|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-1195 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2263.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 3 DVNK--FESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCELCGV 80
Cdd:PRK00566 1 DVNKqdFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 81 QVTTAKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDPKETDLEKKQLLTEREYREQLL 160
Cdd:PRK00566 81 EVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 161 KNGfGSFVAKMGAEAIQDLLNDVDIDKEVSELKEELK-TVTGQRRVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIPPDL 239
Cdd:PRK00566 161 EYG-DEFVAKMGAEAIKELLKNIDLEAEAEELREELKeTGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 240 RPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKSLSH 319
Cdd:PRK00566 240 RPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSD 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 320 MLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDSDVW 399
Cdd:PRK00566 320 MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVW 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 400 DVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEH 479
Cdd:PRK00566 400 DVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNN 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 480 ILNPKDGKPVVTPSQDMVLGNYYLTMEEKGREGEGMIFATPEEVEIAMRNGYVHLHTRIGIATKslnkpwtenqKDKILV 559
Cdd:PRK00566 480 ILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRIT----------SKKLVE 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 560 TTVGKVIFNSIIPEGMPYLNEPtdvnlttstddrffmdagqdikevlagidtvRPFKKGYLGNIIAEVFKRYRTTATSEY 639
Cdd:PRK00566 550 TTVGRVIFNEILPEGLPFINVN-------------------------------KPLKKKEISKIINEVYRRYGLKETVIF 598
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 640 LDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAKE----ALEKR 715
Cdd:PRK00566 599 LDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDevakAMMKN 678
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 716 LIDEQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTDTALKTA 795
Cdd:PRK00566 679 LSKDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTA 758
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 796 DSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEPLFERLVGRYTRKSVLHPETGEMIIADDTLISEDVARK 875
Cdd:PRK00566 759 DSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADK 838
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 876 IIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVasssDITQGLP 955
Cdd:PRK00566 839 IEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV----DITGGLP 914
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 956 RVQEIFEARNPKGEAIITEVTGTVESIVEDPATRTREITVKgKTDTRSYTVGMADVLMVEEGEFIHRGAPLIQGSIEPKH 1035
Cdd:PRK00566 915 RVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPD-DGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHD 993
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1036 LLQVRDALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGSTDILPGTLMDISDFEALNETALLNGEMP 1115
Cdd:PRK00566 994 ILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEP 1073
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1116 ATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMFRYRNIEPLADLTNAP 1195
Cdd:PRK00566 1074 ATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDEEE 1153
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
9-1183 |
0e+00 |
|
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: 1850.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 9 SMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCELCGVQVTTAKSR 88
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 89 RERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDPKETDLEKKQLLTEREYREQLLKNGFGsFV 168
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDG-FR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 169 AKMGAEAIQDLLNDVDIDKEVSELKEELKTVTGQR-RVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIPPDLRPMVQLDG 247
Cdd:TIGR02386 160 AGMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQkRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 248 GRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKSLSHMLKGKQGR 327
Cdd:TIGR02386 240 GRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 328 FRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDSDVWDVLETVVK 407
Cdd:TIGR02386 320 FRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 408 EHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGK 487
Cdd:TIGR02386 400 EHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGK 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 488 PVVTPSQDMVLGNYYLTMEEKGREGEGMIFATPEEVEIAMRNGYVHLHTRIGIATKSlnkpwtenqkdKILVTTVGKVIF 567
Cdd:TIGR02386 480 PIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSG-----------EILETTVGRVIF 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 568 NSIIPEGMPYLNEPtdvnlttstddrffmdagqdikevlagidtvRPFKKGYLGNIIAEVFKRYRTTATSEYLDRLKDLG 647
Cdd:TIGR02386 549 NEILPEGFPYINDN-------------------------------EPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALG 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 648 YHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAKE----ALEKRLIDEQDLT 723
Cdd:TIGR02386 598 FKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDkvtdAMMKLLKKDTYKF 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 724 NPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTDTALKTADSGYLTRR 803
Cdd:TIGR02386 678 NPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRR 757
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 804 LVDVAQDVIIREDDCGTDRGLVISDIATGK-EMVEPLFERLVGRYTRKSVLHPETGEMIIADDTLISEDVARKIIDAGVK 882
Cdd:TIGR02386 758 LVDVAQDVVVREEDCGTEEGIEVEAIVEGKdEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIE 837
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 883 EVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASSS-DITQGLPRVQEIF 961
Cdd:TIGR02386 838 KVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASgDITQGLPRVKELF 917
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 962 EARNPKGEAIITEVTGTVESIVEDPATRtREITVKG-KTDTRSYTVGMADVLMVEEGEFIHRGAPLIQGSIEPKHLLQVR 1040
Cdd:TIGR02386 918 EARTPKDKAVIAEVDGTVEIIEDIVKNK-RVVVIKDeNDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIK 996
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1041 DALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGSTDILPGTLMDISDFEALNETALLNGEMPATGRP 1120
Cdd:TIGR02386 997 GIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIP 1076
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516476482 1121 VLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMFRYR 1183
Cdd:TIGR02386 1077 QLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYK 1139
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-1190 |
0e+00 |
|
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: 1556.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1 MVDVNKFESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCELCGV 80
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 81 QVTTAKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDPKETDLEKKQLLTEREYREQLL 160
Cdd:COG0086 81 EVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 161 KNGfGSFVAKMGAEAIQDLLNDVDIDKEVSELKEELKTVTG-QRRVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIPPDL 239
Cdd:COG0086 161 EYG-DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSeQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 240 RPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKSLSH 319
Cdd:COG0086 240 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSD 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 320 MLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDSDVW 399
Cdd:COG0086 320 MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVW 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 400 DVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEH 479
Cdd:COG0086 400 DILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNN 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 480 ILNPKDGKPVVTPSQDMVLGNYYLTMEEKGREGEGMIFATPEEVEIAMRNGYVHLHTRIGIATKSlnkpwTENQKDKILV 559
Cdd:COG0086 480 ILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITE-----DGEQVGKIVE 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 560 TTVGKVIFNSIIPEGMPYLNEptdvnlttstddrffmdagqdikevlagidtvrPFKKGYLGNIIAEVFKRYRTTATSEY 639
Cdd:COG0086 555 TTVGRYLVNEILPQEVPFYNQ---------------------------------VINKKHIEVIIRQMYRRCGLKETVIF 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 640 LDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAKEALEKRLIDE 719
Cdd:COG0086 602 LDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAA 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 720 QDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTDTALKTADSGY 799
Cdd:COG0086 682 FSSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGY 761
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 800 LTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEPLFERLVGRYTRKSVLHPETGEMIIADDTLISEDVARKIIDA 879
Cdd:COG0086 762 LTRRLVDVAQDVIVTEEDCGTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEA 841
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 880 GVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASSSDITQGLPRVQE 959
Cdd:COG0086 842 GIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAG 921
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 960 IFEARNPKGEAIITEVTGTVESivedpaTRTREITVKGKTDTRSYTVGMADVLMVEEGEFIHRGAPLIQGSIEPKHLLQV 1039
Cdd:COG0086 922 GIVRLNNLKVVVNEEGKGVVVS------RNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIE 995
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1040 RDALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVrqmlRKVRVMDNGSTDILPGTLMDISDFEALNETALLNGEMPATGR 1119
Cdd:COG0086 996 EVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVED----DKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGL 1071
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516476482 1120 PVLMGITKASLETNSFL--SAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMFRYRNIEPLAD 1190
Cdd:COG0086 1072 DVVLGDGVAIGVGAAIAriPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVIT 1144
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
3-1186 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1395.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 3 DVNKFESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCELCGVQV 82
Cdd:PRK14906 5 DVTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 83 TTAKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVI--------------------DPKET 142
Cdd:PRK14906 85 TRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITsvdkeareedaddlrdelaaDLEEL 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 143 DLEKKQL---------------------------LTEREYRE-------------QLLKNGFGSFV-------------- 168
Cdd:PRK14906 165 DAERDRLieatrrlsvdyvpeddefvddigdderLTAEEVRAevadiyeeynerkALRREAFDAFMqiepkqlisdealy 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 169 ------------AKMGAEAIQDLLNDVDIDKEVSELKEELKTVTGQRRVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIP 236
Cdd:PRK14906 245 remrlnysiyfkGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 237 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKS 316
Cdd:PRK14906 325 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKS 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 317 LSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDS 396
Cdd:PRK14906 405 LADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 397 DVWDVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLA 476
Cdd:PRK14906 485 YVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLS 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 477 AEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKGREGEGMIFATPEEVEIAMR-NGYVHLHTRIGI------ATKSLNKPW 549
Cdd:PRK14906 565 SNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDaRADLDLQAKIVVrlsrdmTVRGSYGDL 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 550 TENQKDKILVTTVGKVIFNSIIPEGMPYLNeptdvnlttstddrFFMDagqdikevlagidtvrpfkKGYLGNIIAEVFK 629
Cdd:PRK14906 645 EETKAGERIETTVGRIIFNQVLPEDYPYLN--------------YKMV-------------------KKDIGRLVNDCCN 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 630 RYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAK 709
Cdd:PRK14906 692 RYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEAT 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 710 EALEKRLIDEQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTD 789
Cdd:PRK14906 772 EEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVD 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 790 TALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGlVISDIATGKEMVEplfERLVGRYTRKSVLHPETGEMIIADDTLIS 869
Cdd:PRK14906 852 TALRTADSGYLTRRLVDVAQDVIVREEDCGTDEG-VTYPLVKPKGDVD---TNLIGRCLLEDVCDPNGEVLLSAGDYIES 927
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 870 EDVARKIIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSD 949
Cdd:PRK14906 928 MDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA-GDD 1006
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 950 ITQGLPRVQEIFEARNPKGEAIITEVTGTVeSIVEDPATRTREItVKGKTDTRSYTVGMADVLM--VEEGEFIHRGAPLI 1027
Cdd:PRK14906 1007 ITQGLPRVAELFEARKPKGEAVLAEISGTL-QITGDKTEKTLTI-HDQDGNSREYVVSARVQFMpgVEDGVEVRVGQQIT 1084
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1028 QGSIEPKHLLQVRDALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGSTDILPGTLMDISDFEALNET 1107
Cdd:PRK14906 1085 RGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANN 1164
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516476482 1108 ALLNGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMFRYRNIE 1186
Cdd:PRK14906 1165 LILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLSRYRDVG 1243
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
5-817 |
0e+00 |
|
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: 1235.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 5 NKFESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCELCGVQVTT 84
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 85 AKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFasyvvidpketdlekkqlltereyreqllkngf 164
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 165 gsfvakmgaeaiqdllndvdidkevselkeelktvtgqrrvkiirrldVLSAFRKSGNALSWMVLNVLPVIPPDLRPMVQ 244
Cdd:cd01609 128 ------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQ 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 245 LDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKSLSHMLKGK 324
Cdd:cd01609 160 LDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGK 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 325 QGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDSDVWDVLET 404
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 405 VVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPK 484
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 485 DGKPVVTPSQDMVLGNYYLTMEEKGREGEGMIFatpeeveiamrngyvhlhtrigiatkslnkpwtenqkdkilvTTVGK 564
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTKERKGDKGEGIIE------------------------------------------TTVGR 437
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 565 VIFNSIIPEGMPYLNEptdvnlttstddrffmdagqdikevlagidtvrPFKKGYLGNIIAEVFKRYRTTATSEYLDRLK 644
Cdd:cd01609 438 VIFNEILPEGLPFINK---------------------------------TLKKKVLKKLINECYDRYGLEETAELLDDIK 484
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 645 DLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAKEALEKRLIDE--QDL 722
Cdd:cd01609 485 ELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNldKDP 564
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 723 TNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTDTALKTADSGYLTR 802
Cdd:cd01609 565 FNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTR 644
|
810
....*....|....*
gi 516476482 803 RLVDVAQDVIIREDD 817
Cdd:cd01609 645 RLVDVAQDVIVTEED 659
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-1011 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1091.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 7 FESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKN-QVCELCGVQVTTA 85
Cdd:PRK09603 1396 FSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDiGTCEKCGVAITHS 1475
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 86 KSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDPKET--DLE------KKQLLTEREYRE 157
Cdd:PRK09603 1476 KVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAayDNEgtklvmKYDILNEEQYQN 1555
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 158 QLLKNGFGSFVAKMGAEAIQDLLNDVDIDKEVSELKEELKTVTGQ-RRVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIP 236
Cdd:PRK09603 1556 ISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDaKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLP 1635
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 237 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKS 316
Cdd:PRK09603 1636 PDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKS 1715
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 317 LSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDS 396
Cdd:PRK09603 1716 LSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSN 1795
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 397 DVWDVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLA 476
Cdd:PRK09603 1796 EVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLS 1875
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 477 AEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKGREGEGMIFATPEEVEIAMRNGYVHLHTRIGIAtkslnkpwtenQKDK 556
Cdd:PRK09603 1876 SMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVL-----------DQGN 1944
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 557 ILVTTVGKVIFNSIIPEGMPylneptdVNLTTstddrffmdagqdikevlagidtvRPFKKGYLGNIIAEVFKRYRTTAT 636
Cdd:PRK09603 1945 IIATSAGRMIIKSILPDFIP-------TDLWN------------------------RPMKKKDIGVLVDYVHKVGGIGIT 1993
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 637 SEYLDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAKEALEKRL 716
Cdd:PRK09603 1994 ATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEM 2073
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 717 ID--EQDLT--NPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTDTAL 792
Cdd:PRK09603 2074 MTaiAKDKEgfNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTAL 2153
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 793 KTADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEPLFERLVGRYTRKSVLHPETGEMIIADDTLISEDV 872
Cdd:PRK09603 2154 KTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEG 2233
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 873 ARKIIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASSSD--- 949
Cdd:PRK09603 2234 AKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQder 2313
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516476482 950 ----ITQGLPRVQEIFEARNPKGEAIITEVTGTVESIVE-------------DPATRTREITVKGKTDTRSYTVGMADV 1011
Cdd:PRK09603 2314 eivaSKEGFVRFYNLRTYTNKEGKNIIANRRNASILVVEpkikapfdgelriETVYEEVVVSVKNGDQEAKFVLRRSDI 2392
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-1179 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1083.11 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 7 FESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCELCGVQVTTAK 86
Cdd:PRK14844 1448 FNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSK 1527
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 87 SRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDPKETDLEKKQLLTEREYREQLLKNGFGS 166
Cdd:PRK14844 1528 VRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGIDS 1607
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 167 FVAKMGAEAIQDLLNDVDIDKEVSELKEELKTVTGQ-RRVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIPPDLRPMVQL 245
Cdd:PRK14844 1608 FVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEiRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSL 1687
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 246 DGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLK-SLSHMLKGK 324
Cdd:PRK14844 1688 ESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLKGK 1767
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 325 QGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKRKVERQDSDVWDVLET 404
Cdd:PRK14844 1768 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEE 1847
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 405 VVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPK 484
Cdd:PRK14844 1848 VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPS 1927
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 485 DGKPVVTPSQDMVLGNYYLTMEEKgREGEGMIFATPEEVEIAMRNGYVHLHTRIGIATKSLNKpwTENQKDKILVTTVGK 564
Cdd:PRK14844 1928 NGRPIIVPSKDIVLGIYYLTLQEP-KEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINS--SGETHYKTICTTPGR 2004
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 565 VIFNSIIPE----GMPYLNEPTDVNLTTSTDDRFFMDAGQdikevlagidtvrpfkkgylgniiaevfkryrtTATSEYL 640
Cdd:PRK14844 2005 LILWQIFPKhenlGFDLINQVLTVKEITSIVDLVYRNCGQ---------------------------------SATVAFS 2051
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 641 DRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNAVTGVWRDAKEALEKRLI--- 717
Cdd:PRK14844 2052 DKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLkai 2131
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 718 ---DEQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSVLEMFFSTHGARKGMTDTALKT 794
Cdd:PRK14844 2132 siyDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKT 2211
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 795 ADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEPLFERLVGRYTRKSVLHPETGEMIIADDTLISEDVAR 874
Cdd:PRK14844 2212 ANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVK 2291
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 875 KIIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAS-------- 946
Cdd:PRK14844 2292 QINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTrgvessni 2371
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 --------------------------------------------------------------------------------
Cdd:PRK14844 2372 iasinakiklnnsniiidkngnkivisrscevvlidslgseklkhsvpygaklyvdeggsvkigdkvaewdpytlpiite 2451
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 --------------------------------------------------------------------------------
Cdd:PRK14844 2452 ktgtvsyqdlkdgisitevmdestgisskvvkdwklysgganlrprivllddngkvmtlasgveacyfipigavlnvqdg 2531
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 947 ------------------SSDITQGLPRVQEIFEARNPKGEAIITEVTGTVeSIVEDPATRTREITVKGKTDTRS---YT 1005
Cdd:PRK14844 2532 qkvhagdvitrtpresvkTRDITGGLPRVIELFEARRPKEHAIVSEIDGYV-AFSEKDRRGKRSILIKPVDEQISpveYL 2610
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1006 VGMADVLMVEEGEFIHRGAPLIQGSIEPKHLLQVRDALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDN 1085
Cdd:PRK14844 2611 VSRSKHVIVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDP 2690
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1086 GSTDILPGTLMDISDFEALNETALLNGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKE 1165
Cdd:PRK14844 2691 GDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKE 2770
|
1370
....*....|....
gi 516476482 1166 NVIIGKIIPAGTGM 1179
Cdd:PRK14844 2771 NVIVGRLIPAGTGL 2784
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
5-575 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 799.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 5 NKFESMRIGIASPQKIRYWS---------FGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVC 75
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 76 ELCGVQVTTAKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDP-KETDLEKKQLLTERE 154
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPgNHKNLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 155 YRE---QLLKNG---FGSFVAKMGAEAIQDLLNDVDIDKEVSELKEELKTVTGQRRVKIIRRLDVLSAFRKSGNALSWMV 228
Cdd:PRK02625 167 WLEiedQIYAEDselEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMV 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 229 LNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITG 308
Cdd:PRK02625 247 LDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVG 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 309 AGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAK 388
Cdd:PRK02625 327 ANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAK 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 389 RKVERQDSDVWDVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQA 468
Cdd:PRK02625 407 KLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQA 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 469 EARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKGRE-GEGMIFATPEEVEIAMRNGYVHLHTRI--------- 538
Cdd:PRK02625 487 EARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQkGAGRYFASLEDVIMAFEQGRIDLHAWVwvrfngeve 566
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*...
gi 516476482 539 ----------------GIATKSLNKPWTENQKDKILV-----TTVGKVIFNSIIPEGM 575
Cdd:PRK02625 567 dddedteplktetledGTRIEQYRYRRDRFDEDGNLIsqyilTTVGRVIMNKTIQDAL 624
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
6-575 |
0e+00 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 778.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 6 KFESMRIGIASPQKIRYWS---------FGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVFYKNQVCE 76
Cdd:TIGR02387 1 RFDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 77 LCGVQVTTAKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVVIDP-KETDLEKKQLLTEREY 155
Cdd:TIGR02387 81 RCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPgNAKNLKYKQLLTEDQW 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 156 RE---QLLKNGF---GSFVAKMGAEAIQDLLNDVDIDKEVSELKEELKTVTGQRRVKIIRRLDVLSAFRKSGNALSWMVL 229
Cdd:TIGR02387 161 LEiedQIYAEDSeleNEEVVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 230 NVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGA 309
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 310 GNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKELAANIRAAKR 389
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 390 KVERQDSDVWDVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAE 469
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 470 ARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKGRE-GEGMIFATPEEVEIAMRNGYVHLHTRIGIATKS---L 545
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEkGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGeveT 560
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*..
gi 516476482 546 NKPWTENQKDKIL---------------------------VTTVGKVIFNSIIPEGM 575
Cdd:TIGR02387 561 NDPLDEPIKSEDLsdgtrieqwtyrrdrfdedgalisqyiLTTTGRIIMNHTIIEAL 617
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-573 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 769.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1 MVDVNKFESMRIGIASPQKIRYWS---------FGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECACGKLKGVF-- 69
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAerilpngeiVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGde 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 70 -YKNQVCELCGVQVTTAKSRRERMGHIELAAPISHIWYFKGIPSRMGLALDMSPRALEEVIYFASYVV--IDPKETDLEK 146
Cdd:CHL00018 81 kEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 147 KQLLTE----REYREQLL--KNGFGSFVAK---MGAEAIQDLLNDVD----IDKEVSELKEELKTVT----------GQR 203
Cdd:CHL00018 161 RGLFEYeiqsWKYSIPLFfsTQGFDTFRNReisTGAGAIREQLADLDlriiIDNSLVEWKELGEEGStgnewedrkiGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 204 RVKIIRRLDVLSAFRKSGNALSWMVLNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELN--APNII 281
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 282 VQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPRE 361
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 362 MAIELFKPFVMAQLVKKELAANIRAAKRKVERQDSDVWDVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHP 441
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 442 LACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTME-------------EK 508
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGnrrgiyanrynpcNR 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 509 GREGEGMIFATPEEVEIAMRNGYVHLHT------------------RIGIATKSLN------KPWT--ENQKDKILV--- 559
Cdd:CHL00018 561 KNSTKEPYFSNSYDALGAYRQKRINLDSplwlrwrldqriiasrevPIEVQYESLGtyheiyEHYLivKSRKKEILSiyi 640
|
650
....*....|....*
gi 516476482 560 -TTVGKVIFNSIIPE 573
Cdd:CHL00018 641 rTTVGRILFNREIEE 655
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
15-816 |
3.23e-158 |
|
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: 482.70 E-value: 3.23e-158
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 15 ASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKdwecacgklkgvfyknqvCELCGVQVTTAKSRRERMGH 94
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGGKYDPRLGSIDR------------------CEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 95 IELAAPISHIWYFKGIPSRMGlaldmspraleeviyfasyvvidPketdlekkqlltereyreqllkngfgsfvakmgae 174
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG-----------------------P----------------------------------- 84
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 175 aiqdllndvdidkevselkeelktvtgqrrvkiirrldvlsafrksgnalSWMVLNVLPVIPPDLRPMVqldggrfatsd 254
Cdd:cd00399 85 --------------------------------------------------EWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 255 lndlyrrvinrnnrlkrlmelnapniIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNRPLKSLSHMLKGKQGRFRQNLLG 334
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 335 KRVDYSGRSVIAVGPTLKMYQCGVPREMAIELfkpfvmaqlvkkelaaniraakrkverqdsdvwdvletvvKEHPVLLN 414
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 415 RAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQ 494
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 495 DMVLGNYYLTmeekgregegmifatpeeveiamrngyvhlhtrigiatkslnkpwtenqkdkilvttVGKVIFNSIIPEG 574
Cdd:cd00399 278 DTLLGAYLLT---------------------------------------------------------LGKQIVSAALPGG 300
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 575 MPYLneptdvnlttstddrffmdagqdikevlagidtvrpfkkgylgniiaeVFKRYRTTATSEYLDRLKDLGYHQSTLA 654
Cdd:cd00399 301 LLHT------------------------------------------------VTRELGPEKAAKLLSNLQRVGFVFLTTS 332
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 655 GLTVGIADI----PVVEDKHKIIDAAHKRVEQITKQFRRGLITDDER-------YNAVTGVWRDAKEALEKRLIDEQDLT 723
Cdd:cd00399 333 GFSVGIGDViddgVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNLDLV 412
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 724 ---NPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKI--------------------MELPIISNFREGLSVLEMFFST 780
Cdd:cd00399 413 skfNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHA 492
|
810 820 830
....*....|....*....|....*....|....*.
gi 516476482 781 HGARKGMTDTALKTADSGYLTRRLVDVAQDVIIRED 816
Cdd:cd00399 493 MGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
225-501 |
1.37e-157 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 471.62 E-value: 1.37e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 225 SWMVLNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNG--RR 302
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 303 GRPITGagnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKEL-- 380
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 381 ----------------AANIRAAKR-KVERQDSDVWDVLETVVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLA 443
Cdd:smart00663 158 lvrngpngakyiirgkKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 516476482 444 CEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNY 501
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
617-1028 |
2.49e-124 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 415.55 E-value: 2.49e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 617 KGYLGNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDE 696
Cdd:PRK02597 10 KKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEVE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 697 RYNAVTGVWRDAKEALE---KRLIDEQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSV 773
Cdd:PRK02597 90 RFQKVIDTWNETNERLKdevVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTV 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 774 LEMFFSTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEPLFERLVGRYTRKSVL 853
Cdd:PRK02597 170 TEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLGDRLLGRVLAEDVV 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 854 HPEtGEMIIADDTLISEDVARKIIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQ 933
Cdd:PRK02597 250 DPE-GEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEPGTQ 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 934 LTMRTFHTGGVA---------SSSDITQGLPRVQEIFEARNPKG-EAIITEVTGTVesivedpatrtrEITVKGKTDTRS 1003
Cdd:PRK02597 329 LTMRTFHTGGVFtgevarqvrSPFAGTVEFGKKLRTRPYRTRHGvEALQAEVDFDL------------VLKPSGKGKPQK 396
|
410 420
....*....|....*....|....*
gi 516476482 1004 YTVGMADVLMVEEGEFIHRGAPLIQ 1028
Cdd:PRK02597 397 IEITQGSLLFVDDGQTVEADQLLAE 421
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
8-822 |
1.45e-114 |
|
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: 377.74 E-value: 1.45e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 8 ESMRIGIASPQKIRYWSFGEVKKPETINyRTQKPEREGLFDERIfgpqkdwecacgklkGVFYKNQVCELCGvqvTTAKS 87
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDTYD-EDGYPIEGGLMDPRL---------------GVIEPGLRCKTCG---NTAGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 88 RRERMGHIELAAPISHIWYFKGIPsrmglaldmspRALEEVIYFASYVVIDPKETDLEKKQLLTEREYREQLLKNgfgsF 167
Cdd:cd02582 66 CPGHFGHIELARPVIHVGFAKHIY-----------DLLRATCRSCGRILLPEEEIEKYLERIRRLKEKWPELVKR----V 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 168 VAKMGAEAIQdllndVDI----DKEVSELKEELKTVTGQRRVKIIRRL---DVLSAFRKSGNALS-------------WM 227
Cdd:cd02582 131 IEKVKKKAKK-----RKVcphcGAPQYKIKLEKPTTFYEEKEEGEVKLtpsEIRERLEKIPDEDLellgidpktarpeWM 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 228 VLNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRG-RPI 306
Cdd:cd02582 206 VLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGiPPA 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 307 TGAGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFV--------MAQLVK- 377
Cdd:cd02582 286 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERvtewniekMRKLVLn 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 378 ---KELAAN--IRAAKRKVERQDSDVWDVLET-----VVKEH-----PVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPL 442
Cdd:cd02582 366 gpdKWPGANyvIRPDGRRIRLRYVNREELAERlepgwIVERHlidgdIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLA 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 443 ACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKgregegmiFATPEE 522
Cdd:cd02582 446 VCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTT--------LFTKEE 517
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 523 V-EIAMRNGYVHLhtrigiatksLNKPWTENQKDkiLVTtvGKVIFNSIIPEGmpyLNEPTDVNLTTSTDDRFFMDAGQD 601
Cdd:cd02582 518 AlQLLSAAGYDGL----------LPEPAILEPKP--LWT--GKQLFSLFLPKD---LNFEGKAKVCSGCSECKDEDCPND 580
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 602 ----IK--EVLAG-ID--TVRPFKKgylGNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIPVVEDKHK- 671
Cdd:cd02582 581 gyvvIKngKLLEGvIDkkAIGAEQP---GSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKe 657
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 672 ---IIDAAHKRVEQITKQFRRGLI------TDDE----RYNAVTGVWRD-AKEALEKRLideqDLTNPIVMMMDSGARGN 737
Cdd:cd02582 658 ieeIIKEAEKKVYELIEQYKNGELeplpgrTLEEtlemKIMQVLGKARDeAGKVASKYL----DPFNNAVIMARTGARGS 733
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 738 ISNFSQLAGMRGLMAAPNGKIME------LP--------------IISNFREGLSVLEMFFSTHGARKGMTDTALKTADS 797
Cdd:cd02582 734 MLNLTQMAACLGQQSVRGERINRgyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQS 813
|
890 900
....*....|....*....|....*
gi 516476482 798 GYLTRRLVDVAQDVIIREDdcGTDR 822
Cdd:cd02582 814 GYMQRRLINALQDLYVEYD--GTVR 836
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
617-1028 |
5.92e-114 |
|
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: 384.97 E-value: 5.92e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 617 KGYLGNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLITDDE 696
Cdd:TIGR02388 9 KKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGEITEVE 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 697 RYNAVTGVWRDAKEALE---KRLIDEQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFREGLSV 773
Cdd:TIGR02388 89 RFQKVIDTWNGTNEELKdevVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTV 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 774 LEMFFSTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEpLFERLVGRYTRKSVL 853
Cdd:TIGR02388 169 TEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKIS-LGDRLLGRLVAEDVL 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 854 HPEtGEMIIADDTLISEDVARKIIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQ 933
Cdd:TIGR02388 248 HPE-GEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQ 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 934 LTMRTFHTGGVA---------SSSDITQGLPRVQEIFEARNPKGE-AIITEVTGTVesIVEDpatrtreiTVKGKTDTRS 1003
Cdd:TIGR02388 327 LTMRTFHTGGVFtgevarqvrSKIDGTVEFGKKLRTRGYRTRHGEdAKQVEVAGLL--IIKP--------TGSITNKAQE 396
|
410 420
....*....|....*....|....*
gi 516476482 1004 YTVGMADVLMVEEGEFIHRGAPLIQ 1028
Cdd:TIGR02388 397 IEVTQGSLLFVEDGQTVDAGQLLAE 421
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
613-944 |
5.87e-113 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 384.29 E-value: 5.87e-113
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 613 RPFKKGYLGNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIPVVEDKHKIIDAAHKRVEQITKQFRRGLI 692
Cdd:CHL00117 12 KVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYGNV 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 693 TDDERYNAVTGVWRDAKEALEKRLID---EQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELPIISNFRE 769
Cdd:CHL00117 92 HAVEKLRQSIEIWYATSEYLKQEMNPnfrMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQSNFRE 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 770 GLSVLEMFFSTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIAtgKEMVE-PLFERLVGRYT 848
Cdd:CHL00117 172 GLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRN--GMMIErILIQTLIGRVL 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 849 RKSVLHpeTGEMIIADDTLISEDVARKIIDAGVKEVTIRSVFTCKTPHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIG 928
Cdd:CHL00117 250 ADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIAGQSIG 327
|
330
....*....|....*.
gi 516476482 929 EPGTQLTMRTFHTGGV 944
Cdd:CHL00117 328 EPGTQLTLRTFHTGGV 343
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
913-1179 |
8.44e-106 |
|
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: 331.41 E-value: 8.44e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASssDITQGLPRVQEIFEARNPKGEAIItevtgtvesivedpatrtrE 992
Cdd:cd02655 3 VELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT--DITQGLPRVEELFEARKINPHDLL-------------------R 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 993 ITVKGKTdtrsytvgmadvlmveegefihrgapliqgsiepkhllqvrdalSVETYLLGEVQKTYRSQGVEIGDKHIEVM 1072
Cdd:cd02655 62 IKFLGPE--------------------------------------------AVQKYLVEEIQKVYRSQGVNINDKHIEII 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1073 VRQMLRKVRVMDNGSTDILPGTLMDISDFEALNETALLNGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAA 1152
Cdd:cd02655 98 VRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEAA 177
|
250 260
....*....|....*....|....*..
gi 516476482 1153 IRGKEDHLLGLKENVIIGKIIPAGTGM 1179
Cdd:cd02655 178 IEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
9-822 |
1.90e-105 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 353.39 E-value: 1.90e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 9 SMRIGIASPQKIRYWSFGEVKKPETIN---YrtqkPEREGLFDERIfgpqkdwecacgklkGVFYKNQVCELCGvqvTTA 85
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADTYDddgY----PIDGGLMDPRL---------------GVIDPGLRCKTCG---GRA 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 86 KSRRERMGHIELAAPISHIWYFKGIPsrmglaldmspRALEEVIYFASYVVIDPKETDlekkqllterEYREQLLKNGFG 165
Cdd:PRK08566 69 GECPGHFGHIELARPVIHVGFAKLIY-----------KLLRATCRECGRLKLTEEEIE----------EYLEKLERLKEW 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 166 SFVAKMGAEAIQDLLNDVDIDKEVSELKEELK--------TVTGQRRVKI----IR-RL------DV-LSAFRKSGNALS 225
Cdd:PRK08566 128 GSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKfekpttfyEERKEGLVKLtpsdIReRLekipdeDLeLLGINPEVARPE 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 226 WMVLNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRG-R 304
Cdd:PRK08566 208 WMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGiP 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 305 PITGAGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPF--------VMAQLV 376
Cdd:PRK08566 288 PARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPErvtewnieELREYV 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 377 K----KELAAN--IRAAKRKVERQDSDVWDVLET-----VVKEH-----PVLLNRAPTLHRLGIQAFEPVLIDGKAIRLH 440
Cdd:PRK08566 368 LngpeKHPGANyvIRPDGRRIKLTDKNKEELAEKlepgwIVERHlidgdIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLN 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 441 PLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKgregegmiFATP 520
Cdd:PRK08566 448 LAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKST--------LFTK 519
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 521 EEVEIAMRNGYVHLHTRIGIATKSLNKPWTenqkdkilvttvGKVIFNSIIPEGMpYLNEPTDVNLTTST--DDRFFMDA 598
Cdd:PRK08566 520 EEALDLLRAAGIDELPEPEPAIENGKPYWT------------GKQIFSLFLPKDL-NLEFKAKICSGCDEckKEDCEHDA 586
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 599 GQDIK--EVLAG-IDtvrpfKKGY---LGNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIAD--IP--VVED 668
Cdd:PRK08566 587 YVVIKngKLLEGvID-----KKAIgaeQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDedIPeeAKEE 661
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 669 KHKIIDAAHKRVEQITKQFRRGLI------TDDE----RYNAVTGVWRD-AKEALEKRLideqDLTNPIVMMMDSGARGN 737
Cdd:PRK08566 662 IDEIIEEAEKRVEELIEAYENGELeplpgrTLEEtlemKIMQVLGKARDeAGEIAEKYL----GLDNPAVIMARTGARGS 737
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 738 ISNFSQLAGMRGLMAAPNGKIME------LP--------------IISNFREGLSVLEMFFSTHGARKGMTDTALKTADS 797
Cdd:PRK08566 738 MLNLTQMAACVGQQSVRGERIRRgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQS 817
|
890 900
....*....|....*....|....*
gi 516476482 798 GYLTRRLVDVAQDVIIREDdcGTDR 822
Cdd:PRK08566 818 GYMQRRLINALQDLKVEYD--GTVR 840
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
5-332 |
1.15e-103 |
|
RNA polymerase Rpb1, domain 1; 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 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 330.41 E-value: 1.15e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 5 NKFESMRIGIASPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIFGPQKDWECA-CGKlkgvFYKNqvcelCGVqvt 83
Cdd:pfam04997 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGK----KKKD-----CPG--- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 84 taksrreRMGHIELAAPISHIWYFKgipsrmglaldMSPRALEEVIYFASYVVIDPketdlEKKQLLTEREYREQLLKNg 163
Cdd:pfam04997 70 -------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDP-----GKPKLFNKDKKRLGLENL- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 164 fgsfvaKMGAEAIQDLLNDVD------------------IDKEVSELKEELKT---------VTGQRRVKIIRRL---DV 213
Cdd:pfam04997 126 ------KMGAKAILELCKKKDlcehcggkngvcgsqqpvSRKEGLKLKAAIKKskeeeekeiLNPEKVLKIFKRIsdeDV 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 214 -LSAFRKSGNALSWMVLNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEA 292
Cdd:pfam04997 200 eILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEH 279
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 516476482 293 VDTLIDNGRRG-RPITGAGNRPLKSLSHMLKGKQGRFRQNL 332
Cdd:pfam04997 280 VATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
4-1178 |
8.40e-101 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 349.32 E-value: 8.40e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 4 VNKFESMRIGIASPQKIRYWSFGEVKKPETINyRTQKPEREGLFDERIfgpqkdwecacgklkGVFYKNQVCELCGvqvT 83
Cdd:PRK14977 6 VKAIDGIIFGLISPADARKIGFAEITAPEAYD-EDGLPVQGGLLDGRL---------------GTIEPGQKCLTCG---N 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 84 TAKSRRERMGHIELAAPISHIWYFKGIPSRMG--------LALDMSPRALEEVI--YFASYVVIDPKETDlekKQLLteR 153
Cdd:PRK14977 67 LAANCPGHFGHIELAEPVIHIAFIDNIKDLLNstchkcakLKLPQEDLNVFKLIeeAHAAARDIPEKRID---DEII--E 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 154 EYREQLlkngfgSFVAKM-------GAEAIQDLLNDVDIDKEVSELKEE--LKTVTGQRRVKIIRRLDVLSAFRKSGNAL 224
Cdd:PRK14977 142 EVRDQV------KVYAKKakecphcGAPQHELEFEEPTIFIEKTEIEEHrlLPIEIRDIFEKIIDDDLELIGFDPKKARP 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 225 SWMVLNVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGR 304
Cdd:PRK14977 216 EWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGI 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 305 PIT---GAGnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMA-------------IELFK 368
Cdd:PRK14977 296 PQAhhkGSG-RPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAmkltipeivnennIEKMK 374
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 369 PFVM--------AQLVKKELAANIRA--AKRKVERQDSDVWDVLET--VVKEH-----PVLLNRAPTLHRLGIQAFEPVL 431
Cdd:PRK14977 375 ELVIngpdefpgANAIRKGDGTKIRLdfLEDKGKDALREAAEQLEIgdIVERHladgdIVIFNRQPSLHKLSILAHRVKV 454
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 432 IDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKgre 511
Cdd:PRK14977 455 LPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDA--- 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 512 gegmIFATPEEVEIAMRNGYvhlhtrigiaTKSLNKPWTENqKDKILVTtvGKVIFNSIIPEGMPY--LNEPTDVNLTTS 589
Cdd:PRK14977 532 ----LFDKNEASNIAMLAGI----------TDPLPEPAIKT-KDGPAWT--GKQLFSLFLPKDFNFegIAKWSAGKAGEA 594
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 590 TDDRFFMDAGQDIK--EVLAGI---DTVRPFKKGYLgNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIP 664
Cdd:PRK14977 595 KDPSCLGDGYVLIKegELISGViddNIIGALVEEPE-SLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLI 673
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 665 VVE-DKHKIIDAAHKRVEQITKQFR-RGLITDDERYNAVTGVWRDAK--EALEKRLIDEQ---------------DLTNP 725
Cdd:PRK14977 674 IPDeAKQEIEDDIQGMKDEVSDLIDqRKITRKITIYKGKEELLRGMKeeEALEADIVNELdkardkagssandciDADNA 753
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 726 IVMMMDSGARGNISNFSQLAGMRGLMAAPNGKIMELP----------------------------IISNFREGLSVLEMF 777
Cdd:PRK14977 754 GKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFF 833
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 778 FSTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEP--LF-------ERLVGRY- 847
Cdd:PRK14977 834 FHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPqkLDhgeafnlERIIEKQk 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 848 ---TRKSVLHPETGEMIIADDTLISEDVARKIIDA---------GVKEvtirsvftcktphgVCKHcyGINLATGDAVEV 915
Cdd:PRK14977 914 iedRGKGASKDEIEELAKEYTKTFNANLPKLLADAihgaelkedELEA--------------ICAE--GKEGFEKAKVEP 977
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 916 GEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSDITQGLPRVQEIFEARNP-------------------KGEAIITEVT 976
Cdd:PRK14977 978 GQAIGIISAQSIAEPGTQMTLRTFHAAGIK-AMDVTHGLERFIELVDARAKpstptmdiylddeckedieKAIEIARNLK 1056
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 977 GT-VESIVEDPAT-------------RTRE--------------ITVKGKTDTRSYTVGMADVLMVEEGEFIHRGAPLIQ 1028
Cdd:PRK14977 1057 ELkVRALIADSAIdnaneiklikpdkRALEngcipmerfaeieaALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIA 1136
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1029 GS--IEPKHLLQVRDalsVETYLLGEVQKTYRSQGV--EIGDKHIEVMVRQMLRKVRVMDNGSTDI-------------- 1090
Cdd:PRK14977 1137 IRnkILDKPVKGVPD---IERAWVELVEKDGRDEWIiqTSGSNLAAVLEMKCIDIANTITNDCFEIagtlgieaarnaif 1213
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1091 --LPGTLMDiSDFEALNETALL-------NGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLL 1161
Cdd:PRK14977 1214 neLASILED-QGLEVDNRYIMLvadimcsRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIK 1292
|
1370
....*....|....*..
gi 516476482 1162 GLKENVIIGKIIPAGTG 1178
Cdd:PRK14977 1293 GILDALIMGQNIPIGSG 1309
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
13-816 |
4.46e-83 |
|
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: 287.90 E-value: 4.46e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 13 GIASPQKIRYWSFGEVKKPETINyRTQKPEREGLFDERIfgpqkdwecacgklkGVFYKNQVCELCGvqvttaksrrERM 92
Cdd:cd02733 6 GILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM---------------GTIDRNSRCQTCG----------GDM 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 93 -------GHIELAAPISHIWYfkgipsrmglaLDMSPRALEEVIyfasyvvidpketdleKKQLLTEREYreqllkngfg 165
Cdd:cd02733 60 kecpghfGHIELAKPVFHIGF-----------LTKILKILRCVC----------------KRELSAERVL---------- 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 166 sfvakmgaeaiqdllndvDIDKEVSElkEELKtvtgqrrvkiIRRLDVLSAFRKsgnalsWMVLNVLPVIPPDLRPMVQL 245
Cdd:cd02733 103 ------------------EIFKRISD--EDCR----------ILGFDPKFSRPD------WMILTVLPVPPPAVRPSVVM 146
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 246 DGGRFATSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRP--ITGAGnRPLKSLSHMLKG 323
Cdd:cd02733 147 DGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPqaTQKSG-RPLKSIRQRLKG 225
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 324 KQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIEL-FKPFV-------MAQLVK----KELAAN-------- 383
Cdd:cd02733 226 KEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfnidrLQELVRngpnEYPGAKyiirddge 305
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 384 ---IRAAKR----------KVER--QDSDVwdvletvvkehpVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYN 448
Cdd:cd02733 306 ridLRYLKKasdlhlqygyIVERhlQDGDV------------VLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYN 373
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 449 ADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEkgregegmIFATPEEV-EIAM 527
Cdd:cd02733 374 ADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRD--------TFLEKDQVmNLLM 445
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 528 rngyvHLHTRIG-IATKSLNKP---WTenqkdkilvttvGKVIFNSIIPEGMpylNEPTDVNLTTSTDDRFFMDAGQDIK 603
Cdd:cd02733 446 -----WLPDWDGkIPQPAILKPkplWT------------GKQIFSLIIPKIN---NLIRSSSHHDGDKKWISPGDTKVII 505
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 604 ---EVLAGIDTVRPFKKGYlGNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADI----PVVEDKHKIIDAA 676
Cdd:cd02733 506 engELLSGILCKKTVGASS-GGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTiadkETMKKIQETIKKA 584
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 677 HKRVEQITKQFRRGLITDD---------ERY-NAVTGVWRDAKEALEKRLIDEqdlTNPIVMMMDSGARGNISNFSQLAG 746
Cdd:cd02733 585 KRDVIKLIEKAQNGELEPQpgktlresfENKvNRILNKARDKAGKSAQKSLSE---DNNFKAMVTAGSKGSFINISQIIA 661
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 747 MRGLMAAPNGKIM------ELP--------------IISNFREGLSVLEMFFSTHGARKGMTDTALKTADSGYLTRRLVD 806
Cdd:cd02733 662 CVGQQNVEGKRIPfgfrrrTLPhfikddygpesrgfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVK 741
|
890
....*....|
gi 516476482 807 VAQDVIIRED 816
Cdd:cd02733 742 AMEDVMVKYD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
16-817 |
2.16e-73 |
|
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: 261.71 E-value: 2.16e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 16 SPQKIRYWSFGEVKKPETINYRTQKPEREGLFDERIfgpqkdwecacgklkGVFYKNQVCELCGvqvttaKSRRERMGH- 94
Cdd:cd02583 2 SPEDIIRLSEVEVTNRNLYDIETRKPLPYGVLDPRL---------------GTSDKDGICETCG------LNLADCVGHf 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 95 --IELAAPISHIWYFKGIPSrmglaldmsprALEEVIYFASYVVIDPKETDLEKKQLLtereyreqllkngfgsfvakmg 172
Cdd:cd02583 61 gyIKLELPVFHIGYFKAIIN-----------ILQCICKTCSRVLLPEEEKRKFLKRLR---------------------- 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 173 aEAIQDLLNDVDIDKEVSELKEELKTVT----GQRRVKIIRRLDVLSAFRK-------------SGNALSWMVLNVLPVI 235
Cdd:cd02583 108 -RPNLDNLQKKALKKKILEKCKKVRKCPhcglLKKAQEDLNPLKVLNLFKNippedvelllmnpLAGRPENLILTRIPVP 186
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 236 PPDLRPMVQLDGGrfATSDLNDL---YRRVINRNNRLKRLMELNAPNIIVQNEKRMLQEAVDTLIDNGRRGRPITGAGNR 312
Cdd:cd02583 187 PLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPKK 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 313 PLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMA-------------IELFKPFVM------- 372
Cdd:cd02583 265 PIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAkiltypervtrynIEKLRKLVLngpdvhp 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 373 -AQLVKKE---LAANIRAAKRK-----------VER--QDSDVwdvletvvkehpVLLNRAPTLHRLGIQAFEPVLIDGK 435
Cdd:cd02583 345 gANFVIKRdggKKKFLKYGNRRkiarelkigdiVERhlEDGDI------------VLFNRQPSLHRLSIMAHRAKVMPWR 412
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 436 AIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEkgregegm 515
Cdd:cd02583 413 TFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKD-------- 484
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 516 IFATPEEV-EIA--MRNGYVHLHtrigIATKSLNKP---WTenqkdkilvttvGKVIFNSIIpegMPYLNEPTDVNLTTS 589
Cdd:cd02583 485 VFFDRAQFcQLCsyMLDGEIKID----LPPPAILKPvelWT------------GKQIFSLLL---RPNKKSPVLVNLEAK 545
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 590 TddRFFMDAGQD---------IK--EVLAG-IDtvrpfkKGYLG----NIIAEVFKR-YRTTATSEYLDRLKDLGyhQST 652
Cdd:cd02583 546 E--KSYTKKSPDmcpndgyvvIRnsELLCGrLD------KSTLGsgskNSLFYVLLRdYGPEAAAAAMNRLAKLS--SRW 615
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 653 LA--GLTVGIADI-P---VVEDKHKIIDAAHKRVEQITKQFRRGLITDDERYNA-------VTGVWRDAKEALEKRLIDE 719
Cdd:cd02583 616 LSnrGFSIGIDDVtPskeLLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAeqtleakISGELSKIREDAGKACLKE 695
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 720 QDLTN-PIVMMMdSGARGNISNFSQ---------LAGMRglmaAPNGkiME---LP-------------IISN-FREGLS 772
Cdd:cd02583 696 LHKSNsPLIMAL-CGSKGSNINISQmiacvgqqiISGKR----IPNG--FEdrtLPhfprnsktpaakgFVANsFYSGLT 768
|
890 900 910 920
....*....|....*....|....*....|....*....|....*
gi 516476482 773 VLEMFFSTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDD 817
Cdd:cd02583 769 PTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDG 813
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
945-1178 |
3.02e-69 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 255.31 E-value: 3.02e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 945 ASSSDITQGLPRVQEIFEARNPKGEAIITEVTGTVEsiVEDPATRTREITVKGKTDTRS-YTVGMADVLMVEEGEFIHRG 1023
Cdd:PRK02597 974 AKTGDIIQGLPRIEELLEARKPKESCILAKKPGTVQ--IKYGDDESVDVKVIESDGTITeYPILPGQNVMVSDGQQVDAG 1051
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1024 APLIQGSIEPKHLLQV-----RDAL-----------SVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGS 1087
Cdd:PRK02597 1052 EPLTDGPINPHELLEIffedlRDRKglyeaalealqKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGD 1131
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1088 TDILPGTLMDISDFEALNETALLNGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENV 1167
Cdd:PRK02597 1132 TTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENV 1211
|
250
....*....|.
gi 516476482 1168 IIGKIIPAGTG 1178
Cdd:PRK02597 1212 IIGRLIPAGTG 1222
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
945-1182 |
4.85e-65 |
|
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: 241.68 E-value: 4.85e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 945 ASSSDITQGLPRVQEIFEARNPKGEAIITEVTGTVEsIVEDPATRTREITVKGKTDTRS-YTVGMADVLMVEEGEFIHRG 1023
Cdd:TIGR02388 972 AKTGDIVQGLPRIEELLEARKPKEACILAKRPGVVQ-VKYGTDDESVSIKVIERDGTISeYPLLPGQNIMVSDGQQVTGG 1050
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1024 APLIQGSIEPKHLLQV-------RDAL---------SVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGS 1087
Cdd:TIGR02388 1051 EPLTDGPINPHDILDVffsyykdQDGLyeaaqeslqKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGD 1130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1088 TDILPGTLMDISDFEALNETALLNGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENV 1167
Cdd:TIGR02388 1131 TTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENV 1210
|
250
....*....|....*
gi 516476482 1168 IIGKIIPAGTGMFRY 1182
Cdd:TIGR02388 1211 IIGRLIPAGTGFSSY 1225
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
770-999 |
3.64e-60 |
|
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: 215.68 E-value: 3.64e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 770 GLSVLEMFFSTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLVISDIATGKEMVEPLFERLVGRYTR 849
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 850 KSVLHPETGEMIIadDTLISEDVAR-----------------------------------KIIDAGVKEVTIRSVFTCKT 894
Cdd:pfam04998 81 EFSDLKLEDKFKN--DLLDDLLLLSefslsykkeilvrdsklgrdrlskeaqeratllfeLLLKSGLESKRVRSELTCNS 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 895 PHGVCKHCYGINLATGDAVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASSSdITQGLPRVQEIFearnpKGEAIITE 974
Cdd:pfam04998 159 KAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKN-VTLGVPRLKEII-----NVSKNIKS 232
|
250 260
....*....|....*....|....*
gi 516476482 975 VTGTVESIVEDPATRTREITVKGKT 999
Cdd:pfam04998 233 PSLTVYLFDEVGRELEKAKKVYGAI 257
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
947-1184 |
4.93e-57 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 216.73 E-value: 4.93e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 947 SSDITQGLPRVQEIFEARNpkgeaiitevtgtVESIVEDPatrtrEITVKGktdtrsYTVGMADVLMVEEGEFIhrGAPL 1026
Cdd:CHL00117 1128 SGDITQGLPKVEQLLEARS-------------IDSISMNL-----EKRLEG------WNERITRILGIPWGFLI--GAEL 1181
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1027 iqgSIEpkhllQVRdalsveTYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNG-STDILPGTLMDISDFEALN 1105
Cdd:CHL00117 1182 ---SIA-----QSQ------ISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGmSNVFLPGELIGLLRAERIN 1247
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516476482 1106 EtALlngEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMFRYRN 1184
Cdd:CHL00117 1248 R-AL---EEAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVH 1322
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
944-1185 |
5.53e-57 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 217.48 E-value: 5.53e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 944 VASSSDITQGLPRVQEIFEARN--PKGEAIITEVTGTVESiveDPATRTREITVKGKTDTRS--YTVGMADVLMVEEGEF 1019
Cdd:PRK09603 2637 TVKSRDITGGLPRVSELFEARKpkPKDVAILSEVDGIVSF---GKPIRNKEHIIVTSKDGRSmdYFVDKGKQILVHADEF 2713
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1020 IHRGAPLIQGSIEPKHLLQVRDALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGSTDILPGTLMDIS 1099
Cdd:PRK09603 2714 VHAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKK 2793
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1100 DFEALNETALLNGEMPATGRPVLMGITKASLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGM 1179
Cdd:PRK09603 2794 LFKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGM 2873
|
....*.
gi 516476482 1180 FRYRNI 1185
Cdd:PRK09603 2874 YKNKKI 2879
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
229-805 |
4.32e-54 |
|
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. 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. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 203.57 E-value: 4.32e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 229 LNVLPVIPPDLRPMVQLDGGRFaTSDLNDLYRRVINRNNRLKRLMELNAPNIIVQNEKRM---------------LQEAV 293
Cdd:cd01435 132 LDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLIsgktnseklinawlqLQSAV 210
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 294 DTLIDNGRrgrpITGAGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMAIEL------- 366
Cdd:cd01435 211 NELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLtfpepvt 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 367 -FKPFVMAQLV------------------------------KKELAANIRAAK---------RKVER--QDSDVwdvlet 404
Cdd:cd01435 287 pFNVEELRQAVingpdvypganaiededgrlillsalseerRKALAKLLLLLSsaklllngpKKVYRhlLDGDV------ 360
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 405 vvkehpVLLNRAPTLHRLGIQA-FEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNP 483
Cdd:cd01435 361 ------VLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVP 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 484 KDGKPVVTPSQDMVLGNYYLTMeeKGRegegmiFATPEE----VEIAMRN-GYVHLHTRIGIATKSLNKP---WTENQkd 555
Cdd:cd01435 435 TDGKPLRGLIQDHVVSGVLLTS--RDT------FFTREEyqqlVYAALRPlFTSDKDGRIKLLPPAILKPkplWTGKQ-- 504
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 556 kiLVTTvgkvIFNSIIPEGMPYLNE------PTDVNLTTSTDDrffMDAGQDI---KEVLAGIdtvrpFKKGYLGN---- 622
Cdd:cd01435 505 --VIST----ILKNLIPGNAPLLNLsgkkktKKKVGGGKWGGG---SEESQVIirnGELLTGV-----LDKSQFGAsayg 570
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 623 IIAEVFKRYRTTATSEYLDRLKDLG--YHQSTlaGLTVGIADIPVVEdkhkiiDAAHKRVEQITKQFRRGLITdderyna 700
Cdd:cd01435 571 LVHAVYELYGGETAGKLLSALGRLFtaYLQMR--GFTCGIEDLLLTP------KADEKRRKILRKAKKLGLEA------- 635
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 701 vtgvwrdAKEALEKRLideQDLTNPIV------------------MMMDSGARGNISNFSQLAGMRG----------LMa 752
Cdd:cd01435 636 -------AAEFLGLKL---NKVTSSIIkaclpkgllkpfpennlqLMVQSGAKGSMVNASQISCLLGqqelegrrvpLM- 704
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 516476482 753 aPNGKimELP--------------IISNFREGLSVLEMFFSTHGARKGMTDTALKTADSGYLTRRLV 805
Cdd:cd01435 705 -VSGK--TLPsfppydtspraggfITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
334-476 |
6.97e-50 |
|
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 174.03 E-value: 6.97e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 334 GKRVDYSGRSVIAVGPTLKMYQCGVPREMAIELFKPFVMAQLVKKEL----------------AANIRAAKRKVERQDSD 397
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLrqlvengpnvypganyIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 398 VWDVLET-------VVKEHPVLLNRAPTLHRLGIQAFEPVLIDGKAIRLHPLACEAYNADFDGDQMAIHLPLSEEAQAEA 470
Cdd:pfam00623 81 LDKELEIgdiverhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 516476482 471 RLLMLA 476
Cdd:pfam00623 161 EELMLV 166
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
479-663 |
5.66e-46 |
|
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: 162.41 E-value: 5.66e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 479 HILNPKDGKPVVTPSQDMVLGNYYLTMEEkgregegmIFATPEEVEIAMRNGYVHLHTRIGIATKSLnkpWTenqkdkiL 558
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAILKPIKPL---WT-------G 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 559 VTTVGKVIFNSIIPEGMPYLNEPTDvnltTSTDDRFFMDAGQDIKEVLAGIdtvrpFKKGYLGNIIAEVFKRYRTTATSE 638
Cdd:pfam04983 63 KQTFSRLLPNEINPKGKPKTNEEDL----CENDSYVLINNGELISGVIDKK-----TVGKSLGSLIHIIYKEYGPEETAK 133
|
170 180
....*....|....*....|....*
gi 516476482 639 YLDRLKDLGYHQSTLAGLTVGIADI 663
Cdd:pfam04983 134 FLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
916-1179 |
3.36e-38 |
|
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: 140.25 E-value: 3.36e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 916 GEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSDITQGLPRVQEIFEARNPKgeaiitevtgtvesivedpatrtreitv 995
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVA-SMNVTLGLPRLKEILNAASIH---------------------------- 51
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 996 kgktdtrsytvGMADVLMVEegefihrgapliqgsiepkhllqvrdalSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQ 1075
Cdd:cd00630 52 -----------EMLEALGIE----------------------------AARETIIREIQKVLASQGVSVDRRHIELIADV 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1076 MLRKVrvmdngstdilpgtlmdisdfealnetallngempatgrpVLMGITKASL--ETNSFLSAASFQETTRVLTDAAI 1153
Cdd:cd00630 93 MTYSG----------------------------------------GLRGVTRSGFraSKTSPLMRASFEKTTKHLLDAAA 132
|
250 260
....*....|....*....|....*.
gi 516476482 1154 RGKEDHLLGLKENVIIGKIIPAGTGM 1179
Cdd:cd00630 133 AGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
913-1179 |
1.60e-27 |
|
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: 115.81 E-value: 1.60e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSDITQGLPRVQEIFEAR-NP------------------KGEAIIT 973
Cdd:cd06528 37 IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVA-EINVTLGLPRLIEIVDARkEPstptmtiyleeeykydreKAEEVAR 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 974 EVTGT-VESIVE----DPATRT------------REITV-----------KGK-------------TDTRSYTV------ 1006
Cdd:cd06528 116 KIEETtLENLAEdisiDLFNMRitieldeemledRGITVddvlkaieklkKGKvgeegdvtlivlkAEEPSIKElrklae 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1007 --------GMADVLMV----EEGEFIhrgaPLIQGSIEPKHL---------------LQVRDALSVE---TYLLGEVQKT 1056
Cdd:cd06528 196 kilntkikGIKGIKRVivrkEEDEYV----IYTEGSNLKAVLkvegvdptrtttnniHEIEEVLGIEaarNAIINEIKRT 271
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1057 YRSQGVEIGDKHIevmvrqMLrkvrVMDngstdilpgtLMDISdfealnetallnGEMPATGRPVLMGitkaslETNSFL 1136
Cdd:cd06528 272 LEEQGLDVDIRHI------ML----VAD----------IMTYD------------GEVRQIGRHGIAG------EKPSVL 313
|
330 340 350 360
....*....|....*....|....*....|....*....|...
gi 516476482 1137 SAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGM 1179
Cdd:cd06528 314 ARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGD 356
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
913-1179 |
1.32e-25 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 110.32 E-value: 1.32e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSDITQGLPRVQEIFEAR-NP------------------KGEAIIT 973
Cdd:PRK04309 56 VEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVA-EINVTLGLPRLIEIVDARkEPstpmmtiylkdeyaydreKAEEVAR 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 974 EVTGT-VESIVEDPAT----------------RTREITV-----------KGKTDTRSYTV------------------- 1006
Cdd:PRK04309 135 KIEATtLENLAKDISVdlanmtiiieldeemlEDRGLTVddvkeaiekkkGGEVEIEGNTLiispkepsyrelrklaeki 214
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1007 ------GMADVLMV----EEGEFI--HRGAPLiqgsiepKHLLQVR--DALSVETY-------LLG----------EVQK 1055
Cdd:PRK04309 215 rnikikGIKGIKRViirkEGDEYViyTEGSNL-------KEVLKVEgvDATRTTTNniheieeVLGieaarnaiieEIKN 287
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1056 TYRSQGVEIGDKHIevmvrqMLrkvrVMDNGSTDilpgtlmdisdfealnetallnGEMPATGRpvlMGItkaSLETNSF 1135
Cdd:PRK04309 288 TLEEQGLDVDIRHI------ML----VADMMTWD----------------------GEVRQIGR---HGV---SGEKASV 329
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 516476482 1136 LSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGM 1179
Cdd:PRK04309 330 LARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGD 373
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
913-1180 |
1.89e-25 |
|
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: 108.07 E-value: 1.89e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVASSSdITQGLPRVQEIFEA-------------RNPKGE-------AII 972
Cdd:cd02736 7 VEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMN-ITLGVPRIKEIINAsknistpiitaklENDRDEksarivkGRI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 973 TEVT-GTVESIVEDPATRTrEITVKGKTDTRSYtvgmaDVLMVEEGEFIHR--------------GAPLIQGSIEPKHLL 1037
Cdd:cd02736 86 EKTYlGEVASYIEEVYSPD-DCYILIKLDKKII-----EKLQLSKSNLYFLlqslkrklpdvvvsGIPEVKRAVINKDKK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1038 QVRDALSVETYLLGEVQKTYRSQGVEIGDKHIeVMVRQML-----RKV------RVMDNGSTDILPGTLMdisdfealne 1106
Cdd:cd02736 160 KGKYKLLVEGYGLRAVMNTPGVIGTRTTSNHI-MEVEKVLgieaaRSTiineiqYTMKSHGMSIDPRHIM---------- 228
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516476482 1107 taLLNGEMpaTGRPVLMGITKASLETN--SFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMF 1180
Cdd:cd02736 229 --LLADLM--TFKGEVLGITRFGIAKMkeSVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
913-1183 |
3.22e-25 |
|
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: 108.99 E-value: 3.22e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSDITQGLPRVQEIFEARN---------------PKGEAIITEVTG 977
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVA-ELNVTLGLPRLIEIVDARKtpstpsmtiyledeyEKDREKAEEVAK 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 978 -----TVESIVEDPATRTREITV-----KGKTDTRSYTVGM-----ADVLMVEEGEFIHRGAPLIQGSIEP--KHLLQVR 1040
Cdd:TIGR02389 120 kieatKLEDVAKDISIDLADMTViieldEEQLKERGITVDDvekaiKKAKLGKVIEIDMDNNTITIKPGNPslKELRKLK 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1041 DA-------------------------LSVETYLLGEV--------QKTYRSQGVEIGDK-HIEVMVRQMLRKV-RVMDN 1085
Cdd:TIGR02389 200 EKiknlhikgikgikrvvirkegdeyvIYTEGSNLKEVlklegvdkTRTTTNDIHEIAEVlGIEAARNAIIEEIkRTLEE 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1086 GSTDILPGTLMDISDFEAlnetalLNGEMPATGRPVLMGitkaslETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKE 1165
Cdd:TIGR02389 280 QGLDVDIRHLMLVADLMT------WDGEVRQIGRHGISG------EKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIE 347
|
330
....*....|....*...
gi 516476482 1166 NVIIGKIIPAGTGMFRYR 1183
Cdd:TIGR02389 348 NIIVGQPIPLGTGDVDLV 365
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
75-822 |
7.23e-25 |
|
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 111.73 E-value: 7.23e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 75 CELCGvqvttAKSRRE---RMGHIELAAPISHiWYFkgipsrmglaldmspraLEEVIYFASyvVIDPKETDLEKKQLLT 151
Cdd:cd10506 34 CTTCG-----AKDNKKcegHFGVIKLPVTIYH-PYF-----------------ISEVAQILN--KICPGCKSIKQKKKKP 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 152 EREyreqLLKNGFGSFVAKMGaeaiQDLLNDVDIDKEV---SELKEELKTVTGQRRVKIIRRLDVLsafrksgnalswmV 228
Cdd:cd10506 89 PRE----TLPPDYWDFIPKDG----QQEESCVTKNLPIlslAQVKKILKEIDPKLIAKGLPRQEGL-------------F 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 229 LNVLPVIPPDLR----PMVQLDGGRFATSDLNDLYRRVINrnnrlkrlmelnapniivqnekrmlqeavdtlidngrrgr 304
Cdd:cd10506 148 LKCLPVPPNCHRvtefTHGFSTGSRLIFDERTRAYKKLVD---------------------------------------- 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 305 pITGAGNRplKSLSHMLKGKQgrFRQNLLGKRVDYSGRSVIAVGPTLKMYQCGVPREMA--------------IELFKPF 370
Cdd:cd10506 188 -FIGTANE--SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAerltvservsswnrERLQEYC 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 371 VMAQLVKKEL----AANIRAAKRKVERQDSDVwdVLETVVKEHPVLLNRAPTLHRLGIQAFE-PVLIDGKAIRLHPLACE 445
Cdd:cd10506 263 DLTLLLKGVIgvrrNGRLVGVRSHNTLQIGDV--IHRPLVDGDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCS 340
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 446 AYNADFDGDQMAIHLPLSEEAQAEARLLMLAAEHILNPKDGKPVVTPSQDMVLGNYYLTMEEKGREGEGM----IFATPE 521
Cdd:cd10506 341 PFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGVFLDKAQMqqlqMLCPSQ 420
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 522 EVEIAMrngyvhlhtrigIATKSLNKP-WTenqkdkilvttvGKVIFNSIIPEGMPYlneptdvnltTSTDDRFFMDAGq 600
Cdd:cd10506 421 LPPPAI------------IKSPPSNGPlWT------------GKQLFQMLLPTDLDY----------SFPSNLVFISDG- 465
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 601 dikEVLAGIDtvrpfKKGYL---GNIIAEVFKRYRTTATSEYLDRLKDLGYHQSTLAGLTVGIADIPVVED---KHKIID 674
Cdd:cd10506 466 ---ELISSSG-----GSSWLrdsEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSSDsysRQKMIE 537
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 675 AAHKRVEQ--ITKQFRRGLITDDERYNAVTGVWRDAKEALEKRLIDEQDLT----------------------------N 724
Cdd:cd10506 538 EISLGLREaeIACNIKQLLVDSRKDFLSGSGEENDVSSDVERVIYERQKSAalsqasvsafkqvfrdiqnlvykyaskdN 617
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 725 PIVMMMDSGARGNISNFSQLAGMRGL----------------MAAPN----GKIMELP-------------IISNFREGL 771
Cdd:cd10506 618 SLLAMIKAGSKGSLLKLVQQSGCLGLqlslvklsyriprqlsCAAWNsqksPRVIEKDgsectesyipygvVESSFLDGL 697
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|..
gi 516476482 772 SVLEMFFSTHGARKGMTDtalKTAD-SGYLTRRLVDVAQDVIIREDdcGTDR 822
Cdd:cd10506 698 NPLECFVHSITSRDSSFS---SNADlPGTLFRKLMFFMRDIYVAYD--GTVR 744
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
913-1178 |
2.52e-23 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 105.66 E-value: 2.52e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAsSSDITQGLPRVQEIFEARN---------------PKGEAIITEVTG 977
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVA-EMNVTLGLPRLIEIVDARKkpstptmtiylkkdyREDEEKVREVAK 257
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 978 TVESI----VEDPATRTREITVKGKTDTRSYT---VGMADVL--------MVEEGEFIHRGAPLIQGSIepKHLLQVRDa 1042
Cdd:PRK14897 258 KIENTtlidVADIITDIAEMSVVVELDEEKMKerlIEYDDILaaiskltfKTVEIDDGIIRLKPQQPSF--KKLYLLAE- 334
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1043 lSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMDNGSTDILPGTLMDISDFE------------------AL 1104
Cdd:PRK14897 335 -KVKSLTIKGIKGIKRAIARKENDERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIAtvlgieaarnaiiheakrTL 413
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1105 NETAL---------------LNGEMPATGRpvlMGItkaSLETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVII 1169
Cdd:PRK14897 414 QEQGLnvdirhimlvadmmtFDGSVKAIGR---HGI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIV 487
|
....*....
gi 516476482 1170 GKIIPAGTG 1178
Cdd:PRK14897 488 GQPITLGTG 496
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
692-768 |
5.04e-18 |
|
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: 80.87 E-value: 5.04e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 692 ITDDERYNAVTGVWRDAKEALEKRLI----------------DEQDLTNPIVMMMDSGARGNISNFSQLAGMRGLMA--- 752
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALInnilnkardpagniasKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNveg 80
|
90 100
....*....|....*....|....*...
gi 516476482 753 --APNG----------KIMELPIISNFR 768
Cdd:pfam05000 81 krIPFGfsgrtlphfkKDDEGPESRGFV 108
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
916-1180 |
1.72e-15 |
|
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: 80.33 E-value: 1.72e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 916 GEAVGTIAAQSIGEPGTQLTMRTFHTGGVaSSSDITQGLPRVQEIFE-ARNPKGEAIITEVTGTVESIVED--------P 986
Cdd:cd02584 27 GEMVGTIAAQSIGEPATQMTLNTFHFAGV-SAKNVTLGVPRLKEIINvAKNIKTPSLTVYLEPGFAKDEEKakkiqsrlE 105
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 987 ATRTREITVKGK-------TDT---------RSY--------------------------TVGMaDVLMVEEGEFIHRGA 1024
Cdd:cd02584 106 HTTLKDVTAATEiyydpdpQNTvieedkefvESYfefpdedveqdrlspwllrieldrkkMTDK-KLSMEQIAKKIKEEF 184
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1025 PL---IQGSIEPKHLLQVR----------DALSVETYLLGEVQKTYRSQGVEIGDKHIEVMVRQMLRKVRVMD-NGS--- 1087
Cdd:cd02584 185 KDdlnVIFSDDNAEKLVIRiriinddeekEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVDIeTGEfkk 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1088 -------TDI--------LPG------TLMDISDF------EA-----LNET----------------ALLNGEMPATGR 1119
Cdd:cd02584 265 reewvleTDGvnlrevlsHPGvdptrtTSNDIVEIfevlgiEAarkalLKELrnvisfdgsyvnyrhlALLCDVMTQRGH 344
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516476482 1120 pvLMGITKASL--ETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGTGMF 1180
Cdd:cd02584 345 --LMAITRHGInrQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCF 405
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
913-960 |
2.15e-12 |
|
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: 69.53 E-value: 2.15e-12
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVaSSSDITQGLPRVQEI 960
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGR-GEMNVTLGIPRLREI 53
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
932-1183 |
1.70e-10 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 65.68 E-value: 1.70e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 932 TQLTMRTFHTGGVASSsDITQGLPRVQEIFEARNPKGEAIIT---------------EVTGTVESI-VEDPATrtreiTV 995
Cdd:PRK14898 541 THNTMRTFHYAGVAEI-NVTLGLPRMIEIVDARKEPSTPIMTvhlkgeyatdrekaeEVAKKIESLtLGDVAT-----SI 614
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 996 KGKTDTRSYTVGMADVLMVEEGEFIHRgaplIQGSIEPKhlLQVRDALSVETYLLGEVQKTYRS--QGV----EIGDKHI 1069
Cdd:PRK14898 615 AIDLWTQSIKVELDEETLADRGLTIES----VEEAIEKK--LGVKIDRKGTVLYLKPKTPSYKAlrKRIpkikNIVLKGI 688
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1070 EVMVRQMLRKvRVMDNGSTDIL---PGTLMDISDFEALNET---------------------ALLN-------------- 1111
Cdd:PRK14898 689 PGIERVLVKK-EEHENDEEYVLytqGSNLREVFKIEGVDTSrtttnniieiqevlgieaarnAIINemmntleqqglevd 767
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516476482 1112 --------------GEMPATGRPVLMGitkaslETNSFLSAASFQETTRVLTDAAIRGKEDHLLGLKENVIIGKIIPAGT 1177
Cdd:PRK14898 768 irhlmlvadimtadGEVKPIGRHGVAG------EKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGT 841
|
....*.
gi 516476482 1178 GMFRYR 1183
Cdd:PRK14898 842 GCVDLR 847
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
913-936 |
1.11e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.34 E-value: 1.11e-03
10 20
....*....|....*....|....
gi 516476482 913 VEVGEAVGTIAAQSIGEPGTQLTM 936
Cdd:PRK14898 54 VEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
