|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-1196 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2396.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 3 DVN--NFEYMKIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDRCGV 80
Cdd:PRK00566 1 DVNkqDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 81 EVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDTPLEKKQLLSEREYRVYRE 160
Cdd:PRK00566 81 EVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 161 KYGKGFSAGMGAEAIKKILADIDLEKETNDLKEELKS-AQGQRRTRAIRRLEVMEAFRNSGNNPSWMVLDVLPVIPPEIR 239
Cdd:PRK00566 161 EYGDEFVAKMGAEAIKELLKNIDLEAEAEELREELKEtGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 240 PMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHM 319
Cdd:PRK00566 241 PLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDM 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 320 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIERMAPEIWD 399
Cdd:PRK00566 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 400 VLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNI 479
Cdd:PRK00566 401 VLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 480 LNPKDGKPVVTPSQDMVLGNYYLTLEREKAVGEGTIFKDINEAQLAYQNGYVHLHSRIAVfagsipneRFTDEqrnQLLI 559
Cdd:PRK00566 481 LSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKV--------RITSK---KLVE 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 560 TTVGKLIFNTILPKSFPYINEPTkfnleietpakyfvdtttdvrahiaaqelidPFKKKILGNIIAEVFKKFHITETSKM 639
Cdd:PRK00566 550 TTVGRVIFNEILPEGLPFINVNK-------------------------------PLKKKEISKIINEVYRRYGLKETVIF 598
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 640 LDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAKDEIQGKLILS 719
Cdd:PRK00566 599 LDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKN 678
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 720 LDR----LNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKGLTDTALKTA 795
Cdd:PRK00566 679 LSKdqesFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTA 758
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 796 DSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLEERLEGRYSRKTIRHPETKEVIARENDLITEAIATQ 875
Cdd:PRK00566 759 DSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADK 838
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 876 IVDAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVagdDITQGLPR 955
Cdd:PRK00566 839 IEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPR 915
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 956 IQEIFEARNPKGQAIITEVGGEVVSIEEGRDRqQEITIQGTD-DRRSYNIPYTARLRVEEGTIVERGEALTEGSVDPKAL 1034
Cdd:PRK00566 916 VAELFEARKPKGPAIIAEIDGTVSFGKETKGK-RRIVITPDDgEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHDI 994
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1035 IRVRDVLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNILPGTLMDIHTFTEANREAILSGSQPA 1114
Cdd:PRK00566 995 LRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPA 1074
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1115 TGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGIGRYRKLKSEVIKETAEV 1194
Cdd:PRK00566 1075 TGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDEEEA 1154
|
..
gi 489829083 1195 TD 1196
Cdd:PRK00566 1155 EA 1156
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
9-1182 |
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: 2011.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 9 YMKIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDRCGVEVTKSKVR 88
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 89 RERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDTPLEKKQLLSEREYRVYREKYGKGFSA 168
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 169 GMGAEAIKKILADIDLEKETNDLKEELKSAQGQR-RTRAIRRLEVMEAFRNSGNNPSWMVLDVLPVIPPEIRPMVQLEGG 247
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQkRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 248 RFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRF 327
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 328 RQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIERMAPEIWDVLEEVIRE 407
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 408 HPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKP 487
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 488 VVTPSQDMVLGNYYLTLEREKAVGEGTIFKDINEAQLAYQNGYVHLHSRIAVFAgsipnerftdeqRNQLLITTVGKLIF 567
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRT------------SGEILETTVGRVIF 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 568 NTILPKSFPYINEPTkfnleietpakyfvdtttdvrahiaaqelidPFKKKILGNIIAEVFKKFHITETSKMLDRMKDLG 647
Cdd:TIGR02386 549 NEILPEGFPYINDNE-------------------------------PLSKKEISSLIDLLYEVHGIEETAEMLDKIKALG 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 648 FKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAKDEIQGKLILSLD----RL 723
Cdd:TIGR02386 598 FKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKkdtyKF 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 724 NPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKGLTDTALKTADSGYLTRR 803
Cdd:TIGR02386 678 NPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRR 757
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 804 LVDVAQDVIIREDDCGTDRGLTIKAIREG-TEIIEPLEERLEGRYSRKTIRHPETKEVIARENDLITEAIATQIVDAGIE 882
Cdd:TIGR02386 758 LVDVAQDVVVREEDCGTEEGIEVEAIVEGkDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIE 837
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 883 EVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAG--DDITQGLPRIQEIF 960
Cdd:TIGR02386 838 KVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDITQGLPRVKELF 917
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 961 EARNPKGQAIITEVGGEVVSIEEGRDRQQEITIQG-TDDRRSYNIPYTARLRVEEGTIVERGEALTEGSVDPKALIRVRD 1039
Cdd:TIGR02386 918 EARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDeNDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIKG 997
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1040 VLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNILPGTLMDIHTFTEANREAILSGSQPATGRPV 1119
Cdd:TIGR02386 998 IQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQ 1077
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 489829083 1120 LLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGIGRYRK 1182
Cdd:TIGR02386 1078 LLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYKE 1140
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-1198 |
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: 1678.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1 MLDVNNFEYMKIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDRCGV 80
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 81 EVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDTPLEKKQLLSEREYRVYRE 160
Cdd:COG0086 81 EVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 161 KYGKGFSAGMGAEAIKKILADIDLEKETNDLKEELKSAQG-QRRTRAIRRLEVMEAFRNSGNNPSWMVLDVLPVIPPEIR 239
Cdd:COG0086 161 EYGDEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSeQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 240 PMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHM 319
Cdd:COG0086 241 PLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDM 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 320 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIERMAPEIWD 399
Cdd:COG0086 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 400 VLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNI 479
Cdd:COG0086 401 ILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 480 LNPKDGKPVVTPSQDMVLGNYYLTLEREKAVGEGTIFKDINEAQLAYQNGYVHLHSRIAVFAgsipneRFTDEQRNQLLI 559
Cdd:COG0086 481 LSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRI------TEDGEQVGKIVE 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 560 TTVGKLIFNTILPKSFPYINEptkfnleietpakyfvdtttdvrahiaaqelidPFKKKILGNIIAEVFKKFHITETSKM 639
Cdd:COG0086 555 TTVGRYLVNEILPQEVPFYNQ---------------------------------VINKKHIEVIIRQMYRRCGLKETVIF 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 640 LDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAKDEIQGKLILS 719
Cdd:COG0086 602 LDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAA 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 720 LDRLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKGLTDTALKTADSGY 799
Cdd:COG0086 682 FSSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGY 761
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 800 LTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLEERLEGRYSRKTIRHPETKEVIARENDLITEAIATQIVDA 879
Cdd:COG0086 762 LTRRLVDVAQDVIVTEEDCGTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEA 841
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 880 GIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGdditqglpRIQEI 959
Cdd:COG0086 842 GIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS--------RAAEE 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 960 FEARNPKGQAIITEVGGEVVSIEE----GRDRQQEITIQGTDDRRSYNIPYTARLRVEEGTIVERGEALTEGSVDPKALI 1035
Cdd:COG0086 914 SSIEAKAGGIVRLNNLKVVVNEEGkgvvVSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPI 993
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1036 RVRDVLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQmlRKIRVMDTGDTNILPGTLMDIHTFTEANREAILSGSQPAT 1115
Cdd:COG0086 994 IEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDK--ARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGL 1071
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1116 GRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGIGRYRKLKSEVIKETAEVT 1195
Cdd:COG0086 1072 DVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPI 1151
|
...
gi 489829083 1196 DEI 1198
Cdd:COG0086 1152 EEE 1154
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
3-1184 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1519.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 3 DVNNFEYMKIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDRCGVEV 82
Cdd:PRK14906 5 DVTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 83 TKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVT------------------------- 137
Cdd:PRK14906 85 TRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITsvdkeareedaddlrdelaadleel 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 138 ------------------EPGD-------------TP------------------------------LEKKQLLS-EREY 155
Cdd:PRK14906 165 daerdrlieatrrlsvdyVPEDdefvddigdderlTAeevraevadiyeeynerkalrreafdafmqIEPKQLISdEALY 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 156 RVYREKYGKGFSAGMGAEAIKKILADIDLEKETNDLKEELKSAQGQRRTRAIRRLEVMEAFRNSGNNPSWMVLDVLPVIP 235
Cdd:PRK14906 245 REMRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 236 PEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKS 315
Cdd:PRK14906 325 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKS 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 316 LSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIERMAP 395
Cdd:PRK14906 405 LADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 396 EIWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLA 475
Cdd:PRK14906 485 YVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLS 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 476 AQNILNPKDGKPVVTPSQDMVLGNYYLTLEREKAVGEGTIFKDINEAQLAYQ-NGYVHLHSRIAV-----FAGSIPNERF 549
Cdd:PRK14906 565 SNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDaRADLDLQAKIVVrlsrdMTVRGSYGDL 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 550 TDEQRNQLLITTVGKLIFNTILPKSFPYINeptkfnleietpakYFVDtttdvrahiaaqelidpfkKKILGNIIAEVFK 629
Cdd:PRK14906 645 EETKAGERIETTVGRIIFNQVLPEDYPYLN--------------YKMV-------------------KKDIGRLVNDCCN 691
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 630 KFHITETSKMLDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAK 709
Cdd:PRK14906 692 RYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEAT 771
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 710 DEIQGKLILSLDRLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKGLTD 789
Cdd:PRK14906 772 EEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVD 851
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 790 TALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIieplEERLEGRYSRKTIRHPEtKEVIARENDLIT 869
Cdd:PRK14906 852 TALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKGDV----DTNLIGRCLLEDVCDPN-GEVLLSAGDYIE 926
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 870 EAIA-TQIVDAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDD 948
Cdd:PRK14906 927 SMDDlKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDD 1006
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 949 ITQGLPRIQEIFEARNPKGQAIITEVGGeVVSIeEGRDRQQEITIQGTDDR-RSYNIPYTARLR--VEEGTIVERGEALT 1025
Cdd:PRK14906 1007 ITQGLPRVAELFEARKPKGEAVLAEISG-TLQI-TGDKTEKTLTIHDQDGNsREYVVSARVQFMpgVEDGVEVRVGQQIT 1084
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1026 EGSVDPKALIRVRDVLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNILPGTLMDIHTFTEANRE 1105
Cdd:PRK14906 1085 RGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANN 1164
|
1210 1220 1230 1240 1250 1260 1270
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489829083 1106 AILSGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGIGRYRKLK 1184
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: 1326.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 5 NNFEYMKIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDRCGVEVTK 84
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 85 SKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFasyvvtepgdtplekkqllsereyrvyrekygk 164
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 165 gfsagmgaeaikkiladidleketndlkeelksaqgqrrtrairrleVMEAFRNSGNNPSWMVLDVLPVIPPEIRPMVQL 244
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 245 EGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQ 324
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 325 GRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIERMAPEIWDVLEEV 404
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 405 IREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKD 484
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 485 GKPVVTPSQDMVLGNYYLTLEREKAVGEGTIfkdineaqlayqngyvhlhsriavfagsipnerftdeqrnqllITTVGK 564
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEGII-------------------------------------------ETTVGR 437
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 565 LIFNTILPKSFPYINEptkfnleietpakyfvdtttdvrahiaaqelidPFKKKILGNIIAEVFKKFHITETSKMLDRMK 644
Cdd:cd01609 438 VIFNEILPEGLPFINK---------------------------------TLKKKVLKKLINECYDRYGLEETAELLDDIK 484
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 645 DLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAKDEIQGKL--ILSLDR 722
Cdd:cd01609 485 ELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMmkNLDKDP 564
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 723 LNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKGLTDTALKTADSGYLTR 802
Cdd:cd01609 565 FNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTR 644
|
810
....*....|....*
gi 489829083 803 RLVDVAQDVIIREDD 817
Cdd:cd01609 645 RLVDVAQDVIVTEED 659
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-1177 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1135.88 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 7 FEYMKIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDRCGVEVTKSK 86
Cdd:PRK14844 1448 FNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSK 1527
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 87 VRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDTPLEKKQLLSEREYRVYREKYG-KG 165
Cdd:PRK14844 1528 VRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGiDS 1607
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 166 FSAGMGAEAIKKILADIDLEKETNDLKEELKSAQGQ-RRTRAIRRLEVMEAFRNSGNNPSWMVLDVLPVIPPEIRPMVQL 244
Cdd:PRK14844 1608 FVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEiRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSL 1687
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 245 EGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLK-SLSHMLKGK 323
Cdd:PRK14844 1688 ESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLKGK 1767
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 324 QGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIERMAPEIWDVLEE 403
Cdd:PRK14844 1768 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEE 1847
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 404 VIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPK 483
Cdd:PRK14844 1848 VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPS 1927
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 484 DGKPVVTPSQDMVLGNYYLTLEREKAvGEGTIFKDINEAQLAYQNGYVHLHSRIAVFAGSIPNErftDEQRNQLLITTVG 563
Cdd:PRK14844 1928 NGRPIIVPSKDIVLGIYYLTLQEPKE-DDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSS---GETHYKTICTTPG 2003
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 564 KLIFNTILPKsfpyiNEPTKFNLeietpakyfvdtttdVRAHIAAQELIdpfkkkilgNIIAEVFKKFHITETSKMLDRM 643
Cdd:PRK14844 2004 RLILWQIFPK-----HENLGFDL---------------INQVLTVKEIT---------SIVDLVYRNCGQSATVAFSDKL 2054
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 644 KDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAKDEIQGKLILSLD-- 721
Cdd:PRK14844 2055 MVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISiy 2134
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 722 ----RLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKGLTDTALKTADS 797
Cdd:PRK14844 2135 dgnsKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANS 2214
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 798 GYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLEERLEGRYSRKTIRHPETKEVIARENDLITEAIATQIV 877
Cdd:PRK14844 2215 GYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQIN 2294
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 878 DAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGV------------- 944
Cdd:PRK14844 2295 IAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVmtrgvessniias 2374
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 --------------------------------------------------------------------------------
Cdd:PRK14844 2375 inakiklnnsniiidkngnkivisrscevvlidslgseklkhsvpygaklyvdeggsvkigdkvaewdpytlpiitektg 2454
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 --------------------------------------------------------------------------------
Cdd:PRK14844 2455 tvsyqdlkdgisitevmdestgisskvvkdwklysgganlrprivllddngkvmtlasgveacyfipigavlnvqdgqkv 2534
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 945 -AGD-------------DITQGLPRIQEIFEARNPKGQAIITEVGGEVVSIEEGRDRQQEITIQGTDDRRS---YNIPYT 1007
Cdd:PRK14844 2535 hAGDvitrtpresvktrDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKDRRGKRSILIKPVDEQISpveYLVSRS 2614
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1008 ARLRVEEGTIVERGEALTEGSVDPKALIRVRDVLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTN 1087
Cdd:PRK14844 2615 KHVIVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTM 2694
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1088 ILPGTLMDIHTFTEANREAILSGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIL 1167
Cdd:PRK14844 2695 YLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIV 2774
|
1370
....*....|
gi 489829083 1168 GKLVPAGTGI 1177
Cdd:PRK14844 2775 GRLIPAGTGL 2784
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
3-1035 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1121.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 3 DVNNFEYMkigLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGV-VCDRCGVE 81
Cdd:PRK09603 1395 DFSSFQLT---LASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVA 1471
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 82 VTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDT--------PLEKKQLLSER 153
Cdd:PRK09603 1472 ITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAaydnegtkLVMKYDILNEE 1551
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 154 EYRVYREKY-GKGFSAGMGAEAIKKILADIDLEKETNDLKEELKSAQGQ-RRTRAIRRLEVMEAFRNSGNNPSWMVLDVL 231
Cdd:PRK09603 1552 QYQNISRRYeDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDaKKKKLIKRLKVVESFLNSGNRPEWMMLTVL 1631
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 232 PVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNR 311
Cdd:PRK09603 1632 PVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKR 1711
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 312 PLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRKIE 391
Cdd:PRK09603 1712 PLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIE 1791
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 392 RMAPEIWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARI 471
Cdd:PRK09603 1792 QKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKV 1871
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 472 LMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLEREKAVGEGTIFKDINEAQLAYQNGYVHLHSRIAVFagsipnerftd 551
Cdd:PRK09603 1872 LMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVL----------- 1940
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 552 eQRNQLLITTVGKLIFNTILPKsfpyineptkfnleietpakyFVDTTTDVRahiaaqelidPFKKKILGNIIAEVFKKF 631
Cdd:PRK09603 1941 -DQGNIIATSAGRMIIKSILPD---------------------FIPTDLWNR----------PMKKKDIGVLVDYVHKVG 1988
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 632 HITETSKMLDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDERYERVIAVWNAAKDE 711
Cdd:PRK09603 1989 GIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDK 2068
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 712 IqGKLILSL---DR--LNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTVLEYFISTHGARKG 786
Cdd:PRK09603 2069 M-SKEMMTAiakDKegFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKG 2147
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 787 LTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLEERLEGRYSRKTIRHPETKEVIAREND 866
Cdd:PRK09603 2148 LADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADT 2227
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 867 LITEAIATQIVDAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAG 946
Cdd:PRK09603 2228 LIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTAS 2307
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 947 DDI--------TQGLPRIQEIFEARNPKGQAIITEVGGEVVSIEEGRDRQQ---EITIQGTDDRRSYNI---PYTARLRV 1012
Cdd:PRK09603 2308 RSQdereivasKEGFVRFYNLRTYTNKEGKNIIANRRNASILVVEPKIKAPfdgELRIETVYEEVVVSVkngDQEAKFVL 2387
|
1050 1060
....*....|....*....|....
gi 489829083 1013 EEGTIVERGE-ALTEGSVDPKALI 1035
Cdd:PRK09603 2388 RRSDIVKPSElAGVGGKIEGKVYL 2411
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
5-568 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 872.92 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 5 NNFEYMKIGLASPDKIRSWSH---------GEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVC 75
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGQrtlpngqvvGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 76 DRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDTP-LEKKQLLSERE 154
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKnLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 155 Y-----RVYREK---YGKGFsAGMGAEAIKKILADIDLEKETNDLKEELKSAQGQRRTRAIRRLEVMEAFRNSGNNPSWM 226
Cdd:PRK02625 167 WleiedQIYAEDselEGEEV-VGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWM 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 227 VLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVT 306
Cdd:PRK02625 246 VLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVV 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 307 GPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSA 386
Cdd:PRK02625 326 GANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAA 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 387 KRKIERMAPEIWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQ 466
Cdd:PRK02625 406 KKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 467 AEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLEREKAV-GEGTIFKDINEAQLAYQNGYVHLHSRIAV-FAGSI 544
Cdd:PRK02625 486 AEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQkGAGRYFASLEDVIMAFEQGRIDLHAWVWVrFNGEV 565
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 489829083 545 PNERFTDEQR----------------------------NQLLITTVGKLIFN 568
Cdd:PRK02625 566 EDDDEDTEPLktetledgtrieqyryrrdrfdedgnliSQYILTTVGRVIMN 617
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
7-571 |
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: 835.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 7 FEYMKIGLASPDKIRSWSH---------GEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVRYKGVVCDR 77
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGQrtlpngqvvGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 78 CGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYFASYVVTEPGDTP-LEKKQLLSEREY- 155
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKnLKYKQLLTEDQWl 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 156 RVYREKYGKGFS------AGMGAEAIKKILADIDLEKETNDLKEELKSAQGQRRTRAIRRLEVMEAFRNSGNNPSWMVLD 229
Cdd:TIGR02387 162 EIEDQIYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVLD 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 230 VLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPG 309
Cdd:TIGR02387 242 VIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGAN 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 310 NRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKELVGRGLAHNIKSAKRK 389
Cdd:TIGR02387 322 NRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKL 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 390 IERMAPEIWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEA 469
Cdd:TIGR02387 402 IQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEA 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 470 RILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLEREKAV-GEGTIFKDINEAQLAYQNGYVHLHSRIAV-FAGSIPNE 547
Cdd:TIGR02387 482 RLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEkGRGRYFSSLEDAIHAYEDGRIDLHDWIWVrFNGEVETN 561
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|..
gi 489829083 548 RFTDEQR----------------------------NQLLITTVGKLIFNTIL 571
Cdd:TIGR02387 562 DPLDEPIksedlsdgtrieqwtyrrdrfdedgaliSQYILTTTGRIIMNHTI 613
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-537 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 817.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1 MLDVNNFEYMKIGLASPDKIRSWSH---------GEVKKPETINYRTLKPERDGLFCERIFGPMKDWECSCGKYKRVR-- 69
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGde 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 70 -YKGVVCDRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRALEEIIYF-ASYVVTEP-GDTPLEK 146
Cdd:CHL00018 81 kEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCdFSFARPIAkKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 147 KQLLSE----REYRVYREKYGKGFSA------GMGAEAIKKILADIDLEKETNDLKEELKSAQ--------------GQR 202
Cdd:CHL00018 161 RGLFEYeiqsWKYSIPLFFSTQGFDTfrnreiSTGAGAIREQLADLDLRIIIDNSLVEWKELGeegstgnewedrkiGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 203 RTRAIRRLEVMEAFRNSGNNPSWMVLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLG--APNII 280
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 281 VQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKE 360
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 361 MALELFKPFVMKELVGRGLAHNIKSAKRKIERMAPEIWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHP 440
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 441 LVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLER-------------E 507
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNrrgiyanrynpcnR 560
|
570 580 590
....*....|....*....|....*....|
gi 489829083 508 KAVGEGTIFKDINEAQLAYQNGYVHLHSRI 537
Cdd:CHL00018 561 KNSTKEPYFSNSYDALGAYRQKRINLDSPL 590
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
15-816 |
3.38e-173 |
|
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: 521.61 E-value: 3.38e-173
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 15 ASPDKIRSWSHGEVKKPETINYRTLKPERDGlfcerifgpmkdwecscgKYKRVRYKGVVCDRCGVEVTKSKVRRERMGH 94
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 95 IELAAPVSHIWYFKGIPSRMglvmdmspraleeiiyfasyvvtepgdtplekkqllsereyrvyrekygkgfsagmgaea 174
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFL------------------------------------------------------------ 82
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 175 ikkiladidleketndlkeelksaqgqrrtrairrlevmeafrnsgnNPSWMVLDVLPVIPPEIRPMVqleggrfatsdl 254
Cdd:cd00399 83 -----------------------------------------------GPEWMILTCLPVPPPCLRPSV------------ 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 255 ndlyrrvinrnnrlkrlldlgapniIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGK 334
Cdd:cd00399 104 -------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGK 158
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 335 RVDYSGRSVIVVGPNLKMYQCGLPKEMALELfkpfvmkelvgrglahniksakrkiermapeiwdvleeviREHPVLLNR 414
Cdd:cd00399 159 RVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFNR 198
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 415 APTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQD 494
Cdd:cd00399 199 QPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQD 278
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 495 MVLGNYYLTLerekavgegtifkdineaqlayqngyvhlhsriavfagsipnerftdeqrnqllittvGKLIFNTILPKS 574
Cdd:cd00399 279 TLLGAYLLTL----------------------------------------------------------GKQIVSAALPGG 300
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 575 FPYIneptkfnleietpakyfvdtttdvrahiaaqelidpfkkkilgniiaeVFKKFHITETSKMLDRMKDLGFKISTKA 654
Cdd:cd00399 301 LLHT------------------------------------------------VTRELGPEKAAKLLSNLQRVGFVFLTTS 332
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 655 GMTVGIADIL----TLEEKHEILEKAHDTVEKITKSFRRGLITDDER-------YERVIAVWNAAKDEIQGKLILSLD-- 721
Cdd:cd00399 333 GFSVGIGDVIddgvIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNLDlv 412
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 722 -RLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRI--------------------VELPITSNFREGLTVLEYFIST 780
Cdd:cd00399 413 sKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHA 492
|
810 820 830
....*....|....*....|....*....|....*.
gi 489829083 781 HGARKGLTDTALKTADSGYLTRRLVDVAQDVIIRED 816
Cdd:cd00399 493 MGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
224-500 |
3.72e-162 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 483.56 E-value: 3.72e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 224 SWMVLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNG--RR 301
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 302 GRPVTGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFVMKEL------- 374
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 375 -----------VGRGLAHNIKSAKR-KIERMAPEIWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLV 442
Cdd:smart00663 158 lvrngpngakyIIRGKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 489829083 443 CTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNY 500
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
617-1026 |
1.54e-131 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 435.19 E-value: 1.54e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 617 KKILGNIIAEVFKKFHITETSKMLDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDE 696
Cdd:PRK02597 10 KKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEVE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 697 RYERVIAVWNAAKDEIQGKLILSL---DRLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTV 773
Cdd:PRK02597 90 RFQKVIDTWNETNERLKDEVVKNFrqnDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTV 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 774 LEYFISTHGARKGLTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLEERLEGRYSRKTIR 853
Cdd:PRK02597 170 TEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLGDRLLGRVLAEDVV 249
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 854 HPEtKEVIARENDLITEAIATQIVDAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQ 933
Cdd:PRK02597 250 DPE-GEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEPGTQ 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 934 LTMRTFHTGGV----------AGDDITQGLPRIQEIFEARNPKG-QAIITEVGGEVVSIEEGRDRQQEITI-QGTddrrs 1001
Cdd:PRK02597 329 LTMRTFHTGGVftgevarqvrSPFAGTVEFGKKLRTRPYRTRHGvEALQAEVDFDLVLKPSGKGKPQKIEItQGS----- 403
|
410 420
....*....|....*....|....*
gi 489829083 1002 ynipytaRLRVEEGTIVERGEALTE 1026
Cdd:PRK02597 404 -------LLFVDDGQTVEADQLLAE 421
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
617-1042 |
8.43e-125 |
|
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: 414.63 E-value: 8.43e-125
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 617 KKILGNIIAEVFKKFHITETSKMLDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRGLITDDE 696
Cdd:TIGR02388 9 KKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGEITEVE 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 697 RYERVIAVWNAAKDEIQGKLILSL---DRLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPITSNFREGLTV 773
Cdd:TIGR02388 89 RFQKVIDTWNGTNEELKDEVVNNFrqtDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTV 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 774 LEYFISTHGARKGLTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEpLEERLEGRYSRKTIR 853
Cdd:TIGR02388 169 TEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKIS-LGDRLLGRLVAEDVL 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 854 HPEtKEVIARENDLITEAIATQIVDAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQ 933
Cdd:TIGR02388 248 HPE-GEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQ 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 934 LTMRTFHTGGV----------AGDDITQGLPRIQEIFEARNPKGQ-AIITEVGGEVVSIEEGrdrqqeitiQGTDDRRSY 1002
Cdd:TIGR02388 327 LTMRTFHTGGVftgevarqvrSKIDGTVEFGKKLRTRGYRTRHGEdAKQVEVAGLLIIKPTG---------SITNKAQEI 397
|
410 420 430 440
....*....|....*....|....*....|....*....|...
gi 489829083 1003 NIPYTARLRVEEGTIVERGEALTE---GSVDPKALIRVRDVLS 1042
Cdd:TIGR02388 398 EVTQGSLLFVEDGQTVDAGQLLAEialGAVRKSTEKATKDVAS 440
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
611-944 |
2.83e-124 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 415.88 E-value: 2.83e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 611 LIDpfkKKILGNIIAEVFKKFHITETSKMLDRMKDLGFKISTKAGMTVGIADILTLEEKHEILEKAHDTVEKITKSFRRG 690
Cdd:CHL00117 13 VID---KTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYG 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 691 LITDDERYERVIAVWNAA----KDEI--QGKLIlslDRLNPIFMMQDSGARGNISNFTQLAGMRGLMADPSGRIVELPIT 764
Cdd:CHL00117 90 NVHAVEKLRQSIEIWYATseylKQEMnpNFRMT---DPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 765 SNFREGLTVLEYFISTHGARKGLTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAiREGTEIIEPLEERLE 844
Cdd:CHL00117 167 SNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSP-RNGMMIERILIQTLI 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 845 GRYSRKTIRHpeTKEVIARENDLITEAIATQIVDAGIEEVTIRSAFTCNTKHGVCKKCYGKNLATGTEVEVGEAVGIIAA 924
Cdd:CHL00117 246 GRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIAG 323
|
330 340
....*....|....*....|
gi 489829083 925 QSIGEPGTQLTMRTFHTGGV 944
Cdd:CHL00117 324 QSIGEPGTQLTLRTFHTGGV 343
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
8-822 |
1.51e-116 |
|
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: 383.14 E-value: 1.51e-116
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 8 EYMKIGLASPDKIRSWSHGEVKKPETinYrtlkpERDGLFCERifGPMKdwecscgkyKR--VRYKGVVCDRCGVevtks 85
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGYPIEG--GLMD---------PRlgVIEPGLRCKTCGN----- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 86 kvRRER----MGHIELAAPVSHIWYFKGIPSrmglVMDMSPRALEEIIYfasyvvtepgdTPLEKKQLLSE-REYRVYRE 160
Cdd:cd02582 62 --TAGEcpghFGHIELARPVIHVGFAKHIYD----LLRATCRSCGRILL-----------PEEEIEKYLERiRRLKEKWP 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 161 KYGKGFSAGMGAEAIK--------KILADIDLEKETNdlKEELKSAQGQRRTRA-IR-RLE-------VMEAFRNSGNNP 223
Cdd:cd02582 125 ELVKRVIEKVKKKAKKrkvcphcgAPQYKIKLEKPTT--FYEEKEEGEVKLTPSeIReRLEkipdedlELLGIDPKTARP 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 224 SWMVLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGR 303
Cdd:cd02582 203 EWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGI 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 304 PV----TGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFV--------M 371
Cdd:cd02582 283 PParhrSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERvtewniekM 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 372 KELVGRGLAH----N--IKSAKRKI-----------ERMAPEiWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGR 434
Cdd:cd02582 360 RKLVLNGPDKwpgaNyvIRPDGRRIrlryvnreelaERLEPG-WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGK 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 435 AIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLT-----LEREKA 509
Cdd:cd02582 439 TFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTrkttlFTKEEA 518
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 510 vgegtifkdineAQLAYQNGYVHLHSRIAVfagSIPNERFTdeqrnqllittvGKLIFNTILPKSFPYInEPTKFNLEIE 589
Cdd:cd02582 519 ------------LQLLSAAGYDGLLPEPAI---LEPKPLWT------------GKQLFSLFLPKDLNFE-GKAKVCSGCS 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 590 TPAKYFVDTTTDVRahIAAQELID-PFKKKILG-----NIIAEVFKKFHITETSKMLDRMKDLGFKISTKAGMTVGIADI 663
Cdd:cd02582 571 ECKDEDCPNDGYVV--IKNGKLLEgVIDKKAIGaeqpgSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDE 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 664 LTLEEKH----EILEKAHDTVEKITKSFRRGLI------TDDERYE-RVIAVWNAAKDEIQGKLILSLDRLNPIFMMQDS 732
Cdd:cd02582 649 DIPEEARkeieEIIKEAEKKVYELIEQYKNGELeplpgrTLEETLEmKIMQVLGKARDEAGKVASKYLDPFNNAVIMART 728
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 733 GARGNISNFTQLAGMRGLMADPSGRIVE------LP--------------ITSNFREGLTVLEYFISTHGARKGLTDTAL 792
Cdd:cd02582 729 GARGSMLNLTQMAACLGQQSVRGERINRgyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGREGLVDTAV 808
|
890 900 910
....*....|....*....|....*....|
gi 489829083 793 KTADSGYLTRRLVDVAQDVIIREDdcGTDR 822
Cdd:cd02582 809 RTSQSGYMQRRLINALQDLYVEYD--GTVR 836
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
11-822 |
3.90e-109 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 363.41 E-value: 3.90e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 11 KIGLASPDKIRSWSHGEVKKPETinYrtlkpERDGLFCERifGPMKdwecscgkyKR--VRYKGVVCDRCGvevTKSKVR 88
Cdd:PRK08566 13 KFGLLSPEEIRKMSVTKIITADT--Y-----DDDGYPIDG--GLMD---------PRlgVIDPGLRCKTCG---GRAGEC 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 89 RERMGHIELAAPVSHIWYFKGIpsRMGLvmdmspRAleeiiyfasyVVTEPGdtplekKQLLSEREYRVYREKYGK---- 164
Cdd:PRK08566 72 PGHFGHIELARPVIHVGFAKLI--YKLL------RA----------TCRECG------RLKLTEEEIEEYLEKLERlkew 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 165 GFSAGMGAEAIKKILA-------------DIDLEKETNdLKEELKSAQGQRRTRAIR-RLEVM--EAFRNSGNNPS---- 224
Cdd:PRK08566 128 GSLADDLIKEVKKEAAkrmvcphcgekqyKIKFEKPTT-FYEERKEGLVKLTPSDIReRLEKIpdEDLELLGINPEvarp 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 225 -WMVLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGR 303
Cdd:PRK08566 207 eWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGI 286
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 304 PV----TGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPF--------VM 371
Cdd:PRK08566 287 PParhrSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPErvtewnieEL 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 372 KELVGRGL-AHN-----IKSAKRKI-----------ERMAPEiWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGR 434
Cdd:PRK08566 364 REYVLNGPeKHPganyvIRPDGRRIkltdknkeelaEKLEPG-WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGK 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 435 AIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLerekavgEGT 514
Cdd:PRK08566 443 TFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTR-------KST 515
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 515 IFkdiNEAQLAYQNGYVHLHsriavfagSIPNERFTDEQRNQLLittVGKLIFNTILPKSFPYiNEPTKFNLEIETPAKY 594
Cdd:PRK08566 516 LF---TKEEALDLLRAAGID--------ELPEPEPAIENGKPYW---TGKQIFSLFLPKDLNL-EFKAKICSGCDECKKE 580
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 595 FVDTTTDVRahIAAQEL----IDpfKKKI---LGNIIAEVFKKFHITETSKMLDRMKDLGFKISTKAGMTVGIADI---- 663
Cdd:PRK08566 581 DCEHDAYVV--IKNGKLlegvID--KKAIgaeQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEdipe 656
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 664 LTLEEKHEILEKAHDTVEKITKSFRRGLI------TDDERYE-RVIAVWNAAKDEIqGKLILS-LDRLNPIFMMQDSGAR 735
Cdd:PRK08566 657 EAKEEIDEIIEEAEKRVEELIEAYENGELeplpgrTLEETLEmKIMQVLGKARDEA-GEIAEKyLGLDNPAVIMARTGAR 735
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 736 GNISNFTQLAGMRGLMADPSGRIVE------LP--------------ITSNFREGLTVLEYFISTHGARKGLTDTALKTA 795
Cdd:PRK08566 736 GSMLNLTQMAACVGQQSVRGERIRRgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTS 815
|
890 900
....*....|....*....|....*..
gi 489829083 796 DSGYLTRRLVDVAQDVIIREDdcGTDR 822
Cdd:PRK08566 816 QSGYMQRRLINALQDLKVEYD--GTVR 840
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
913-1177 |
1.31e-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: 333.34 E-value: 1.31e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 913 VEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDdITQGLPRIQEIFEARNpkgqaiitevggevvsieegrdrqqeit 992
Cdd:cd02655 3 VELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVATD-ITQGLPRVEELFEARK---------------------------- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 993 iqgtddrrsynipytarlrveegtivergealtegsVDPKALIRVRD--VLSVQEYLLAEVQKVYRMQGVEIGDKHVEVM 1070
Cdd:cd02655 54 ------------------------------------INPHDLLRIKFlgPEAVQKYLVEEIQKVYRSQGVNINDKHIEII 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1071 VRQMLRKIRVMDTGDTNILPGTLMDIHTFTEANREAILSGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAA 1150
Cdd:cd02655 98 VRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEAA 177
|
250 260
....*....|....*....|....*..
gi 489829083 1151 IKGKRDELLGLKENVILGKLVPAGTGI 1177
Cdd:cd02655 178 IEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
11-331 |
1.75e-102 |
|
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: 326.94 E-value: 1.75e-102
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 11 KIGLASPDKIRSWSHGEVKKPETINYRTLKPERDGLFCERIFGPMKDWECS-CGKYKRvrykgvvcdRCGVevtkskvrr 89
Cdd:pfam04997 8 QFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGKKKK---------DCPG--------- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 90 eRMGHIELAAPVSHIWYFKgipsrmglvmdMSPRALEEIIYFASYVVTEPGdtpleKKQLLSEREYRVYREKYGkgfsag 169
Cdd:pfam04997 70 -HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENLK------ 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 170 MGAEAIKKILADIDL------------------EKETNDLKEELKSAQGQRRTRAIRRLEVM-------------EAFRN 218
Cdd:pfam04997 127 MGAKAILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKKSKEEEEKEILNPEKVLkifkrisdedveiLGFNP 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 219 SGNNPSWMVLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDN 298
Cdd:pfam04997 207 SGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDN 286
|
330 340 350
....*....|....*....|....*....|....
gi 489829083 299 GRRG-RPVTGPGNRPLKSLSHMLKGKQGRFRQNL 331
Cdd:pfam04997 287 EIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
1-1176 |
3.50e-97 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 338.92 E-value: 3.50e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1 MLDVNNFEYMKIGLASPDKIRSWSHGEVKKPETINYRTLkPERDGLFCERIfGPMKdwecscgkykrvryKGVVCDRCGv 80
Cdd:PRK14977 3 ILAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIE--------------PGQKCLTCG- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 81 evTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLVMDMSPRAL---EEIIYFASYVVTEPGDTPLEKKQLLSE--REY 155
Cdd:PRK14977 66 --NLAANCPGHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKlpqEDLNVFKLIEEAHAAARDIPEKRIDDEiiEEV 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 156 RVYREKYGKGFSAgmgAEAIKKILADIDLEKETndlKEELKSAQGQRRTRAIRRLEVME----------AFRNSGNNPSW 225
Cdd:PRK14977 144 RDQVKVYAKKAKE---CPHCGAPQHELEFEEPT---IFIEKTEIEEHRLLPIEIRDIFEkiidddleliGFDPKKARPEW 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 226 MVLDVLPVIPPEIRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPV 305
Cdd:PRK14977 218 AVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQ 297
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 306 T--GPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFV--------MKELV 375
Cdd:PRK14977 298 AhhKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenniekMKELV 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 376 GRG---------------LAHNIKSAKRKIERMAPEIWDVLE--EVIREH-----PVLLNRAPTLHRLGIQAFEPTLVEG 433
Cdd:PRK14977 378 INGpdefpganairkgdgTKIRLDFLEDKGKDALREAAEQLEigDIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPG 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 434 RAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTlerekavGEG 513
Cdd:PRK14977 458 ATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT-------KDD 530
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 514 TIFkDINEAqlayqngyvhlhSRIAVFAG-SIPNERFTDEQRNQLLITtvGKLIFNTILPKSFPYINePTKFNLEIETPA 592
Cdd:PRK14977 531 ALF-DKNEA------------SNIAMLAGiTDPLPEPAIKTKDGPAWT--GKQLFSLFLPKDFNFEG-IAKWSAGKAGEA 594
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 593 KYfVDTTTDVRAHIAAQELIDP-FKKKILGNIIAEVFKKFHITETS-------KMLDRMKDLGFKISTKAGMTVGIADIL 664
Cdd:PRK14977 595 KD-PSCLGDGYVLIKEGELISGvIDDNIIGALVEEPESLIDRIAKDygeavaiEFLNKILIIAKKEILHYGFSNGPGDLI 673
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 665 TLEE-KHEILEKAHDTVEKITKSFRRGLITDDERYER------------------VIAVWNAAKDEIQGKLILSLDRLNP 725
Cdd:PRK14977 674 IPDEaKQEIEDDIQGMKDEVSDLIDQRKITRKITIYKgkeellrgmkeeealeadIVNELDKARDKAGSSANDCIDADNA 753
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 726 IFMMQDSGARGNISNFTQLAG--------MRGLMADPSGRIVE---------------LP-----ITSNFREGLTVLEYF 777
Cdd:PRK14977 754 GKIMAKTGARGSMANLAQIAGalgqqkrkTRIGFVLTGGRLHEgykdralshfqegddNPdahgfVKNNYREGLNAAEFF 833
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 778 ISTHGARKGLTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLE---------ERLEGRYS 848
Cdd:PRK14977 834 FHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKldhgeafnlERIIEKQK 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 849 RKTIRHPETKEVI------------ARENDLITEAI-ATQIVDAGIEEvtirsaftcntkhgVCKKcyGKNLATGTEVEV 915
Cdd:PRK14977 914 IEDRGKGASKDEIeelakeytktfnANLPKLLADAIhGAELKEDELEA--------------ICAE--GKEGFEKAKVEP 977
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 916 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFEARNP-------------------KGQAIITEVGG 976
Cdd:PRK14977 978 GQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKpstptmdiylddeckedieKAIEIARNLKE 1057
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 977 EVVS--IEEGR-DRQQEITIQGTDDRRSYN--IPYTARLRVEEGTIV-ERGEALTEGSVDPKALIRVRDVLSVQEYLLAE 1050
Cdd:PRK14977 1058 LKVRalIADSAiDNANEIKLIKPDKRALENgcIPMERFAEIEAALAKgKKFEMELEDDLIILDLVEAADRDKPLATLIAI 1137
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1051 VQKVYR--MQGVEIGDKHVEVMVRQMLRKIRVMDTGDTN---ILPGTLMDI-HTFT------------EANREAIL---- 1108
Cdd:PRK14977 1138 RNKILDkpVKGVPDIERAWVELVEKDGRDEWIIQTSGSNlaaVLEMKCIDIaNTITndcfeiagtlgiEAARNAIFnela 1217
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1109 ------------------------SGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKEN 1164
Cdd:PRK14977 1218 siledqglevdnryimlvadimcsRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDA 1297
|
1370
....*....|..
gi 489829083 1165 VILGKLVPAGTG 1176
Cdd:PRK14977 1298 LIMGQNIPIGSG 1309
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
13-816 |
2.54e-82 |
|
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: 285.58 E-value: 2.54e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 13 GLASPDKIRSWSHGEVKKPETINyRTLKPERDGLFCERIfGPMKdwecscgkykrvryKGVVCDRCGvevtkskvrrERM 92
Cdd:cd02733 6 GILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG----------GDM 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 93 -------GHIELAAPVSHIWYfkgipsrmglvMDMSPRALEEIIyfasyvvtepgdtplekKQLLSEReyRVYrekygkg 165
Cdd:cd02733 60 kecpghfGHIELAKPVFHIGF-----------LTKILKILRCVC-----------------KRELSAE--RVL------- 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 166 fsagmgaEAIKKILaDIDLEKETNDLKeelksaqgqrRTRairrlevmeafrnsgnnPSWMVLDVLPVIPPEIRPMVQLE 245
Cdd:cd02733 103 -------EIFKRIS-DEDCRILGFDPK----------FSR-----------------PDWMILTVLPVPPPAVRPSVVMD 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 246 GGRFATSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRP-VTGPGNRPLKSLSHMLKGKQ 324
Cdd:cd02733 148 GSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPqATQKSGRPLKSIRQRLKGKE 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 325 GRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALEL-FKPFV-------MKELVGRGLAHN------IKSAKRKI 390
Cdd:cd02733 228 GRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfnidrLQELVRNGPNEYpgakyiIRDDGERI 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 391 E-RMAPEIWDV-LEE--VIREH-----PVLLNRAPTLHRLGIQafeptlveGRAIRLHPL--------VCTAYNADFDGD 453
Cdd:cd02733 308 DlRYLKKASDLhLQYgyIVERHlqdgdVVLFNRQPSLHKMSMM--------GHRVKVLPYstfrlnlsVTTPYNADFDGD 379
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 454 QMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERekavgegtIFKDINEAQlayqngyvHL 533
Cdd:cd02733 380 EMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRD--------TFLEKDQVM--------NL 443
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 534 HSRIAVFAGSIPNERFTdeqRNQLLITtvGKLIFNTILPKsfpyINEPTKFNLEIETPAKYFvdTTTDVRAHIAAQELID 613
Cdd:cd02733 444 LMWLPDWDGKIPQPAIL---KPKPLWT--GKQIFSLIIPK----INNLIRSSSHHDGDKKWI--SPGDTKVIIENGELLS 512
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 614 -PFKKKILG----NIIAEVFKKFHITETSKMLDRMKDLgfkIST---KAGMTVGIADIL----TLEEKHEILEKAHDTVE 681
Cdd:cd02733 513 gILCKKTVGassgGLIHVIWLEYGPEAARDFIGNIQRV---VNNwllHNGFSIGIGDTIadkeTMKKIQETIKKAKRDVI 589
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 682 KITKSFRRGLITDD------ERYE-RVIAVWNAAKDEIQGKLILSLDRLNPIFMMQDSGARGNISNFTQLAGMRGLMADP 754
Cdd:cd02733 590 KLIEKAQNGELEPQpgktlrESFEnKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVE 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 755 SGRIV------ELP--------------ITSNFREGLTVLEYFISTHGARKGLTDTALKTADSGYLTRRLVDVAQDVIIR 814
Cdd:cd02733 670 GKRIPfgfrrrTLPhfikddygpesrgfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVK 749
|
..
gi 489829083 815 ED 816
Cdd:cd02733 750 YD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
93-817 |
2.06e-74 |
|
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: 264.41 E-value: 2.06e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 93 GHIELAAPVSHIWYFKGIPSrmglvmdmsprALEEIIYFASYVvtepgdtplekkqLLSEREYRVYREKY-GKGFSAGMG 171
Cdd:cd02583 61 GYIKLELPVFHIGYFKAIIN-----------ILQCICKTCSRV-------------LLPEEEKRKFLKRLrRPNLDNLQK 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 172 AEAIKKILadiDLEKETN--DLKEELKSAQGQrrtraIRRLEVMEAFRN-------------SGNNPSWMVLDVLPVIPP 236
Cdd:cd02583 117 KALKKKIL---EKCKKVRkcPHCGLLKKAQED-----LNPLKVLNLFKNippedvelllmnpLAGRPENLILTRIPVPPL 188
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 237 EIRPMVQLEGGrfATSDLNDL---YRRVINRNNRLKRLLDLGAPNIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPL 313
Cdd:cd02583 189 CIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPKKPI 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 314 KSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPF--------VMKELVGRG------- 378
Cdd:cd02583 267 RGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPErvtrynieKLRKLVLNGpdvhpga 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 379 ---------LAHNIKSAKRKIERMAPEIWDVLEEVIREHP-VLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNA 448
Cdd:cd02583 347 nfvikrdggKKKFLKYGNRRKIARELKIGDIVERHLEDGDiVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNA 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 449 DFDGDQMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLerekavgegtifKDI--NEAQLAY 526
Cdd:cd02583 427 DFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTS------------KDVffDRAQFCQ 494
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 527 QNGYVHL-HSRIAVFAGSI--PNERFTdeqrnqllittvGKLIFNTILpksFPYINEPTKFNLEIETPAKYFVDTT---T 600
Cdd:cd02583 495 LCSYMLDgEIKIDLPPPAIlkPVELWT------------GKQIFSLLL---RPNKKSPVLVNLEAKEKSYTKKSPDmcpN 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 601 DVRAHIAAQELI----DpfkKKILG-----NIIAEVFKKFHITETSKMLDRMKDLGFK-ISTKaGMTVGIADILT----L 666
Cdd:cd02583 560 DGYVVIRNSELLcgrlD---KSTLGsgsknSLFYVLLRDYGPEAAAAAMNRLAKLSSRwLSNR-GFSIGIDDVTPskelL 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 667 EEKHEILEKAHDTVEKITKSFRRGLI------TDDERYERVI-AVWNAAKDEIqGKLILS-LDRLNPIFMMQDSGARGNI 738
Cdd:cd02583 636 KKKEELVDNGYAKCDEYIKQYKKGKLelqpgcTAEQTLEAKIsGELSKIREDA-GKACLKeLHKSNSPLIMALCGSKGSN 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 739 SNFTQ---------LAGMR---GLMA-----------DPSGR-IVElpitSNFREGLTVLEYFISTHGARKGLTDTALKT 794
Cdd:cd02583 715 INISQmiacvgqqiISGKRipnGFEDrtlphfprnskTPAAKgFVA----NSFYSGLTPTEFFFHTMSGREGLVDTAVKT 790
|
810 820
....*....|....*....|...
gi 489829083 795 ADSGYLTRRLVDVAQDVIIREDD 817
Cdd:cd02583 791 AETGYMQRRLMKALEDLSVQYDG 813
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
770-1022 |
6.62e-70 |
|
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: 243.80 E-value: 6.62e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 770 GLTVLEYFISTHGARKGLTDTALKTADSGYLTRRLVDVAQDVIIREDDCGTDRGLTIKAIREGTEIIEPLEERLEGRYSR 849
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 850 KTIRHPETKEVIARENDLITEA---------------------------------IATQIVDAGIEEVTIRSAFTCNTKH 896
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLsefslsykkeilvrdsklgrdrlskeaqeratlLFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 897 GVCKKCYGKNLATGTEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFearnpKGQAIITEVGG 976
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEII-----NVSKNIKSPSL 235
|
250 260 270 280
....*....|....*....|....*....|....*....|....*.
gi 489829083 977 EvVSIEEGRdrqqeitiqgTDDRRSYNIPYTARLRVEEGTIVERGE 1022
Cdd:pfam04998 236 T-VYLFDEV----------GRELEKAKKVYGAIEKVTLGSVVESGE 270
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
948-1176 |
1.64e-69 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 256.08 E-value: 1.64e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 948 DITQGLPRIQEIFEARNPKGQAIITEVGGeVVSIEEGRDRQQEITIQGTDDRRS-YNIPYTARLRVEEGTIVERGEALTE 1026
Cdd:PRK02597 978 DIIQGLPRIEELLEARKPKESCILAKKPG-TVQIKYGDDESVDVKVIESDGTITeYPILPGQNVMVSDGQQVDAGEPLTD 1056
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1027 GSVDPKALIRV-----RDVL-----------SVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNILP 1090
Cdd:PRK02597 1057 GPINPHELLEIffedlRDRKglyeaalealqKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLP 1136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1091 GTLMDIHTFTEANREAILSGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKL 1170
Cdd:PRK02597 1137 GELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRL 1216
|
....*.
gi 489829083 1171 VPAGTG 1176
Cdd:PRK02597 1217 IPAGTG 1222
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
948-1180 |
7.34e-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: 240.91 E-value: 7.34e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 948 DITQGLPRIQEIFEARNPKGQAIITEVGGEVVSIEEGRDRQQEITIQGTDDRRS-YNIPYTARLRVEEGTIVERGEALTE 1026
Cdd:TIGR02388 976 DIVQGLPRIEELLEARKPKEACILAKRPGVVQVKYGTDDESVSIKVIERDGTISeYPLLPGQNIMVSDGQQVTGGEPLTD 1055
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1027 GSVDPKALIRV----------------RDVLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNILP 1090
Cdd:TIGR02388 1056 GPINPHDILDVffsyykdqdglyeaaqESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLP 1135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1091 GTLMDIHTFTEANREAILSGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKL 1170
Cdd:TIGR02388 1136 GELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRL 1215
|
250
....*....|
gi 489829083 1171 VPAGTGIGRY 1180
Cdd:TIGR02388 1216 IPAGTGFSSY 1225
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
948-1193 |
9.00e-59 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 223.26 E-value: 9.00e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 948 DITQGLPRIQEIFEARN--PKGQAIITEVGGeVVSIEEGRDRQQEITIQGTDDRRS-YNIPYTARLRVEEGTIVERGEAL 1024
Cdd:PRK09603 2642 DITGGLPRVSELFEARKpkPKDVAILSEVDG-IVSFGKPIRNKEHIIVTSKDGRSMdYFVDKGKQILVHADEFVHAGEAM 2720
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1025 TEGSVDPKALIRVRDVLSVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNILPGTLMDIHTFTEANR 1104
Cdd:PRK09603 2721 TDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENA 2800
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1105 EAILSGSQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGIGRYRKLK 1184
Cdd:PRK09603 2801 RVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNKKIV 2880
|
....*....
gi 489829083 1185 SEVIKETAE 1193
Cdd:PRK09603 2881 LRTLEDDPK 2889
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
948-1201 |
6.40e-55 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 210.18 E-value: 6.40e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 948 DITQGLPRIQEIFEARnpKGQAIitevggeVVSIEEgRDR--QQEITiqgtddrRSYNIPY----TARLrveegTIVErg 1021
Cdd:CHL00117 1130 DITQGLPKVEQLLEAR--SIDSI-------SMNLEK-RLEgwNERIT-------RILGIPWgfliGAEL-----SIAQ-- 1185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1022 ealtegsvdpkalirvrdvlsVQEYLLAEVQKVYRMQGVEIGDKHVEVMVRQMLRKIRVMDTGDTNI-LPGTLMDIHTFT 1100
Cdd:CHL00117 1186 ---------------------SQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNVfLPGELIGLLRAE 1244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1101 EANReaILSgsQPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGIGRY 1180
Cdd:CHL00117 1245 RINR--ALE--EAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGL 1320
|
250 260
....*....|....*....|....*..
gi 489829083 1181 ------RKLKSEVIKETAEVTDEITNI 1201
Cdd:CHL00117 1321 vhrskqHKNKNLEIKKKNLFEGEMRDI 1347
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
333-475 |
8.37e-52 |
|
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: 179.42 E-value: 8.37e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 333 GKRVDYSGRSVIVVGPNLKMYQCGLPKEMALELFKPFV--------MKELVGRG--------LAHNIKSAKRKIE----R 392
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpynikrLRQLVENGpnvypganYIIRINGARRDLRyqkrR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 393 MAPEIW--DVLEE-VIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEA 469
Cdd:pfam00623 81 LDKELEigDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 489829083 470 RILMLA 475
Cdd:pfam00623 161 EELMLV 166
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
221-805 |
8.81e-52 |
|
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: 196.25 E-value: 8.81e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 221 NNPSWMVLDVLPVIPPEIRPMVQLEGGRFaTSDLNDLYRRVINRNNRLKRLLDLGAPNIIVQNEKRM------------- 287
Cdd:cd01435 125 FGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLIsgktnseklinaw 203
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 288 --LQEAVDALIDNGRrgrpVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALEL 365
Cdd:cd01435 204 lqLQSAVNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 366 --------FKPFVMKELVGRGlAH---------------NIKSAKRKIERMAPEIWDVLEEVIREHP------------- 409
Cdd:cd01435 280 tfpepvtpFNVEELRQAVING-PDvypganaiededgrlILLSALSEERRKALAKLLLLLSSAKLLLngpkkvyrhlldg 358
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 410 --VLLNRAPTLHRLGIQAF-------EptlvegRAIRLHPLVCTAYNADFDGDQMAVHVPLSAEAQAEARILMLAAQNIL 480
Cdd:cd01435 359 dvVLLNRQPTLHKPSIMAHkvrvlpgE------KTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYL 432
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 481 NPKDGKPVVTPSQDMVLGNYYLTLerekavgEGTIFKDINEAQLAYQ----NGYVHLHSRIAVFAGSI--PNERFTDEQr 554
Cdd:cd01435 433 VPTDGKPLRGLIQDHVVSGVLLTS-------RDTFFTREEYQQLVYAalrpLFTSDKDGRIKLLPPAIlkPKPLWTGKQ- 504
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 555 nqlLITTvgklIFNTILPKSFPYINEPTKFNLEIETPAKYFVDTTTD----VR-----------AHIAA---------QE 610
Cdd:cd01435 505 ---VIST----ILKNLIPGNAPLLNLSGKKKTKKKVGGGKWGGGSEEsqviIRngelltgvldkSQFGAsayglvhavYE 577
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 611 LIDPFKKKILGNIIAEVFKKFhitetskmLdRMKdlGFkistkagmTVGIADILTLEE----KHEILEKAHDTVEKITKS 686
Cdd:cd01435 578 LYGGETAGKLLSALGRLFTAY--------L-QMR--GF--------TCGIEDLLLTPKadekRRKILRKAKKLGLEAAAE 638
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 687 FrrglitdderyerviavWNAAKDEIQGKLILSL--DRL------NPIFMMQDSGARGNISNFTQLAGMRG--------- 749
Cdd:cd01435 639 F-----------------LGLKLNKVTSSIIKAClpKGLlkpfpeNNLQLMVQSGAKGSMVNASQISCLLGqqelegrrv 701
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489829083 750 -LMadPSGRivELP--------------ITSNFREGLTVLEYFISTHGARKGLTDTALKTADSGYLTRRLV 805
Cdd:cd01435 702 pLM--VSGK--TLPsfppydtspraggfITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
478-663 |
2.61e-44 |
|
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: 157.79 E-value: 2.61e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 478 NILNPKDGKPVVTPSQDMVLGNYYLTLERekavgegtIFKDINEAQLAYQNGYVHLHSRIAVFAgsipNERFTdeqrnql 557
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAILKPI----KPLWT------- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 558 LITTVGKLIFNTILPKSFPYINEPtkfnLEIETPAKYFVDTTTDVRAHIAAQELIdpfkkKILGNIIAEVFKKFHITETS 637
Cdd:pfam04983 62 GKQTFSRLLPNEINPKGKPKTNEE----DLCENDSYVLINNGELISGVIDKKTVG-----KSLGSLIHIIYKEYGPEETA 132
|
170 180
....*....|....*....|....*.
gi 489829083 638 KMLDRMKDLGFKISTKAGMTVGIADI 663
Cdd:pfam04983 133 KFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
916-1176 |
4.20e-39 |
|
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: 142.94 E-value: 4.20e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 916 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFEARNPkgQAIItevggEVVSIEEGRdrqqeitiqg 995
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAASI--HEML-----EALGIEAAR---------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 996 tddrrsynipytarlrveegtivergealtegsvdpkalirvrdvlsvqEYLLAEVQKVYRMQGVEIGDKHVEVMVRQML 1075
Cdd:cd00630 64 -------------------------------------------------ETIIREIQKVLASQGVSVDRRHIELIADVMT 94
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1076 RkirvmdTGDtnilpgtlmdihtfteanreailsgsqpatgrpvLLGITKASL--ETDSFLSAASFQETTRVLTDAAIKG 1153
Cdd:cd00630 95 Y------SGG----------------------------------LRGVTRSGFraSKTSPLMRASFEKTTKHLLDAAAAG 134
|
250 260
....*....|....*....|...
gi 489829083 1154 KRDELLGLKENVILGKLVPAGTG 1176
Cdd:cd00630 135 EKDELEGVSENIILGRPAPLGTG 157
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
913-1177 |
3.06e-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: 115.04 E-value: 3.06e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 913 VEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFEARNPKGQAIIT-EVGGEVvsiEEGRDRQQEI 991
Cdd:cd06528 37 IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTPTMTiYLEEEY---KYDREKAEEV 113
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 992 T--IQGT---DDRRSYNIPY---TARLRVEEGTIVERG------------EALTEGSVDPKALIRVR--DVLSVQE-YLL 1048
Cdd:cd06528 114 ArkIEETtleNLAEDISIDLfnmRITIELDEEMLEDRGitvddvlkaiekLKKGKVGEEGDVTLIVLkaEEPSIKElRKL 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1049 AEVQKVYRMQGVEiGDKHveVMVRQM------------LRKIRVMDTGD-----TNilpgtlmDIHTF-----TEANREA 1106
Cdd:cd06528 194 AEKILNTKIKGIK-GIKR--VIVRKEedeyviytegsnLKAVLKVEGVDptrttTN-------NIHEIeevlgIEAARNA 263
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1107 IL----------------------------SGSQPATGRpvlLGItkaSLETDSFLSAASFQETTRVLTDAAIKGKRDEL 1158
Cdd:cd06528 264 IIneikrtleeqgldvdirhimlvadimtyDGEVRQIGR---HGI---AGEKPSVLARAAFEVTVKHLLDAAVRGEVDEL 337
|
330
....*....|....*....
gi 489829083 1159 LGLKENVILGKLVPAGTGI 1177
Cdd:cd06528 338 RGVIENIIVGQPIPLGTGD 356
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
913-1177 |
8.34e-26 |
|
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: 109.23 E-value: 8.34e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 913 VEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEI----------------------FEARNPKGQAI 970
Cdd:cd02736 7 VEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIinasknistpiitaklendrdeKSARIVKGRIE 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 971 ITEVGGEVVSIEEGRDRQQ---EITI--------QGTDDRRSYNIpytARLRVEEGTIVERGEALTEgsvdpKALIRVRD 1039
Cdd:cd02736 87 KTYLGEVASYIEEVYSPDDcyiLIKLdkkiieklQLSKSNLYFLL---QSLKRKLPDVVVSGIPEVK-----RAVINKDK 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1040 VLSVQEyLLAE---VQKVYRMQGVeIGDK----HVeVMVRQML-----RKIRVMDTGDTnilpgtlMDIHTFTEANREAI 1107
Cdd:cd02736 159 KKGKYK-LLVEgygLRAVMNTPGV-IGTRttsnHI-MEVEKVLgieaaRSTIINEIQYT-------MKSHGMSIDPRHIM 228
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489829083 1108 LSGSQpATGRPVLLGITKASLE--TDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGI 1177
Cdd:cd02736 229 LLADL-MTFKGEVLGITRFGIAkmKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGL 299
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
911-1177 |
7.52e-24 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 105.31 E-value: 7.52e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 911 TEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFEARNPKGQAIIT-----------EVGGEVV 979
Cdd:PRK04309 54 SLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTiylkdeyaydrEKAEEVA 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 980 -SIEE------GRD-----RQQEITIQGTDDRRSYnipytARLRVEEgtIVERGEALT--EGSVDPKALIRVRDVLSVQE 1045
Cdd:PRK04309 134 rKIEAttlenlAKDisvdlANMTIIIELDEEMLED-----RGLTVDD--VKEAIEKKKggEVEIEGNTLIISPKEPSYRE 206
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1046 YL-LAEVQKVYRMQGVEiGDKHveVMVRQ------------MLRKIRVMDTGD-----TNilpgtlmDIHTF-----TEA 1102
Cdd:PRK04309 207 LRkLAEKIRNIKIKGIK-GIKR--VIIRKegdeyviytegsNLKEVLKVEGVDatrttTN-------NIHEIeevlgIEA 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1103 NREAI----------------------------LSGSQPATGRpvlLGItkaSLETDSFLSAASFQETTRVLTDAAIKGK 1154
Cdd:PRK04309 277 ARNAIieeikntleeqgldvdirhimlvadmmtWDGEVRQIGR---HGV---SGEKASVLARAAFEVTVKHLLDAAVRGE 350
|
330 340
....*....|....*....|...
gi 489829083 1155 RDELLGLKENVILGKLVPAGTGI 1177
Cdd:PRK04309 351 VDELKGVTENIIVGQPIPLGTGD 373
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
911-1176 |
1.15e-23 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 106.43 E-value: 1.15e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 911 TEVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFEARN-PKGQAIITEVGGEVvsiEEGRDRQQ 989
Cdd:PRK14897 177 ARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKkPSTPTMTIYLKKDY---REDEEKVR 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 990 EI--TIQGTDDRRSYNI-----PYTARLRVEEGTIVERGEALTE--GSVDPKALIRV-----RDVLSVQE------YLLA 1049
Cdd:PRK14897 254 EVakKIENTTLIDVADIitdiaEMSVVVELDEEKMKERLIEYDDilAAISKLTFKTVeiddgIIRLKPQQpsfkklYLLA 333
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1050 EVQKVYRMQGVE---------IGDKHVEVMVRQMLRKIRVMDTGDTNILPGTLMDIHTFT-----EANREAIL------- 1108
Cdd:PRK14897 334 EKVKSLTIKGIKgikraiarkENDERRWVIYTQGSNLKDVLEIDEVDPTRTYTNDIIEIAtvlgiEAARNAIIheakrtl 413
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1109 ---------------------SGSQPATGRPvllGItkaSLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVIL 1167
Cdd:PRK14897 414 qeqglnvdirhimlvadmmtfDGSVKAIGRH---GI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIV 487
|
....*....
gi 489829083 1168 GKLVPAGTG 1176
Cdd:PRK14897 488 GQPITLGTG 496
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
913-1177 |
1.19e-23 |
|
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: 104.36 E-value: 1.19e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 913 VEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFEAR----------------------------- 963
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARktpstpsmtiyledeyekdrekaeevakk 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 964 ------NPKGQAIITEVGGEVVSIE------EGRD-----------------------RQQEITIQGTDDR-RSY----- 1002
Cdd:TIGR02389 121 ieatklEDVAKDISIDLADMTVIIEldeeqlKERGitvddvekaikkaklgkvieidmDNNTITIKPGNPSlKELrklke 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1003 -----------NIPY-TARLRVEEGTIVERG----EALTEGSVDPKA-----LIRVRDVLSVQ---EYLLAEVQKVYRMQ 1058
Cdd:TIGR02389 201 kiknlhikgikGIKRvVIRKEGDEYVIYTEGsnlkEVLKLEGVDKTRtttndIHEIAEVLGIEaarNAIIEEIKRTLEEQ 280
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1059 GVEIGDKHVevmvrqMLrkirvmdtgdtnilpgtLMDIHTFteanreailSGSQPATGRpvlLGITKaslETDSFLSAAS 1138
Cdd:TIGR02389 281 GLDVDIRHL------ML-----------------VADLMTW---------DGEVRQIGR---HGISG---EKASVLARAA 322
|
330 340 350
....*....|....*....|....*....|....*....
gi 489829083 1139 FQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGI 1177
Cdd:TIGR02389 323 FEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGD 361
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
314-822 |
2.22e-21 |
|
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: 100.56 E-value: 2.22e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 314 KSLSHMLKGKQgrFRQNLLGKRVDYSGRSVIVVGPNLKMYQCGLPKEMALEL-FKPFV-------MKELVGRGLAHNIKS 385
Cdd:cd10506 195 SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLtVSERVsswnrerLQEYCDLTLLLKGVI 272
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 386 AKRKIERMAP-------EIWDVLEEVIRE-HPVLLNRAPTLHRLGIQAFEPTLVE-GRAIRLHPLVCTAYNADFDGDQMA 456
Cdd:cd10506 273 GVRRNGRLVGvrshntlQIGDVIHRPLVDgDVVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRGDFDGDCLH 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 457 VHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTlerekavgEGTIFKDINEAQlayqngyvhlhsR 536
Cdd:cd10506 353 GYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMT--------ERGVFLDKAQMQ------------Q 412
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 537 IAVFAGSI--PNERFTDEQRNQLLITtvGKLIFNTILPKSFPYinEPTKFNLEIETpakyfvdtttdvrahiaaQELIDP 614
Cdd:cd10506 413 LQMLCPSQlpPPAIIKSPPSNGPLWT--GKQLFQMLLPTDLDY--SFPSNLVFISD------------------GELISS 470
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 615 FKK----KILGNIIAEVFKKFHITETSKMLDRMKDLGFKISTKAGMTVGIADILT----------LEEKHEILEKAHDTV 680
Cdd:cd10506 471 SGGsswlRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLssdsysrqkmIEEISLGLREAEIAC 550
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 681 EK---ITKSFRRGLITDDERY------ERVI-------AVWNAAKDEIQGKL--ILSL-----DRLNPIFMMQDSGARGN 737
Cdd:cd10506 551 NIkqlLVDSRKDFLSGSGEENdvssdvERVIyerqksaALSQASVSAFKQVFrdIQNLvykyaSKDNSLLAMIKAGSKGS 630
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 738 ISNFTQLAGMRGL----------------------------MADPSGRIVELPIT-----SNFREGLTVLEYFISTHGAR 784
Cdd:cd10506 631 LLKLVQQSGCLGLqlslvklsyriprqlscaawnsqksprvIEKDGSECTESYIPygvveSSFLDGLNPLECFVHSITSR 710
|
570 580 590
....*....|....*....|....*....|....*....
gi 489829083 785 KGLTDtalKTAD-SGYLTRRLVDVAQDVIIREDdcGTDR 822
Cdd:cd10506 711 DSSFS---SNADlPGTLFRKLMFFMRDIYVAYD--GTVR 744
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
692-768 |
4.24e-20 |
|
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 86.65 E-value: 4.24e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 692 ITDDERYERVIAVWNAAKDEIQGKLIL----------------SLDRLNPIFMMQDSGARGNISNFTQLAGMRGLMADPS 755
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINnilnkardpagniaskSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 489829083 756 GRIV---------------ELPITSNFR 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 ... |
916-1177 |
5.80e-17 |
|
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: 84.56 E-value: 5.80e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 916 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEIFE-ARNPKGQAIITEVGGEVVSIEEG----RDRQQE 990
Cdd:cd02584 27 GEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINvAKNIKTPSLTVYLEPGFAKDEEKakkiQSRLEH 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 991 IT---------------IQGT---DDR---RSYNI------------PYTARLRVEEGTIVERGeaLTEGSV-------- 1029
Cdd:cd02584 107 TTlkdvtaateiyydpdPQNTvieEDKefvESYFEfpdedveqdrlsPWLLRIELDRKKMTDKK--LSMEQIakkikeef 184
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1030 ------------DPKALIRVRDVLS-VQEYLLAEVQKVYR-----------MQGVEIGDKHV-----EVMV---RQMLRK 1077
Cdd:cd02584 185 kddlnvifsddnAEKLVIRIRIINDdEEKEEDSEDDVFLKkiesnmlsdmtLKGIEGIRKVFireenKKKVdieTGEFKK 264
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1078 IR--VMDTGDTN---ILPGTLMD-IHTFT------------EANREAIL---------SGS-----------QPATGRPV 1119
Cdd:cd02584 265 REewVLETDGVNlreVLSHPGVDpTRTTSndiveifevlgiEAARKALLkelrnvisfDGSyvnyrhlallcDVMTQRGH 344
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1120 LLGITKASL-ETD-SFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTGI 1177
Cdd:cd02584 345 LMAITRHGInRQDtGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
913-959 |
4.67e-14 |
|
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: 74.54 E-value: 4.67e-14
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 489829083 913 VEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGLPRIQEI 959
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREI 53
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
932-1176 |
4.81e-13 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 73.77 E-value: 4.81e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 932 TQLTMRTFHTGGVAGDDITQGLPRIQEIFEARNPKGQAIIT-----EVGGEVVSIEEGRDRQQEITIQGTDDRRSYNIpY 1006
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTvhlkgEYATDREKAEEVAKKIESLTLGDVATSIAIDL-W 619
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1007 TARLRVE--EGTIVERG-------EAL---------TEGSV------DP--KALI-RVRDVLSVQEYLLAEVQKVY-RMQ 1058
Cdd:PRK14898 620 TQSIKVEldEETLADRGltiesveEAIekklgvkidRKGTVlylkpkTPsyKALRkRIPKIKNIVLKGIPGIERVLvKKE 699
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489829083 1059 GVEIGDKHVEVMVRQMLR---KIRVMDTGDTniLPGTLMDIHTF--TEANREAILSGSQ--------------------- 1112
Cdd:PRK14898 700 EHENDEEYVLYTQGSNLRevfKIEGVDTSRT--TTNNIIEIQEVlgIEAARNAIINEMMntleqqglevdirhlmlvadi 777
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489829083 1113 -PATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLGLKENVILGKLVPAGTG 1176
Cdd:PRK14898 778 mTADGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
911-936 |
7.46e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.73 E-value: 7.46e-04
10 20
....*....|....*....|....*.
gi 489829083 911 TEVEVGEAVGIIAAQSIGEPGTQLTM 936
Cdd:PRK14898 52 ALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
