|
Name |
Accession |
Description |
Interval |
E-value |
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
35-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 2676.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 35 PPFRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERY 114
Cdd:PRK02597 1 PIFRNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 115 RLGEITEVERHTKVIDTWTETNERLVDAVKKNFDENAPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIR 194
Cdd:PRK02597 81 RRGEITEVERFQKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIK 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 195 TNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDAEDG------KFGSRLV 268
Cdd:PRK02597 161 TNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDgdrvliPLGDRLL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 269 GRLTAAQVVNADGEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQ 348
Cdd:PRK02597 241 GRVLAEDVVDPEGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 349 SIGEPGTQLTMRTFHTGGVSTAETG-VVRSKVAGTVEFGSKARVRPYRTPHGVNAQQAEVDFNLTIKPSGKGKAQKIEIT 427
Cdd:PRK02597 321 SIGEPGTQLTMRTFHTGGVFTGEVArQVRSPFAGTVEFGKKLRTRPYRTRHGVEALQAEVDFDLVLKPSGKGKPQKIEIT 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 428 NGSLLFVDNGADIDADVTVAQIAAGAVKKSVEKATKDVICDLAGQVRYEEAIqPREVTDRQGNITLKAQRLGRMWVLSGD 507
Cdd:PRK02597 401 QGSLLFVDDGQTVEADQLLAEVAAGAVKKSTEKATKDVICDLAGEVRFADLI-PEEKTDRQGNTTRKAQRGGLLWVLSGD 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 508 VYNLPPNAQPVVSSETQVTEGQVLAEASQRSEYGGEVRLRDSIGDSREVQIVTTAMTLKDFKLLEESTHSGEIWNLEAKD 587
Cdd:PRK02597 480 VYNLPPGAEPVVSNGDRVEEGDVLAETKLVSEHGGVVRLRESSGDSREVEIITASVLLDQAKVLEESTHGREQYNLETKD 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 588 GTRYRLNTIPGSKIGSGEVIAELADDRFRTGTGGLVKFApGLAIKKARSAKNGYEVNKGGTLLWIPQETHEINKDISLLM 667
Cdd:PRK02597 560 GQRFRLNATPGTKVQNGEVVAELIDDRYRTKTGGLVKYA-GLEVKKAGSAKNGYEVSKGGTLLWIPEETHEVNKDISLLM 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 668 ITDGQWIEAGTEVVKDIFSQTAGIVTVTQKNDILREIIVRSGEFHLCTDAKALERFEGDGQMVNPGEDIAKGLSVDTMKY 747
Cdd:PRK02597 639 VEDGQYVEAGTEVVKDIFCQTSGVVEVTQKNDILREIIIKPGELHLCDDPEALERFTGDGQLVNPGEEVLPGVVTDELRY 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 748 VQTVETPEGKGLLLRPVEEYTIPNEAQLPELSHVKQANGPHLGIKATQRLAFKDNELIKSVEGVELLKTQLLLETFDTTP 827
Cdd:PRK02597 719 VEWVETPEGPGLLLRPVEEFTIPDEPQVPSQGSVKQEKGRSIGLRAVQRLPYKDGERVKSVEGVELLRTQLVLEIFDTTP 798
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 828 QMTVDVEKAPDKRAKTISRLRLVILESILVRRDTMSDSSHGSTHTELQVEDGVSVKAGDVVATTQILCKQAGLAQlPEAT 907
Cdd:PRK02597 799 QLTADIELIPDEKDKEIQRLQLVILESLLVRRDTASDSSHGSTHTELLVKDGQQIKPGDVVARTQILCKEAGEVR-GIRV 877
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 908 EADPVRRMIVERPEDTTTLSTSGKPVVSVGQRIVDGDALADGETATCCGEIEAVSGNSVTLRLGRPYMVSPDSVLHVRDG 987
Cdd:PRK02597 878 GGEAVRRLLVERDEDTITIPLSGKPTVKVGDLVVAGDELAPGVPAPESGEVEAVSGGSVTLRLGRPYRVSPGAVLHVRDG 957
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 988 DLVQRGDGLALLVFERQKTGDIVQGLPRIEELLEARRPRESAILCKKPGTVEIKQGeDDESLAVNVIESDDAIGEYPILL 1067
Cdd:PRK02597 958 DLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCILAKKPGTVQIKYG-DDESVDVKVIESDGTITEYPILP 1036
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1068 GRNIMVSDGQQVTAGELLTDGPINPHELLECYFEDLRSRKPLMEAAQEAIANLQHRLVTEVQNVYKSQGVSIDDKHIEVI 1147
Cdd:PRK02597 1037 GQNVMVSDGQQVDAGEPLTDGPINPHELLEIFFEDLRDRKGLYEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVI 1116
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1148 VRQMTSKVRVEDAGDTTLLPGELIELRQVEDTNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAA 1227
Cdd:PRK02597 1117 VRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAA 1196
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1228 IEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELQKEAGPHPDILSEDPAGYRRMQNLRPDYTVDMPPAASASAVLDDPS 1307
Cdd:PRK02597 1197 IEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELSAEAGPHPDILAEDPAGYRRMQNLRPDYTVDMPARPYASSLDDPSD 1276
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*.
gi 1896202387 1308 DADlEATRTRHNIDPSASNFAAFTRPDADNELK-EEQVVDAEAVEGLQEEGLLSDE 1362
Cdd:PRK02597 1277 EDL-EATRSRHGIDPSSSNFAAFARPDADDELLiDDQLPDPAALEGLQEEGLLSDE 1331
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
37-1259 |
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: 1968.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 37 FRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYRL 116
Cdd:TIGR02388 2 FKNRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 117 GEITEVERHTKVIDTWTETNERLVDAVKKNFDENAPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRTN 196
Cdd:TIGR02388 82 GEITEVERFQKVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTN 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 197 FREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDA--EDGK---FGSRLVGRL 271
Cdd:TIGR02388 162 FREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAmtEGDKkisLGDRLLGRL 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 272 TAAQVVNADGEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQSIG 351
Cdd:TIGR02388 242 VAEDVLHPEGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIG 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 352 EPGTQLTMRTFHTGGVSTAETG-VVRSKVAGTVEFGSKARVRPYRTPHGVNAQQAEVDFNLTIKPSGKG--KAQKIEITN 428
Cdd:TIGR02388 322 EPGTQLTMRTFHTGGVFTGEVArQVRSKIDGTVEFGKKLRTRGYRTRHGEDAKQVEVAGLLIIKPTGSItnKAQEIEVTQ 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 429 GSLLFVDNGADIDADVTVAQIAAGAVKKSVEKATKDVICDLAGQVRYEEAIqPREVTDRQGNITLKAQRLGRMWVLSGDV 508
Cdd:TIGR02388 402 GSLLFVEDGQTVDAGQLLAEIALGAVRKSTEKATKDVASDLAGEVKFDKVV-PEEKTDRQGNTTRIAQRGGLIWVLSGEV 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 509 YNLPPNAQPVVSSETQVTEGQVLAEASQRSEYGGEVRLRDSIGDSREVQIVTTAMTLKDFKLLEESTHSGEIWNLEAKDG 588
Cdd:TIGR02388 481 YNLPPGAEPVVKNGDRVEQGTVLAETKLSTEHGGVVRLPESVGDSREVEIITASVLLDQAKVIEESSQGRELYHIETADG 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 589 TRYRLNTIPGSKIGSGEVIAELADDRFRTGTGGLVKFApGLAIKKARSAKNGYEVNKGGTLLWIPQETHEINKDISLLMI 668
Cdd:TIGR02388 561 QRFRLKAAPGTKVQNGQVVAELIDDRYRTTTGGLLKYA-GVEVAKKGKAKQGYEVSQGGTLLWIPEETHEINKDISLLMV 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 669 TDGQWIEAGTEVVKDIFSQTAGIVTVTQKNDILREIIVRSGEFHLCTDAKALeRFEgDGQMVNPGEDIAKGLSVDTMKYV 748
Cdd:TIGR02388 640 EDGQYVEAGTEVVKDIFCQNSGIVEVTQKNDILREIIVKPGEFHEVDDPEAV-STE-EGTLLQPGEEVLPGVVVDELSQV 717
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 749 QTVETPEGKGLLLRPVEEYTIPNEAQLPELSHVKQANGPHLGIKATQRLAFKDNELIKSVEGVELLKTQLLLETFDTTPQ 828
Cdd:TIGR02388 718 QYLETPEGPGLLLRPVEEYTVPDEPEVPSQSSVSQEKGRSIALRAVQRLPYKDGERVKSVEGVELLRTQLVLEIFDEGPQ 797
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 829 MTVDVEKAPDKRAKTISRLRLVILESILVRRDTMSDSSHGSTHTELQVEDGVSVKAGDVVATTQILCKQAGLAQLPEATe 908
Cdd:TIGR02388 798 LAADIELIQDEEDKDIQRLQLVILESLVLRRDIASDSTQGSTHTSLLVKDGDLIKPGAVIARTQILCKEAGVVQGIDSG- 876
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 909 ADPVRRMIVERPEDTTTLSTSGKPVVSVGQRIVDGDALADGETATCCGEIEAVSGNSVTLRLGRPYMVSPDSVLHVRDGD 988
Cdd:TIGR02388 877 GESIRRLLVERNSDRLKVNIKAKPVVKTGDLVVAGDELAKGVKAEESGEIEEVASDYVILRIGRPYRVSPGAVLHIEDGD 956
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 989 LVQRGDGLALLVFERQKTGDIVQGLPRIEELLEARRPRESAILCKKPGTVEIKQGEDDESLAVNVIESDDAIGEYPILLG 1068
Cdd:TIGR02388 957 LVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARKPKEACILAKRPGVVQVKYGTDDESVSIKVIERDGTISEYPLLPG 1036
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1069 RNIMVSDGQQVTAGELLTDGPINPHELLECYFEDLRSRKPLMEAAQEAIANLQHRLVTEVQNVYKSQGVSIDDKHIEVIV 1148
Cdd:TIGR02388 1037 QNIMVSDGQQVTGGEPLTDGPINPHDILDVFFSYYKDQDGLYEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIV 1116
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1149 RQMTSKVRVEDAGDTTLLPGELIELRQVEDTNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAAI 1228
Cdd:TIGR02388 1117 RQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAI 1196
|
1210 1220 1230
....*....|....*....|....*....|.
gi 1896202387 1229 EGKSDWLRGLKENVIIGRLIPAGTGFSGFEE 1259
Cdd:TIGR02388 1197 EGKSDWLRGLKENVIIGRLIPAGTGFSSYEE 1227
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
35-1257 |
0e+00 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 1066.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 35 PPFRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERY 114
Cdd:CHL00117 7 LVFHNKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHY 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 115 RLGEITEVERHTKVIDTWTETNERLVDAVKKNFDENAPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIR 194
Cdd:CHL00117 87 HYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 195 TNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDAEDGK-----FGSRLVG 269
Cdd:CHL00117 167 SNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGMmieriLIQTLIG 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 270 RLTAAQVVNaDGEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQS 349
Cdd:CHL00117 247 RVLADDIYI-GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIAGQS 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 350 IGEPGTQLTMRTFHTGGVSTAET-GVVRSKVAGTVEFgSKARVRPYRTPHGVNAQQAEVDFNLTIKpsGKGKAQKIEITN 428
Cdd:CHL00117 326 IGEPGTQLTLRTFHTGGVFTGGTaEQVRAPFNGKIKF-NEDLVHPTRTRHGHPAFLCKIDLYVTIE--SEDIIHNVNIPP 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 429 GSLLFVDNGADIDADVTVAQIAAGAVKKSV-EKATKDVICDLAGQVRYEEAIQ-PREVTDRQGNITLKAqrlGRMWVLSG 506
Cdd:CHL00117 403 KSLLLVQNDQYVESEQVIAEIRAGTSTLNFkEKVRKHIYSDSEGEMHWSTDVYhAPEFTYGNVHLLPKT---SHLWILSG 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 507 DVYNLPPNAQPVVSSETQV-----TEGQVLAEASQRSEYGGEVRLR---------DSIGDSREVQIVTTamtlKDFKLLE 572
Cdd:CHL00117 480 GVYRSSLVSFSLHKDQDQInihlsVERRYISRLSVINTNNGQVRHKlfssdgkkeKRILDYSELNRIIS----NGHCNFI 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 573 ESTHSGEIWNLEAKDG--------------------TRYRLNTIPGSKIGSGEVIAELADDRFRTGTGGLVKFAPG--LA 630
Cdd:CHL00117 556 YPAILHENSDLLAKRRrnrflipfqsiqerekelmpCGISIEIPINGILRRNSIFAYFDDPRYRTKSSGITKYGTIevDS 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 631 IKKARSAKNGYEVN--------KGGTLLWIPQETHEINKdISLLMITDGQWIEAGTEVVKDIFSQTAGIVTVtQKNDILR 702
Cdd:CHL00117 636 IVKKEDLIEYRGVKefkpkyqmKVDRFFFIPEEVHILPE-SSSILVRNNSIIGVDTQITLNIRSKVGGLVRI-EKKKKRI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 703 EIIVRSGEFHLCTDAKALERFegdGQM-VNPGEDIAKGLSVDTMK---YVQTVETPEGKG-LLLRPVEEYTIPNEAQLPE 777
Cdd:CHL00117 714 ELKIFSGDIHFPGETDKISRH---SGIlIPPGTGKKNSKESKKIKnwiYVQRITPTKKKYfVLVRPVVTYEIADGINLAT 790
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 778 LSHVKQANGP-HLGIKATQRLAFKDNELIKSVEGVELLKTQLLL---ETFDTTPQMTVDVEKAPdKRAKTISR--LRLVI 851
Cdd:CHL00117 791 LFPQDLLQEKdNLQLRVVNYILYGNGKPIRGISSIQLVRTCLVLnwdQDKKSSSIEEARASFVE-VRTNGLIRdfLRINL 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 852 LES---------------ILVRRDTMSDSSHGSTHTELQVEDgVSVKAGDVVATTQ---------IL----CKQAGLAQ- 902
Cdd:CHL00117 870 VKSpisyirkrndpsssgLLVQSNNFLDSTNIYSKAEIQSQS-LSQNQGTIRTLLNrnkesqsllILsssdCFRIGPFNg 948
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 903 ----LPEATEADPVRRMIVE---------------------------------------------------------RPE 921
Cdd:CHL00117 949 kkskYHNIKESNPLIPIRNSlgplgtvlqianfsssyhllthnqilvtkylqldnlkqtfqvkvlkyylidengkiyNPD 1028
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 922 DTTTL----------------STSGKPVVSVGQRIVDGDALADGETATcCGEIEAVSGNSVTLRLGRPYMVSPDSVLHVR 985
Cdd:CHL00117 1029 PCSNIilnpfnlnwyflhhnyCEETSTIISLGQFICENVCISKNGPHK-SGQIIIVQVDSLVIRSAKPYLATPGATVHGH 1107
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 986 DGDLVQRGDGLALLVFERQKTGDIVQGLPRIEELLEARrpresailckkpgtvEIKqgeddeSLAVNVIESDDAIGEypi 1065
Cdd:CHL00117 1108 YGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEAR---------------SID------SISMNLEKRLEGWNE--- 1163
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1066 llgrnimvsdgqqvtagelltdgpiNPHELLECYFedlrsrkPLMEAAQEAIANLQHRLVTEVQNVYKSQGVSIDDKHIE 1145
Cdd:CHL00117 1164 -------------------------RITRILGIPW-------GFLIGAELSIAQSQISLVNKIQKVYRSQGVQISDKHIE 1211
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1146 VIVRQMTSKVRVEDAGDTT-LLPGELIELRQVEDTNQAMAItggaPAEFTPVLLGITKASLNTDSFISAASFQETTRVLT 1224
Cdd:CHL00117 1212 IIVRQMTSKVLVSEDGMSNvFLPGELIGLLRAERINRALEE----AICYRPILLGITKASLNTQSFISEASFQETTRVLA 1287
|
1370 1380 1390
....*....|....*....|....*....|...
gi 1896202387 1225 EAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGF 1257
Cdd:CHL00117 1288 KAALRGRIDWLKGLKENVILGGLIPAGTGFKGL 1320
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
37-390 |
2.15e-179 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 563.54 E-value: 2.15e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 37 FRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYRL 116
Cdd:PRK00566 569 NVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRR 648
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 117 GEITEVERHTKVIDTWTETNERLVDAVKKNFD-ENAPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRT 195
Cdd:PRK00566 649 GLITDGERYNKVIDIWSKATDEVAKAMMKNLSkDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIKS 728
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 196 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDA--EDG----KFGSRLVG 269
Cdd:PRK00566 729 NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAiiEGGeviePLEERILG 808
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 270 RLTAAQVVNAD-GEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQ 348
Cdd:PRK00566 809 RVLAEDVVDPEtGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQ 888
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*...
gi 1896202387 349 SIGEPGTQLTMRTFHTGGVS-T------AE---------TGVVrSKVAGTVEFGSKAR 390
Cdd:PRK00566 889 SIGEPGTQLTMRTFHTGGVDiTgglprvAElfearkpkgPAII-AEIDGTVSFGKETK 945
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
34-1253 |
8.89e-143 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 483.66 E-value: 8.89e-143
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 34 PPPFRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEER 113
Cdd:PRK09603 1964 PTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQ 2043
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 114 YRLGEITEVERHTKVIDTWTETNERL-------VDAVKKNFdenaplNSVWMMANSGARGNMSQVRQLVGMRGLMANPQG 186
Cdd:PRK09603 2044 YDQGLLTDQERYNKIIDTWTEVNDKMskemmtaIAKDKEGF------NSIYMMADSGARGSAAQIRQLSAMRGLMTKPDG 2117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 187 EIIDLPIRTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTtrHIVVDAEDGKFGS- 265
Cdd:PRK09603 2118 SIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGT--HEGIEITDIAVGSe 2195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 266 -------RLVGRLTAAQVVNA-DGEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVD 337
Cdd:PRK09603 2196 liepleeRIFGRVLLEDVIDPiTNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSY 2275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 338 LGEAVGIIAAQSIGEPGTQLTMRTFHTGGV---STAETGVVRSKvAGTVEFgskarvrpyrtphgvnaqqaevdFNLTIK 414
Cdd:PRK09603 2276 PGEAVGVVAAQSIGEPGTQLTLRTFHVGGTasrSQDEREIVASK-EGFVRF-----------------------YNLRTY 2331
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 415 PSGKGKAQKIEITNGSLLFVDN--GADIDADVTVaQIAAGAVKKSVEKATKDVICDLagqvRYEEAIQPREVTDRQGNIt 492
Cdd:PRK09603 2332 TNKEGKNIIANRRNASILVVEPkiKAPFDGELRI-ETVYEEVVVSVKNGDQEAKFVL----RRSDIVKPSELAGVGGKI- 2405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 493 lkaqrlgrmwvlSGDVYnLPpnaqpvVSSETQVTEGQVLAEASQ-------RSEYGGEVRLRDSigdsrevQIVTTAMTL 565
Cdd:PRK09603 2406 ------------EGKVY-LP------YASGHKVHKGGSIADIIQegwnvpnRIPYASELLVKDN-------DPIAQDVYA 2459
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 566 KDFKLLeesthsgEIWNLEAKDGTRYRlNTIPGSKIGSGEVIAELADDRFRTgtgglvkfapglAIKkarsakngyevnk 645
Cdd:PRK09603 2460 KEKGII-------KYYVLEANHLERTH-GIKKGDIVSEKGLFAVIADDNGRE------------AAR------------- 2506
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 646 ggtllwipqetHEINKDiSLLMITDGQWIEAGTEVVKDIFSQTAGIVTVtqknDILREIIVrsgefhlcTDAKALERFeg 725
Cdd:PRK09603 2507 -----------HYIARG-SEILIDDNSEVSANSVISKPTTNTFKTIATW----DPYNTPII--------ADFKGKVSF-- 2560
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 726 dgqmvnpgEDIAKGLSVdtmkyvqTVETPEGKGLLLRPVEEYtIPNeaqlpelshvkqangphlGIKATQRLAFKDNELI 805
Cdd:PRK09603 2561 --------VDIIAGVTV-------AEKEDENTGITSLVVNDY-IPS------------------GYKPSLFLEGANGEEI 2606
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 806 ksvegvellktqllletfdttpqmtvdvekapdkraktisRLRLvilesilvrrdtmsdsshgSTHTELQVEDGVSVKAG 885
Cdd:PRK09603 2607 ----------------------------------------RYFL-------------------EPKTSIAISDGSSVEQA 2627
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 886 DVvattqilckqagLAQLPEATeadpvrrmiverpedtttlstsgkpvvsvgqrivdgdaladgetatccgeieavsgns 965
Cdd:PRK09603 2628 EV------------LAKIPKAT---------------------------------------------------------- 2637
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 966 vtlrlgrpymvspdsvlhvrdgdlvqrgdglallVFERQKTGdivqGLPRIEELLEAR--RPRESAILCKKPGTVEI-KQ 1042
Cdd:PRK09603 2638 ----------------------------------VKSRDITG----GLPRVSELFEARkpKPKDVAILSEVDGIVSFgKP 2679
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1043 GEDDESLavnVIESDDA-IGEYPILLGRNIMVSDGQQVTAGELLTDGPINPHELLECYFEDlrsrkplmeaaqeaiaNLQ 1121
Cdd:PRK09603 2680 IRNKEHI---IVTSKDGrSMDYFVDKGKQILVHADEFVHAGEAMTDGVVSSHDILRISGEK----------------ELY 2740
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1122 HRLVTEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGDTTLLPGELIELRQVEDTNQAMAITGGAPAEFTPVLLGIT 1201
Cdd:PRK09603 2741 KYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALKGEPAIAEPVLLGIT 2820
|
1210 1220 1230 1240 1250
....*....|....*....|....*....|....*....|....*....|..
gi 1896202387 1202 KASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:PRK09603 2821 RAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
38-388 |
8.00e-142 |
|
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: 462.60 E-value: 8.00e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 38 RNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYRLG 117
Cdd:TIGR02386 561 DNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKG 640
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 118 EITEVERHTKVIDTWTETNERLVDAVKKNFDENAP-LNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRTN 196
Cdd:TIGR02386 641 LITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYkFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSS 720
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 197 FREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDA-EDGKFGS------RLVG 269
Cdd:TIGR02386 721 FREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAiVEGKDEIieslkdRIVG 800
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 270 RLTAAQVVNAD-GEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQ 348
Cdd:TIGR02386 801 RYSAEDVYDPDtGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQ 880
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 349 SIGEPGTQLTMRTFHTGGVSTAE---TG-----------------VVRSKVAGTVEFGSK 388
Cdd:TIGR02386 881 SIGEPGTQLTMRTFHTGGVAGASgdiTQglprvkelfeartpkdkAVIAEVDGTVEIIED 940
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
36-500 |
4.51e-132 |
|
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: 436.51 E-value: 4.51e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 36 PFRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYR 115
Cdd:COG0086 571 PFYNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYA 650
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 116 LGEITEVERHTKVIDTWTETNERLVDAVKKNFDenaPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRT 195
Cdd:COG0086 651 EGLITEPERYNKVIDGWTKASLETESFLMAAFS---SQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGS 727
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 196 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDA--EDG----KFGSRLVG 269
Cdd:COG0086 728 NFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDRGITVTAikEGGeviePLKERILG 807
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 270 RLTAAQVVNAD-GEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQ 348
Cdd:COG0086 808 RVAAEDVVDPGtGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQ 887
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 349 SIGEPGTQLTMRTFHTGGVST--AETGVVRSKVAGTVEFGSKARVrpyrtphgVNAQQAEVDFN----LTIKPSGKGKAQ 422
Cdd:COG0086 888 SIGEPGTQLTMRTFHIGGAASraAEESSIEAKAGGIVRLNNLKVV--------VNEEGKGVVVSrnseLVIVDDGGRREE 959
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1896202387 423 KIEITNGSLLFVDNGADIDADVTVAQIAAGAVKKSVEKATKDVICDLAGQVRYEEAIQPREVTDRQGNITLKAQRLGR 500
Cdd:COG0086 960 EYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGG 1037
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
36-368 |
3.73e-111 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 383.45 E-value: 3.73e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 36 PFRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYR 115
Cdd:PRK14906 671 PYLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYE 750
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 116 LGEITEVERHTKVIDTWTETNERLVDAVKKNFDENAPlnsVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRT 195
Cdd:PRK14906 751 DGFLSERERHKQVVDIWTEATEEVGEAMLAGFDEDNP---IYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKA 827
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 196 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVD--AEDGKFGSRLVGRLTA 273
Cdd:PRK14906 828 NFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPlvKPKGDVDTNLIGRCLL 907
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 274 AQVVNADGEVLAERDTEIDPPLS-KAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQSIGE 352
Cdd:PRK14906 908 EDVCDPNGEVLLSAGDYIESMDDlKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGE 987
|
330
....*....|....*.
gi 1896202387 353 PGTQLTMRTFHTGGVS 368
Cdd:PRK14906 988 PGTQLTMRTFHSGGVA 1003
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1006-1259 |
3.91e-108 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 369.78 E-value: 3.91e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1006 TG--DIVQGLPRIEELLEARRPRESAILCKKPGTVEIkqGEDDESLAVNVIESDDA-IGEYPILLGRNIMVSDGQQVTAG 1082
Cdd:PRK00566 904 TGgvDITGGLPRVAELFEARKPKGPAIIAEIDGTVSF--GKETKGKRRIVITPDDGeEREYLIPKGKHLLVQEGDHVEAG 981
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1083 ELLTDGPINPHELLecyfedlRSRKPlmeaaqEAianLQHRLVTEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGD 1162
Cdd:PRK00566 982 DKLTDGSIDPHDIL-------RVLGV------EA---VQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGD 1045
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1163 TTLLPGELIELRQVEDTNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENV 1242
Cdd:PRK00566 1046 TDFLPGELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENV 1125
|
250
....*....|....*..
gi 1896202387 1243 IIGRLIPAGTGFSGFEE 1259
Cdd:PRK00566 1126 IIGRLIPAGTGLARYRN 1142
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
36-247 |
1.72e-106 |
|
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: 352.21 E-value: 1.72e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 36 PFRNQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYR 115
Cdd:cd01609 449 PFINKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYE 528
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 116 LGEITEVERHTKVIDTWTETNERLVDAVKKNFDENaPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRT 195
Cdd:cd01609 529 KGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKD-PFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPIKS 607
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 1896202387 196 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDD 247
Cdd:cd01609 608 NFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
1004-1259 |
2.67e-90 |
|
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: 318.15 E-value: 2.67e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1004 QKTGDIVQGLPRIEELLEARRPRESAILCKKPGTVEIKQGEDDESLAVNVIESDDAIGEYPILLGRNIMVSDGQQVTAGE 1083
Cdd:TIGR02386 901 GASGDITQGLPRVKELFEARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGD 980
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1084 LLTDGPINPHELLECyfedlrsrkplmeaaqEAIANLQHRLVTEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGDT 1163
Cdd:TIGR02386 981 KLTEGSIDPHDLLRI----------------KGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDS 1044
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1164 TLLPGELIELRQVEDTNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVI 1243
Cdd:TIGR02386 1045 NLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVI 1124
|
250
....*....|....*.
gi 1896202387 1244 IGRLIPAGTGFSGFEE 1259
Cdd:TIGR02386 1125 IGNLIPAGTGLKTYKE 1140
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
39-513 |
7.77e-90 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 323.11 E-value: 7.77e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 39 NQVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKDLLGQAEEQITATEERYRLGE 118
Cdd:PRK14844 2023 NQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGL 2102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 119 ITEVERHTKVIDTWTETNERLVDAVKKN---FDENAPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIRT 195
Cdd:PRK14844 2103 ITRSERYNKVIDEWSKCTDMIANDMLKAisiYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIIS 2182
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 196 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHIVVDA--EDG----KFGSRLVG 269
Cdd:PRK14844 2183 NFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRAtvEGStivaSLESVVLG 2262
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 270 RLTAAQVVN-ADGEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANRSVCRKCYGWALAHNELVDLGEAVGIIAAQ 348
Cdd:PRK14844 2263 RTAANDIYNpVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQ 2342
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 349 SIGEPGTQLTMRTFHTGGVST--AETGVVRSKVAGTVEFGSKARVRPYRTPHGVNAQQAEVdfnLTIKPSGKGKAqKIEI 426
Cdd:PRK14844 2343 SVGEPGTQLTMRTFHIGGVMTrgVESSNIIASINAKIKLNNSNIIIDKNGNKIVISRSCEV---VLIDSLGSEKL-KHSV 2418
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 427 TNGSLLFVDNGADIDADVTVAQIaagavkksvEKATKDVICDLAGQVRYE---EAIQPREVTDRQGNITlkaQRLGRMWV 503
Cdd:PRK14844 2419 PYGAKLYVDEGGSVKIGDKVAEW---------DPYTLPIITEKTGTVSYQdlkDGISITEVMDESTGIS---SKVVKDWK 2486
|
490
....*....|
gi 1896202387 504 LSGDVYNLPP 513
Cdd:PRK14844 2487 LYSGGANLRP 2496
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1007-1254 |
4.71e-84 |
|
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: 273.25 E-value: 4.71e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1007 GDIVQGLPRIEELLEARrpresailckkpgtveikqgeddeslavnviesddaigeypillgrnimvsdgqqvtagellt 1086
Cdd:cd02655 36 TDITQGLPRVEELFEAR--------------------------------------------------------------- 52
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1087 dgPINPHELLECYFEDLRsrkplmeaaqeaiaNLQHRLVTEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGDTTLL 1166
Cdd:cd02655 53 --KINPHDLLRIKFLGPE--------------AVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFL 116
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1167 PGELIELRQVEDTNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1246
Cdd:cd02655 117 PGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGR 196
|
....*...
gi 1896202387 1247 LIPAGTGF 1254
Cdd:cd02655 197 LIPAGTGL 204
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
816-1254 |
3.99e-63 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 238.37 E-value: 3.99e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 816 TQLLLETFDTTPQMTVDVEKApDKRAKTISRLRL----VILE----SILVRRD---TMSDS--SHGSTHT-----ELQVE 877
Cdd:PRK14844 2349 TQLTMRTFHIGGVMTRGVESS-NIIASINAKIKLnnsnIIIDkngnKIVISRScevVLIDSlgSEKLKHSvpygaKLYVD 2427
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 878 DGVSVKAGDVVA-----TTQILCKQAGLAQLPEATEADPvrrmIVERPEDTTTLST---------SGkpVVSVGQRIVDG 943
Cdd:PRK14844 2428 EGGSVKIGDKVAewdpyTLPIITEKTGTVSYQDLKDGIS----ITEVMDESTGISSkvvkdwklySG--GANLRPRIVLL 2501
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 944 DAlaDGETATCCGEIEAVsgnsvtlrlgrpYMVSPDSVLHVRDGDLVQRGDGLALLVFERQKTGDIVQGLPRIEELLEAR 1023
Cdd:PRK14844 2502 DD--NGKVMTLASGVEAC------------YFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELFEAR 2567
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1024 RPRESAILCKKPGTVEIKQGEDDESLAVNVIESDDAIG--EYPILLGRNIMVSDGQQVTAGELLTDGPINPHELLecyfe 1101
Cdd:PRK14844 2568 RPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVDEQISpvEYLVSRSKHVIVNEGDFVRKGDLLMDGDPDLHDIL----- 2642
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1102 dlrsRKPLMEAaqeaianLQHRLVTEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGDTTLLPGELIELRQVEDTNQ 1181
Cdd:PRK14844 2643 ----RVLGLEA-------LAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDREND 2711
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1896202387 1182 AMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1254
Cdd:PRK14844 2712 AMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
1008-1287 |
3.35e-60 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 227.83 E-value: 3.35e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1008 DIVQGLPRIEELLEARRPRESAILCKKPGTVEIkQGEDDESLaVNVIESDDAIGEYPILLGRNIM--VSDGQQVTAGELL 1085
Cdd:PRK14906 1006 DITQGLPRVAELFEARKPKGEAVLAEISGTLQI-TGDKTEKT-LTIHDQDGNSREYVVSARVQFMpgVEDGVEVRVGQQI 1083
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1086 TDGPINPHELLEcyFEDLRSRkplmeaaqeaianlQHRLVTEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGDTTL 1165
Cdd:PRK14906 1084 TRGSVNPHDLLR--LTDPNTT--------------LRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDY 1147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1166 LPGELIELRQVEDTNQAMAITGGAPAEFTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIG 1245
Cdd:PRK14906 1148 LPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIG 1227
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1896202387 1246 RLIPAGTGFSGFEE-EL----QKEAGPHPDILSE-DPAGYRRMQNLRP 1287
Cdd:PRK14906 1228 KPIPAGTGLSRYRDvGLtyhgQKVDGPTSKSLPDwAPEELRDIEELLP 1275
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
200-376 |
2.28e-53 |
|
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: 196.04 E-value: 2.28e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 200 GLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDDCGTTRHI----VVDAEDG-------------- 261
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGeivqFLYGEDGldplkiekqgrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 262 ----------------------KFGSRLVGRLTAAQVVNADGEVLAERDTEIDPPLSKAFEAAGVKAVSVRSPLTCEANR 319
Cdd:pfam04998 81 efsdlkledkfkndllddllllSEFSLSYKKEILVRDSKLGRDRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 1896202387 320 SVCRKCYGWALAHNELVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVSTA--ETGVVR 376
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKnvTLGVPR 219
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
40-246 |
9.23e-50 |
|
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: 185.71 E-value: 9.23e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 40 QVIDKRALKQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDL----KVPEAKKDLLGQAEEQITATEERYR 115
Cdd:cd00399 291 QIVSAALPGGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDViddgVIPEEKTELIEEAKKKVDEVEEAFQ 370
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 116 LGEITEVERHT-------KVIDTWTETNERLVDAVKKNFDENAPLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEI 188
Cdd:cd00399 371 AGLLTAQEGMTleesledNILDFLNEARDKAGSAASVNLDLVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRI 450
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1896202387 189 IDL--------------------PIRTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVRED 246
Cdd:cd00399 451 PRGfsdrtlphfskddyspeakgFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
41-252 |
2.06e-28 |
|
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: 123.90 E-value: 2.06e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 41 VIDKRAL-----KQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKKD----LLGQAEEQITATE 111
Cdd:cd02582 594 VIDKKAIgaeqpGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKeieeIIKEAEKKVYELI 673
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 112 ERYRLGEItEVER--------HTKVIDTWTETNERLVDAVKKNFDenaPLNSVWMMANSGARGNMSQVRQLVGMRGLMAn 183
Cdd:cd02582 674 EQYKNGEL-EPLPgrtleetlEMKIMQVLGKARDEAGKVASKYLD---PFNNAVIMARTGARGSMLNLTQMAACLGQQS- 748
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 184 PQGEIID-------LP--------------IRTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVI 242
Cdd:cd02582 749 VRGERINrgyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLY 828
|
250
....*....|
gi 1896202387 243 VREDdcGTTR 252
Cdd:cd02582 829 VEYD--GTVR 836
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
41-252 |
3.01e-26 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 116.88 E-value: 3.01e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 41 VIDKRAL----KQLVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVP-EAKK---DLLGQAEEQITATEE 112
Cdd:PRK08566 599 VIDKKAIgaeqGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPeEAKEeidEIIEEAEKRVEELIE 678
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 113 RYRLGEIT-------EVERHTKVIDTWTETNERLVDAVKKNFDenaPLNSVWMMANSGARGNMSQVRQLVGMRGLMAnPQ 185
Cdd:PRK08566 679 AYENGELEplpgrtlEETLEMKIMQVLGKARDEAGEIAEKYLG---LDNPAVIMARTGARGSMLNLTQMAACVGQQS-VR 754
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 186 GEIID-------LP--------------IRTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVR 244
Cdd:PRK08566 755 GERIRrgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVE 834
|
....*...
gi 1896202387 245 EDdcGTTR 252
Cdd:PRK08566 835 YD--GTVR 840
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
56-367 |
3.23e-24 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 110.89 E-value: 3.23e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 56 KNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDLKVPEAKK----DLLGQAEEQITATEERYRLGEITEVERHTKVIDT 131
Cdd:PRK14977 638 KDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKqeieDDIQGMKDEVSDLIDQRKITRKITIYKGKEELLR 717
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 132 WTETNERL----VDAVKKNFDENA--------PLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQGEIIDLP------- 192
Cdd:PRK14977 718 GMKEEEALeadiVNELDKARDKAGssandcidADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTggrlheg 797
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 193 ---------------------IRTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDdcGTT 251
Cdd:PRK14977 798 ykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYD--ETV 875
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 252 R----HIV--VDAEDGKFGSRL-------VGRLTAAQVVNADGE-VLAERDTEIDPPLSKAFEAAGVKAVS---VRSPLT 314
Cdd:PRK14977 876 RdphgHIIqfKFGEDGIDPQKLdhgeafnLERIIEKQKIEDRGKgASKDEIEELAKEYTKTFNANLPKLLAdaiHGAELK 955
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|...
gi 1896202387 315 CEANRSVCRKcyGWALAHNELVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 367
Cdd:PRK14977 956 EDELEAICAE--GKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGI 1006
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1091-1253 |
5.26e-21 |
|
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: 90.94 E-value: 5.26e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1091 NPHELLECYFedlrsrkplMEAAQEAIanlqhrlVTEVQNVYKSQGVSIDDKHIEVIVRQMTskvrvedagdttllpgel 1170
Cdd:cd00630 49 SIHEMLEALG---------IEAARETI-------IREIQKVLASQGVSVDRRHIELIADVMT------------------ 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1171 ielrqvedtnqamaitggapaeFTPVLLGITKASLN--TDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLI 1248
Cdd:cd00630 95 ----------------------YSGGLRGVTRSGFRasKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPA 152
|
....*
gi 1896202387 1249 PAGTG 1253
Cdd:cd00630 153 PLGTG 157
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
335-369 |
7.27e-21 |
|
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: 92.21 E-value: 7.27e-21
10 20 30
....*....|....*....|....*....|....*
gi 1896202387 335 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVST 369
Cdd:cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT 36
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
119-198 |
4.22e-20 |
|
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: 86.65 E-value: 4.22e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 119 ITEVERHTKVIDTWTETNERLVDAVKKNFDENA-------------PLNSVWMMANSGARGNMSQVRQLVGMRGLMANPQ 185
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKArdpagniasksldPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 1896202387 186 GEI---------------IDLPIRTNFR 198
Cdd:pfam05000 81 KRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1139-1254 |
1.34e-14 |
|
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: 79.43 E-value: 1.34e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1139 IDDKHIEVIVRQMTSKVRVE------------------DAGDTTLLPGELI-------------ELRQVEDTNQAMAITg 1187
Cdd:COG0086 577 INKKHIEVIIRQMYRRCGLKetvifldrlkklgfkyatRAGISIGLDDMVVpkekqeifeeankEVKEIEKQYAEGLIT- 655
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1188 gAPAEFTPVLLGITKASLNTDSFISAA-SFQETTRVLTEAAIEGKSDWLRGL----------KENVI---IGRLIPAGTG 1253
Cdd:COG0086 656 -EPERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmakpSGNIIetpIGSNFREGLG 734
|
.
gi 1896202387 1254 F 1254
Cdd:COG0086 735 V 735
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
999-1163 |
3.81e-14 |
|
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: 77.01 E-value: 3.81e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 999 LVFERQKTGDIVQGLPRIEELLEARRPRESAILCKKPGTVEIKQGEDDESLAVNVIESDDAIGEYPIL-----LGRNIMV 1073
Cdd:pfam04998 358 IIKISKKIRQDTGGLRRVDELFMEEDPKLAILVASLLGNITLRGIPGIKRILVNEDDKGKVEPDWVLEtegvnLLRVLLV 437
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1074 SDgqQVTAGELLTDgpiNPHELLECYFEdlrsrkplmEAAQEAIanlqhrlVTEVQNVYKSQGVSIDDKHIEVIVRQMTS 1153
Cdd:pfam04998 438 PG--FVDAGRILSN---DIHEILEILGI---------EAARNAL-------LNEIRNVYRFQGIYINDRHLELIADQMTR 496
|
170
....*....|
gi 1896202387 1154 KVRVEDAGDT 1163
Cdd:pfam04998 497 KGYIMAIGRH 506
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
332-367 |
8.47e-13 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 71.80 E-value: 8.47e-13
10 20 30
....*....|....*....|....*....|....*.
gi 1896202387 332 HNELVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 367
Cdd:PRK04309 52 LRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGV 87
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
333-368 |
1.53e-12 |
|
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: 70.85 E-value: 1.53e-12
10 20 30
....*....|....*....|....*....|....*.
gi 1896202387 333 NELVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVS 368
Cdd:TIGR02389 38 RSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVA 73
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
335-368 |
3.96e-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: 69.59 E-value: 3.96e-12
10 20 30
....*....|....*....|....*....|....
gi 1896202387 335 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVS 368
Cdd:cd06528 36 LIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVA 69
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
333-367 |
4.75e-12 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 70.22 E-value: 4.75e-12
10 20 30
....*....|....*....|....*....|....*
gi 1896202387 333 NELVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 367
Cdd:PRK14897 176 RARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGV 210
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
339-378 |
3.19e-11 |
|
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: 62.82 E-value: 3.19e-11
10 20 30 40
....*....|....*....|....*....|....*....|..
gi 1896202387 339 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVST--AETGVVRSK 378
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASmnVTLGLPRLK 42
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1111-1253 |
4.44e-11 |
|
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: 65.70 E-value: 4.44e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1111 EAAQEAIANlqhrlvtEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVedagdttllpgelielrqvedtnqamaitggap 1190
Cdd:cd02736 201 EAARSTIIN-------EIQYTMKSHGMSIDPRHIMLLADLMTFKGEV--------------------------------- 240
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1896202387 1191 aeftpvlLGITKASL--NTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:cd02736 241 -------LGITRFGIakMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1111-1253 |
7.17e-11 |
|
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: 65.73 E-value: 7.17e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1111 EAAQEAIANlqhrlvtEVQNVYKSQGVSIDDKHIEVIVRQMTSkvrvedagdttllPGELielRQVedtnQAMAITGgap 1190
Cdd:cd06528 258 EAARNAIIN-------EIKRTLEEQGLDVDIRHIMLVADIMTY-------------DGEV---RQI----GRHGIAG--- 307
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1896202387 1191 aeftpvllgiTKASLntdsfISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:cd06528 308 ----------EKPSV-----LARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
141-252 |
9.68e-11 |
|
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: 66.42 E-value: 9.68e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 141 DAVKKNFDENAPLNSVWMMANSGARG---NMSQV-----RQLV-GMRglmanPQGEIID--LP--------------IRT 195
Cdd:cd02583 687 DAGKACLKELHKSNSPLIMALCGSKGsniNISQMiacvgQQIIsGKR-----IPNGFEDrtLPhfprnsktpaakgfVAN 761
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*..
gi 1896202387 196 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREDdcGTTR 252
Cdd:cd02583 762 SFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYD--GTVR 816
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
335-366 |
1.15e-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: 1.15e-10
10 20 30
....*....|....*....|....*....|..
gi 1896202387 335 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGG 366
Cdd:cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
335-368 |
4.49e-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: 62.62 E-value: 4.49e-10
10 20 30
....*....|....*....|....*....|....
gi 1896202387 335 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVS 368
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVA 39
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1111-1253 |
5.12e-10 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 62.94 E-value: 5.12e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1111 EAAQEAIANlqhrlvtEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGdttllpgelielRqvedtnqaMAITGgap 1190
Cdd:PRK04309 275 EAARNAIIE-------EIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIG------------R--------HGVSG--- 324
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1896202387 1191 aeftpvllgiTKASLntdsfISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:PRK04309 325 ----------EKASV-----LARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
335-378 |
2.46e-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: 61.07 E-value: 2.46e-09
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 1896202387 335 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVSTAE--TGVVRSK 378
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNvtLGVPRLK 68
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
141-246 |
1.10e-08 |
|
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: 59.86 E-value: 1.10e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 141 DAVKKNFDENAPLNSVWMMANSGARG---NMSQVRQLVGM-----------------------------RGLMANpqgei 188
Cdd:cd02733 626 KAGKSAQKSLSEDNNFKAMVTAGSKGsfiNISQIIACVGQqnvegkripfgfrrrtlphfikddygpesRGFVEN----- 700
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 1896202387 189 idlpirtNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVAQDVIVRED 246
Cdd:cd02733 701 -------SYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1197-1254 |
7.88e-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: 56.44 E-value: 7.88e-08
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1197 LLGITKASLN-TD-SFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1254
Cdd:cd02584 345 LMAITRHGINrQDtGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1110-1253 |
3.39e-07 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 54.43 E-value: 3.39e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1110 MEAAQEAIANlqhrlvtEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGDTtllpgelielrqvedtnqamaitgga 1189
Cdd:PRK14897 398 IEAARNAIIH-------EAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRH-------------------------- 444
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1896202387 1190 paeftpvllGItkaSLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:PRK14897 445 ---------GI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1110-1253 |
4.78e-07 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 54.51 E-value: 4.78e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1110 MEAAQEAIANlqhrlvtEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGdttllpgelielRQvedtnqamAITGga 1189
Cdd:PRK14898 744 IEAARNAIIN-------EMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIG------------RH--------GVAG-- 794
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1896202387 1190 paeftpvllgitkaslNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:PRK14898 795 ----------------EKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
41-90 |
5.28e-07 |
|
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: 50.70 E-value: 5.28e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1896202387 41 VIDKRALKQ----LVAWSYKNHGTAVTSAMADNLKDLGFKYATQAAVSISVDDL 90
Cdd:pfam04983 105 VIDKKTVGKslgsLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
1110-1253 |
8.58e-05 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 47.33 E-value: 8.58e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1896202387 1110 MEAAQEAIANlqhrlvtEVQNVYKSQGVSIDDKHIEVIVRQMTSKVRVEDAGdttllpgelielrqvedtNQAMAITGGA 1189
Cdd:PRK14977 1205 IEAARNAIFN-------ELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIG------------------LQAAGVRHGF 1259
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1896202387 1190 PAEftpvllgitkaslnTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1253
Cdd:PRK14977 1260 AGE--------------KDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
307-367 |
1.11e-04 |
|
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: 46.69 E-value: 1.11e-04
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1896202387 307 VSVRSPLTCEANRSVCR--KCYGWALAHneLVDLG---EAVGI------IAAQSIGEpgTQLTMRTFHTGGV 367
Cdd:COG0086 40 KPERDGLFCERIFGPCKdyECYCGKYKR--MVYKGvvcEKCGVevtlskVRRERMGH--IELAMPVFHIWGL 107
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
333-359 |
2.70e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 45.65 E-value: 2.70e-04
10 20
....*....|....*....|....*..
gi 1896202387 333 NELVDLGEAVGIIAAQSIGEPGTQLTM 359
Cdd:PRK14898 51 NALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
