|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
15-1369 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2382.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 15 QSFDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIICEKCGVEVTL 94
Cdd:PRK00566 5 QDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTR 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 95 SKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVVIEPGLTPLKLHQLLSEEEFVSAQDEYGe 174
Cdd:PRK00566 85 SKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYG- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 175 DAFTASIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKLVKRLKLIDAFLSSQSRPEWMILEVIPVIPPELRPLV 254
Cdd:PRK00566 164 DEFVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 255 PLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKG 334
Cdd:PRK00566 244 QLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 335 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEKERPEVWDILE 414
Cdd:PRK00566 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 415 EVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSP 494
Cdd:PRK00566 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 495 ANGKPIIVPSQDIVLGLYYITMDRPGEKGEGMTFANVGEIEQALDAKVVTLHAKVKARYKGvdengdekISIVETTPGRM 574
Cdd:PRK00566 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITS--------KKLVETTVGRV 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 575 LLSEILPRNpaVPFSLINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLVN 654
Cdd:PRK00566 556 IFNEILPEG--LPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 655 DSKERVKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISdtAPGKPVNSVYMMAHSGARGSAAQIRQLAGMR 734
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLS--KDQESFNPIYMMADSGARGSASQIRQLAGMR 711
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 735 GLMAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVKA 814
Cdd:PRK00566 712 GLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTA 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 815 VIDGGEVISPLGDRILGRTVVGDLIDPLNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDLA 894
Cdd:PRK00566 792 IIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLA 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 895 RGTLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGgaaqrgaeqsqveaafdatvrihnrnvvinssnipvvmgrstevil 974
Cdd:PRK00566 872 TGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTG---------------------------------------------- 905
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 975 ldeqgrerarhrvpygaklladeGVkvergqklaewdpytlpiiteregtahyvdlvegismrevmdeatgisskvvvdw 1054
Cdd:PRK00566 906 -----------------------GV------------------------------------------------------- 907
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1055 rqqprgadlkpritlrdergeiitlanglearyfmsvdailsvengahvragdvlaripressktrDITGGLPRVAELFE 1134
Cdd:PRK00566 908 ------------------------------------------------------------------DITGGLPRVAELFE 921
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1135 ARRPKDFAIISDLDGRVEFGKDYKTKRRIVVRNDEtGDEREYLIPKGKHISVQEGDYVQRGDLLMDGNPVPHDILSVMGV 1214
Cdd:PRK00566 922 ARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDD-GEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHDILRVLGV 1000
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1215 EALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFDEENEKTVGEGLKPAAGHPVL 1294
Cdd:PRK00566 1001 EAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRPVL 1080
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1719390878 1295 QGITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSVVNRLKQIAAERDRALAE 1369
Cdd:PRK00566 1081 LGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDEEEAE 1155
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
14-1189 |
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: 1862.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 14 PQSFDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIICEKCGVEVT 93
Cdd:COG0086 4 VEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 94 LSKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVVIEPGLTPLKLHQLLSEEEFVSAQDEYG 173
Cdd:COG0086 84 LSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 174 eDAFTASIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKLVKRLKLIDAFLSSQSRPEWMILEVIPVIPPELRPL 253
Cdd:COG0086 164 -DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPL 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 254 VPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLK 333
Cdd:COG0086 243 VPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLK 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 334 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEKERPEVWDIL 413
Cdd:COG0086 323 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDIL 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 414 EEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILS 493
Cdd:COG0086 403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILS 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 494 PANGKPIIVPSQDIVLGLYYITMDRPGEKGEGMTFANVGEIEQALDAKVVTLHAKVKARykgVDENGDEKISIVETTPGR 573
Cdd:COG0086 483 PANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVR---ITEDGEQVGKIVETTVGR 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 574 MLLSEILPRNpaVPFslINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLV 653
Cdd:COG0086 560 YLVNEILPQE--VPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIF 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 654 NDSKERVKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISdtapgkPVNSVYMMAHSGARGSAAQIRQLAGM 733
Cdd:COG0086 636 EEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS------SQNTTYMMADSGARGSADQLRQLAGM 709
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 734 RGLMAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVK 813
Cdd:COG0086 710 RGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDRGITVT 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 814 AVIDGGEVISPLGDRILGRTVVGDLIDPLNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDL 893
Cdd:COG0086 790 AIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKCYGRDL 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 894 ARGTLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRGAEQSQVEAAFDATVRIHNRNVVINSSNIPVVMGRSTEVI 973
Cdd:COG0086 870 ARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELV 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 974 LLDEQGRERARHRVPYGAKLLADEGVKVERGQKLAEWDPYTLPIITEREGTAHYVDLVEGISMREVMDEATGISSKVVVD 1053
Cdd:COG0086 950 IVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVED 1029
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1054 WRQQPRGADLKPRITLRDERGEIITLANGLEARYFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDITGGLPRVAELF 1133
Cdd:COG0086 1030 DKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLARVAA 1109
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*.
gi 1719390878 1134 EARRPKDFAIISDLDGRVEFGKDYKTKRRIVVRNDETGDEREYLIPKGKHISVQEG 1189
Cdd:COG0086 1110 AAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
20-1350 |
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: 1826.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 20 IRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIICEKCGVEVTLSKVRR 99
Cdd:TIGR02386 2 IKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVRR 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 100 ERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVVIEPGLTPLKLHQLLSEEEFVSAQDEYGeDAFTA 179
Cdd:TIGR02386 82 ERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYG-DGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 180 SIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKLVKRLKLIDAFLSSQSRPEWMILEVIPVIPPELRPLVPLDGG 259
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 260 RFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRF 339
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 340 RQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEKERPEVWDILEEVIRE 419
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 420 HPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKP 499
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 500 IIVPSQDIVLGLYYITMDRPGEKGEGMTFANVGEIEQALDAKVVTLHAKVKARYKGvdengdekiSIVETTPGRMLLSEI 579
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSG---------EILETTVGRVIFNEI 551
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 580 LPRNpaVPFSLINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLVNDSKER 659
Cdd:TIGR02386 552 LPEG--FPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKE 629
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 660 VKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISDTAPGKpvNSVYMMAHSGARGSAAQIRQLAGMRGLMAK 739
Cdd:TIGR02386 630 VAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTYKF--NPIFMMADSGARGNISQFRQLAGMRGLMAK 707
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 740 PSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVKAVIDG- 818
Cdd:TIGR02386 708 PSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAIVEGk 787
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 819 GEVISPLGDRILGRTVVGDLIDPLNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDLARGTL 898
Cdd:TIGR02386 788 DEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKL 867
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 899 VNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRgaeqsqveaafdatvrihnrnvvinssnipvvmgrstevilldeq 978
Cdd:TIGR02386 868 VEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGA--------------------------------------------- 902
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 979 grerarhrvpygaklladegvkvergqklaewdpytlpiiteregtahyvdlvegismrevmdeatgisskvvvdwrqqp 1058
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1059 rgadlkpritlrdergeiitlanglearyfmsvdailsvengahvragdvlaripresskTRDITGGLPRVAELFEARRP 1138
Cdd:TIGR02386 903 ------------------------------------------------------------SGDITQGLPRVKELFEARTP 922
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1139 KDFAIISDLDGRVEFGKDYKTKRRIVVRNDETGDEREYLIPKGKHISVQEGDYVQRGDLLMDGNPVPHDILSVMGVEALA 1218
Cdd:TIGR02386 923 KDKAVIAEVDGTVEIIEDIVKNKRVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIKGIQAVQ 1002
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1219 NYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFDEENEKTVGEGLKPAAGHPVLQGIT 1298
Cdd:TIGR02386 1003 EYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLLGIT 1082
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
gi 1719390878 1299 KASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTG 1350
Cdd:TIGR02386 1083 KASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1360 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1806.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 15 QSFDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIICEKCGVEVTL 94
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 95 SKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVVIEPGLTPLKLHQLLSEEEFVSAQDEYGE 174
Cdd:PRK14844 1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGI 1605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 175 DAFTASIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKLVKRLKLIDAFLSSQSRPEWMILEVIPVIPPELRPLV 254
Cdd:PRK14844 1606 DSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLV 1685
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 255 PLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLK-SLSDMLK 333
Cdd:PRK14844 1686 SLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLK 1765
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 334 GKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEKERPEVWDIL 413
Cdd:PRK14844 1766 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDML 1845
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 414 EEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILS 493
Cdd:PRK14844 1846 EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 494 PANGKPIIVPSQDIVLGLYYITMDRPgEKGEGMTFANVGEIEQALDAKVVTLHAKVKARYKGVDENGDEKISIVETTPGR 573
Cdd:PRK14844 1926 PSNGRPIIVPSKDIVLGIYYLTLQEP-KEDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSSGETHYKTICTTPGR 2004
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 574 MLLSEILPRNPAVPFSLINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLV 653
Cdd:PRK14844 2005 LILWQIFPKHENLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHV 2084
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 654 NDSKERVKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISDTAPGKPVNSVYMMAHSGARGSAAQIRQLAGM 733
Cdd:PRK14844 2085 DHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIYDGNSKYNSVYMMVNSGARGSTSQMKQLAGM 2164
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 734 RGLMAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVK 813
Cdd:PRK14844 2165 RGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVR 2244
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 814 AVIDGGEVISPLGDRILGRTVVGDLIDPLNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDL 893
Cdd:PRK14844 2245 ATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDL 2324
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 894 ARGTLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRGAEQSQVEAAFDATVRIHNRNVVINSSNIPVVMGRSTEVI 973
Cdd:PRK14844 2325 ATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIVISRSCEVV 2404
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 974 LLDEQGRERARHRVPYGAKLLADEGVKVERGQKLAEWDPYTLPIITEREGTAHYVDLVEGISMREVMDEATGISSKVVVD 1053
Cdd:PRK14844 2405 LIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEVMDESTGISSKVVKD 2484
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1054 WRQQPRGADLKPRITLRDERGEIITLANGLEARYFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDITGGLPRVAELF 1133
Cdd:PRK14844 2485 WKLYSGGANLRPRIVLLDDNGKVMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGLPRVIELF 2564
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1134 EARRPKDFAIISDLDGRVEFG-KDYKTKRRIVVRN-DETGDEREYLIPKGKHISVQEGDYVQRGDLLMDGNPVPHDILSV 1211
Cdd:PRK14844 2565 EARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPvDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLMDGDPDLHDILRV 2644
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1212 MGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFDEENEKTVGEGLKPAAGH 1291
Cdd:PRK14844 2645 LGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYL 2724
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1719390878 1292 PVLQGITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSVVNRLKQIA 1360
Cdd:PRK14844 2725 PILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLIMNKVRALS 2793
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
14-1355 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1582.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 14 PQSFDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGI-ICEKCGVEV 92
Cdd:PRK09603 1393 PKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVAI 1472
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 93 TLSKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVVIEPG--------LTPLKLHQLLSEEE 164
Cdd:PRK09603 1473 THSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGeaaydnegTKLVMKYDILNEEQ 1552
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 165 FVSAQDEYGEDAFTASIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKLVKRLKLIDAFLSSQSRPEWMILEVIP 244
Cdd:PRK09603 1553 YQNISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLP 1632
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 245 VIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRP 324
Cdd:PRK09603 1633 VLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRP 1712
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 325 LKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEK 404
Cdd:PRK09603 1713 LKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQ 1792
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 405 ERPEVWDILEEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVL 484
Cdd:PRK09603 1793 KSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVL 1872
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 485 MMSTNNILSPANGKPIIVPSQDIVLGLYYITMDRPGEKGEGMTFANVGEIEQALDAKVVTLHAKVKArykgVDENgdeki 564
Cdd:PRK09603 1873 MLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRV----LDQG----- 1943
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 565 SIVETTPGRMLLSEILPrnPAVPFSLINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMV 644
Cdd:PRK09603 1944 NIIATSAGRMIIKSILP--DFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDII 2021
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 645 IPEAKKKLVNDSKERVKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISDTAPGkpVNSVYMMAHSGARGSA 724
Cdd:PRK09603 2022 TPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDKEG--FNSIYMMADSGARGSA 2099
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 725 AQIRQLAGMRGLMAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDC 804
Cdd:PRK09603 2100 AQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDC 2179
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 805 GTDKGITVKAVIDGGEVISPLGDRILGRTVVGDLIDPLNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGV 884
Cdd:PRK09603 2180 GTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGV 2259
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 885 CAKCYGRDLARGTLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRGAEQSQVEAAFDATVRIHN---------RNV 955
Cdd:PRK09603 2260 CAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGFVRFYNlrtytnkegKNI 2339
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 956 VINSSNIPV---------------------------VMGRSTEV------------------------------------ 972
Cdd:PRK09603 2340 IANRRNASIlvvepkikapfdgelrietvyeevvvsVKNGDQEAkfvlrrsdivkpselagvggkiegkvylpyasghkv 2419
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 973 ---------------------------------------------------------------------------ILLDE 977
Cdd:PRK09603 2420 hkggsiadiiqegwnvpnripyasellvkdndpiaqdvyakekgiikyyvleanhlerthgikkgdivsekglfaVIADD 2499
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 978 QGRERARHRVPYGAKLLADEGVKV---------ERGQK--LAEWDPYTLPIITEREGTAHYVDLVEGISMREVMDEATGI 1046
Cdd:PRK09603 2500 NGREAARHYIARGSEILIDDNSEVsansviskpTTNTFktIATWDPYNTPIIADFKGKVSFVDIIAGVTVAEKEDENTGI 2579
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1047 SSKVVVDWrqQPRGadLKPRItlrdergeIITLANGLEARYFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDITGGL 1126
Cdd:PRK09603 2580 TSLVVNDY--IPSG--YKPSL--------FLEGANGEEIRYFLEPKTSIAISDGSSVEQAEVLAKIPKATVKSRDITGGL 2647
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1127 PRVAELFEAR--RPKDFAIISDLDGRVEFGKDYKTKRRIVVRNDEtGDEREYLIPKGKHISVQEGDYVQRGDLLMDGNPV 1204
Cdd:PRK09603 2648 PRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKD-GRSMDYFVDKGKQILVHADEFVHAGEAMTDGVVS 2726
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1205 PHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFDEENEKTVGEG 1284
Cdd:PRK09603 2727 SHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARVIALK 2806
|
1450 1460 1470 1480 1490 1500 1510
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1719390878 1285 LKPAAGHPVLQGITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSVVNR 1355
Cdd:PRK09603 2807 GEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNK 2877
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
17-803 |
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: 1333.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 17 FDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIICEKCGVEVTLSK 96
Cdd:cd01609 3 FDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 97 VRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFenyvviepgltplklhqllseeefvsaqdeygeda 176
Cdd:cd01609 83 VRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF----------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 177 ftasigaealrimlsaldmeeekktcreelrdtsseakrkklvkrlkLIDAFLSSQSRPEWMILEVIPVIPPELRPLVPL 256
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 257 DGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQ 336
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 337 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEKERPEVWDILEEV 416
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 417 IREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPAN 496
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 497 GKPIIVPSQDIVLGLYYITMDRPGEKGEGmtfanvgeieqaldakvvtlhakvkarykgvdengdekisIVETTPGRMLL 576
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEG----------------------------------------IIETTVGRVIF 440
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 577 SEILPrnPAVPFslINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLVNDS 656
Cdd:cd01609 441 NEILP--EGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEA 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 657 KERVKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISDTapgkPVNSVYMMAHSGARGSAAQIRQLAGMRGL 736
Cdd:cd01609 517 EEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKD----PFNPIYMMADSGARGSKSQIRQLAGMRGL 592
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1719390878 737 MAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETD 803
Cdd:cd01609 593 MAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
17-1350 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1281.35 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 17 FDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIICEKCGVEVTLSK 96
Cdd:PRK14906 9 FDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRAK 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 97 VRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVV------------------------------ 146
Cdd:PRK14906 89 VRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleeldaer 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 147 ---------------------------IEPgLTP------------------------------LKLHQLLSEEEFVSAQ 169
Cdd:PRK14906 169 drlieatrrlsvdyvpeddefvddigdDER-LTAeevraevadiyeeynerkalrreafdafmqIEPKQLISDEALYREM 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 170 DEYGEDAFTASIGAEALRIMLSALDMEEEKktcrEELRD---TSSEAKRKKLVKRLKLIDAFLSSQSRPEWMILEVIPVI 246
Cdd:PRK14906 248 RLNYSIYFKGGMGAEAVRDLLDAIDLEKEA----EELRAiiaNGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVI 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 247 PPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLK 326
Cdd:PRK14906 324 PPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLK 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 327 SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAAKRMVEKER 406
Cdd:PRK14906 404 SLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGA 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 407 PEVWDILEEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMM 486
Cdd:PRK14906 484 SYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLML 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 487 STNNILSPANGKPIIVPSQDIVLGLYYITMDRPGEKGEGMTFANVGEIEQALDAKV-VTLHAKVKAR----YKGVDENGD 561
Cdd:PRK14906 564 SSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDARAdLDLQAKIVVRlsrdMTVRGSYGD 643
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 562 EKISI----VETTPGRMLLSEILPRNpaVPFslINRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGIS 637
Cdd:PRK14906 644 LEETKagerIETTVGRIIFNQVLPED--YPY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLT 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 638 FGKDDMVIPEAKKKLVNDSKERVKEFEQQYLDGLITQGEKYNKVVDVWSECTEKVATEMMKVISDTAPgkpvnsVYMMAH 717
Cdd:PRK14906 720 VSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFDEDNP------IYMMAD 793
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 718 SGARGSAAQIRQLAGMRGLMAKPSGEIIETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDA 797
Cdd:PRK14906 794 SGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDV 873
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 798 IIVETDCGTDKGITVKAVIDGGEVISPLgdriLGRTVVGDLIDPlNGELIVPNAGLIDE-PTVDRIERSGIDSVMIRSVL 876
Cdd:PRK14906 874 IVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDP-NGEVLLSAGDYIESmDDLKRLVEAGVTKVQIRTLM 948
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 877 TCETKDGVCAKCYGRDLARGTLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAaqrgaeqsqveaafdatvrihnrnvv 956
Cdd:PRK14906 949 TCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGV-------------------------- 1002
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 957 inssnipvvmgrstevilldeqgrerarhrvpygaklladegvkvergqklaewdpytlpiiteregtahyvdlvegism 1036
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1037 revmdeatgisskvvvdwrqqprgadlkpritlrdergeiitlanglearyfmsvdailsvengahvrAGDvlaripres 1116
Cdd:PRK14906 1003 --------------------------------------------------------------------AGD--------- 1005
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1117 sktrDITGGLPRVAELFEARRPKDFAIISDLDGRVEFGKDYKTKRRIVVrnDETGDEREYLIPKGKHI--SVQEGDYVQR 1194
Cdd:PRK14906 1006 ----DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEKTLTIH--DQDGNSREYVVSARVQFmpGVEDGVEVRV 1079
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1195 GDLLMDGNPVPHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFD 1274
Cdd:PRK14906 1080 GQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFE 1159
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1719390878 1275 EENEKTVGEGLKPAAGHPVLQGITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTG 1350
Cdd:PRK14906 1160 DTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
15-571 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 842.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 15 QSFDQIRIQIASPERIRSWS---------FGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYRGIIC 85
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 86 EKCGVEVTLSKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVVIEPGLTP-LKLHQLLSEEE 164
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKnLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 165 FVSAQDE-YGEDAF-----TASIGAEALRIMLSALDMEEEKKTCREELrDTSSEAKRKKLVKRLKLIDAFLSSQSRPEWM 238
Cdd:PRK02625 167 WLEIEDQiYAEDSElegeeVVGIGAEALKRLLEDLNLEEEAEQLREEI-ANSKGQKRAKLIKRLRVIDNFIATGSRPEWM 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 239 ILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRGRVIT 318
Cdd:PRK02625 246 VLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVV 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 319 GANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKLELYGLASTIKAA 398
Cdd:PRK02625 326 GANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAA 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 399 KRMVEKERPEVWDILEEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQ 478
Cdd:PRK02625 406 KKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 479 LEARVLMMSTNNILSPANGKPIIVPSQDIVLGLYYITMDRPG-EKGEGMTFANVGEIEQALDAKVVTLHAKVKARYKG-- 555
Cdd:PRK02625 486 AEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGaQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNGev 565
|
570
....*....|....*.
gi 1719390878 556 VDENGDEKISIVETTP 571
Cdd:PRK02625 566 EDDDEDTEPLKTETLE 581
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
15-519 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 815.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 15 QSFDQIRIQIASPERIRSWS---------FGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRM---KYRG 82
Cdd:CHL00018 5 YKHQQLRIGLASPQQIRAWAerilpngeiVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdeKEDP 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 83 IICEKCGVEVTLSKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLKDLERILYFENYVV--IEPGLTPLKLHQLL 160
Cdd:CHL00018 85 KFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRLRGLF 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 161 SEE---------EFVSAQdeyGEDAF---TASIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKLVKRLKL---- 224
Cdd:CHL00018 165 EYEiqswkysipLFFSTQ---GFDTFrnrEISTGAGAIREQLADLDLRIIIDNSLVEWKELGEEGSTGNEWEDRKIgrrk 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 225 ---------IDAFLSSQSRPEWMILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIEL--KAPDIIV 293
Cdd:CHL00018 242 dflvrriklAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTsrSTPGELV 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 294 RNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKM 373
Cdd:CHL00018 322 MCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREI 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 374 ALELFKPFIYAKLELYGLASTIKAAKRMVEKERPEVWDILEEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPL 453
Cdd:CHL00018 402 AIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPL 481
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1719390878 454 VCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPSQDIVLGLYYITMDRP 519
Cdd:CHL00018 482 VCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNR 547
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
25-803 |
0e+00 |
|
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: 567.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 25 ASPERIRSWSFGEIKKPETINYRTFKPERDGlfcarifgpikdyeclcgKYKRMKYRGIICEKCGVEVTLSKVRRERMGH 104
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 105 IELASPVAHIWFLKSLPSRIGllldmtlkdlerilyfenyvviepgltplklhqllseeefvsaqdeygedaftasigae 184
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 185 alrimlsaldmeeekktcreelrdtsseakrkklvkrlklidaflssqsrPEWMILEVIPVIPPELRPLVpldggrfats 264
Cdd:cd00399 84 --------------------------------------------------PEWMILTCLPVPPPCLRPSV---------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 265 dlndlyrrvinrnnrlkrlielkapdiIVRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLL 344
Cdd:cd00399 104 ---------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLM 156
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 345 GKRVDYSGRSVIVVGPELKLHQCGLPKKMALELfkpfiyaklelyglastikaakrmvekerpevwdileeviREHPVML 424
Cdd:cd00399 157 GKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLF 196
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 425 NRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPS 504
Cdd:cd00399 197 NRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLS 276
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 505 QDIVLGLYYITMdrpgekgegmtfanvgeieqaldakvvtlhakvkarykgvdengdekisivettpGRMLLSEILPrnp 584
Cdd:cd00399 277 QDTLLGAYLLTL-------------------------------------------------------GKQIVSAALP--- 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 585 avpfslinrlltkkdvGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDD----MVIPEAKKKLVNDSKERV 660
Cdd:cd00399 299 ----------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDviddGVIPEEKTELIEEAKKKV 362
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 661 KEFEQQYLDGLITQGEK-------YNKVVDVWSECTEKVATEMMKVISDTAPgkpVNSVYMMAHSGARGSAAQIRQLAGM 733
Cdd:cd00399 363 DEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNLDLVSK---FNSIYVMAMSGAKGSFINIRQMSAC 439
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 734 RGLMAKPSGEI--------------------IETPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDV 793
Cdd:cd00399 440 VGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKA 519
|
810
....*....|
gi 1719390878 794 AQDaIIVETD 803
Cdd:cd00399 520 LED-LVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
236-512 |
5.51e-162 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 487.41 E-value: 5.51e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 236 EWMILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNG--RR 313
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 314 GRVITGankRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIY---------- 383
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVtplnidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 384 --------AKLELYGLASTIKAAKRM-VEKERPEVWDILEEVIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLV 454
Cdd:smart00663 158 lvrngpngAKYIIRGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 1719390878 455 CTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPSQDIVLGLY 512
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
592-1122 |
2.39e-132 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 441.74 E-value: 2.39e-132
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 592 NRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLVNDSKERVKEFEQQYLDGL 671
Cdd:PRK02597 5 NRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 672 ITQGEKYNKVVDVWSECTEKVATEMMKVISDTAPgkpVNSVYMMAHSGARGSAAQIRQLAGMRGLMAKPSGEIIETPIIS 751
Cdd:PRK02597 85 ITEVERFQKVIDTWNETNERLKDEVVKNFRQNDP---LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 752 NFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVKAVIDGGEVISPLGDRILG 831
Cdd:PRK02597 162 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLGDRLLG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 832 RTVVGDLIDPlNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDLARGTLVNVGEAVGVIAAQ 911
Cdd:PRK02597 242 RVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQ 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 912 SIGEPGTQLTMRTFHIGGAAQrGAEQSQVEAAFDATVRIhnrnvvinSSNIPVVMGRS------------TEVILLDEQG 979
Cdd:PRK02597 321 SIGEPGTQLTMRTFHTGGVFT-GEVARQVRSPFAGTVEF--------GKKLRTRPYRTrhgvealqaevdFDLVLKPSGK 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 980 RERARHRVPYGAKLLADEGVKVERGQKLAEwdpytlpiiteregtahyvdlVEGISMREVMDEATgisSKVVVDWRQQPR 1059
Cdd:PRK02597 392 GKPQKIEITQGSLLFVDDGQTVEADQLLAE---------------------VAAGAVKKSTEKAT---KDVICDLAGEVR 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1060 GADLKPRiTLRDERGEIITLANGLEARYFMSVD-------AILSVENGAHVRAGDVLA------------RIPRESSKTR 1120
Cdd:PRK02597 448 FADLIPE-EKTDRQGNTTRKAQRGGLLWVLSGDvynlppgAEPVVSNGDRVEEGDVLAetklvsehggvvRLRESSGDSR 526
|
..
gi 1719390878 1121 DI 1122
Cdd:PRK02597 527 EV 528
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
592-1137 |
1.25e-121 |
|
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: 409.63 E-value: 1.25e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 592 NRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLVNDSKERVKEFEQQYLDGL 671
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 672 ITQGEKYNKVVDVWSECTEKVATEMMKVISDTapgKPVNSVYMMAHSGARGSAAQIRQLAGMRGLMAKPSGEIIETPIIS 751
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNFRQT---DPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKT 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 752 NFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVKAVIDGGEVISpLGDRILG 831
Cdd:TIGR02388 161 NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKIS-LGDRLLG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 832 RTVVGDLIDPlNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDLARGTLVNVGEAVGVIAAQ 911
Cdd:TIGR02388 240 RLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQ 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 912 SIGEPGTQLTMRTFHIGGAAQrGAEQSQVEAAFDATVRIHNRNVVINSSNIPVVMGRSTEV--ILLDEQGRERA----RH 985
Cdd:TIGR02388 319 SIGEPGTQLTMRTFHTGGVFT-GEVARQVRSKIDGTVEFGKKLRTRGYRTRHGEDAKQVEVagLLIIKPTGSITnkaqEI 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 986 RVPYGAKLLADEGVKVERGQKLAEWDPYTLPIITEregtahyvdlvegismREVMDEATGISSKVVVDWRQQPRGADLKP 1065
Cdd:TIGR02388 398 EVTQGSLLFVEDGQTVDAGQLLAEIALGAVRKSTE----------------KATKDVASDLAGEVKFDKVVPEEKTDRQG 461
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1719390878 1066 RITLRDERGEIITLANGleARYFMSVDAILSVENGAHVRAGDVLARipresSKTRDITGGLPRVAELFEARR 1137
Cdd:TIGR02388 462 NTTRIAQRGGLIWVLSG--EVYNLPPGAEPVVKNGDRVEQGTVLAE-----TKLSTEHGGVVRLPESVGDSR 526
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
756-1260 |
5.30e-121 |
|
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: 387.48 E-value: 5.30e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 756 GLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVKAVIDGGEVISPLGDRILGRTVV 835
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 836 GDLIDPLNGELIVPNAGLID-----------EPTVDR----------------------IERSGIDSVMIRSVLTCETKD 882
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLllsefslsykkEILVRDsklgrdrlskeaqeratllfelLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 883 GVCAKCYGRDLARGTLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRGAEQsqveaafdATVRIHNrnvVINSSNI 962
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTL--------GVPRLKE---IINVSKN 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 963 pvVMGRSTEVILLDEQGRERARHRVPYGAKLLADEGVKVERGQKLAEWDPYTLPIITEREGTAHYVDLVEGISMREVMDE 1042
Cdd:pfam04998 230 --IKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1043 ATGISSKVVvdwrqqprgadlkpritlrDERGEIITLANGLEARYFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDI 1122
Cdd:pfam04998 308 ETGLLILVI-------------------RLLKILNKSIKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQD 368
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1123 TGGLPRVAELFEARRPKDFAIISDLDGRVeFGKDYKTKRRIVVRNDETGDE------REYLIPKGKHISVQEgdYVQRGD 1196
Cdd:pfam04998 369 TGGLRRVDELFMEEDPKLAILVASLLGNI-TLRGIPGIKRILVNEDDKGKVepdwvlETEGVNLLRVLLVPG--FVDAGR 445
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1719390878 1197 LLMDgnpVPHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGET 1260
Cdd:pfam04998 446 ILSN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
592-929 |
6.20e-115 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 393.54 E-value: 6.20e-115
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 592 NRLLTKKDVGNVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLVNDSKERVKEFEQQYLDGL 671
Cdd:CHL00117 11 NKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYGN 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 672 ITQGEKYNKVVDVW---SECTEKvatEMMKV--ISDtapgkPVNSVYMMAHSGARGSAAQIRQLAGMRGLMAKPSGEIIE 746
Cdd:CHL00117 91 VHAVEKLRQSIEIWyatSEYLKQ---EMNPNfrMTD-----PLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIID 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 747 TPIISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIIVETDCGTDKGITVKaVIDGGEVISPLG 826
Cdd:CHL00117 163 LPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVS-PRNGMMIERILI 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 827 DRILGRtVVGDLIDpLNGELIVPNAGLIDEPTVDRIERSGIDSVMIRSVLTCETKDGVCAKCYGRDLARGTLVNVGEAVG 906
Cdd:CHL00117 242 QTLIGR-VLADDIY-IGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVG 319
|
330 340
....*....|....*....|...
gi 1719390878 907 VIAAQSIGEPGTQLTMRTFHIGG 929
Cdd:CHL00117 320 IIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
14-806 |
3.57e-101 |
|
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: 343.85 E-value: 3.57e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 14 PQSFDQIRIQIASPERIRSWSFGEIKKPETinYrtfkpERDGLfcaRIFGPIKDyeclcgkyKRMkyrGII-----CEKC 88
Cdd:cd02582 1 PKRIKGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTC 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 89 GVevtlskvRRER----MGHIELASPVAHIWFLKslpsRIGLLLDMTLKDLERILyfenyvviepgLTPLKLHQLLSEEE 164
Cdd:cd02582 60 GN-------TAGEcpghFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEIEKYLERIR 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 165 FVSAQDEYGEDAFTASI-------------GAEALRIML------SALDMEEEKK----TCREELRDTSSEakrkklvkr 221
Cdd:cd02582 118 RLKEKWPELVKRVIEKVkkkakkrkvcphcGAPQYKIKLekpttfYEEKEEGEVKltpsEIRERLEKIPDE--------- 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 222 lkliDAFL----SSQSRPEWMILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEK 297
Cdd:cd02582 189 ----DLELlgidPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLW 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 298 RMLQEAVDALFDNGRRG-RVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALE 376
Cdd:cd02582 265 DLLQYHVTTYFDNEIPGiPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKE 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 377 LFKPFIYAKLelyglasTIKAAKRMVEKeRPEVW--------------DILEE-------------VIREH-----PVML 424
Cdd:cd02582 345 LTVPERVTEW-------NIEKMRKLVLN-GPDKWpganyvirpdgrriRLRYVnreelaerlepgwIVERHlidgdIVLF 416
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 425 NRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPS 504
Cdd:cd02582 417 NRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGI 496
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 505 QDIVLGLYYITMDRPG-EKGEGMTFANVGEIEQALDakvvtlhakvkaryKGVDENGDEKISivettpGRMLLSEILP-- 581
Cdd:cd02582 497 QDYISGAYLLTRKTTLfTKEEALQLLSAAGYDGLLP--------------EPAILEPKPLWT------GKQLFSLFLPkd 556
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 582 ----------------RNPAVPFS---------LINRLLTKKDVG-----NVIDAVYRHCGQKETVIFADRLMKLGFGHA 631
Cdd:cd02582 557 lnfegkakvcsgcsecKDEDCPNDgyvvikngkLLEGVIDKKAIGaeqpgSLLHRIAKEYGNEVARRFLDSVTRLAIRFI 636
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 632 CRAGISFGKDDMVIPEAKKK----LVNDSKERVKEFEQQYLDGLI------TQGEKY-NKVVDVWSEC---TEKVATEMM 697
Cdd:cd02582 637 ELRGFTIGIDDEDIPEEARKeieeIIKEAEKKVYELIEQYKNGELeplpgrTLEETLeMKIMQVLGKArdeAGKVASKYL 716
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 698 kvisdtapgKPVNSVYMMAHSGARGSAAQIRQLAGMRGLMAKpSGEIIET-------P--------------IISNFKEG 756
Cdd:cd02582 717 ---------DPFNNAVIMARTGARGSMLNLTQMAACLGQQSV-RGERINRgyrnrtlPhfkpgdlgpeargfVRSSFRDG 786
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|
gi 1719390878 757 LTVLEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDaIIVETDcGT 806
Cdd:cd02582 787 LSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD-LYVEYD-GT 834
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-343 |
5.35e-98 |
|
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: 316.92 E-value: 5.35e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 14 PQSFDQIRIQIASPERIRSWSFGEIKKPETINYRTFKPERDGLFCARIFGPIKDYEC-LCGKYKRmkyrgiiceKCGVev 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 93 tlskvrreRMGHIELASPVAHIWFLKslpsrigllldMTLKDLERILYFENYVVIEPGLtplklHQLLSEEEFVSAQDEY 172
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPGK-----PKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 173 ------------------GEDAFTASIGAEALRIMLSALDMEEEKKTCREELRDTSSEAKRKKL-----VKRLKLIDAFL 229
Cdd:pfam04997 126 kmgakailelckkkdlceHCGGKNGVCGSQQPVSRKEGLKLKAAIKKSKEEEEKEILNPEKVLKifkriSDEDVEILGFN 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 230 SSQSRPEWMILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFD 309
Cdd:pfam04997 206 PSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFD 285
|
330 340 350
....*....|....*....|....*....|....*
gi 1719390878 310 NGRRG-RVITGANKRPLKSLSDMLKGKQGRFRQNL 343
Cdd:pfam04997 286 NEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
14-806 |
1.91e-89 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 311.02 E-value: 1.91e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 14 PQSFDQIRIQIASPERIRSWSFGEIKKPETinYrtfkpERDGLfcaRIFGPIKDyeclcgkyKRMkyrGII-----CEKC 88
Cdd:PRK08566 6 PKRIGSIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTC 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 89 GvevtlSKVRR--ERMGHIELASPVAHIWFLKslpsRIGLLLDMT--------LKDLERILYFENY-VVIEPGLTPLKLH 157
Cdd:PRK08566 65 G-----GRAGEcpGHFGHIELARPVIHVGFAK----LIYKLLRATcrecgrlkLTEEEIEEYLEKLeRLKEWGSLADDLI 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 158 qllseeefvsaqDEYGEDAFTASI----GAEALRIML------SALDMEEEKK----TCREELRDTSSEakrkklvkrlk 223
Cdd:PRK08566 136 ------------KEVKKEAAKRMVcphcGEKQYKIKFekpttfYEERKEGLVKltpsDIRERLEKIPDE----------- 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 224 liDAFL----SSQSRPEWMILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRM 299
Cdd:PRK08566 193 --DLELlginPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWEL 270
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 300 LQEAVDALFDN---G------RRGRvitgankrPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLP 370
Cdd:PRK08566 271 LQYHVTTYFDNeipGipparhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVP 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 371 KKMALELFKP-----FIYAKLELY---------GLASTIKAAKR---MVEKERPEVWDILEE--VIREH-----PVMLNR 426
Cdd:PRK08566 343 EAIAKELTVPervteWNIEELREYvlngpekhpGANYVIRPDGRrikLTDKNKEELAEKLEPgwIVERHlidgdIVLFNR 422
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 427 APTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPSQD 506
Cdd:PRK08566 423 QPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQD 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 507 IVLGLYYITMDrpgekgegMTFANVGEIEQALDakvvtlhakvKARYKGVDENGDEKISIVETTPGRMLLSEILPRNPAV 586
Cdd:PRK08566 503 HISGAYLLTRK--------STLFTKEEALDLLR----------AAGIDELPEPEPAIENGKPYWTGKQIFSLFLPKDLNL 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 587 PFS---------------------------LINRLLTKKDVGN----VIDAVYRHCGQKETVIFADRLMKLGFGHACRAG 635
Cdd:PRK08566 565 EFKakicsgcdeckkedcehdayvvikngkLLEGVIDKKAIGAeqgsILDRIVKEYGPERARRFLDSVTRLAIRFIMLRG 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 636 ISFGKDDMVIP-EAKKK---LVNDSKERVKEFEQQYLDGLI------TQGEKY-NKVVDVWSEC---TEKVATEMMkvis 701
Cdd:PRK08566 645 FTTGIDDEDIPeEAKEEideIIEEAEKRVEELIEAYENGELeplpgrTLEETLeMKIMQVLGKArdeAGEIAEKYL---- 720
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 702 dtapgKPVNSVYMMAHSGARGSAAQIRQLAGMRGLMAKpSGEIIE-------TP--------------IISNFKEGLTVL 760
Cdd:PRK08566 721 -----GLDNPAVIMARTGARGSMLNLTQMAACVGQQSV-RGERIRrgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPT 794
|
890 900 910 920
....*....|....*....|....*....|....*....|....*.
gi 1719390878 761 EYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDaIIVETDcGT 806
Cdd:PRK08566 795 EFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD-LKVEYD-GT 838
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
10-1352 |
5.15e-86 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 308.11 E-value: 5.15e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 10 QVQGPQSFDQIRIQIASPERIRSWSFGEIKKPETINYRTFkPERDGLFCARIfGPIKDyeclcgkykrmkyrGIICEKCG 89
Cdd:PRK14977 2 EILAVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIEP--------------GQKCLTCG 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 90 vevTLSKVRRERMGHIELASPVAHIWFLKslpsRIGLLLDMTLKDLERILY--------------FENYVVIEPGLTPLK 155
Cdd:PRK14977 66 ---NLAANCPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLpqedlnvfklieeaHAAARDIPEKRIDDE 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 156 LHQLLSEEEFVSAQdeygEDAFTASIGAEALRIMLSALDMEEEKKTCRE------ELRDTSSEakrkkLVKRLKLIDAFL 229
Cdd:PRK14977 139 IIEEVRDQVKVYAK----KAKECPHCGAPQHELEFEEPTIFIEKTEIEEhrllpiEIRDIFEK-----IIDDDLELIGFD 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 230 SSQSRPEWMILEVIPVIPPELRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFD 309
Cdd:PRK14977 210 PKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFD 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 310 NGRRG--RVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIY---- 383
Cdd:PRK14977 290 NATAGipQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVnenn 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 384 --------------------------AKLELYGLASTIKAAKRMVeKERPEVWDILEEVIREHP-VMLNRAPTLHRLGIQ 436
Cdd:PRK14977 370 iekmkelvingpdefpganairkgdgTKIRLDFLEDKGKDALREA-AEQLEIGDIVERHLADGDiVIFNRQPSLHKLSIL 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 437 AFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPSQDIVLGLYYITM 516
Cdd:PRK14977 449 AHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITK 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 517 -DRPGEKGEGMTFANVGEIEQALDAKVVTlhAKVKARYKG-----------VDENGDEKISIVETT----PGRMLLSEIL 580
Cdd:PRK14977 529 dDALFDKNEASNIAMLAGITDPLPEPAIK--TKDGPAWTGkqlfslflpkdFNFEGIAKWSAGKAGeakdPSCLGDGYVL 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 581 PRNPavpfSLINRLLTKKDVG-------NVIDAVYRHCGQKETVIFADRLMKLGFGHACRAGISFGKDDMVIPEAKKKLV 653
Cdd:PRK14977 607 IKEG----ELISGVIDDNIIGalveepeSLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEI 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 654 ND----SKERVKEFEQQY-LDGLITQGEKYNKVVDVWSE---CTEKVATEMMK-------VISDTAPgkPVNSVYMMAHS 718
Cdd:PRK14977 683 EDdiqgMKDEVSDLIDQRkITRKITIYKGKEELLRGMKEeeaLEADIVNELDKardkagsSANDCID--ADNAGKIMAKT 760
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 719 GARGSAAQIRQLAG--------MRGLMAKPSGEIIE---------------TP-----IISNFKEGLTVLEYFNSTHGAR 770
Cdd:PRK14977 761 GARGSMANLAQIAGalgqqkrkTRIGFVLTGGRLHEgykdralshfqegddNPdahgfVKNNYREGLNAAEFFFHAMGGR 840
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 771 KGLADTALKTANSGYLTRRLVDVAQDAI-------------IVETDCGTDkGITVKAvIDGGEVISPlgDRIL------- 830
Cdd:PRK14977 841 EGLIDKARRTEDSGYFQRRLANALEDIRleydetvrdphghIIQFKFGED-GIDPQK-LDHGEAFNL--ERIIekqkied 916
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 831 -GRTVVGDLIDPLNGELIVPNAGLIDEPTVDRIERSGIdsvmirsvltceTKDGVCAKCY-GRDLARGTLVNVGEAVGVI 908
Cdd:PRK14977 917 rGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAEL------------KEDELEAICAeGKEGFEKAKVEPGQAIGII 984
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 909 AAQSIGEPGTQLTMRTFHIGGAAQRgaeqsqveaafDATVRIHNRNVVINSSNIPVVmgrSTEVILLDEQGRERarhrvp 988
Cdd:PRK14977 985 SAQSIAEPGTQMTLRTFHAAGIKAM-----------DVTHGLERFIELVDARAKPST---PTMDIYLDDECKED------ 1044
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 989 ygakllADEGVKVERGQKlaewdpytlpiiteregTAHYVDLVEgismREVMDEATGISSkvvvdwrqqprgadLKPRIT 1068
Cdd:PRK14977 1045 ------IEKAIEIARNLK-----------------ELKVRALIA----DSAIDNANEIKL--------------IKPDKR 1083
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1069 LRdERGEIitlanglEARYFMSVDAILSVENGAHVragdvlaripressktrDITGGLPRVAELFEARRPKDFAIISDLD 1148
Cdd:PRK14977 1084 AL-ENGCI-------PMERFAEIEAALAKGKKFEM-----------------ELEDDLIILDLVEAADRDKPLATLIAIR 1138
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1149 GRV--EFGKDYKTKRRIVVRNDETGDEREYLI-PKGKHIS-VQEGDYVQRGDLLMDGnpvPHDILSVMGVEALANYLINE 1224
Cdd:PRK14977 1139 NKIldKPVKGVPDIERAWVELVEKDGRDEWIIqTSGSNLAaVLEMKCIDIANTITND---CFEIAGTLGIEAARNAIFNE 1215
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1225 IQDVYRLQGVKINDKHIEVIVRQM-----LQKVEITDAGETTFLVGEQvdrqefdeenektvgeglkpaaghpvlqgitk 1299
Cdd:PRK14977 1216 LASILEDQGLEVDNRYIMLVADIMcsrgtIEAIGLQAAGVRHGFAGEK-------------------------------- 1263
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|...
gi 1719390878 1300 aslqtRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:PRK14977 1264 -----DSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKV 1311
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
898-1350 |
6.77e-85 |
|
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: 275.56 E-value: 6.77e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 898 LVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQrgaeqsqveaafdatvrihnrnvvinssnipvvmgrstevillde 977
Cdd:cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT--------------------------------------------- 36
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 978 qgrerarhrvpygaklladegvkvergqklaewdpytlpiiteregtahyvdlvegismrevmdeatgisskvvvdwrqq 1057
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1058 prgadlkpritlrdergeiitlanglearyfmsvdailsvengahvragdvlaripressktrDITGGLPRVAELFEARr 1137
Cdd:cd02655 37 ---------------------------------------------------------------DITQGLPRVEELFEAR- 52
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1138 pkdfaiisdldgrvefgkdyktkrrivvrndetgdereylipkgkhisvqegdyvqrgdllmdgNPVPHDIL--SVMGVE 1215
Cdd:cd02655 53 ----------------------------------------------------------------KINPHDLLriKFLGPE 68
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1216 ALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFDEENEKTVGEGLKPAAGHPVLQ 1295
Cdd:cd02655 69 AVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLL 148
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 1719390878 1296 GITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTG 1350
Cdd:cd02655 149 GITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTG 203
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1060-1380 |
2.40e-79 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 288.05 E-value: 2.40e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1060 GADLKPRITLrDERGEIITLANG-----LEARYFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDITGGLPRVAELFE 1134
Cdd:PRK02597 913 GDELAPGVPA-PESGEVEAVSGGsvtlrLGRPYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLE 991
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1135 ARRPKDFAIISDLDGRVEfgkdyktkrrIVVRNDET---------GDEREYLIPKGKHISVQEGDYVQRGDLLMDGNPVP 1205
Cdd:PRK02597 992 ARKPKESCILAKKPGTVQ----------IKYGDDESvdvkviesdGTITEYPILPGQNVMVSDGQQVDAGEPLTDGPINP 1061
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1206 HDILSVM----------------GVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVD 1269
Cdd:PRK02597 1062 HELLEIFfedlrdrkglyeaaleALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIE 1141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1270 RQEFDEENEKTVGEGLKPAAGHPVLQGITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGT 1349
Cdd:PRK02597 1142 LRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGT 1221
|
330 340 350
....*....|....*....|....*....|...
gi 1719390878 1350 G--SVVNRLKQIAAERDRALAEGETGDGEAPAL 1380
Cdd:PRK02597 1222 GfsGFEEELSAEAGPHPDILAEDPAGYRRMQNL 1254
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1060-1350 |
3.72e-73 |
|
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: 267.87 E-value: 3.72e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1060 GADLKPRITLrDERGEIITLANG-----LEARYFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDITGGLPRVAELFE 1134
Cdd:TIGR02388 911 GDELAKGVKA-EESGEIEEVASDyvilrIGRPYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLE 989
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1135 ARRPKDFAIISDLDG--RVEFGKDYKTKRRIVVRNDetGDEREYLIPKGKHISVQEGDYVQRGDLLMDGNPVPHDILSVM 1212
Cdd:TIGR02388 990 ARKPKEACILAKRPGvvQVKYGTDDESVSIKVIERD--GTISEYPLLPGQNIMVSDGQQVTGGEPLTDGPINPHDILDVF 1067
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1213 ----------------GVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITDAGETTFLVGEQVDRQEFDEE 1276
Cdd:TIGR02388 1068 fsyykdqdglyeaaqeSLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQV 1147
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1719390878 1277 NEKTVGEGLKPAAGHPVLQGITKASLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTG 1350
Cdd:TIGR02388 1148 NEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1221
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
20-799 |
1.07e-69 |
|
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: 250.15 E-value: 1.07e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 20 IRIQ--IASPERIRSWSFGEIKKPETINyRTFKPERDGLFCARIfGPIKdyeclcgkykrmkyRGIICEKCGvevtlskv 97
Cdd:cd02733 1 KRVQfgILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 98 rrERM-------GHIELASPVAHIWFLkslpsriglllDMTLKDLErilyfenyVVIEPGLTPLKLHQLLSEeefvsaqd 170
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILR--------CVCKRELSAERVLEIFKR-------- 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 171 eygedaftasIGAEALRIMlsaldmeeekktcreelrdtsseakrkklvkrlklidAFLSSQSRPEWMILEVIPVIPPEL 250
Cdd:cd02733 108 ----------ISDEDCRIL-------------------------------------GFDPKFSRPDWMILTVLPVPPPAV 140
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 251 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAVDALFDNGRRG--RVITGaNKRPLKSL 328
Cdd:cd02733 141 RPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQK-SGRPLKSI 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 329 SDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL-----ELFKPFIYAKL-EL--YGLASTIKAakR 400
Cdd:cd02733 220 RQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLqELvrNGPNEYPGA--K 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 401 MVEKERPEVWD----------ILEE--VIREH-----PVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFD 463
Cdd:cd02733 298 YIIRDDGERIDlrylkkasdlHLQYgyIVERHlqdgdVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 464 GDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPI--IVpsQDIVLGLYYITMDRpgekgegmTFANVGEIEQAL--- 538
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTKRD--------TFLEKDQVMNLLmwl 447
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 539 --DAKVVTLHAKVKARykgvdengdekisivETTPGRMLLSEILPRN------------PAVPFS------------LIN 592
Cdd:cd02733 448 pdWDGKIPQPAILKPK---------------PLWTGKQIFSLIIPKInnlirssshhdgDKKWISpgdtkviiengeLLS 512
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 593 RLLTKKDVG----NVIDAVYRHCGQKETVIFADR--------LMKLGFghacragiSFGKDDMVIPEAKKKLVND----S 656
Cdd:cd02733 513 GILCKKTVGassgGLIHVIWLEYGPEAARDFIGNiqrvvnnwLLHNGF--------SIGIGDTIADKETMKKIQEtikkA 584
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 657 KERVKEFEQQYLDGLITQGEKY-------NKVVDVWSECTEKVATEMMKVISDTapgkpvNSVYMMAHSGARGSAAQIRQ 729
Cdd:cd02733 585 KRDVIKLIEKAQNGELEPQPGKtlresfeNKVNRILNKARDKAGKSAQKSLSED------NNFKAMVTAGSKGSFINISQ 658
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 730 lagMRGLMAKPSGEIIETP-----------------------IISNFKEGLTVLEYFNSTHGARKGLADTALKTANSGYL 786
Cdd:cd02733 659 ---IIACVGQQNVEGKRIPfgfrrrtlphfikddygpesrgfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYI 735
|
890
....*....|...
gi 1719390878 787 TRRLVDVAQDAII 799
Cdd:cd02733 736 QRRLVKAMEDVMV 748
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
228-791 |
1.42e-63 |
|
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: 233.21 E-value: 1.42e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 228 FLSSQSRPEWMILEVIPVIPPELRPLVPLDGGrfATSDLNDL---YRRVINRNNRLKRLIELKAPDIIVRNEKRMLQEAV 304
Cdd:cd02583 168 MNPLAGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQC 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 305 DALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP---- 380
Cdd:cd02583 246 ALYINSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPervt 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 381 ----------------------FIYAKLElyGLASTIKAAKRMVEKERPEVWDILEEVIREHPVML-NRAPTLHRLGIQA 437
Cdd:cd02583 326 rynieklrklvlngpdvhpganFVIKRDG--GKKKFLKYGNRRKIARELKIGDIVERHLEDGDIVLfNRQPSLHRLSIMA 403
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 438 FEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPSQDIVLGLYYITM- 516
Cdd:cd02583 404 HRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSk 483
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 517 DrpgekgegmTFANVGEIEQAldakVVTLHAkvkarykgvdenGDEKISIVETT---P-----GRMLLSEILPRNPAVP- 587
Cdd:cd02583 484 D---------VFFDRAQFCQL----CSYMLD------------GEIKIDLPPPAilkPvelwtGKQIFSLLLRPNKKSPv 538
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 588 ---FSLINRLLTKKDVG-NVIDA--VYRH----CGQ--KETV-------IFADRLMKLGFGHACRA-------------- 634
Cdd:cd02583 539 lvnLEAKEKSYTKKSPDmCPNDGyvVIRNsellCGRldKSTLgsgsknsLFYVLLRDYGPEAAAAAmnrlaklssrwlsn 618
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 635 -GISFGKDDmVIP-----EAKKKLVNDSKERVKEFEQQYLDG-LITQgekynkvvdvwSECTEKVATEMMK-----VISD 702
Cdd:cd02583 619 rGFSIGIDD-VTPskellKKKEELVDNGYAKCDEYIKQYKKGkLELQ-----------PGCTAEQTLEAKIsgelsKIRE 686
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 703 TApGK-------PVNSVYMMAHSGARGSAAQIRQ---------LAGMR--------GL--MAKPSgeiiETPI----ISN 752
Cdd:cd02583 687 DA-GKaclkelhKSNSPLIMALCGSKGSNINISQmiacvgqqiISGKRipngfedrTLphFPRNS----KTPAakgfVAN 761
|
650 660 670 680
....*....|....*....|....*....|....*....|
gi 1719390878 753 -FKEGLTVLEYFNSTHGARKGLADTALKTANSGYLTRRLV 791
Cdd:cd02583 762 sFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLM 801
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1087-1358 |
1.09e-61 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 232.52 E-value: 1.09e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1087 YFMSVDAILSVENGAHVRAGDVLARIPRESSKTRDITGGLPRVAELFEARrpkDFAIIS-DLDGRVE-FGKDYKtkrriv 1164
Cdd:CHL00117 1096 YLATPGATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEAR---SIDSISmNLEKRLEgWNERIT------ 1166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1165 vrndetgdeREYLIPKGKHISVQegdyvqrgdllmdgnpvphdiLSVmgvEALANYLINEIQDVYRLQGVKINDKHIEVI 1244
Cdd:CHL00117 1167 ---------RILGIPWGFLIGAE---------------------LSI---AQSQISLVNKIQKVYRSQGVQISDKHIEII 1213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1245 VRQMLQKVEITDAGETT-FLVGEQVDRQEFdeenEKTvGEGLKPAAGH-PVLQGITKASLQTRSFISAASFQETTRVLTE 1322
Cdd:CHL00117 1214 VRQMTSKVLVSEDGMSNvFLPGELIGLLRA----ERI-NRALEEAICYrPILLGITKASLNTQSFISEASFQETTRVLAK 1288
|
250 260 270
....*....|....*....|....*....|....*...
gi 1719390878 1323 AAVSGKTDNLEGLKENVIVGRLIPAGTGS--VVNRLKQ 1358
Cdd:CHL00117 1289 AALRGRIDWLKGLKENVILGGLIPAGTGFkgLVHRSKQ 1326
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
345-486 |
7.40e-46 |
|
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: 162.47 E-value: 7.40e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 345 GKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYAKL-------------ELYGLASTIK---------AAKRMV 402
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYnikrlrqlvengpNVYPGANYIIringarrdlRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 403 EKERPEVWDILEE-VIREHPVMLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEA 481
Cdd:pfam00623 81 LDKELEIGDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 1719390878 482 RVLMM 486
Cdd:pfam00623 161 EELML 165
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
235-791 |
3.88e-44 |
|
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: 173.14 E-value: 3.88e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 235 PEWMILEVIPVIPPELRPLVPLDGGRFaTSDLNDLYRRVINRNNRLKRLIELKAPDIIVRNEKRM--------------- 299
Cdd:cd01435 127 YDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLIsgktnseklinawlq 205
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 300 LQEAVDALFDNGRrgrvITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALEL-F 378
Cdd:cd01435 206 LQSAVNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLtF 281
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 379 ----KPFIYAKLE-------------------------LYGLASTIKAAKRMVEKERPE----------VW------DIl 413
Cdd:cd01435 282 pepvTPFNVEELRqavingpdvypganaiededgrlilLSALSEERRKALAKLLLLLSSaklllngpkkVYrhlldgDV- 360
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 414 eevirehpVMLNRAPTLHRLGIQAFEPTLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNIL 492
Cdd:cd01435 361 --------VLLNRQPTLHKPSIMAHKVRVLPGeKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYL 432
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 493 SPANGKPI---IvpsQDIVLGLYYITM-DRPGEKGEGMTF---ANVGEIEQALDAKVVTLHA---KVKARYKGvdengde 562
Cdd:cd01435 433 VPTDGKPLrglI---QDHVVSGVLLTSrDTFFTREEYQQLvyaALRPLFTSDKDGRIKLLPPailKPKPLWTG------- 502
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 563 K--ISivettpgrMLLSEILPRNPAVPFSLINRLLTKKDVGNVIDAvyrhcGQKE-TVIFAD-RLM-----KLGFG---- 629
Cdd:cd01435 503 KqvIS--------TILKNLIPGNAPLLNLSGKKKTKKKVGGGKWGG-----GSEEsQVIIRNgELLtgvldKSQFGasay 569
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 630 ---HAC-------------------------RAGISFGKDDMVI-PEA---KKKLVNDSKERVKEFEQQYLdglitqGEK 677
Cdd:cd01435 570 glvHAVyelyggetagkllsalgrlftaylqMRGFTCGIEDLLLtPKAdekRRKILRKAKKLGLEAAAEFL------GLK 643
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 678 YNKVVDvwsectekvatemmKVISDTAPG-----KPVNSVYMMAHSGARGS---AAQI------RQLAGMR-GLMAK--- 739
Cdd:cd01435 644 LNKVTS--------------SIIKACLPKgllkpFPENNLQLMVQSGAKGSmvnASQIscllgqQELEGRRvPLMVSgkt 709
|
650 660 670 680 690 700
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1719390878 740 -PSGEIIET-P-----IISNFKEGLTVLEYFnsTH---GaRKGLADTALKTANSGYLTRRLV 791
Cdd:cd01435 710 lPSFPPYDTsPraggfITDRFLTGIRPQEYF--FHcmaG-REGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
490-643 |
1.31e-35 |
|
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: 133.14 E-value: 1.31e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 490 NILSPANGKPIIVPSQDIVLGLYYITMDRpgekgegmTFANVGEIEQALDAKVVTLHAKVKARYKgvdengdeKISIVET 569
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAILKPIK--------PLWTGKQ 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 570 TPGRMLLSEILPRNPAVPFS----------------LINRLLTKKDVG----NVIDAVYRHCGQKETVIFADRLMKLGFG 629
Cdd:pfam04983 65 TFSRLLPNEINPKGKPKTNEedlcendsyvlinngeLISGVIDKKTVGkslgSLIHIIYKEYGPEETAKFLDRLQKLGFR 144
|
170
....*....|....
gi 1719390878 630 HACRAGISFGKDDM 643
Cdd:pfam04983 145 YLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1205-1351 |
5.06e-25 |
|
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: 102.50 E-value: 5.06e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1205 PHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITdagettflvgeQVDRQEFDEENEktvgeg 1284
Cdd:cd00630 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLR-----------GVTRSGFRASKT------ 112
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1719390878 1285 lkpaaghpvlqgitkaslqtrSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGS 1351
Cdd:cd00630 113 ---------------------SPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
672-754 |
2.00e-21 |
|
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: 90.50 E-value: 2.00e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 672 ITQGEKYNKVVDVWSECTEKVATEMMKVISDTA----------PGKPVNSVYMMAHSGARGSAAQIRQLAGMRGLMAKPS 741
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKArdpagniaskSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 1719390878 742 GEI---------------IETPIISNFK 754
Cdd:pfam05000 81 KRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
897-1352 |
7.96e-21 |
|
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: 96.17 E-value: 7.96e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 897 TLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAaqrgaeqsqveAAFDATV---RIhnrnvvinssnIPVVMGRST--- 970
Cdd:cd06528 35 SLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGV-----------AEINVTLglpRL-----------IEIVDARKEpst 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 971 ---EVILLDEQG--RERARhRVpygAKLLadEGVKVERGQKLAEWDPYTLPIITEREgtahyVDLVE--GISMREVMdEA 1043
Cdd:cd06528 93 ptmTIYLEEEYKydREKAE-EV---ARKI--EETTLENLAEDISIDLFNMRITIELD-----EEMLEdrGITVDDVL-KA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1044 TGISSKVVVDwrqqprgadlkpritlRDERGEIITLANGLEaryfmSVDAILSVENgahvragdvlaripressKTRDIT 1123
Cdd:cd06528 161 IEKLKKGKVG----------------EEGDVTLIVLKAEEP-----SIKELRKLAE------------------KILNTK 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1124 gglprvaelfearrpkdfaiISDLDGrvefgkdyktKRRIVVRNDETgderEYLIpkgkhisVQEGDYVqRGDLLMDG-N 1202
Cdd:cd06528 202 --------------------IKGIKG----------IKRVIVRKEED----EYVI-------YTEGSNL-KAVLKVEGvD 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1203 PV------PHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMlqkveiTDAGETtflvgEQVDRqefdee 1276
Cdd:cd06528 240 PTrtttnnIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIM------TYDGEV-----RQIGR------ 302
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1719390878 1277 nektvgeglkpaaghpvlQGI--TKASLQTRsfisaASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:cd06528 303 ------------------HGIagEKPSVLAR-----AAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDV 357
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
872-1350 |
3.00e-20 |
|
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: 97.92 E-value: 3.00e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 872 IRSVLTCETKDGVC--AKCYGRDLARgtLVNVG---EAVGV------IAAQSIGEpgTQLTMRTFHIGGAAqrgaeqsqv 940
Cdd:COG0086 42 ERDGLFCERIFGPCkdYECYCGKYKR--MVYKGvvcEKCGVevtlskVRRERMGH--IELAMPVFHIWGLK--------- 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 941 eaafdatvrihnrnvvinssNIPVVMGrstevILLDEQGRERARHRVpYGAKLLADEGVK-VERGQKLAEwDPYtLPIIT 1019
Cdd:COG0086 109 --------------------SLPSRIG-----LLLDMSLRDLERVLY-FESYVVIDPGDTpLEKGQLLTE-DEY-REILE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1020 E-------REGTAHYVDLVEGI-------SMREVMDEATGISSK-------VVVDWRQQ----------------PRGA- 1061
Cdd:COG0086 161 EygdefvaKMGAEAIKDLLGRIdlekeseELREELKETTSEQKRkklikrlKVVEAFREsgnrpewmildvlpviPPDLr 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1062 ----------------DLKPRITLRDER---------GEIItLANglEARyfM---SVDAILsvENGAHVRAGDVLARIP 1113
Cdd:COG0086 241 plvpldggrfatsdlnDLYRRVINRNNRlkrllelkaPDII-VRN--EKR--MlqeAVDALF--DNGRRGRAVTGANKRP 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1114 RES-----------------SKTRD-------ITG--------GLPR--VAELFearrpKDFaIISDLDGRVEFGKDYKT 1159
Cdd:COG0086 314 LKSlsdmlkgkqgrfrqnllGKRVDysgrsviVVGpelklhqcGLPKkmALELF-----KPF-IYRKLEERGLATTIKSA 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1160 KRRIVVRNDETGDEREYLI----------PKGKHISVQ-------EGDYVQ-------------RGD------------- 1196
Cdd:COG0086 388 KKMVEREEPEVWDILEEVIkehpvllnraPTLHRLGIQafepvliEGKAIQlhplvctafnadfDGDqmavhvplsleaq 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1197 ----LLM----------DGNPV------------------------------PHDILSVMGVEALA-------------- 1218
Cdd:COG0086 468 learLLMlstnnilspaNGKPIivpsqdmvlglyyltreregakgegmifadPEEVLRAYENGAVDlharikvritedge 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1219 -----------NYLINEI--QDVYRLQGVkINDKHIEVIVRQM---------------LQKVEI---TDAGETTFLVGEQ 1267
Cdd:COG0086 548 qvgkivettvgRYLVNEIlpQEVPFYNQV-INKKHIEVIIRQMyrrcglketvifldrLKKLGFkyaTRAGISIGLDDMV 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1268 VDRQE---FDEENEKTVG------EGL--KPAAGHPVLQGITKASLQTRSFISAA-SFQETTRVLTEAAVSGKTDNLEGL 1335
Cdd:COG0086 627 VPKEKqeiFEEANKEVKEiekqyaEGLitEPERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQL 706
|
730 740
....*....|....*....|....*...
gi 1719390878 1336 ----------KENVI---VGRLIPAGTG 1350
Cdd:COG0086 707 agmrglmakpSGNIIetpIGSNFREGLG 734
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
326-517 |
7.09e-20 |
|
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: 95.93 E-value: 7.09e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 326 KSLSDMLKGKQgrFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFkpfIYAKLELYGLAS-TIKAAKRMVEK 404
Cdd:cd10506 195 SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLT---VSERVSSWNRERlQEYCDLTLLLK 269
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 405 ER--PEVWDILEEVIREHP----------------VMLNRAPTLHRLGIQAFEPTLIE-GKAIQLHPLVCTAFNADFDGD 465
Cdd:cd10506 270 GVigVRRNGRLVGVRSHNTlqigdvihrplvdgdvVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRGDFDGD 349
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|..
gi 1719390878 466 QMAVHVPLSLEAQLEARVLMMSTNNILSPANGKPIIVPSQDIVLGLYYITMD 517
Cdd:cd10506 350 CLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTER 401
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
897-1352 |
1.24e-19 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 92.60 E-value: 1.24e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 897 TLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQrgaeqsqveaaFDATV---RIhnrnvvinssnIPVVMGR---ST 970
Cdd:PRK04309 54 SLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAE-----------INVTLglpRL-----------IEIVDARkepST 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 971 ---EVILLDEQGRERARhrvpygAKLLAD--EGVKVERGQKLAEWDPYTLPIIteregtahyvdlvegISMREVMDEATG 1045
Cdd:PRK04309 112 pmmTIYLKDEYAYDREK------AEEVARkiEATTLENLAKDISVDLANMTII---------------IELDEEMLEDRG 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1046 ISSKVVVdwrqqprgadlkpritlrdergEIITLANGLEARyfmsvdailsvengahvRAGDVLARIPREssktrditgg 1125
Cdd:PRK04309 171 LTVDDVK----------------------EAIEKKKGGEVE-----------------IEGNTLIISPKE---------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1126 lPRVAELFEARRPKDFAIISDLDGrvefgkdyktKRRIVVRNdetgDEREYLIpkgkhisVQEGDYVqRGDLLMDG---- 1201
Cdd:PRK04309 202 -PSYRELRKLAEKIRNIKIKGIKG----------IKRVIIRK----EGDEYVI-------YTEGSNL-KEVLKVEGvdat 258
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1202 -----NpvPHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMlqkveiTDAGEttflvgeqvdrqefdee 1276
Cdd:PRK04309 259 rtttnN--IHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMM------TWDGE----------------- 313
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1719390878 1277 nektvgegLKPAAGHpvlqGIT--KASLQTRsfisaASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:PRK04309 314 --------VRQIGRH----GVSgeKASVLAR-----AAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDV 374
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
897-1352 |
3.47e-17 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 86.40 E-value: 3.47e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 897 TLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQrgaeqsqveaaFDATVRIHNRNVVINSSNIPvvmgrSTEV--IL 974
Cdd:PRK14897 177 ARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAE-----------MNVTLGLPRLIEIVDARKKP-----STPTmtIY 240
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 975 LDEQGRErarhrvpygakllaDEGVKVERGQKLaewdpytlpiiteregtahyvdlvEGISMREVMDEATGISSKVVVdw 1054
Cdd:PRK14897 241 LKKDYRE--------------DEEKVREVAKKI------------------------ENTTLIDVADIITDIAEMSVV-- 280
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1055 rqqprgADLKPRITlrdergeiitlanglearyfmsvdailsveNGAHVRAGDVLARIPRESSKTRDITGGL-------P 1127
Cdd:PRK14897 281 ------VELDEEKM------------------------------KERLIEYDDILAAISKLTFKTVEIDDGIirlkpqqP 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1128 RVAELFEARRPKDFAIISDLDGrvefgkdyktKRRIVVRNDetGDEREYLI-PKGKHI-SVQEGDYVqrgdllmDG---- 1201
Cdd:PRK14897 325 SFKKLYLLAEKVKSLTIKGIKG----------IKRAIARKE--NDERRWVIyTQGSNLkDVLEIDEV-------DPtrty 385
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1202 -NPVpHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIevivrqMLQKVEITDAGETtflvgEQVDRqefdeenekt 1280
Cdd:PRK14897 386 tNDI-IEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHI------MLVADMMTFDGSV-----KAIGR---------- 443
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1719390878 1281 vgeglkpaaghpvlQGItkaSLQTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:PRK14897 444 --------------HGI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAV 498
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
897-1352 |
4.62e-17 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 84.72 E-value: 4.62e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 897 TLVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQrgaeqsqveaaFDATVRIHNRNVVINSSNIPvvmgrST---EVI 973
Cdd:TIGR02389 39 SLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAE-----------LNVTLGLPRLIEIVDARKTP-----STpsmTIY 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 974 LLDE--QGRERARHRVpygAKLladEGVKVErgqklaewdpytlpiiteregtahyvDLVEGISmrevmdeaTGISSKVV 1051
Cdd:TIGR02389 103 LEDEyeKDREKAEEVA---KKI---EATKLE--------------------------DVAKDIS--------IDLADMTV 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1052 VdwrqqprgADLKPRITlrDERGeiITLANGLEA--RYFMSVDAILSVENGahvragdvlaripresskTRDITGGLPRV 1129
Cdd:TIGR02389 143 I--------IELDEEQL--KERG--ITVDDVEKAikKAKLGKVIEIDMDNN------------------TITIKPGNPSL 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1130 AELFE-ARRPKDFAIisdldgrvefgKDYKTKRRIVVRndETGDEReYLIPKGKHIsvqegdyvqRGDLLMDG------- 1201
Cdd:TIGR02389 193 KELRKlKEKIKNLHI-----------KGIKGIKRVVIR--KEGDEY-VIYTEGSNL---------KEVLKLEGvdktrtt 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1202 -NPVpHDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMlqkveiTDAGEttflvgeqvdrqefdeenekt 1280
Cdd:TIGR02389 250 tNDI-HEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLM------TWDGE--------------------- 301
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1719390878 1281 vgegLKPAAGHpvlqGIT--KASLQTRsfisaASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:TIGR02389 302 ----VRQIGRH----GISgeKASVLAR-----AAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDV 362
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
898-1351 |
1.42e-13 |
|
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: 74.55 E-value: 1.42e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 898 LVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGaaqrgaeqsqVEAafdatvrihnRNV---------VIN-SSNI--Pvv 965
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG----------VSA----------KNVtlgvprlkeIINvAKNIktP-- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 966 mgrSTEVILLDEQGRErarhrvPYGAK--LLADEGVKVERGQKLAE--WDP-YTLPIITEREgtahyvDLVEG-ISMREV 1039
Cdd:cd02584 81 ---SLTVYLEPGFAKD------EEKAKkiQSRLEHTTLKDVTAATEiyYDPdPQNTVIEEDK------EFVESyFEFPDE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1040 MDEATGISS---KVVVDwrqqprgadlkpRITLRDERGEIITLANGLEARYFMSVDAILSVENGAHVRagdVLARIPRES 1116
Cdd:cd02584 146 DVEQDRLSPwllRIELD------------RKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKLV---IRIRIINDD 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1117 SkTRDITGGLPRVAELFEARRPKDFAIISDLDGRVEFGKdyktKRRIVVRNDETGDERE----YLIPKGKHI----SVQE 1188
Cdd:cd02584 211 E-EKEEDSEDDVFLKKIESNMLSDMTLKGIEGIRKVFIR----EENKKKVDIETGEFKKreewVLETDGVNLrevlSHPG 285
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1189 GDYVQ--RGDLLmdgnpvphDILSVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKveitdagettflvge 1266
Cdd:cd02584 286 VDPTRttSNDIV--------EIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLCDVMTQR--------------- 342
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1267 qvdrqefdeenektvgeglkpaaGHpvLQGITKASL--QTRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRL 1344
Cdd:cd02584 343 -----------------------GH--LMAITRHGInrQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQL 397
|
....*..
gi 1719390878 1345 IPAGTGS 1351
Cdd:cd02584 398 APIGTGC 404
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
902-1352 |
1.09e-11 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 67.24 E-value: 1.09e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 902 GEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRGAEQsqveaafdATVRIhnrNVVIN-SSNIpvvmgrSTEVI---LLDE 977
Cdd:cd02736 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITL--------GVPRI---KEIINaSKNI------STPIItakLEND 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 978 QGRERARhRVpygaklladegvkveRGQklaewdpytlpiiteregtahyvdlVEGISMREVmdeatgiSSKVvvdwrqq 1057
Cdd:cd02736 73 RDEKSAR-IV---------------KGR-------------------------IEKTYLGEV-------ASYI------- 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1058 prgadlkpritlrdergEIITLANGlearYFMSVDAILSVENGAHVRAGDVLARIpressktRDITGGLPRVaelfearr 1137
Cdd:cd02736 98 -----------------EEVYSPDD----CYILIKLDKKIIEKLQLSKSNLYFLL-------QSLKRKLPDV-------- 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1138 pkdfaIISdldgrvefgkDYKTKRRIVVRNDETGDEREYLIpkgkhisvqEGdYVQRGDLLMDG--------NPVpHDIL 1209
Cdd:cd02736 142 -----VVS----------GIPEVKRAVINKDKKKGKYKLLV---------EG-YGLRAVMNTPGvigtrttsNHI-MEVE 195
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1210 SVMGVEALANYLINEIQDVYRLQGVKINDKHIEVIVRQMLQKVEITdaGETTFlvgeqvdrqefdeenektvgeglkpaa 1289
Cdd:cd02736 196 KVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEVL--GITRF--------------------------- 246
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1719390878 1290 ghpvlqGITKASlqtRSFISAASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:cd02736 247 ------GIAKMK---ESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
902-937 |
7.52e-11 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 62.05 E-value: 7.52e-11
10 20 30
....*....|....*....|....*....|....*.
gi 1719390878 902 GEAVGVIAAQSIGEPGTQLTMRTFHIGGAAQRGAEQ 937
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTL 36
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1162-1352 |
1.60e-10 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 65.68 E-value: 1.60e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1162 RIVVRNDETGDEREYLIpkgkhisvqegdYVQRGDLL----MDG--------NPVpHDILSVMGVEALANYLINEIQDVY 1229
Cdd:PRK14898 693 RVLVKKEEHENDEEYVL------------YTQGSNLRevfkIEGvdtsrtttNNI-IEIQEVLGIEAARNAIINEMMNTL 759
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719390878 1230 RLQGVKINDKHIEVIVRQMlqkveiTDAGEttflvgeqvdrqefdeenektvgegLKPAAGHPVlqgitkaSLQTRSFIS 1309
Cdd:PRK14898 760 EQQGLEVDIRHLMLVADIM------TADGE-------------------------VKPIGRHGV-------AGEKGSVLA 801
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1719390878 1310 AASFQETTRVLTEAAVSGKTDNLEGLKENVIVGRLIPAGTGSV 1352
Cdd:PRK14898 802 RAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCV 844
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
898-935 |
4.43e-10 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 62.59 E-value: 4.43e-10
10 20 30
....*....|....*....|....*....|....*...
gi 1719390878 898 LVNVGEAVGVIAAQSIGEPGTQLTMRTFHIGGaaqRGA 935
Cdd:cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG---RGE 40
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
895-922 |
1.26e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.34 E-value: 1.26e-03
10 20
....*....|....*....|....*...
gi 1719390878 895 RGTLVNVGEAVGVIAAQSIGEPGTQLTM 922
Cdd:PRK14898 50 LNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
