|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-1194 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2334.30 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 3 DVNK--FDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCDRCGV 80
Cdd:PRK00566 1 DVNKqdFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 81 EVTKAKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTALEKKQLLTEREYREKRD 160
Cdd:PRK00566 81 EVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 161 QYGQGFKASMGADAIRTLLRDVDLEKECAELKEELRE-ATGQKRTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIPPDLR 239
Cdd:PRK00566 161 EYGDEFVAKMGAEAIKELLKNIDLEAEAEELREELKEtGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 240 PMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHM 319
Cdd:PRK00566 241 PLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDM 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 320 LKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDEDIWD 399
Cdd:PRK00566 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 400 VVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHI 479
Cdd:PRK00566 401 VLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 480 LAPKDGKPIISPSQDMTIGNYYLSIEEANREGEGMIFKDINEIRTAYQNGYVHLHTRVGLQTDclvaqgkpfsdwqKDRI 559
Cdd:PRK00566 481 LSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRIT-------------SKKL 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 560 LVTTVGKVFFNEILPEDFIYLNEPTqenltkatpdkyflepgqdihaflaaqelvaPFKSGFLADIIAEVYKEYKVTATA 639
Cdd:PRK00566 548 VETTVGRVIFNEILPEGLPFINVNK-------------------------------PLKKKEISKIINEVYRRYGLKETV 596
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 640 ELLDRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNAKDEIQAKLV 719
Cdd:PRK00566 597 IFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMM 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 720 E----DVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMTDTALK 795
Cdd:PRK00566 677 KnlskDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALK 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 796 TADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLYDRILGRYAMKTVKNPETGEVIVPADTMMNEKLA 875
Cdd:PRK00566 757 TADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIA 836
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 876 QAVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVaggdDITQG 955
Cdd:PRK00566 837 DKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV----DITGG 912
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 956 LPRVQEIFEARNPKGRATITEVTGVVDSIEENPAERTKEITiSGKTDTRTYNLPYTAVLSVAEGDEVVRGQALTIGSVDP 1035
Cdd:PRK00566 913 LPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVIT-PDDGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDP 991
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1036 KELIKVRDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQNAKTVISGG 1115
Cdd:PRK00566 992 HDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGK 1071
|
1130 1140 1150 1160 1170 1180 1190
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 428147636 1116 VPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTGMKKYRDIQPEEVGA 1194
Cdd:PRK00566 1072 EPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVD 1150
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
9-1186 |
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: 1914.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 9 SMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCDRCGVEVTKAKVR 88
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 89 RERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTALEKKQLLTEREYREKRDQYGQGFKA 168
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 169 SMGADAIRTLLRDVDLEKECAELKEELREATG-QKRTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIPPDLRPMVQLEGG 247
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSdQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 248 RFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRF 327
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 328 RQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDEDIWDVVEDVIKE 407
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 408 HPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKP 487
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 488 IISPSQDMTIGNYYLSIEEANREGEGMIFKDINEIRTAYQNGYVHLHTRVGLQTdclvaqgkpfsdwqKDRILVTTVGKV 567
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRT--------------SGEILETTVGRV 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 568 FFNEILPEDFIYLNEPTqenltkatpdkyflepgqdihaflaaqelvaPFKSGFLADIIAEVYKEYKVTATAELLDRMKD 647
Cdd:TIGR02386 547 IFNEILPEGFPYINDNE-------------------------------PLSKKEISSLIDLLYEVHGIEETAEMLDKIKA 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 648 LGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNAKDEIQAKLVE----DVD 723
Cdd:TIGR02386 596 LGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKllkkDTY 675
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 724 PSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMTDTALKTADSGYLT 803
Cdd:TIGR02386 676 KFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLT 755
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 804 RRLVDVAQDVIVREFDCHTDRGLEVSAIMEGN-QMVEPLYDRILGRYAMKTVKNPETGEVIVPADTMMNEKLAQAVIDAG 882
Cdd:TIGR02386 756 RRLVDVAQDVVVREEDCGTEEGIEVEAIVEGKdEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSG 835
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 883 VKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAG-GDDITQGLPRVQE 961
Cdd:TIGR02386 836 IEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGaSGDITQGLPRVKE 915
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 962 IFEARNPKGRATITEVTGVVDSIEENPAERTKEITISGKTDTRTYNLPYTAVLSVAEGDEVVRGQALTIGSVDPKELIKV 1041
Cdd:TIGR02386 916 LFEARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRI 995
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1042 RDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQNAKTVISGGVPATAR 1121
Cdd:TIGR02386 996 KGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAI 1075
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 428147636 1122 PVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTGMKKYRD 1186
Cdd:TIGR02386 1076 PQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYKE 1140
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-1202 |
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: 1611.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1 MIDVNKFDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCDRCGV 80
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 81 EVTKAKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTALEKKQLLTEREYREKRD 160
Cdd:COG0086 81 EVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 161 QYGQGFKASMGADAIRTLLRDVDLEKECAELKEELREATG-QKRTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIPPDLR 239
Cdd:COG0086 161 EYGDEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSeQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 240 PMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHM 319
Cdd:COG0086 241 PLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDM 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 320 LKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDEDIWD 399
Cdd:COG0086 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 400 VVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHI 479
Cdd:COG0086 401 ILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 480 LAPKDGKPIISPSQDMTIGNYYLSIEEANREGEGMIFKDINEIRTAYQNGYVHLHTRVGLQTdclvaqgkPFSDWQKDRI 559
Cdd:COG0086 481 LSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRI--------TEDGEQVGKI 552
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 560 LVTTVGKVFFNEILPEDFIYLNEptqenltkatpdkyflepgqdihaflaaqelvaPFKSGFLADIIAEVYKEYKVTATA 639
Cdd:COG0086 553 VETTVGRYLVNEILPQEVPFYNQ---------------------------------VINKKHIEVIIRQMYRRCGLKETV 599
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 640 ELLDRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNAKDEIQAKLV 719
Cdd:COG0086 600 IFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLM 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 720 EDVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMTDTALKTADS 799
Cdd:COG0086 680 AAFSSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADS 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 800 GYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLYDRILGRYAMKTVKNPETGEVIVPADTMMNEKLAQAVI 879
Cdd:COG0086 760 GYLTRRLVDVAQDVIVTEEDCGTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIE 839
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 880 DAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAGGDDITQGLPRV 959
Cdd:COG0086 840 EAGIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAK 919
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 960 QEIFEARNPKGRATITEVTGVVDSIEEnpaerTKEITISGKTDTRTYNLPYTAVLSVAEGDEVVRGQALTIGSVDPKELI 1039
Cdd:COG0086 920 AGGIVRLNNLKVVVNEEGKGVVVSRNS-----ELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPII 994
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1040 KVRDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQNAKTVISGGVPAT 1119
Cdd:COG0086 995 EEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVV 1074
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1120 ARPVLLGITKASLETnsfLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTGMKKYRDIQPEEVGAVSKSV 1199
Cdd:COG0086 1075 LGDGVAIGVGAAIAR---IPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPI 1151
|
...
gi 428147636 1200 YSI 1202
Cdd:COG0086 1152 EEE 1154
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
3-1187 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1438.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 3 DVNKFDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCDRCGVEV 82
Cdd:PRK14906 5 DVTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 83 TKAKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTA------------------- 143
Cdd:PRK14906 85 TRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITSVDKEAreedaddlrdelaadleel 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 144 -------------------------------------------------------------------LEKKQLLT-EREY 155
Cdd:PRK14906 165 daerdrlieatrrlsvdyvpeddefvddigdderltaeevraevadiyeeynerkalrreafdafmqIEPKQLISdEALY 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 156 REKRDQYGQGFKASMGADAIRTLLRDVDLEKECAELKEELREATGQKRTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIP 235
Cdd:PRK14906 245 REMRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 236 PDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKS 315
Cdd:PRK14906 325 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKS 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 316 LSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDE 395
Cdd:PRK14906 405 LADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 396 DIWDVVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLA 475
Cdd:PRK14906 485 YVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLS 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 476 AHHILAPKDGKPIISPSQDMTIGNYYLSIEEANREGEGMIFKDINEIRTAYQ-NGYVHLHTRVGLQTDCLVAQGKPFSDW 554
Cdd:PRK14906 565 SNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDaRADLDLQAKIVVRLSRDMTVRGSYGDL 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 555 QK----DRIlVTTVGKVFFNEILPEDFIYLNeptqenltkatpdkYFLEPGQdihaflaaqelvapfksgfLADIIAEVY 630
Cdd:PRK14906 645 EEtkagERI-ETTVGRIIFNQVLPEDYPYLN--------------YKMVKKD-------------------IGRLVNDCC 690
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 631 KEYKVTATAELLDRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNA 710
Cdd:PRK14906 691 NRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEA 770
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 711 KDEIQAKLVEDVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMT 790
Cdd:PRK14906 771 TEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLV 850
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 791 DTALKTADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLydriLGRYAMKTVKNPEtGEVIVPADTMM 870
Cdd:PRK14906 851 DTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDPN-GEVLLSAGDYI 925
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 871 NEKLA-QAVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAgG 949
Cdd:PRK14906 926 ESMDDlKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA-G 1004
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 950 DDITQGLPRVQEIFEARNPKGRATITEVTGVvdsIEENPAERTKEITISGKTD-TRTYNLPYTAVL--SVAEGDEVVRGQ 1026
Cdd:PRK14906 1005 DDITQGLPRVAELFEARKPKGEAVLAEISGT---LQITGDKTEKTLTIHDQDGnSREYVVSARVQFmpGVEDGVEVRVGQ 1081
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1027 ALTIGSVDPKELIKVRDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQ 1106
Cdd:PRK14906 1082 QITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDT 1161
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1107 NAKTVISGGVPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTGMKKYRD 1186
Cdd:PRK14906 1162 ANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLSRYRD 1241
|
.
gi 428147636 1187 I 1187
Cdd:PRK14906 1242 V 1242
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
5-819 |
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: 1252.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 5 NKFDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCDRCGVEVTK 84
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 85 AKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFasyvvtdpgdtalekkqlltereyrekrdqygq 164
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 165 gfkasmgadairtllrdvdlekecaelkeelreatgqkrtravrrldILEAFLTSGNKPEWMVMDTIPVIPPDLRPMVQL 244
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 245 EGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQ 324
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 325 GRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDEDIWDVVEDV 404
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 405 IKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKD 484
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 485 GKPIISPSQDMTIGNYYLSIEEANREGEGMIFkdineirtayqngyvhlhtrvglqtdclvaqgkpfsdwqkdrilvTTV 564
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEGIIE---------------------------------------------TTV 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 565 GKVFFNEILPEDFIYLNEptqenltkatpdkyflepgqdihaflaaqelvaPFKSGFLADIIAEVYKEYKVTATAELLDR 644
Cdd:cd01609 436 GRVIFNEILPEGLPFINK---------------------------------TLKKKVLKKLINECYDRYGLEETAELLDD 482
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 645 MKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNAKDEIQAKLVEDVD- 723
Cdd:cd01609 483 IKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDk 562
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 724 -PSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMTDTALKTADSGYL 802
Cdd:cd01609 563 dPFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYL 642
|
810
....*....|....*..
gi 428147636 803 TRRLVDVAQDVIVREFD 819
Cdd:cd01609 643 TRRLVDVAQDVIVTEED 659
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-1185 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1084.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 7 FDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCDRCGVEVTKAK 86
Cdd:PRK14844 1448 FNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSK 1527
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 87 VRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTALEKKQLLTEREYREKRDQYG-QG 165
Cdd:PRK14844 1528 VRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGiDS 1607
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 166 FKASMGADAIRTLLRDVDLEKECAELKEELRE-ATGQKRTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIPPDLRPMVQL 244
Cdd:PRK14844 1608 FVAMQGVEAIRELLTRLDLHEIRKDLRLELESvASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSL 1687
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 245 EGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLK-SLSHMLKGK 323
Cdd:PRK14844 1688 ESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLKGK 1767
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 324 QGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDEDIWDVVED 403
Cdd:PRK14844 1768 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEE 1847
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 404 VIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPK 483
Cdd:PRK14844 1848 VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPS 1927
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 484 DGKPIISPSQDMTIGNYYLSIEEAnREGEGMIFKDINEIRTAYQNGYVHLHTRVGLQTDCLVAQGKpfsdwQKDRILVTT 563
Cdd:PRK14844 1928 NGRPIIVPSKDIVLGIYYLTLQEP-KEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSSGE-----THYKTICTT 2001
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 564 VGKVFFNEILPEdfiylneptQENLtkatpdkyflepGQD-IHAFLAAQELVApfksgfladIIAEVYKEYKVTATAELL 642
Cdd:PRK14844 2002 PGRLILWQIFPK---------HENL------------GFDlINQVLTVKEITS---------IVDLVYRNCGQSATVAFS 2051
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 643 DRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNAKDEIQAKLVEDV 722
Cdd:PRK14844 2052 DKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAI 2131
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 723 D------PSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMTDTALKT 796
Cdd:PRK14844 2132 SiydgnsKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKT 2211
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 797 ADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLYDRILGRYAMKTVKNPETGEVIVPADTMMNEKLAQ 876
Cdd:PRK14844 2212 ANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVK 2291
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 877 AVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVA--------- 947
Cdd:PRK14844 2292 QINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMtrgvessni 2371
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 --------------------------------------------------------------------------------
Cdd:PRK14844 2372 iasinakiklnnsniiidkngnkivisrscevvlidslgseklkhsvpygaklyvdeggsvkigdkvaewdpytlpiite 2451
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 --------------------------------------------------------------------------------
Cdd:PRK14844 2452 ktgtvsyqdlkdgisitevmdestgisskvvkdwklysgganlrprivllddngkvmtlasgveacyfipigavlnvqdg 2531
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 948 ----GGD-------------DITQGLPRVQEIFEARNPKGRATITEVTGVVDSIEENpaERTKEITISGKTDTRTYNLPY 1010
Cdd:PRK14844 2532 qkvhAGDvitrtpresvktrDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSEKD--RRGKRSILIKPVDEQISPVEY 2609
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1011 TAVLS----VAEGDEVVRGQALTIGSVDPKELIKVRDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMD 1086
Cdd:PRK14844 2610 LVSRSkhviVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITD 2689
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1087 PGETDLLPGILMDIDQFKDQNAKTVISGGVPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLK 1166
Cdd:PRK14844 2690 PGDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLK 2769
|
1370 1380
....*....|....*....|.
gi 428147636 1167 ENVIIGKIIPAGTG--MKKYR 1185
Cdd:PRK14844 2770 ENVIVGRLIPAGTGliMNKVR 2790
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-947 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1059.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 7 FDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGV-VCDRCGVEVTKA 85
Cdd:PRK09603 1396 FSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVAITHS 1475
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 86 KVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTALE--------KKQLLTEREYRE 157
Cdd:PRK09603 1476 KVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDnegtklvmKYDILNEEQYQN 1555
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 158 KRDQY-GQGFKASMGADAIRTLLRDVDLEKECAELKEELREATGQ-KRTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIP 235
Cdd:PRK09603 1556 ISRRYeDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDaKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLP 1635
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 236 PDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKS 315
Cdd:PRK09603 1636 PDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKS 1715
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 316 LSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKRKIDRRDE 395
Cdd:PRK09603 1716 LSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSN 1795
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 396 DIWDVVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLA 475
Cdd:PRK09603 1796 EVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLS 1875
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 476 AHHILAPKDGKPIISPSQDMTIGNYYLSIEEANREGEGMIFKDINEIRTAYQNGYVHLHTRVGLQTDclvaqgkpfsdwq 555
Cdd:PRK09603 1876 SMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ------------- 1942
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 556 kDRILVTTVGKVFFNEILPeDFIYLNEPTQenltkatpdkyflepgqdihaflaaqelvaPFKSGFLADIIAEVYKEYKV 635
Cdd:PRK09603 1943 -GNIIATSAGRMIIKSILP-DFIPTDLWNR------------------------------PMKKKDIGVLVDYVHKVGGI 1990
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 636 TATAELLDRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDERYNRVISIWNNAKD--- 712
Cdd:PRK09603 1991 GITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDkms 2070
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 713 -EIQAKLVEDVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLEMFISTHGARKGMTD 791
Cdd:PRK09603 2071 kEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLAD 2150
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 792 TALKTADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLYDRILGRYAMKTVKNPETGEVIVPADTMMN 871
Cdd:PRK09603 2151 TALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLID 2230
|
890 900 910 920 930 940 950
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 428147636 872 EKLAQAVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVA 947
Cdd:PRK09603 2231 EEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTA 2306
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
5-575 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 836.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 5 NKFDSMQIGLASSDKIRQWS---------YGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVC 75
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 76 DRCGVEVTKAKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGD-TALEKKQLLTERE 154
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNhKNLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 155 YREKRDQ-YGQGFK------ASMGADAIRTLLRDVDLEKECAELKEELREATGQKRTRAVRRLDILEAFLTSGNKPEWMV 227
Cdd:PRK02625 167 WLEIEDQiYAEDSElegeevVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMV 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 228 MDTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTG 307
Cdd:PRK02625 247 LDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVG 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 308 PGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAK 387
Cdd:PRK02625 327 ANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAK 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 388 RKIDRRDEDIWDVVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQA 467
Cdd:PRK02625 407 KLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQA 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 468 ESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEEANRE-GEGMIFKDINEIRTAYQNGYVHLHTRVGLQTDCLVA 546
Cdd:PRK02625 487 EARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQkGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNGEVE 566
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*.
gi 428147636 547 QGKPFSD---------------WQKDRI------------LVTTVGKVFFNEILPE 575
Cdd:PRK02625 567 DDDEDTEplktetledgtrieqYRYRRDrfdedgnlisqyILTTVGRVIMNKTIQD 622
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
6-579 |
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: 811.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 6 KFDSMQIGLASSDKIRQWS---------YGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIRYKGVVCD 76
Cdd:TIGR02387 1 RFDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 77 RCGVEVTKAKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYFASYVVTDPGDTA-LEKKQLLTEREY 155
Cdd:TIGR02387 81 RCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKnLKYKQLLTEDQW 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 156 REKRDQ-YGQGFK------ASMGADAIRTLLRDVDLEKECAELKEELREATGQKRTRAVRRLDILEAFLTSGNKPEWMVM 228
Cdd:TIGR02387 161 LEIEDQiYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 229 DTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGP 308
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 309 GNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFVMRELVKRDMASNIKNAKR 388
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 389 KIDRRDEDIWDVVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAE 468
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 469 SRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEEANRE-GEGMIFKDINEIRTAYQNGYVHLHTRVGLQTDCLVAQ 547
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEkGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVET 560
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*....
gi 428147636 548 GKPFSD---------------WQKDRI------------LVTTVGKVFFNEILPEDFIY 579
Cdd:TIGR02387 561 NDPLDEpiksedlsdgtrieqWTYRRDrfdedgalisqyILTTTGRIIMNHTIIEALVA 619
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-575 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 798.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1 MIDVNKFDSMQIGLASSDKIRQWSY---------GEVKKPETINYRTLKPERDGLFDERIFGPSKDWECACGKYKRIR-- 69
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGde 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 70 -YKGVVCDRCGVEVTKAKVRRERMGHIELAAPVTHIWYFKGIPSRMGLVLDMSPRALEEIIYF-ASYVVTDP-GDTALEK 146
Cdd:CHL00018 81 kEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCdFSFARPIAkKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 147 KQLLTE----REYREKRDQYGQGFKA------SMGADAIRTLLRDVDLEK-------ECAELKEELREAT-------GQK 202
Cdd:CHL00018 161 RGLFEYeiqsWKYSIPLFFSTQGFDTfrnreiSTGAGAIREQLADLDLRIiidnslvEWKELGEEGSTGNewedrkiGRR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 203 RTRAVRRLDILEAFLTSGNKPEWMVMDTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLH--APGII 280
Cdd:CHL00018 241 KDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGEL 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 281 VQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHE 360
Cdd:CHL00018 321 VMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPRE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 361 MALELFKPFVMRELVKRDMASNIKNAKRKIDRRDEDIWDVVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHP 440
Cdd:CHL00018 401 IAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 441 LVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEE-----ANREGEGM- 514
Cdd:CHL00018 481 LVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNrrgiyANRYNPCNr 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 515 -------IFKDINEIRTAYQNGYVHLHT----RVGLQTDCLVAQGKP--------------FSDWQ-----KDRILV--- 561
Cdd:CHL00018 561 knstkepYFSNSYDALGAYRQKRINLDSplwlRWRLDQRIIASREVPievqyeslgtyheiYEHYLivksrKKEILSiyi 640
|
650
....*....|....*
gi 428147636 562 -TTVGKVFFNEILPE 575
Cdd:CHL00018 641 rTTVGRILFNREIEE 655
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
15-817 |
1.14e-163 |
|
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: 497.34 E-value: 1.14e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 15 ASSDKIRQWSYGEVKKPETINYRTLKPERDGlfderifgpskdwecacgKYKRIRYKGVVCDRCGVEVTKAKVRRERMGH 94
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 95 IELAAPVTHIWYFKGIPSRMGlvldmspraleeiiyfasyvvtdpgdtalekkqlltereyrekrdqygqgfkasmgada 174
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 175 irtllrdvdlekecaelkeelreatgqkrtravrrldileafltsgnkPEWMVMDTIPVIPPDLRPMVqleggrfatsdl 254
Cdd:cd00399 84 ------------------------------------------------PEWMILTCLPVPPPCLRPSV------------ 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 255 ndlyrrvinrnnrlkrlldlhapgiIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGK 334
Cdd:cd00399 104 -------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGK 158
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 335 RVDYSGRSVIDVGPKLRLTQMGLPHEMALELfkpfvmrelvkrdmasniknakrkidrrdediwdvvedviKEHPVLLNR 414
Cdd:cd00399 159 RVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFNR 198
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 415 APTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQD 494
Cdd:cd00399 199 QPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQD 278
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 495 MTIGNYYLsieeanregegmifkdineirtayqngyvhlhtrvglqtdclvaqgkpfsdwqkdrilvtTVGKVFFNEILP 574
Cdd:cd00399 279 TLLGAYLL------------------------------------------------------------TLGKQIVSAALP 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 575 EDFIYLneptqenltkatpdkyflepgqdihaflaaqelvapfksgfladiiaeVYKEYKVTATAELLDRMKDLGYYEST 654
Cdd:cd00399 299 GGLLHT------------------------------------------------VTRELGPEKAAKLLSNLQRVGFVFLT 330
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 655 KSGLTVGIADITDL----KEKPEIIANARHKVEQVAKQFRRGLITDDER-------YNRVISIWNNAKDEI-QAKLVED- 721
Cdd:cd00399 331 TSGFSVGIGDVIDDgvipEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAgSAASVNLd 410
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 722 -VDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKT--------------------MELPILSNFREGLSVLEMFI 780
Cdd:cd00399 411 lVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFF 490
|
810 820 830
....*....|....*....|....*....|....*..
gi 428147636 781 STHGARKGMTDTALKTADSGYLTRRLVDVAQDVIVRE 817
Cdd:cd00399 491 HAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHY 527
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
224-500 |
2.25e-153 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 461.22 E-value: 2.25e-153
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 224 EWMVMDTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNG--RR 301
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 302 GRPVTGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFV--------MRE 373
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIvtplnidkLRK 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 374 LVK----------RDMASNIKNAKR-KIDRRDEDIWDVVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLV 442
Cdd:smart00663 158 LVRngpngakyiiRGKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 428147636 443 CTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNY 500
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
620-1028 |
2.33e-112 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 382.42 E-value: 2.33e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 620 GFLADIIAEVYKEYKVTATAELLDRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDER 699
Cdd:PRK02597 11 KALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEVER 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 700 YNRVISIWNNAKDEiqakLVEDV-------DPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREG 772
Cdd:PRK02597 91 FQKVIDTWNETNER----LKDEVvknfrqnDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREG 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 773 LSVLEMFISTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLYDRILGRYAMK 852
Cdd:PRK02597 167 LTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLGDRLLGRVLAE 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 853 TVKNPEtGEVIVPADTMMNEKLAQAVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEP 932
Cdd:PRK02597 247 DVVDPE-GEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEP 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 933 GTQLTMRNFHQGGVAGGD---------DITQGLPRVQEIFEARNPKG-RATITEVTGvvdsieenpaerTKEITISGKTD 1002
Cdd:PRK02597 326 GTQLTMRTFHTGGVFTGEvarqvrspfAGTVEFGKKLRTRPYRTRHGvEALQAEVDF------------DLVLKPSGKGK 393
|
410 420
....*....|....*....|....*.
gi 428147636 1003 TRTYNLPYTAVLSVAEGDEVVRGQAL 1028
Cdd:PRK02597 394 PQKIEITQGSLLFVDDGQTVEADQLL 419
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
13-819 |
2.19e-110 |
|
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: 366.57 E-value: 2.19e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 13 GLASSDKIRQWSYGEVKKPETINYRTLkPERDGLFDERiFG---PskdwecacgkykrirykGVVCDRCGvevTKAKVRR 89
Cdd:cd02582 10 GLLSPEEIRKMSVVEIITPDTYDEDGY-PIEGGLMDPR-LGvieP-----------------GLRCKTCG---NTAGECP 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 90 ERMGHIELAAPVTHIWYFKGIPSrmglVLDMSPRALEEIIyfasyvVTDPgdtalEKKQLLTEREYREKRDQYGQGfkas 169
Cdd:cd02582 68 GHFGHIELARPVIHVGFAKHIYD----LLRATCRSCGRIL------LPEE-----EIEKYLERIRRLKEKWPELVK---- 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 170 mgaDAIRTLLRDVDLEKECAELKEELREATGQKRTR-------AVRRL------DILE----------AFLTSGNKPEWM 226
Cdd:cd02582 129 ---RVIEKVKKKAKKRKVCPHCGAPQYKIKLEKPTTfyeekeeGEVKLtpseirERLEkipdedlellGIDPKTARPEWM 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 227 VMDTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPV- 305
Cdd:cd02582 206 VLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPa 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 306 ---TGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFV--------MREL 374
Cdd:cd02582 286 rhrSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERvtewniekMRKL 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 375 VKR-----DMASN-IKNAKRKIDRRDEDIWDVVE-----DVIKEH-----PVLLNRAPTLHRLGIQAFEPVLVSGKSMRL 438
Cdd:cd02582 363 VLNgpdkwPGANYvIRPDGRRIRLRYVNREELAErlepgWIVERHlidgdIVLFNRQPSLHRMSIMAHRVRVLPGKTFRL 442
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 439 HPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEEANREGEGMIFkd 518
Cdd:cd02582 443 NLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQ-- 520
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 519 ineirtayqngyvhlhtrvglqtdcLVAQGKPFSDWQKDRI-----LVTtvGKVFFNEILPEDFIY-----LNEPTQENL 588
Cdd:cd02582 521 -------------------------LLSAAGYDGLLPEPAIlepkpLWT--GKQLFSLFLPKDLNFegkakVCSGCSECK 573
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 589 TKATP-DKYFL-EPGQDIHAFLaAQELVAPFKSGFLADIIAevyKEYKVTATAELLDRMKDLGYYESTKSGLTVGIADIT 666
Cdd:cd02582 574 DEDCPnDGYVViKNGKLLEGVI-DKKAIGAEQPGSLLHRIA---KEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDED 649
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 667 ----DLKEKPEIIANARHKVEQVAKQFRRGLI------TDDE-RYNRVISIWNNAKDEIQAKLVEDVDPSNPIQMMSDSG 735
Cdd:cd02582 650 ipeeARKEIEEIIKEAEKKVYELIEQYKNGELeplpgrTLEEtLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTG 729
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 736 ARGNISNFTQLSGMRGLMAAPNGKTME------LP--------------ILSNFREGLSVLEMFISTHGARKGMTDTALK 795
Cdd:cd02582 730 ARGSMLNLTQMAACLGQQSVRGERINRgyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGREGLVDTAVR 809
|
890 900
....*....|....*....|....
gi 428147636 796 TADSGYLTRRLVDVAQDVIVrEFD 819
Cdd:cd02582 810 TSQSGYMQRRLINALQDLYV-EYD 832
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
625-946 |
3.13e-107 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 368.50 E-value: 3.13e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 625 IIAEVYKEYKVTATAELLDRMKDLGYYESTKSGLTVGIaDitDLKEKP---EIIANARHKVEQVAKQFRRGLITDDERYN 701
Cdd:CHL00117 22 LISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGI-D--DLLTPPskgWLVQDAEQQSLILEKHYHYGNVHAVEKLR 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 702 RVISIWNNA----KDEIQAKLVEdVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVLE 777
Cdd:CHL00117 99 QSIEIWYATseylKQEMNPNFRM-TDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQSNFREGLSLTE 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 778 MFISTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAiMEGNQMVEPLYDRILGRYAMKTVKNp 857
Cdd:CHL00117 178 YIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSP-RNGMMIERILIQTLIGRVLADDIYI- 255
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 858 eTGEVIVPADTMMNEKLAQAVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLT 937
Cdd:CHL00117 256 -GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIAGQSIGEPGTQLT 334
|
....*....
gi 428147636 938 MRNFHQGGV 946
Cdd:CHL00117 335 LRTFHTGGV 343
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
620-1029 |
1.26e-106 |
|
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: 364.56 E-value: 1.26e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 620 GFLADIIAEVYKEYKVTATAELLDRMKDLGYYESTKSGLTVGIADITDLKEKPEIIANARHKVEQVAKQFRRGLITDDER 699
Cdd:TIGR02388 10 KALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGEITEVER 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 700 YNRVISIWNNAKDEIQAKLV---EDVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMAAPNGKTMELPILSNFREGLSVL 776
Cdd:TIGR02388 90 FQKVIDTWNGTNEELKDEVVnnfRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTVT 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 777 EMFISTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEpLYDRILGRYAMKTVKN 856
Cdd:TIGR02388 170 EYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKIS-LGDRLLGRLVAEDVLH 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 857 PEtGEVIVPADTMMNEKLAQAVIDAGVKTVTIRSVFTCNTRHGVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQL 936
Cdd:TIGR02388 249 PE-GEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGTQL 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 937 TMRNFHQGGVAGGD---------DITQGLPRVQEIFEARNPKGR-ATITEVTGVVDSIEENpaertkeitiSGKTDTRTY 1006
Cdd:TIGR02388 328 TMRTFHTGGVFTGEvarqvrskiDGTVEFGKKLRTRGYRTRHGEdAKQVEVAGLLIIKPTG----------SITNKAQEI 397
|
410 420
....*....|....*....|...
gi 428147636 1007 NLPYTAVLSVAEGDEVVRGQALT 1029
Cdd:TIGR02388 398 EVTQGSLLFVEDGQTVDAGQLLA 420
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
915-1181 |
9.10e-106 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 331.41 E-value: 9.10e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 915 VEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAGgdDITQGLPRVQEIFEARNpkgratitevtgvvdsieenpaertke 994
Cdd:cd02655 3 VELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT--DITQGLPRVEELFEARK--------------------------- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 995 itisgktdtrtynlpytavlsvaegdevvrgqaltigsVDPKELIKVRD--VLTTENYILREIQKVYRMQGVDISDKHVE 1072
Cdd:cd02655 54 --------------------------------------INPHDLLRIKFlgPEAVQKYLVEEIQKVYRSQGVNINDKHIE 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1073 VMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQNAKTVISGGVPATARPVLLGITKASLETNSFLSAASFQETTRVLTD 1152
Cdd:cd02655 96 IIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTE 175
|
250 260
....*....|....*....|....*....
gi 428147636 1153 AAIRGKNDPLVGLKENVIIGKIIPAGTGM 1181
Cdd:cd02655 176 AAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
5-331 |
5.17e-105 |
|
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: 334.26 E-value: 5.17e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 5 NKFDSMQIGLASSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIFGPSKDWECA-CGKYKRirykgvvcdRCGVevt 83
Cdd:pfam04997 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGKKKK---------DCPG--- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 84 kakvrreRMGHIELAAPVTHIWYFKgipsrmglvldMSPRALEEIIYFASYVVTDPGdtaleKKQLLTEREYREKRDQYG 163
Cdd:pfam04997 70 -------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENLK 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 164 QGFKAsmgadaIRTLLRDVDL------------------EKECAELKEELR---EATGQKRTRAVRRLDIL--------- 213
Cdd:pfam04997 127 MGAKA------ILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKkskEEEEKEILNPEKVLKIFkrisdedve 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 214 -EAFLTSGNKPEWMVMDTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAV 292
Cdd:pfam04997 201 iLGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHV 280
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 428147636 293 DALIDNGRRG-RPVTGPGNRPLKSLSHMLKGKQGRFRQNL 331
Cdd:pfam04997 281 ATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
13-819 |
1.78e-99 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 337.21 E-value: 1.78e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 13 GLASSDKIRQWSYGEVKKPETIN---YrtlkPERDGLFDERiFG---PskdwecacgkykrirykGVVCDRCGvevTKAK 86
Cdd:PRK08566 15 GLLSPEEIRKMSVTKIITADTYDddgY----PIDGGLMDPR-LGvidP-----------------GLRCKTCG---GRAG 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 87 VRRERMGHIELAAPVTHIWYFKGIpsRMglVLDMSPRALEEIiyfasyvvtdpgdtalekkqLLTEREYREKRDQYGQG- 165
Cdd:PRK08566 70 ECPGHFGHIELARPVIHVGFAKLI--YK--LLRATCRECGRL--------------------KLTEEEIEEYLEKLERLk 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 166 FKASMGADAIRTLLRDVDLEKECAELKEELREATGQK-------RTRAVRRL------DILE------AFLTSGN----K 222
Cdd:PRK08566 126 EWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKFEKpttfyeeRKEGLVKLtpsdirERLEkipdedLELLGINpevaR 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 223 PEWMVMDTIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRG 302
Cdd:PRK08566 206 PEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPG 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 303 RPV----TGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPF--------V 370
Cdd:PRK08566 286 IPParhrSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPErvtewnieE 362
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 371 MRELVKRdmASN--------IKNAKRKIDRRDEDIWDVVE-----DVIKEH-----PVLLNRAPTLHRLGIQAFEPVLVS 432
Cdd:PRK08566 363 LREYVLN--GPEkhpganyvIRPDGRRIKLTDKNKEELAEklepgWIVERHlidgdIVLFNRQPSLHRMSIMAHRVRVLP 440
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 433 GKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEEANrege 512
Cdd:PRK08566 441 GKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTL---- 516
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 513 gmifkdINEIRTAYQNGYVHLHtrVGLQTDCLVAQGKPFsdWqkdrilvttVGKVFFNEILPEDFIY-----LNEPTQEN 587
Cdd:PRK08566 517 ------FTKEEALDLLRAAGID--ELPEPEPAIENGKPY--W---------TGKQIFSLFLPKDLNLefkakICSGCDEC 577
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 588 LTKATP-DKYFL-EPGQDIHAFLAAQElVAPFKsGFLADIIAevyKEYKVTATAELLDRMKDLGYYESTKSGLTVGIADI 665
Cdd:PRK08566 578 KKEDCEhDAYVViKNGKLLEGVIDKKA-IGAEQ-GSILDRIV---KEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE 652
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 666 T----DLKEKPEIIANARHKVEQVAKQFRRGLI------TDDE-RYNRVISIWNNAKDEIqAKLVED-VDPSNPIQMMSD 733
Cdd:PRK08566 653 DipeeAKEEIDEIIEEAEKRVEELIEAYENGELeplpgrTLEEtLEMKIMQVLGKARDEA-GEIAEKyLGLDNPAVIMAR 731
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 734 SGARGNISNFTQLSGMRGLMAAPNGKTME------LP--------------ILSNFREGLSVLEMFISTHGARKGMTDTA 793
Cdd:PRK08566 732 TGARGSMLNLTQMAACVGQQSVRGERIRRgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHAMGGREGLVDTA 811
|
890 900
....*....|....*....|....*.
gi 428147636 794 LKTADSGYLTRRLVDVAQDVIVrEFD 819
Cdd:PRK08566 812 VRTSQSGYMQRRLINALQDLKV-EYD 836
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
4-1180 |
2.34e-94 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 330.83 E-value: 2.34e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 4 VNKFDSMQIGLASSDKIRQWSYGEVKKPETINYRTLkPERDGLFDERIFGPSKDWEC-ACGKYKRirykgvvcdRCgvev 82
Cdd:PRK14977 6 VKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRLGTIEPGQKClTCGNLAA---------NC---- 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 83 tkakvrRERMGHIELAAPVTHIWYFKGIPSRMG--------LVLDMSPRALEEIIYFASYVVTDPGDTALEKKQLlteRE 154
Cdd:PRK14977 72 ------PGHFGHIELAEPVIHIAFIDNIKDLLNstchkcakLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEII---EE 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 155 YREKRDQYGQGFKAS--MGADAIRTLLRDVDLEKECAELkEELREATGQKRTRAVRRLD---ILEAFLTSGNKPEWMVMD 229
Cdd:PRK14977 143 VRDQVKVYAKKAKECphCGAPQHELEFEEPTIFIEKTEI-EEHRLLPIEIRDIFEKIIDddlELIGFDPKKARPEWAVLQ 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 230 TIPVIPPDLRPMVQLEGGRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVT--G 307
Cdd:PRK14977 222 AFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAhhK 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 308 PGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFV--------MRELVKRD- 378
Cdd:PRK14977 302 GSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenniekMKELVINGp 381
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 379 --------------MASNIKNAKRKIDRRDEDIWDVVE--DVIKEH-----PVLLNRAPTLHRLGIQAFEPVLVSGKSMR 437
Cdd:PRK14977 382 defpganairkgdgTKIRLDFLEDKGKDALREAAEQLEigDIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPGATFR 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 438 LHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEEAnregegmiFK 517
Cdd:PRK14977 462 LHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDA--------LF 533
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 518 DINEI-RTAYQNGYVHLHTRVGLQTdclvaqgkpfsdwqKDRILVTtvGKVFFNEILPEDFIYLNEPTQENLTKA----- 591
Cdd:PRK14977 534 DKNEAsNIAMLAGITDPLPEPAIKT--------------KDGPAWT--GKQLFSLFLPKDFNFEGIAKWSAGKAGeakdp 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 592 --TPDKYFLEPGQDIHAFLAAQELVAPFKSGFLAdIIAEVYKEYKVTATAELLDRMKDLGYYESTKSGLTVGIADIT--- 666
Cdd:PRK14977 598 scLGDGYVLIKEGELISGVIDDNIIGALVEEPES-LIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIipd 676
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 667 -DLKEKPEIIANARHKVEQVAKQFR---------------RGLITDDERYNRVISIWNNAKDEIQAKLVEDVDPSNPIQM 730
Cdd:PRK14977 677 eAKQEIEDDIQGMKDEVSDLIDQRKitrkitiykgkeellRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKI 756
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 731 MSDSGARGNISNFTQLSGMRGLMAAPNGKTMELP----------------------------ILSNFREGLSVLEMFIST 782
Cdd:PRK14977 757 MAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHA 836
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 783 HGARKGMTDTALKTADSGYLTRRLVDVAQDV------IVREFDCHT------DRGLEVSAIMEgNQMVEPlyDRILGRYA 850
Cdd:PRK14977 837 MGGREGLIDKARRTEDSGYFQRRLANALEDIrleydeTVRDPHGHIiqfkfgEDGIDPQKLDH-GEAFNL--ERIIEKQK 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 851 M----KTVKNPETGEVIVPADTMMNEKLAQAVIDAgvktvTIRSVFTCNTRHGVCVKcyGRNMATGDTVEVGEAVGTVAA 926
Cdd:PRK14977 914 IedrgKGASKDEIEELAKEYTKTFNANLPKLLADA-----IHGAELKEDELEAICAE--GKEGFEKAKVEPGQAIGIISA 986
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 927 QSIGEPGTQLTMRNFHQGGVAgGDDITQGLPRVQEIFEARNP---------------KGRATITEV------TGVVDSIE 985
Cdd:PRK14977 987 QSIAEPGTQMTLRTFHAAGIK-AMDVTHGLERFIELVDARAKpstptmdiylddeckEDIEKAIEIarnlkeLKVRALIA 1065
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 986 ENPAERTKEI-TISGKTDTRTYN-LPYTAVLSV-------AEGDEVVRGQALTIGSVDPKELIK---------------- 1040
Cdd:PRK14977 1066 DSAIDNANEIkLIKPDKRALENGcIPMERFAEIeaalakgKKFEMELEDDLIILDLVEAADRDKplatliairnkildkp 1145
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1041 ---VRDV----LTT------ENYILR----EIQKVYRMQGVDIsdkhvevmarqmlRKVRVMDPGETDLLPGILMDIDQF 1103
Cdd:PRK14977 1146 vkgVPDIerawVELvekdgrDEWIIQtsgsNLAAVLEMKCIDI-------------ANTITNDCFEIAGTLGIEAARNAI 1212
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1104 KDQNAKTVISGGVPATARPVLL--------------GITKASL------ETNSFLSAASFQETTRVLTDAAIRGKNDPLV 1163
Cdd:PRK14977 1213 FNELASILEDQGLEVDNRYIMLvadimcsrgtieaiGLQAAGVrhgfagEKDSPLAKAAFEITTHTIAHAALGGEIEKIK 1292
|
1370
....*....|....*..
gi 428147636 1164 GLKENVIIGKIIPAGTG 1180
Cdd:PRK14977 1293 GILDALIMGQNIPIGSG 1309
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
8-816 |
1.12e-74 |
|
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: 264.01 E-value: 1.12e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 8 DSMQIGLASSDKIRQWSYGEVKKPETINyRTLKPERDGLFDERIFGPSKDWECA-CGKykriryKGVVCDrcGvevtkak 86
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRMGTIDRNSRCQtCGG------DMKECP--G------- 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 87 vrreRMGHIELAAPVTHIWYfkgipsrMGLVLdmspRALEEIIyfasyvvtdpgdtalekKQLLTereyrekrdqygqgf 166
Cdd:cd02733 65 ----HFGHIELAKPVFHIGF-------LTKIL----KILRCVC-----------------KRELS--------------- 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 167 kasmgADAIRTLLRDVDLEkECAELKEELREAtgqkrtravrrldileafltsgnKPEWMVMDTIPVIPPDLRPMVQLEG 246
Cdd:cd02733 98 -----AERVLEIFKRISDE-DCRILGFDPKFS-----------------------RPDWMILTVLPVPPPAVRPSVVMDG 148
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 247 GRFATSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRP-VTGPGNRPLKSLSHMLKGKQG 325
Cdd:cd02733 149 SARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPqATQKSGRPLKSIRQRLKGKEG 228
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 326 RFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALEL-FKPFV-------MRELVKRDMASN------IKNAKRKID 391
Cdd:cd02733 229 RIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfnidrLQELVRNGPNEYpgakyiIRDDGERID 308
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 392 ----RRDEDI----WDVVE------DVikehpVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAI 457
Cdd:cd02733 309 lrylKKASDLhlqyGYIVErhlqdgDV-----VLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNL 383
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 458 HVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSieeanregegmiFKDIneIRTAYQNGYVHLHtrv 537
Cdd:cd02733 384 HVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLT------------KRDT--FLEKDQVMNLLMW--- 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 538 gLQTDclvaQGK-PFSDWQKDRILVTtvGKVFFNEILPEDfIYLNEPTQENLTKATP----DKYFLEPGQDIHAFLAAQE 612
Cdd:cd02733 447 -LPDW----DGKiPQPAILKPKPLWT--GKQIFSLIIPKI-NNLIRSSSHHDGDKKWispgDTKVIIENGELLSGILCKK 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 613 LVAPfKSGFLADIIaevYKEYKVTATAELLDRMKDLGYYESTKSGLTVGIAD-ITD---LKEKPEIIANARHKVEQVAKQ 688
Cdd:cd02733 519 TVGA-SSGGLIHVI---WLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDtIADketMKKIQETIKKAKRDVIKLIEK 594
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 689 FRRGLITDDERY-------NRVISIWNNAKDEIQAKLVEDVDPSNPIQMMSDSGARGNISNFTQLSGMRG-------LMa 754
Cdd:cd02733 595 AQNGELEPQPGKtlresfeNKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGqqnvegkRI- 673
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 428147636 755 aPNG---KTmeLP--------------ILSNFREGLSVLEMFISTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIVR 816
Cdd:cd02733 674 -PFGfrrRT--LPhfikddygpesrgfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVK 749
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
16-816 |
1.60e-73 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 262.10 E-value: 1.60e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 16 SSDKIRQWSYGEVKKPETINYRTLKPERDGLFDERIfGPSKdwecacgkykriryKGVVCDRCGvevtkaKVRRERMGH- 94
Cdd:cd02583 2 SPEDIIRLSEVEVTNRNLYDIETRKPLPYGVLDPRL-GTSD--------------KDGICETCG------LNLADCVGHf 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 95 --IELAAPVTHIWYFKGIPSrmglVLDMspraleeIIYFASYVVTDPGDTALEKKQLltereyREKRDQYGQGfkaSMGA 172
Cdd:cd02583 61 gyIKLELPVFHIGYFKAIIN----ILQC-------ICKTCSRVLLPEEEKRKFLKRL------RRPNLDNLQK---KALK 120
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 173 DAIRTLLRDVDLEKECAELK---EELREATGQKRTRAVRRLDI-LEAFLTSGNKPEWMVMDTIPVIPPDLRPMVQLEGGr 248
Cdd:cd02583 121 KKILEKCKKVRKCPHCGLLKkaqEDLNPLKVLNLFKNIPPEDVeLLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEK- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 249 fATSDLNDL---YRRVINRNNRLKRLLDLHAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQG 325
Cdd:cd02583 200 -SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPKKPIRGFCQRLKGKQG 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 326 RFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPF--------VMRELVKR----------------DMAS 381
Cdd:cd02583 279 RFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPErvtrynieKLRKLVLNgpdvhpganfvikrdgGKKK 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 382 NIKNAKRKIDRRDEDIWDVVE------DVikehpVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQM 455
Cdd:cd02583 359 FLKYGNRRKIARELKIGDIVErhledgDI-----VLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEM 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 456 AIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQDMTIGNYYLSIEEA--NREgegmifkDINEIRTAYQNGYVHL 533
Cdd:cd02583 434 NLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVffDRA-------QFCQLCSYMLDGEIKI 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 534 HtrvgLQTDCLVaqgKPFSDWqkdrilvttVGKVFFNEILpedFIYLNEPTQENLTKATPDKYFLEPGQDIH-AFLAAQ- 611
Cdd:cd02583 507 D----LPPPAIL---KPVELW---------TGKQIFSLLL---RPNKKSPVLVNLEAKEKSYTKKSPDMCPNdGYVVIRn 567
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 612 -ELVA----------PFKSGFLADIIaevyKEYKVTATAELLDRMKDLG-YYESTKsGLTVGIADITD----LKEKPEII 675
Cdd:cd02583 568 sELLCgrldkstlgsGSKNSLFYVLL----RDYGPEAAAAAMNRLAKLSsRWLSNR-GFSIGIDDVTPskelLKKKEELV 642
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 676 ANARHKVEQVAKQFRRGLI------TDDERY-NRVISIWNNAKDEIQAKLVEDVDPSNPIQMMSDSGARGNISNFTQ--- 745
Cdd:cd02583 643 DNGYAKCDEYIKQYKKGKLelqpgcTAEQTLeAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQmia 722
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 746 ------LSGMRglmaAPNGktME---LP--------------ILSNFREGLSVLEMFISTHGARKGMTDTALKTADSGYL 802
Cdd:cd02583 723 cvgqqiISGKR----IPNG--FEdrtLPhfprnsktpaakgfVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYM 796
|
890
....*....|....
gi 428147636 803 TRRLVDVAQDVIVR 816
Cdd:cd02583 797 QRRLMKALEDLSVQ 810
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
951-1193 |
2.41e-69 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 255.69 E-value: 2.41e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 951 DITQGLPRVQEIFEARNPKGRATITEVTGVVDsIEENPAERTkEITISGKTDTRT-YNLPYTAVLSVAEGDEVVRGQALT 1029
Cdd:PRK02597 978 DIIQGLPRIEELLEARKPKESCILAKKPGTVQ-IKYGDDESV-DVKVIESDGTITeYPILPGQNVMVSDGQQVDAGEPLT 1055
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1030 IGSVDPKELIKV-----RDVL-----------TTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLL 1093
Cdd:PRK02597 1056 DGPINPHELLEIffedlRDRKglyeaalealqKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTML 1135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1094 PGILMDIDQFKDQNAKTVISGGVPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGK 1173
Cdd:PRK02597 1136 PGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1215
|
250 260
....*....|....*....|
gi 428147636 1174 IIPAGTGMKKYRDIQPEEVG 1193
Cdd:PRK02597 1216 LIPAGTGFSGFEEELSAEAG 1235
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
951-1184 |
4.68e-64 |
|
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: 238.60 E-value: 4.68e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 951 DITQGLPRVQEIFEARNPKGRATITEVTGVVdSIEENPAERTKEITISGKTDTRT-YNLPYTAVLSVAEGDEVVRGQALT 1029
Cdd:TIGR02388 976 DIVQGLPRIEELLEARKPKEACILAKRPGVV-QVKYGTDDESVSIKVIERDGTISeYPLLPGQNIMVSDGQQVTGGEPLT 1054
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1030 IGSVDPKELIKV----------------RDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLL 1093
Cdd:TIGR02388 1055 DGPINPHDILDVffsyykdqdglyeaaqESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLL 1134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1094 PGILMDIDQFKDQNAKTVISGGVPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGK 1173
Cdd:TIGR02388 1135 PGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGR 1214
|
250
....*....|.
gi 428147636 1174 IIPAGTGMKKY 1184
Cdd:TIGR02388 1215 LIPAGTGFSSY 1225
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
772-1090 |
6.37e-62 |
|
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: 220.69 E-value: 6.37e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 772 GLSVLEMFISTHGARKGMTDTALKTADSGYLTRRLVDVAQDVIVREFDCHTDRGLEVSAIMEGNQMVEPLYDRILGRYAM 851
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 852 KTVKNPETGE---------------------------------VIVPADTMMNEKLAQAVIDAGVKTVTIRSVFTCNTRH 898
Cdd:pfam04998 81 EFSDLKLEDKfkndllddllllsefslsykkeilvrdsklgrdRLSKEAQERATLLFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 899 GVCVKCYGRNMATGDTVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAgGDDITQGLPRVQEIFE-------------- 964
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVA-SKNVTLGVPRLKEIINvsknikspsltvyl 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 965 ----------ARNPKGRATITEVTGVVDSIE--ENP-------------------------------------------- 988
Cdd:pfam04998 240 fdevgrelekAKKVYGAIEKVTLGSVVESGEilYDPdpfntpiisdvkgvvkffdiidevtneeeidpetgllilvirll 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 989 -----------------------------------------------------------------------AERTKEITI 997
Cdd:pfam04998 320 kilnksikkvvkseviprsirnkvdegrdiaigeitafiikiskkirqdtgglrrvdelfmeedpklailvASLLGNITL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 998 SG-KTDTRTYNLPYTAVLSVAEGDEVVRGQALTI-----GSVDPKELI--KVRDVLTT------ENYILREIQKVYRMQG 1063
Cdd:pfam04998 400 RGiPGIKRILVNEDDKGKVEPDWVLETEGVNLLRvllvpGFVDAGRILsnDIHEILEIlgieaaRNALLNEIRNVYRFQG 479
|
490 500
....*....|....*....|....*..
gi 428147636 1064 VDISDKHVEVMARQMLRKVRVMDPGET 1090
Cdd:pfam04998 480 IYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
951-1186 |
1.36e-58 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 221.74 E-value: 1.36e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 951 DITQGLPRVQEIFEARNpkgratitevtgvVDSIEENPAERTKeitISGKTDTRTYNLPYTAVLSVAegdevvrgqaLTI 1030
Cdd:CHL00117 1130 DITQGLPKVEQLLEARS-------------IDSISMNLEKRLE---GWNERITRILGIPWGFLIGAE----------LSI 1183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1031 GsvdpkeliKVRdvltteNYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETD-LLPGILmdIDQFKDQNAK 1109
Cdd:CHL00117 1184 A--------QSQ------ISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSNvFLPGEL--IGLLRAERIN 1247
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 428147636 1110 TVISggVPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTGMKKYRD 1186
Cdd:CHL00117 1248 RALE--EAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVH 1322
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
951-1187 |
3.55e-55 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 212.09 E-value: 3.55e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 951 DITQGLPRVQEIFEARNPKGR--ATITEVTGVVDSieeNPAERTKEITISGKTDTRT--YNLPYTAVLSVAEGDEVVRGQ 1026
Cdd:PRK09603 2642 DITGGLPRVSELFEARKPKPKdvAILSEVDGIVSF---GKPIRNKEHIIVTSKDGRSmdYFVDKGKQILVHADEFVHAGE 2718
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1027 ALTIGSVDPKELIKVRDVLTTENYILREIQKVYRMQGVDISDKHVEVMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQ 1106
Cdd:PRK09603 2719 AMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEE 2798
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1107 NAKTVISGGVPATARPVLLGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTGMKKYRD 1186
Cdd:PRK09603 2799 NARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNKK 2878
|
.
gi 428147636 1187 I 1187
Cdd:PRK09603 2879 I 2879
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
221-807 |
5.06e-49 |
|
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: 188.16 E-value: 5.06e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 221 NKPEWMVMDTIPVIPPDLRPMVQLEGGRFaTSDLNDLYRRVINRNNRLKRLLDLHAPGIIVQNEKRM------------- 287
Cdd:cd01435 125 FGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLIsgktnseklinaw 203
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 288 --LQEAVDALIDNGRrgrpVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALEL 365
Cdd:cd01435 204 lqLQSAVNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKL 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 366 --------FKPFVMRELV------------------KRDMASNIKNAKRKIDRRDE----------DIWDVVE------D 403
Cdd:cd01435 280 tfpepvtpFNVEELRQAVingpdvypganaiededgRLILLSALSEERRKALAKLLlllssaklllNGPKKVYrhlldgD 359
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 404 VikehpVLLNRAPTLHRLGIQA-FEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAESRLLMLAAHHILAP 482
Cdd:cd01435 360 V-----VLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVP 434
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 483 KDGKPI---IspsQD-------MTIGNYYLSIEEanregegmifkdineirtaYQN---------GYVHLHTRVGLQTDC 543
Cdd:cd01435 435 TDGKPLrglI---QDhvvsgvlLTSRDTFFTREE-------------------YQQlvyaalrplFTSDKDGRIKLLPPA 492
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 544 LVaqgKPFSDW---QkdriLVTTVgkvfFNEILPEDFIYLNEPTQENLTKATPDKYFLEPGQD----------------- 603
Cdd:cd01435 493 IL---KPKPLWtgkQ----VISTI----LKNLIPGNAPLLNLSGKKKTKKKVGGGKWGGGSEEsqviirngelltgvldk 561
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 604 ----------IHAFlaaQELVAPFKSGFLADIIAEVykeykvtATAELldRMKdlgyyestksGLTVGIADITdLKEKPE 673
Cdd:cd01435 562 sqfgasayglVHAV---YELYGGETAGKLLSALGRL-------FTAYL--QMR----------GFTCGIEDLL-LTPKAD 618
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 674 -----IIANARHKVEQVAKQFrRGLITDDerynrvisIWNNAKDEIQAKLVEDVDPSNPIQMMSDSGARGNISNFTQLSG 748
Cdd:cd01435 619 ekrrkILRKAKKLGLEAAAEF-LGLKLNK--------VTSSIIKACLPKGLLKPFPENNLQLMVQSGAKGSMVNASQISC 689
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 749 MRG----------LMaaPNGKTmeLP--------------ILSNFREGLSVLEMFISTHGARKGMTDTALKTADSGYLTR 804
Cdd:cd01435 690 LLGqqelegrrvpLM--VSGKT--LPsfppydtspraggfITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQR 765
|
...
gi 428147636 805 RLV 807
Cdd:cd01435 766 CLI 768
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
333-475 |
3.02e-48 |
|
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: 169.41 E-value: 3.02e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 333 GKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELFKPFV--------MRELV-----KRDMASNIKN---AKRKI----DR 392
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpynikrLRQLVengpnVYPGANYIIRingARRDLryqkRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 393 RDEDIWD---VVEDVIKEHPVLLNRAPTLHRLGIQAFEPVLVSGKSMRLHPLVCTAYNADFDGDQMAIHVPLSAEAQAES 469
Cdd:pfam00623 81 LDKELEIgdiVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 428147636 470 RLLMLA 475
Cdd:pfam00623 161 EELMLV 166
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
478-665 |
8.12e-41 |
|
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: 147.77 E-value: 8.12e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 478 HILAPKDGKPIISPSQDMTIGNYYLSIEEanregegmIFKDINEIRTAYQNGYVHLHTRVGlqtdclvaqgKPFSdwqKD 557
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAIL----------KPIK---PL 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 558 RILVTTVGKVFFNEILPEDFIYLNEPtqenLTKATPDKYFLEPGQDIHAFLAAQELVapfksGFLADIIAEVYKEYKVTA 637
Cdd:pfam04983 60 WTGKQTFSRLLPNEINPKGKPKTNEE----DLCENDSYVLINNGELISGVIDKKTVG-----KSLGSLIHIIYKEYGPEE 130
|
170 180
....*....|....*....|....*...
gi 428147636 638 TAELLDRMKDLGYYESTKSGLTVGIADI 665
Cdd:pfam04983 131 TAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
918-1181 |
2.54e-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: 143.33 E-value: 2.54e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 918 GEAVGTVAAQSIGEPGTQLTMRNFHQGGVAGGdDITQGLPRVQEIFEARNPKgraTITEVTGVvdsieenpaertkeiti 997
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASM-NVTLGLPRLKEILNAASIH---EMLEALGI----------------- 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 998 sgktdtrtynlpytavlsvaegdEVVRgqaltigsvdpkelikvrdvltteNYILREIQKVYRMQGVDISDKHVEVMARQ 1077
Cdd:cd00630 60 -----------------------EAAR------------------------ETIIREIQKVLASQGVSVDRRHIELIADV 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1078 MLRKVRVMdpgetdllpgilmdidqfkdqnaktvisggvpatarpvllGITKASL--ETNSFLSAASFQETTRVLTDAAI 1155
Cdd:cd00630 93 MTYSGGLR----------------------------------------GVTRSGFraSKTSPLMRASFEKTTKHLLDAAA 132
|
250 260
....*....|....*....|....*.
gi 428147636 1156 RGKNDPLVGLKENVIIGKIIPAGTGM 1181
Cdd:cd00630 133 AGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
872-1181 |
9.80e-27 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 113.79 E-value: 9.80e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 872 EKLAQAVIDAGVKTVTIRSVFTcntrhgVCVKCYGRNMatgdtVEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAgGDD 951
Cdd:PRK04309 24 EELREKLEERKLTEEEVEEIIE------EVVREYLRSL-----VEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVA-EIN 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 952 ITQGLPRVQEIFEAR-NP------------------KGRA---TITEVT--GVVDSIEENPAERT--------------- 992
Cdd:PRK04309 92 VTLGLPRLIEIVDARkEPstpmmtiylkdeyaydreKAEEvarKIEATTleNLAKDISVDLANMTiiieldeemledrgl 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 993 --------------KEITISGKTDTRTYNLP-YTAVLSVA---------------------EGDE---VVRG----QALT 1029
Cdd:PRK04309 172 tvddvkeaiekkkgGEVEIEGNTLIISPKEPsYRELRKLAekirnikikgikgikrviirkEGDEyviYTEGsnlkEVLK 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1030 IGSVDPK-----ELIKVRDVLTTE---NYILREIQKVYRMQGVDISDKHVEVMARQMlrkvrvmdpgetdllpgilmdid 1101
Cdd:PRK04309 252 VEGVDATrtttnNIHEIEEVLGIEaarNAIIEEIKNTLEEQGLDVDIRHIMLVADMM----------------------- 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1102 qfkdqnaktvisggvpaTARPVLLGITKASL--ETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGT 1179
Cdd:PRK04309 309 -----------------TWDGEVRQIGRHGVsgEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGT 371
|
..
gi 428147636 1180 GM 1181
Cdd:PRK04309 372 GD 373
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
915-1181 |
1.20e-26 |
|
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: 113.11 E-value: 1.20e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 915 VEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAgGDDITQGLPRVQEIFEARNPKGRATI-------------------- 974
Cdd:cd06528 37 IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVA-EINVTLGLPRLIEIVDARKEPSTPTMtiyleeeykydrekaeevar 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 975 ----TEVTGVVDSIEENPAERTKEITI-SGKTDTR--TYNLPYTAVLSVAEGDEVVRGQALTI----GSVDPKELIKVRD 1043
Cdd:cd06528 116 kieeTTLENLAEDISIDLFNMRITIELdEEMLEDRgiTVDDVLKAIEKLKKGKVGEEGDVTLIvlkaEEPSIKELRKLAE 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1044 ----------------VLTTEN--YILR----EIQKVYRMQGVDIsdkhvevmarqmlRKVRVMDPGETDLLPGI----- 1096
Cdd:cd06528 196 kilntkikgikgikrvIVRKEEdeYVIYtegsNLKAVLKVEGVDP-------------TRTTTNNIHEIEEVLGIeaarn 262
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1097 -----LMDI--DQFKDQNAKTVI--------SGGVpataRPVllGITKASLETNSFLSAASFQETTRVLTDAAIRGKNDP 1161
Cdd:cd06528 263 aiineIKRTleEQGLDVDIRHIMlvadimtyDGEV----RQI--GRHGIAGEKPSVLARAAFEVTVKHLLDAAVRGEVDE 336
|
330 340
....*....|....*....|
gi 428147636 1162 LVGLKENVIIGKIIPAGTGM 1181
Cdd:cd06528 337 LRGVIENIIVGQPIPLGTGD 356
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
915-1181 |
1.04e-25 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 108.84 E-value: 1.04e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 915 VEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAgGDDITQGLPRVQEI----------------------FEARNPKGRA 972
Cdd:cd02736 7 VEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVA-SMNITLGVPRIKEIinasknistpiitaklendrdeKSARIVKGRI 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 973 TITEVTGVVDSIEE--NPAERTKEITISGKT--------DTRTYN-------LPYTAVLSVAEGDEVVRGQ--------- 1026
Cdd:cd02736 86 EKTYLGEVASYIEEvySPDDCYILIKLDKKIieklqlskSNLYFLlqslkrkLPDVVVSGIPEVKRAVINKdkkkgkykl 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1027 ---------ALTIGSVDPKEL-----IKVRDVLTTE---NYILREIQKVYRMQGVDISDKHVEVMARQMlrkvrvmdpge 1089
Cdd:cd02736 166 lvegyglraVMNTPGVIGTRTtsnhiMEVEKVLGIEaarSTIINEIQYTMKSHGMSIDPRHIMLLADLM----------- 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1090 tdllpgilmdidqfkdqnaktvisggvpaTARPVLLGITKASLETN--SFLSAASFQETTRVLTDAAIRGKNDPLVGLKE 1167
Cdd:cd02736 235 -----------------------------TFKGEVLGITRFGIAKMkeSVLMLASFEKTTDHLFNAALHGRKDSIEGVSE 285
|
330
....*....|....
gi 428147636 1168 NVIIGKIIPAGTGM 1181
Cdd:cd02736 286 CIIMGKPMPIGTGL 299
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
915-1180 |
6.92e-21 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 97.96 E-value: 6.92e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 915 VEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAGGdDITQGLPRVQEIFEAR---------------------------N 967
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEM-NVTLGLPRLIEIVDARkkpstptmtiylkkdyredeekvrevaK 257
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 968 PKGRATITEV--------------------------------------TGVVDSIEENP----------------AERTK 993
Cdd:PRK14897 258 KIENTTLIDVadiitdiaemsvvveldeekmkerlieyddilaaisklTFKTVEIDDGIirlkpqqpsfkklyllAEKVK 337
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 994 EITISGKTDTRTynlpytaVLSVAEGDE---VVRGQA------LTIGSVDP-----KELIKVRDVLTTE---NYILREIQ 1056
Cdd:PRK14897 338 SLTIKGIKGIKR-------AIARKENDErrwVIYTQGsnlkdvLEIDEVDPtrtytNDIIEIATVLGIEaarNAIIHEAK 410
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1057 KVYRMQGVDISDKHVEVMARQMlrkvrvmdpgetdllpgilmdidqfkdqnaktVISGGVPATARPvllGItkaSLETNS 1136
Cdd:PRK14897 411 RTLQEQGLNVDIRHIMLVADMM--------------------------------TFDGSVKAIGRH---GI---SGEKSS 452
|
330 340 350 360
....*....|....*....|....*....|....*....|....
gi 428147636 1137 FLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTG 1180
Cdd:PRK14897 453 VLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
694-770 |
6.18e-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: 86.26 E-value: 6.18e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 694 ITDDERYNRVISIWNNAKDEIQAKLV----------------EDVDPSNPIQMMSDSGARGNISNFTQLSGMRGLMA--- 754
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALInnilnkardpagniasKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNveg 80
|
90 100
....*....|....*....|....*...
gi 428147636 755 --APNG----------KTMELPILSNFR 770
Cdd:pfam05000 81 krIPFGfsgrtlphfkKDDEGPESRGFV 108
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
314-508 |
2.12e-19 |
|
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: 94.39 E-value: 2.12e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 314 KSLSHMLKGKQgrFRQNLLGKRVDYSGRSVIDVGPKLRLTQMGLPHEMALELfkpfVMRELVKRdmaSNIKNAKRKIDRR 393
Cdd:cd10506 195 SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERL----TVSERVSS---WNRERLQEYCDLT 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 394 ----------------------DEDIWDVVEDVIKE-HPVLLNRAPTLHRLGIQAFE-PVLVSGKSMRLHPLVCTAYNAD 449
Cdd:cd10506 266 lllkgvigvrrngrlvgvrshnTLQIGDVIHRPLVDgDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGD 345
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 428147636 450 FDGDQMAIHVPLSAEAQAESRLLMLAAHHILAPKDGKPIISPSQD-------MTIGNYYLSIEEAN 508
Cdd:cd10506 346 FDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDsllaahlMTERGVFLDKAQMQ 411
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
918-969 |
5.53e-12 |
|
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: 69.16 E-value: 5.53e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 428147636 918 GEAVGTVAAQSIGEPGTQLTMRNFHQGGVAgGDDITQGLPRVQEIFE-ARNPK 969
Cdd:cd02584 27 GEMVGTIAAQSIGEPATQMTLNTFHFAGVS-AKNVTLGVPRLKEIINvAKNIK 78
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
915-962 |
5.93e-11 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 64.91 E-value: 5.93e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 428147636 915 VEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVaGGDDITQGLPRVQEI 962
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGR-GEMNVTLGIPRLREI 53
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
934-1180 |
6.40e-10 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 63.76 E-value: 6.40e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 934 TQLTMRNFHQGGVAGgDDITQGLPRVQEIFEARNPKGRATIT-EVTGVVDSIEENPAERTKEIT--ISGKTDTRTYNLPY 1010
Cdd:PRK14898 541 THNTMRTFHYAGVAE-INVTLGLPRMIEIVDARKEPSTPIMTvHLKGEYATDREKAEEVAKKIEslTLGDVATSIAIDLW 619
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1011 TAVLSVAEGDEVVRGQALTIGSVD---------------------PKE---------------------------LIKVR 1042
Cdd:PRK14898 620 TQSIKVELDEETLADRGLTIESVEeaiekklgvkidrkgtvlylkPKTpsykalrkripkiknivlkgipgiervLVKKE 699
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 1043 DVLTTENYIL----REIQKVYRMQGVDISDKHV-------EVMARQMLRKVRVMDPGETDLLPGILMDIDQFKDQNAKTV 1111
Cdd:PRK14898 700 EHENDEEYVLytqgSNLREVFKIEGVDTSRTTTnniieiqEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMT 779
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 428147636 1112 ISGGVPATARPVLLGitkaslETNSFLSAASFQETTRVLTDAAIRGKNDPLVGLKENVIIGKIIPAGTG 1180
Cdd:PRK14898 780 ADGEVKPIGRHGVAG------EKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
915-1063 |
5.25e-05 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 47.58 E-value: 5.25e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 915 VEVGEAVGTVAAQSIGEPGTQLTMRNFHQGGVAGGD--DITQGLPRVQEIFEARnpkGRATI--TEVTGVVDSIE----- 985
Cdd:PRK14898 54 VEPYEAVGIVAAQSIGEPGTQMSLPYDEKIIVKEGGetRVTEIGKLVDELIDKF---GFEKIggHEVCDLPIEIYalsld 130
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 428147636 986 ----------------ENPAERTKEITISGKTDTRTynlPYTAVLsVAEGDEV--VRGQALTIGS---------VDPKEL 1038
Cdd:PRK14898 131 qdekvhwkriisvirhKANGKLIKIKTESGRTIRAT---PYHSFV-TRKDNEVipVEGSELKIGDwlpvvrslpANCQEA 206
|
170 180
....*....|....*....|....*
gi 428147636 1039 IKVRDVLTTENYILREIQKVYRMQG 1063
Cdd:PRK14898 207 IDLREYLPASDYGEIEEHAVYPVQG 231
|
|
| |
