspgeligllraermgraleeaicYRAILLGITRASLN--TQSFI 1285
Cdd:cd00630 73 VLASQGVSVDRRHIELIADVMT-------------------------------------YSGGLRGVTRSGFRasKTSPL 115
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 1732474081 1286 SEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:cd00630 116 MRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
314-349 |
2.35e-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: 90.66 E-value: 2.35e-20
10 20 30
....*....|....*....|....*....|....*.
gi 1732474081 314 DLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFT 349
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT 36
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
15-347 |
3.78e-20 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 97.79 E-value: 3.78e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 15 NKAIDGTAMK---RLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLLtIPSKGW------------LVQDA 79
Cdd:PRK14977 618 DDNIIGALVEepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLI-IPDEAKqeieddiqgmkdEVSDL 696
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 80 EQQSLILEKHHHYgnvHAVEKLRQSIEIWYATSEYLRQEMNpNFR---------MTDPFNPVHIMSFSGARGNASQVHQL 150
Cdd:PRK14977 697 IDQRKITRKITIY---KGKEELLRGMKEEEALEADIVNELD-KARdkagssandCIDADNAGKIMAKTGARGSMANLAQI 772
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 151 VGMRGLMSDPQGQMIDLP----------------------------IQSNLREGLSLTEYIISCYGARKGVVDTAVRTSD 202
Cdd:PRK14977 773 AGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGLIDKARRTED 852
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 203 AGYLTRRLVEVVQHIVVRRTdcGTVR--------------GISV--SPRN-GMMPERIFIQTLI---GR-VLADDI-YMG 260
Cdd:PRK14977 853 SGYFQRRLANALEDIRLEYD--ETVRdphghiiqfkfgedGIDPqkLDHGeAFNLERIIEKQKIedrGKgASKDEIeELA 930
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 261 PRCIATRNQDIGIGLINRFITFRAQPISIRTpftcrstswICR---LCYGRSPthgdlVELGEAVGIIAGQSIGEPGTQL 337
Cdd:PRK14977 931 KEYTKTFNANLPKLLADAIHGAELKEDELEA---------ICAegkEGFEKAK-----VEPGQAIGIISAQSIAEPGTQM 996
|
410
....*....|
gi 1732474081 338 TLRTFHTGGV 347
Cdd:PRK14977 997 TLRTFHAAGI 1006
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
16-228 |
1.67e-17 |
|
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: 88.46 E-value: 1.67e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 16 KAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLlTIPSKGW-----LVQDAEQ--QSLIleK 88
Cdd:cd02582 598 KAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDE-DIPEEARkeieeIIKEAEKkvYELI--E 674
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 89 HHHYGNVHAV--EKLRQSIEI---------WYATSEYLRQEMnpnfrmtDPFNPVHIMSFSGARGNASQVHQLVGMRGLM 157
Cdd:cd02582 675 QYKNGELEPLpgRTLEETLEMkimqvlgkaRDEAGKVASKYL-------DPFNNAVIMARTGARGSMLNLTQMAACLGQQ 747
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 158 SdPQGQMID-------LP--------------IQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQH 216
Cdd:cd02582 748 S-VRGERINrgyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD 826
|
250
....*....|..
gi 1732474081 217 IVVrrTDCGTVR 228
Cdd:cd02582 827 LYV--EYDGTVR 836
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
16-228 |
9.67e-15 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 79.51 E-value: 9.67e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 16 KAIdGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDLlTIPSKGW-----LVQDAEQQSLILEKHH 90
Cdd:PRK08566 603 KAI-GAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE-DIPEEAKeeideIIEEAEKRVEELIEAY 680
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 91 HYGNVHAV--EKLRQSIEIwyatseYLRQEMN-----------PNFrmtDPFNPVHIMSFSGARG---NASQVHQLVG-- 152
Cdd:PRK08566 681 ENGELEPLpgRTLEETLEM------KIMQVLGkardeageiaeKYL---GLDNPAVIMARTGARGsmlNLTQMAACVGqq 751
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 153 -------MRGLMSDPqgqmidLP--------------IQSNLREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRLV 211
Cdd:PRK08566 752 svrgeriRRGYRDRT------LPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLI 825
|
250
....*....|....*..
gi 1732474081 212 EVVQHIVVrRTDcGTVR 228
Cdd:PRK08566 826 NALQDLKV-EYD-GTVR 840
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
95-160 |
2.89e-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: 64.31 E-value: 2.89e-12
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1732474081 95 VHAVEKLRQSIEIWYATSEYLRQEMNPNFRM-------------TDPFNPVHIMSFSGARGNASQVHQLVGMRGLMSDP 160
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNkardpagniasksLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
315-347 |
3.81e-12 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 69.87 E-value: 3.81e-12
10 20 30
....*....|....*....|....*....|...
gi 1732474081 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 |
6.17e-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: 6.17e-12
10 20 30
....*....|....*....|....*....|...
gi 1732474081 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 |
2.37e-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: 2.37e-11
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1732474081 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 |
1.09e-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: 61.66 E-value: 1.09e-10
10 20
....*....|....*....|....*....
gi 1732474081 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 |
1.17e-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: 1.17e-10
10 20 30
....*....|....*....|....*....|..
gi 1732474081 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGG 346
Cdd:cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
315-347 |
1.84e-10 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 65.22 E-value: 1.84e-10
10 20 30
....*....|....*....|....*....|...
gi 1732474081 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 |
2.18e-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: 2.18e-10
10 20 30
....*....|....*....|....*....|...
gi 1732474081 315 LVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGV 38
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1192-1327 |
1.58e-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: 61.50 E-value: 1.58e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1192 LTIAQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSNvfsPGEL--IGllraeRMGRALEEAicyra 1269
Cdd:cd06528 255 LGIEAARNAIINEIKRTLEEQGLDVDIRHI----------MLVA-DIMTY---DGEVrqIG-----RHGIAGEKP----- 310
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1732474081 1270 illgitraslntqSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:cd06528 311 -------------SVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1265-1328 |
4.77e-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: 4.77e-09
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1732474081 1265 ICYRAILLGITRASLNTQSF--ISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTGF 1328
Cdd:cd02584 339 MTQRGHLMAITRHGINRQDTgpLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1192-1327 |
2.21e-08 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 57.93 E-value: 2.21e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1192 LTIAQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSNvfsPGEL--IGllraeRMGRALEEAicyra 1269
Cdd:PRK04309 272 LGIEAARNAIIEEIKNTLEEQGLDVDIRHI----------MLVA-DMMTW---DGEVrqIG-----RHGVSGEKA----- 327
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1732474081 1270 illgitraslntqSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:PRK04309 328 -------------SVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1192-1327 |
2.98e-08 |
|
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: 56.84 E-value: 2.98e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1192 LTIAQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskvlvsedgmsnvfspgeligLLRAERMgraleeaiCYRAIL 1271
Cdd:cd02736 198 LGIEAARSTIINEIQYTMKSHGMSIDPRHI-----------------------------MLLADLM--------TFKGEV 240
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1732474081 1272 LGITRASL--NTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:cd02736 241 LGITRFGIakMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
300-347 |
3.43e-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: 3.43e-08
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1732474081 300 WIC---RLCYGRSpthgdLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 347
Cdd:cd02584 10 WILgeiETRFNRS-----LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGV 55
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
1149-1327 |
9.62e-08 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 56.96 E-value: 9.62e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1149 VEQVLEVRSIDsismnleKRVEGWNEC--ITRILGIpwgfligaeltiAQSRISLVNKIQKVYRSQGVQIHNRHIEIIVR 1226
Cdd:PRK14977 1177 LAAVLEMKCID-------IANTITNDCfeIAGTLGI------------EAARNAIFNELASILEDQGLEVDNRYIMLVAD 1237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1227 QITSKVLVsedgmsnvfspgELIGLLRAE-RMGRALEEaicyraillgitraslntQSFISEASFQETARVLAKAALRGR 1305
Cdd:PRK14977 1238 IMCSRGTI------------EAIGLQAAGvRHGFAGEK------------------DSPLAKAAFEITTHTIAHAALGGE 1287
|
170 180
....*....|....*....|..
gi 1732474081 1306 IDWLKGLKENVVLGGMIPVGTG 1327
Cdd:PRK14977 1288 IEKIKGILDALIMGQNIPIGSG 1309
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1188-1327 |
3.68e-06 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 51.43 E-value: 3.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1188 IGAELTIAQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSNvfsPGELigllraERMGRAleeaicy 1267
Cdd:PRK14898 738 IQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHL----------MLVA-DIMTA---DGEV------KPIGRH------- 790
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1268 raillGItraSLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:PRK14898 791 -----GV---AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1188-1327 |
1.69e-05 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 49.04 E-value: 1.69e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1188 IGAELTIAQSRISLVNKIQKVYRSQGVQIHNRHIeiivrqitskVLVSeDGMSnvFSpgeliGLLRAerMGRAleeaicy 1267
Cdd:PRK14897 392 IATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHI----------MLVA-DMMT--FD-----GSVKA--IGRH------- 444
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 1268 raillGItraSLNTQSFISEASFQETARVLAKAALRGRIDWLKGLKENVVLGGMIPVGTG 1327
Cdd:PRK14897 445 -----GI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
127-220 |
3.09e-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: 3.09e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 127 DPFNPVHIMSFSGARG---NASQVHQLVG--------------MRGLmsdPQGQMIDLPIQS------NLREGLSLTEYI 183
Cdd:cd02733 636 SEDNNFKAMVTAGSKGsfiNISQIIACVGqqnvegkripfgfrRRTL---PHFIKDDYGPESrgfvenSYLRGLTPQEFF 712
|
90 100 110
....*....|....*....|....*....|....*..
gi 1732474081 184 ISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVR 220
Cdd:cd02733 713 FHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVK 749
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
127-228 |
4.45e-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: 47.93 E-value: 4.45e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1732474081 127 DPFNPVHIMSFSGARG---NASQVHQLVG------MRglmsdPQGQMID--LP--------------IQSNLREGLSLTE 181
Cdd:cd02583 697 HKSNSPLIMALCGSKGsniNISQMIACVGqqiisgKR-----IPNGFEDrtLPhfprnsktpaakgfVANSFYSGLTPTE 771
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 1732474081 182 YIISCYGARKGVVDTAVRTSDAGYLTRRLVEVVQHIVVrRTDcGTVR 228
Cdd:cd02583 772 FFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSV-QYD-GTVR 816
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1267-1321 |
6.15e-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: 47.85 E-value: 6.15e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 1732474081 1267 YRAILLGITRASLNTQSFISEA-SFQETARVLAKAALRGRIDWLKGlkenvvLGGM 1321
Cdd:COG0086 660 YNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQ------LAGM 709
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
1201-1234 |
6.33e-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: 47.35 E-value: 6.33e-05
10 20 30
....*....|....*....|....*....|....
gi 1732474081 1201 LVNKIQKVYRSQGVQIHNRHIEIIVRQITSKVLV 1234
Cdd:pfam04998 467 LLNEIRNVYRFQGIYINDRHLELIADQMTRKGYI 500
|
|
| 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 ... |
16-66 |
1.24e-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: 41.07 E-value: 1.24e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1732474081 16 KAIDGTAMKRLISRLIDHFGMAYTSHILDQVKTLGFQQATATSISLGIDDL 66
Cdd:pfam04983 108 KKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| |
