|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
446-1497 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 1712.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 446 VVESY--DIDARMGAEAIQQLLKELDLEALEKELLEEMKHP-SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPP 522
Cdd:PRK00566 158 ALEEYgdEFVAKMGAEAIKELLKNIDLEAEAEELREELKETgSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPP 237
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 523 DLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGsDRPLRS 602
Cdd:PRK00566 238 DLRPLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPN-NRPLKS 316
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 603 LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRD 682
Cdd:PRK00566 317 LSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDP 396
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 683 ikdEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQ 762
Cdd:PRK00566 397 ---EVWDVLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVL 473
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 763 MLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVagretsvgRLKyv 842
Cdd:PRK00566 474 MLSSNNILSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKV--------RIT-- 543
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 843 fanpdeallavahgivdlqdvvtvryMGKRLETSPGRILFARIVAEAVEdekvaweLIQLDVPQEKNSLKDLVYQAFLRL 922
Cdd:PRK00566 544 --------------------------SKKLVETTVGRVIFNEILPEGLP-------FINVNKPLKKKEISKIINEVYRRY 590
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 923 GMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK 1002
Cdd:PRK00566 591 GLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDE 670
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1003 VTQAVFKNFE-ENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG 1081
Cdd:PRK00566 671 VAKAMMKNLSkDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGL 750
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1082 ADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISV-PLFQPDEVTRSLRLRkradieagLYGRVLAREV------E 1154
Cdd:PRK00566 751 ADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVtAIIEGGEVIEPLEER--------ILGRVLAEDVvdpetgE 822
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1155 VLgvrLEEGRYLSMDDVHLLIKAAeageIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGT 1234
Cdd:PRK00566 823 VI---VPAGTLIDEEIADKIEEAG----IEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGT 895
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1235 QLTMRTFHTGGVagaaDITQGLPRVIELFEARRPKAKAVISEIDGVVR-IEETEEKLSVFVESE-GFSKEYKLPKEARLL 1312
Cdd:PRK00566 896 QLTMRTFHTGGV----DITGGLPRVAELFEARKPKGPAIIAEIDGTVSfGKETKGKRRIVITPDdGEEREYLIPKGKHLL 971
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1313 VKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEG 1392
Cdd:PRK00566 972 VQEGDHVEAGDKLTDGSIDPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPG 1051
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1393 QVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLI 1472
Cdd:PRK00566 1052 ELVDRSEFEEENRKLIAEGKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLI 1131
|
1050 1060
....*....|....*....|....*
gi 78101264 1473 PAGTGSDFVRFTQVVDQKTLKAIEE 1497
Cdd:PRK00566 1132 PAGTGLARYRNIKVEPAVDEEEAEA 1156
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
453-1477 |
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: 1368.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 453 DARMGAEAIQQLLKELDLEALEKELLEEM-KHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVD 531
Cdd:TIGR02386 159 RAGMGAEAIKELLEKIDLDKEIEELKIQLrESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLD 238
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 532 GGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSdRPLRSLTDILSGKQ 611
Cdd:TIGR02386 239 GGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNN-RPLKSLSDMLKGKQ 317
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 612 GRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQrdiKDEVWDAL 691
Cdd:TIGR02386 318 GRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQE---DPEVWDVL 394
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 692 EEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS 771
Cdd:TIGR02386 395 EDVIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILN 474
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 772 PASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVagretsvgrlkyvfanpdeall 851
Cdd:TIGR02386 475 PKDGKPIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGV---------------------- 532
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 852 avahgivdlqdvvtvRYMGKRLETSPGRILFARIVAEAVEdekvaweLIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLL 931
Cdd:TIGR02386 533 ---------------RTSGEILETTVGRVIFNEILPEGFP-------YINDNEPLSKKEISSLIDLLYEVHGIEETAEML 590
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 932 DALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNF 1011
Cdd:TIGR02386 591 DKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLL 670
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1012 EEN-YPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTAD 1090
Cdd:TIGR02386 671 KKDtYKFNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTAD 750
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1091 SGYLTRKLVDVTHEIVVREADCGTTNYISVP-LFQ-PDEVTRSLRLRkradieagLYGRVLAREV---EVLGVRLEEGRY 1165
Cdd:TIGR02386 751 SGYLTRRLVDVAQDVVVREEDCGTEEGIEVEaIVEgKDEIIESLKDR--------IVGRYSAEDVydpDTGKLIAEANTL 822
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1166 LSMDDVHLLIKAAeageIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGG 1245
Cdd:TIGR02386 823 ITEEIAEKIENSG----IEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGG 898
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1246 VAGAA-DITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEK---LSVFVESEGFSKEYKLPKEARLLVKDGDYVEA 1321
Cdd:TIGR02386 899 VAGASgDITQGLPRVKELFEARTPKDKAVIAEVDGTVEIIEDIVKnkrVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSA 978
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1322 GQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVE 1401
Cdd:TIGR02386 979 GDKLTEGSIDPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFN 1058
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 78101264 1402 ALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Cdd:TIGR02386 1059 EENRKLLEQGKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
8-1477 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1299.46 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 8 VRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRR 87
Cdd:PRK14906 12 LRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRAKVRR 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 88 YRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDpkgailngVPVEKRqlltDEEYRELRygkqe 167
Cdd:PRK14906 92 ERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITS--------VDKEAR----EEDADDLR----- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 168 typlppgvDALVKDGEEVVkgqelapgvVSRLDGVALyrfPRRVRVEYVKkeraglrlplaawvekeaykpgeilaelpe 247
Cdd:PRK14906 155 --------DELAADLEELD---------AERDRLIEA---TRRLSVDYVP------------------------------ 184
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 248 pylfraeeegvvelkelEEGAFLVLRREDEPVAtyflpvgmtplvvhgeivekgqplaeakgllrmPRQVRAAQVEAEEE 327
Cdd:PRK14906 185 -----------------EDDEFVDDIGDDERLT---------------------------------AEEVRAEVADIYEE 214
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 328 getvyltlfleWTEPKDYRVqphmnvvvpegarvEAGDKIVaaidpeeeviaeaegvvhlhepasilvvkarvypfeddv 407
Cdd:PRK14906 215 -----------YNERKALRR--------------EAFDAFM--------------------------------------- 230
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 408 evstgdRVAPGDVLADGGkvksdvygrvevdLVRNVVRVVESYdIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRA 487
Cdd:PRK14906 231 ------QIEPKQLISDEA-------------LYREMRLNYSIY-FKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQ 290
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 488 RRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIII 567
Cdd:PRK14906 291 KREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIV 370
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 568 RNEKRMLQEAVDALLDNGRRGAPVTNPGsDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKR 647
Cdd:PRK14906 371 NNEKRMLQEAVDSLFDNGRRGRPVTGPG-NRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSA 449
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 648 MALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIkdeVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQ 727
Cdd:PRK14906 450 MALELFKPFVMKRLVELEYAANIKAAKRAVDRGASY---VWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIK 526
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 728 LHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFA 807
Cdd:PRK14906 527 LHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFA 606
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 808 TPEEALAAHE-RGEVALNAPIKVAGRETSVGRLKYVFANPDEAllavahgivdlqdvvtvrymGKRLETSPGRILFARIV 886
Cdd:PRK14906 607 DFDDALNAYDaRADLDLQAKIVVRLSRDMTVRGSYGDLEETKA--------------------GERIETTVGRIIFNQVL 666
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 887 AEavedekvawELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEE 966
Cdd:PRK14906 667 PE---------DYPYLNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAE 737
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 967 ADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENypfNPLYVMAQSGARGNPQQIRQLCGLRGLMQ 1046
Cdd:PRK14906 738 ADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFDED---NPIYMMADSGARGNIKQIRQLAGMRGLMA 814
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1047 KPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPd 1126
Cdd:PRK14906 815 DMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKP- 893
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1127 evtrslrlrkRADIEAGLYGRVLAREV-EVLGVRL-EEGRYL-SMDDVHLLIKAAeageIQEVPVRSPLTCQTRYGVCQK 1203
Cdd:PRK14906 894 ----------KGDVDTNLIGRCLLEDVcDPNGEVLlSAGDYIeSMDDLKRLVEAG----VTKVQIRTLMTCHAEYGVCQK 959
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1204 CYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGaADITQGLPRVIELFEARRPKAKAVISEIDGVVRI 1283
Cdd:PRK14906 960 CYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAG-DDITQGLPRVAELFEARKPKGEAVLAEISGTLQI 1038
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1284 E-ETEEKLSVFVESEGFSKEYKLPKEARLL--VKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQG 1360
Cdd:PRK14906 1039 TgDKTEKTLTIHDQDGNSREYVVSARVQFMpgVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQG 1118
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1361 VKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASF 1440
Cdd:PRK14906 1119 VDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASF 1198
|
1450 1460 1470
....*....|....*....|....*....|....*..
gi 78101264 1441 QNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Cdd:PRK14906 1199 QETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
453-1397 |
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: 1067.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 453 DARMGAEAIQQLLKELDLEALEKELLEEMKH-PSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVD 531
Cdd:COG0086 167 VAKMGAEAIKDLLGRIDLEKESEELREELKEtTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLD 246
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 532 GGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSdRPLRSLTDILSGKQ 611
Cdd:COG0086 247 GGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANK-RPLKSLSDMLKGKQ 325
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 612 GRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQrdiKDEVWDAL 691
Cdd:COG0086 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVERE---EPEVWDIL 402
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 692 EEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLS 771
Cdd:COG0086 403 EEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILS 482
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 772 PASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRlkyvfanpdeall 851
Cdd:COG0086 483 PANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGEQV------------- 549
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 852 avahgivdlqdvvtvrymGKRLETSPGRILFARIVAEavedekvawELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLL 931
Cdd:COG0086 550 ------------------GKIVETTVGRYLVNEILPQ---------EVPFYNQVINKKHIEVIIRQMYRRCGLKETVIFL 602
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 932 DALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNF 1011
Cdd:COG0086 603 DRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAF 682
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1012 EenyPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADS 1091
Cdd:COG0086 683 S---SQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADS 759
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1092 GYLTRKLVDVTHEIVVREADCGTTNYISV-PLFQPDEVTRSLRLRkradieagLYGRVLAREVEVLGVRLEEGRYLSMDD 1170
Cdd:COG0086 760 GYLTRRLVDVAQDVIVTEEDCGTDRGITVtAIKEGGEVIEPLKER--------ILGRVAAEDVVDPGTGEVLVPAGTLID 831
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1171 VHLLIKAAEAGeIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAA 1250
Cdd:COG0086 832 EEVAEIIEEAG-IDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRA 910
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1251 DITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEklsVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAI 1330
Cdd:COG0086 911 AEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSEL---VIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWD 987
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 78101264 1331 DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEK 1397
Cdd:COG0086 988 PHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSL 1054
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
498-1111 |
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: 988.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 498 VVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEA 577
Cdd:cd01609 128 VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEA 207
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 578 VDALLDNGRRGAPVTNPGsDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFL 657
Cdd:cd01609 208 VDALIDNGRRGKPVTGAN-NRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFV 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 658 LKKMEEKGIAPNVKAARRMLERQRDikdEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFN 737
Cdd:cd01609 287 IRELIERGLAPNIKSAKKMIERKDP---EVWDILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFN 363
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 738 ADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLefatpeealaahe 817
Cdd:cd01609 364 ADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKGEGI------------- 430
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 818 rgevalnapikvagretsvgrlkyvfanpdeallavahgivdlqdvvtvrymgkrLETSPGRILFARIVAEAVEDekvaw 897
Cdd:cd01609 431 -------------------------------------------------------IETTVGRVIFNEILPEGLPF----- 450
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 898 eliqLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQA 977
Cdd:cd01609 451 ----INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQ 526
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 978 YEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEEnYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPV 1057
Cdd:cd01609 527 YEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDK-DPFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPI 605
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....
gi 78101264 1058 RSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREAD 1111
Cdd:cd01609 606 KSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
448-1477 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 887.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 448 ESYDID---ARMGAEAIQQLLKELDLEALEKELLEEMKH-PSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPD 523
Cdd:PRK14844 1601 DSYGIDsfvAMQGVEAIRELLTRLDLHEIRKDLRLELESvASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPD 1680
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 524 LRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSL 603
Cdd:PRK14844 1681 LRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKKSI 1760
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 604 TDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLerqRDI 683
Cdd:PRK14844 1761 SDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLI---RAE 1837
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 684 KDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQM 763
Cdd:PRK14844 1838 KPEVWDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLM 1917
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 764 LSAHNLLSPASGEPLAKPSRDIILGLYYITqVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVagretsvgRLKYVF 843
Cdd:PRK14844 1918 MSTNNVLSPSNGRPIIVPSKDIVLGIYYLT-LQEPKEDDLPSFGAFCEVEHSLSDGTLHIHSSIKY--------RMEYIN 1988
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 844 ANPDeallavahgivdlqdvvtVRYmgKRLETSPGRILFARIVAEaveDEKVAWELI-QLDVPQEKNSLKDLVYQAflrL 922
Cdd:PRK14844 1989 SSGE------------------THY--KTICTTPGRLILWQIFPK---HENLGFDLInQVLTVKEITSIVDLVYRN---C 2042
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 923 GMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK 1002
Cdd:PRK14844 2043 GQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDM 2122
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1003 VTQAVFKN---FEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARK 1079
Cdd:PRK14844 2123 IANDMLKAisiYDGNSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARK 2202
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1080 GGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVplfqpdevtrslrlrkRADIEAGLYgrVLAREVEVLGVR 1159
Cdd:PRK14844 2203 GLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVV----------------RATVEGSTI--VASLESVVLGRT 2264
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1160 LEEGRYLSMDDvHLLIKAAE---AGEIQE--------VPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQS 1228
Cdd:PRK14844 2265 AANDIYNPVTK-ELLVKAGElidEDKVKQiniagldvVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQS 2343
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1229 IGEPGTQLTMRTFHTGGV-------------------------------------------------------------- 1246
Cdd:PRK14844 2344 VGEPGTQLTMRTFHIGGVmtrgvessniiasinakiklnnsniiidkngnkivisrscevvlidslgseklkhsvpygak 2423
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1247 -----------------------------------------------------------------AGAA----------- 1250
Cdd:PRK14844 2424 lyvdeggsvkigdkvaewdpytlpiitektgtvsyqdlkdgisitevmdestgisskvvkdwklySGGAnlrprivlldd 2503
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1251 ------------------------------------------------DITQGLPRVIELFEARRPKAKAVISEIDGVVR 1282
Cdd:PRK14844 2504 ngkvmtlasgveacyfipigavlnvqdgqkvhagdvitrtpresvktrDITGGLPRVIELFEARRPKEHAIVSEIDGYVA 2583
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1283 IEETEE--KLSVF---VESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYR 1357
Cdd:PRK14844 2584 FSEKDRrgKRSILikpVDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYR 2663
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1358 AQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSA 1437
Cdd:PRK14844 2664 LQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISA 2743
|
1210 1220 1230 1240
....*....|....*....|....*....|....*....|
gi 78101264 1438 ASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Cdd:PRK14844 2744 ASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTG 2783
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
454-1307 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 781.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 454 ARMGAEAIQQLLKELDLEALEKELLEEMKHP-SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDG 532
Cdd:PRK09603 1567 AQMGGEAIKDLLEEIDLITLLQSLKEEVKDTnSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLPPDLRPLVALDG 1646
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 533 GRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNpGSDRPLRSLTDILSGKQG 612
Cdd:PRK09603 1647 GKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKG-ANKRPLKSLSEIIKGKQG 1725
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 613 RFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQrdiKDEVWDALE 692
Cdd:PRK09603 1726 RFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQK---SNEVWECLQ 1802
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 693 EVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSP 772
Cdd:PRK09603 1803 EITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLP 1882
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 773 ASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRetsvgrlkyvfanpdealla 852
Cdd:PRK09603 1883 ASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQ-------------------- 1942
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 853 vahgivdlqdvvtvrymGKRLETSPGRILFARIVAEAVEDEkvAWeliqlDVPQEKNSLKDLVYQAFLRLGMEKTARLLD 932
Cdd:PRK09603 1943 -----------------GNIIATSAGRMIIKSILPDFIPTD--LW-----NRPMKKKDIGVLVDYVHKVGGIGITATFLD 1998
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 933 ALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFE 1012
Cdd:PRK09603 1999 NLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA 2078
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1013 ENYP-FNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADS 1091
Cdd:PRK09603 2079 KDKEgFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANA 2158
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1092 GYLTRKLVDVTHEIVVREADCGTTNYISVP-LFQPDEVTRSLRLRkradieagLYGRVLAREV------EVLgvrLEEGr 1164
Cdd:PRK09603 2159 GYLTRKLIDVSQNVKVVSDDCGTHEGIEITdIAVGSELIEPLEER--------IFGRVLLEDVidpitnEIL---LYAD- 2226
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1165 ylSMDDVHLLIKAAEAGeIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTG 1244
Cdd:PRK09603 2227 --TLIDEEGAKKVVEAG-IKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVG 2303
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1245 GVAGAAD-------ITQGLPRVIELFEARRPKAKAVI----------------SEIDGVVRIEETEEKLSVFVESEGFSK 1301
Cdd:PRK09603 2304 GTASRSQdereivaSKEGFVRFYNLRTYTNKEGKNIIanrrnasilvvepkikAPFDGELRIETVYEEVVVSVKNGDQEA 2383
|
....*.
gi 78101264 1302 EYKLPK 1307
Cdd:PRK09603 2384 KFVLRR 2389
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
509-1110 |
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: 567.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 509 PEWMILEAVPVLPPDLRPMVqvdggrfatsdlndlyrrlinrnnrlkkllaqgapeiIIRNEKRMLQEAVDALLDNGRRG 588
Cdd:cd00399 84 PEWMILTCLPVPPPCLRPSV-------------------------------------IIEERWRLLQEHVDTYLDNGIAG 126
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 589 APVTnPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELfkpfllkkmeekgiap 668
Cdd:cd00399 127 QPQT-QKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL---------------- 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 669 nvkaarrmlerqrdikdevwdaleeviHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVH 748
Cdd:cd00399 190 ---------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLH 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 749 VPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQvrkekkgaglefatpeealaahergevalnapik 828
Cdd:cd00399 243 VPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLTL---------------------------------- 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 829 vagretsvgrlkyvfanpdeallavahgivdlqdvvtvrymgkrletspgrilFARIVAEAVEdekvaweliqldvpqek 908
Cdd:cd00399 289 -----------------------------------------------------GKQIVSAALP----------------- 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 909 nslKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIG----IDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLT 984
Cdd:cd00399 299 ---GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGigdvIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLT 375
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 985 DRER-------YDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETF---- 1053
Cdd:cd00399 376 AQEGmtleeslEDNILDFLNEARDKAGSAASVNLDLVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPrgfs 455
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 78101264 1054 ----------------EVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREA 1110
Cdd:cd00399 456 drtlphfskddyspeaKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
496-890 |
1.11e-180 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 554.51 E-value: 1.11e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 496 LEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQG--APEIIIRNEKRM 573
Cdd:CHL00018 248 IKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQKKL 327
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 574 LQEAVDALLDNGRRGAPVTNpGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELF 653
Cdd:CHL00018 328 LQEAVDALLDNGIRGQPMRD-GHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELF 406
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 654 KPFLLKKMEEKGIAPNVKAARRMLERQRDIkdeVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVC 733
Cdd:CHL00018 407 QPFVIRGLIRQHLASNIRAAKSKIREKEPI---VWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVC 483
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 734 EAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYIT-------------QVRKEKK 800
Cdd:CHL00018 484 KGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTignrrgiyanrynPCNRKNS 563
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 801 GAGLEFATPEEALAAHERGEVALNAPIKVagRETSVGRLKYVFANPDEAL---LAVAHGIVDLQDVVTVRYMGKR---LE 874
Cdd:CHL00018 564 TKEPYFSNSYDALGAYRQKRINLDSPLWL--RWRLDQRIIASREVPIEVQyesLGTYHEIYEHYLIVKSRKKEILsiyIR 641
|
410
....*....|....*.
gi 78101264 875 TSPGRILFARIVAEAV 890
Cdd:CHL00018 642 TTVGRILFNREIEEAI 657
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
456-890 |
1.57e-169 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 523.54 E-value: 1.57e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 456 MGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRF 535
Cdd:PRK02625 189 IGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRF 268
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 536 ATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNpGSDRPLRSLTDILSGKQGRFR 615
Cdd:PRK02625 269 ATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVG-ANNRPLKSLSDIIEGKQGRFR 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 616 QNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQrdiKDEVWDALEEVI 695
Cdd:PRK02625 348 QNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRA---DPEVWQVLEEVI 424
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 696 HGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASG 775
Cdd:PRK02625 425 EGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATG 504
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 776 EPLAKPSRDIILGLYYITQVR-KEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGREtsvgrlKYVFANPDEALLAVa 854
Cdd:PRK02625 505 EPIVTPSQDMVLGCYYLTAENpGAQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNG------EVEDDDEDTEPLKT- 577
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|
gi 78101264 855 hgiVDLQD-VVTVRYMGKRLE-------------TSPGRILFARIVAEAV 890
Cdd:PRK02625 578 ---ETLEDgTRIEQYRYRRDRfdedgnlisqyilTTVGRVIMNKTIQDAL 624
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
454-890 |
7.21e-167 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 516.45 E-value: 7.21e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 454 ARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGG 533
Cdd:TIGR02387 180 VGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVLDVIPVIPPDLRPMVQLDGG 259
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 534 RFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNpGSDRPLRSLTDILSGKQGR 613
Cdd:TIGR02387 260 RFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVG-ANNRPLKSLSDIIEGKQGR 338
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 614 FRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQrdiKDEVWDALEE 693
Cdd:TIGR02387 339 FRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKLIQRA---DDEIWSVLQE 415
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 694 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPA 773
Cdd:TIGR02387 416 VITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEARLLMLASNNVLSPA 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 774 SGEPLAKPSRDIILGLYYITQVRKE-KKGAGLEFATPEEALAAHERGEVALNAPIKVAGREtsvgrlKYVFANPDEALLA 852
Cdd:TIGR02387 496 TGEPIVTPSQDMVLGCYYLTALNPGaEKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNG------EVETNDPLDEPIK 569
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|..
gi 78101264 853 VAhgivDLQDVVTVRYMGKR--------------LETSPGRILFARIVAEAV 890
Cdd:TIGR02387 570 SE----DLSDGTRIEQWTYRrdrfdedgalisqyILTTTGRIIMNHTIIEAL 617
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
510-790 |
2.98e-148 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 453.90 E-value: 2.98e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 510 EWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGrrGA 589
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 590 PVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEK----- 664
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDklrkl 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 665 -------------GIAPNVKAARRM-LERQRDIKDEVwdaLEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHP 730
Cdd:smart00663 159 vrngpngakyiirGKKTNLKLAKKSkIANHLKIGDIV---ERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNP 235
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 731 LVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLY 790
Cdd:smart00663 236 LVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
908-1323 |
1.80e-117 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 402.78 E-value: 1.80e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 908 KNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRE 987
Cdd:CHL00117 16 KTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYGNVHAVE 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 988 RYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTV 1067
Cdd:CHL00117 96 KLRQSIEIWYATSEYLKQEMNPNFRMTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQSNFREGLSL 175
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1068 LEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRkradieagLYGR 1147
Cdd:CHL00117 176 TEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGMMIERILIQT--------LIGR 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1148 VLAREVeVLGVRLEEGR--YLSMDDVHLLIKAaeagEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVA 1225
Cdd:CHL00117 248 VLADDI-YIGSRCIATRnqDIGIGLANRFITF----RAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIA 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1226 AQSIGEPGTQLTMRTFHTGGVagaadITQGLprvielfearrpkAKAVISEIDGVVRIEE----------------TEEK 1289
Cdd:CHL00117 323 GQSIGEPGTQLTLRTFHTGGV-----FTGGT-------------AEQVRAPFNGKIKFNEdlvhptrtrhghpaflCKID 384
|
410 420 430
....*....|....*....|....*....|....
gi 78101264 1290 LSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQ 1323
Cdd:CHL00117 385 LYVTIESEDIIHNVNIPPKSLLLVQNDQYVESEQ 418
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
908-1325 |
4.25e-114 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 392.44 E-value: 4.25e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 908 KNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRE 987
Cdd:PRK02597 10 KKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEVE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 988 RYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTV 1067
Cdd:PRK02597 90 RFQKVIDTWNETNERLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLTV 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1068 LEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISV-PLFQPDEVTRSLRLRkradieagLYG 1146
Cdd:PRK02597 170 TEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVeAMDDGDRVLIPLGDR--------LLG 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1147 RVLAREV-----EVLGVRLEEgrylsmDDVHLLIKAAEAGeIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAV 1221
Cdd:PRK02597 242 RVLAEDVvdpegEVIAERNTA------IDPDLAKKIEKAG-VEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAV 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1222 GIVAAQSIGEPGTQLTMRTFHTGGVAGAaditqglprvielfEArrpkAKAVISEIDGVVR------------------- 1282
Cdd:PRK02597 315 GIIAAQSIGEPGTQLTMRTFHTGGVFTG--------------EV----ARQVRSPFAGTVEfgkklrtrpyrtrhgveal 376
|
410 420 430 440
....*....|....*....|....*....|....*....|...
gi 78101264 1283 IEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPL 1325
Cdd:PRK02597 377 QAEVDFDLVLKPSGKGKPQKIEITQGSLLFVDDGQTVEADQLL 419
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1213-1477 |
1.20e-110 |
|
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: 348.36 E-value: 1.20e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1213 RPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGaaDITQGLPRVIELFEARRpkakaviseidgvvrieeteeklsv 1292
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT--DITQGLPRVEELFEARK------------------------- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1293 fvesegfskeyklpkearllvkdgdyveagqpltrgaIDPHQLLE--AKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEI 1370
Cdd:cd02655 54 -------------------------------------INPHDLLRikFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEI 96
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1371 VVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEA 1450
Cdd:cd02655 97 IVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEA 176
|
250 260
....*....|....*....|....*..
gi 78101264 1451 AIAGKKDELIGLKENVILGRLIPAGTG 1477
Cdd:cd02655 177 AIEGKIDWLRGLKENVILGRLIPAGTG 203
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
907-1326 |
1.36e-106 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 369.18 E-value: 1.36e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 907 EKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDR 986
Cdd:TIGR02388 8 DKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGEITEV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 987 ERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLT 1066
Cdd:TIGR02388 88 ERFQKVIDTWNGTNEELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLT 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1067 VLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNyiSVPLFQPDEVTRSLRLRKRadieagLYG 1146
Cdd:TIGR02388 168 VTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTER--SIVVRAMTEGDKKISLGDR------LLG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1147 RVLAREV-----EVLGVRLEEgryLSMDdvhlLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAV 1221
Cdd:TIGR02388 240 RLVAEDVlhpegEVIVPKNTA---IDPD----LAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAV 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1222 GIVAAQSIGEPGTQLTMRTFHTGGVAGAA---------DITQGLPRVIELFEARRPKAK-AVISEIDGVVRIEETEEKLS 1291
Cdd:TIGR02388 313 GIIAAQSIGEPGTQLTMRTFHTGGVFTGEvarqvrskiDGTVEFGKKLRTRGYRTRHGEdAKQVEVAGLLIIKPTGSITN 392
|
410 420 430
....*....|....*....|....*....|....*
gi 78101264 1292 VfvesegfSKEYKLPKEARLLVKDGDYVEAGQPLT 1326
Cdd:TIGR02388 393 K-------AQEIEVTQGSLLFVEDGQTVDAGQLLA 420
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1-164 |
5.50e-100 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 348.60 E-value: 5.50e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1 MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEV 80
Cdd:PRK00566 3 NKQDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 81 TKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAilngvPVEKRQLLTDEEYRE 160
Cdd:PRK00566 83 TRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDT-----PLEKKQLLTEEEYRE 157
|
....*.
gi 78101264 161 L--RYG 164
Cdd:PRK00566 158 AleEYG 163
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
508-1107 |
7.49e-86 |
|
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: 300.70 E-value: 7.49e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRR 587
Cdd:cd02582 201 RPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIP 280
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 588 GAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPfllkkmeEKGIA 667
Cdd:cd02582 281 GIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVP-------ERVTE 353
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 668 PNVKAARRMLERQRDI---------------------KDEVWDALE-------EVIHGKVVLLNRAPTLHRLGIQAFQPV 719
Cdd:cd02582 354 WNIEKMRKLVLNGPDKwpganyvirpdgrrirlryvnREELAERLEpgwiverHLIDGDIVLFNRQPSLHRMSIMAHRVR 433
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 720 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITqvrkeK 799
Cdd:cd02582 434 VLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLT-----R 508
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 800 KGAGLEFatpEEA--LAAHERGEVALNAPIKVAGRETSVGR----------LKYVFANPDEALLAVAHGIVDLQD--VVT 865
Cdd:cd02582 509 KTTLFTK---EEAlqLLSAAGYDGLLPEPAILEPKPLWTGKqlfslflpkdLNFEGKAKVCSGCSECKDEDCPNDgyVVI 585
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 866 VRymgkrletspGRILfarivaEAVEDEKVaweliqldVPQEKNSlkDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTS 945
Cdd:cd02582 586 KN----------GKLL------EGVIDKKA--------IGAEQPG--SLLHRIAKEYGNEVARRFLDSVTRLAIRFIELR 639
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 946 GITIGIDDAVIPEEKKQYLEE----ADRKLLQIEQAYEMGFL-------TDRERYDQILQLWTETTEKVTQAVFKNFEen 1014
Cdd:cd02582 640 GFTIGIDDEDIPEEARKEIEEiikeAEKKVYELIEQYKNGELeplpgrtLEETLEMKIMQVLGKARDEAGKVASKYLD-- 717
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1015 yPFNPLYVMAQSGARGNPQQIRQLCGLRGlMQKPSGE-----------TFEVP----------VRSSFREGLTVLEYFIS 1073
Cdd:cd02582 718 -PFNNAVIMARTGARGSMLNLTQMAACLG-QQSVRGErinrgyrnrtlPHFKPgdlgpeargfVRSSFRDGLSPTEFFFH 795
|
650 660 670
....*....|....*....|....*....|....
gi 78101264 1074 SHGARKGGADTALRTADSGYLTRKLVDVTHEIVV 1107
Cdd:cd02582 796 AMGGREGLVDTAVRTSQSGYMQRRLINALQDLYV 829
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
3-147 |
1.17e-82 |
|
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: 286.34 E-value: 1.17e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTK 82
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 78101264 83 SIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFskyIV-------LDPKGAILNGVPV 147
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF---VVesfrksgNRPEWMILTVLPV 149
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
508-1107 |
2.10e-80 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 285.21 E-value: 2.10e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRR 587
Cdd:PRK08566 205 RPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIP 284
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 588 GAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPfllkkmeEKGIA 667
Cdd:PRK08566 285 GIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVP-------ERVTE 357
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 668 PNVKAARRMLERQRDI---------------------KDEVWDALEE-------VIHGKVVLLNRAPTLHRLGIQAFQPV 719
Cdd:PRK08566 358 WNIEELREYVLNGPEKhpganyvirpdgrrikltdknKEELAEKLEPgwiverhLIDGDIVLFNRQPSLHRMSIMAHRVR 437
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 720 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITqvRKEK 799
Cdd:PRK08566 438 VLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLT--RKST 515
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 800 kgagleFATPEEA---LAAHERGEVALNAPIKVAGRETSVGR----------LKYVF-ANPDEALLAVAHGIVDLQDVVT 865
Cdd:PRK08566 516 ------LFTKEEAldlLRAAGIDELPEPEPAIENGKPYWTGKqifslflpkdLNLEFkAKICSGCDECKKEDCEHDAYVV 589
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 866 VRymgkrletsPGRILfarivaEAVEDEKVaweliqldVPQEKNSLKDLVyqaFLRLGMEKTARLLDALKYYGFTFSTTS 945
Cdd:PRK08566 590 IK---------NGKLL------EGVIDKKA--------IGAEQGSILDRI---VKEYGPERARRFLDSVTRLAIRFIMLR 643
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 946 GITIGIDDAVIPEEKKQ----YLEEADRKLLQIEQAYEMGFLT-------DRERYDQILQLWTETTEKVTQAVFKNFEen 1014
Cdd:PRK08566 644 GFTTGIDDEDIPEEAKEeideIIEEAEKRVEELIEAYENGELEplpgrtlEETLEMKIMQVLGKARDEAGEIAEKYLG-- 721
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1015 yPFNPLYVMAQSGARGNPQQIRQLCGLRGlMQKPSGET------------FEVP---------VRSSFREGLTVLEYFIS 1073
Cdd:PRK08566 722 -LDNPAVIMARTGARGSMLNLTQMAACVG-QQSVRGERirrgyrdrtlphFKPGdlgaeargfVRSSYKSGLTPTEFFFH 799
|
650 660 670
....*....|....*....|....*....|....
gi 78101264 1074 SHGARKGGADTALRTADSGYLTRKLVDVTHEIVV 1107
Cdd:PRK08566 800 AMGGREGLVDTAVRTSQSGYMQRRLINALQDLKV 833
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
508-1478 |
5.67e-80 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 290.39 E-value: 5.67e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRR 587
Cdd:PRK14977 214 RPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATA 293
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 588 GAPVT-NPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFL-----LKKM 661
Cdd:PRK14977 294 GIPQAhHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnennIEKM 373
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 662 EEKGIA-----PNVKAARR----------MLERQRDIKDEVWDALE-------EVIHGKVVLLNRAPTLHRLGIQAFQPV 719
Cdd:PRK14977 374 KELVINgpdefPGANAIRKgdgtkirldfLEDKGKDALREAAEQLEigdiverHLADGDIVIFNRQPSLHKLSILAHRVK 453
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 720 LVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITqvrkeK 799
Cdd:PRK14977 454 VLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT-----K 528
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 800 KGAGLefaTPEEALAAHERGevALNAPIKVAGRETSVGRL---KYVFAnpdeALLAvahgiVDLQDVVTVRY-MGKRLET 875
Cdd:PRK14977 529 DDALF---DKNEASNIAMLA--GITDPLPEPAIKTKDGPAwtgKQLFS----LFLP-----KDFNFEGIAKWsAGKAGEA 594
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 876 SPGRILFARIVA-------EAVEDEKVAWELIqldvpQEKNSLKDLVYQAFlrlGMEKTARLLDALKYYGFTFSTTSGIT 948
Cdd:PRK14977 595 KDPSCLGDGYVLikegeliSGVIDDNIIGALV-----EEPESLIDRIAKDY---GEAVAIEFLNKILIIAKKEILHYGFS 666
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 949 IGIDDAVIPEEKKQYLEEA-------------DRKLLQIEQAYEMGF-LTDRERYDQILQLWTETT-----EKVTQAVFK 1009
Cdd:PRK14977 667 NGPGDLIIPDEAKQEIEDDiqgmkdevsdlidQRKITRKITIYKGKEeLLRGMKEEEALEADIVNEldkarDKAGSSAND 746
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1010 NFEenyPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVP----------------------------VRSSF 1061
Cdd:PRK14977 747 CID---ADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNY 823
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1062 REGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VTHEIVVREA-------DCGTTNYISVPLFQPDEV 1128
Cdd:PRK14977 824 REGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANaledirLEYDETVRDPhghiiqfKFGEDGIDPQKLDHGEAF 903
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1129 TRSLRLRKRADIEAGlyGRVLAREVEVLGVrlEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSpltcqtrygVCQKcyGYD 1208
Cdd:PRK14977 904 NLERIIEKQKIEDRG--KGASKDEIEELAK--EYTKTFNANLPKLLADAIHGAELKEDELEA---------ICAE--GKE 968
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1209 LSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIELFEARRP------------KAKAVISE 1276
Cdd:PRK14977 969 GFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIK-AMDVTHGLERFIELVDARAKpstptmdiylddECKEDIEK 1047
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1277 IDGVVR----------IEETE-----EKLSVFVE---------------------SEGFSKEYKLPKEaRLLVKDGDYVE 1320
Cdd:PRK14977 1048 AIEIARnlkelkvralIADSAidnanEIKLIKPDkralengcipmerfaeieaalAKGKKFEMELEDD-LIILDLVEAAD 1126
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1321 AGQPLTRGAIDPHQLLE--AKGPEAVERYLVEEIQKVYRAQGVklhdkhIEIVVRQMMKYVEVTDPGDSRLLEGQVLE-- 1396
Cdd:PRK14977 1127 RDKPLATLIAIRNKILDkpVKGVPDIERAWVELVEKDGRDEWI------IQTSGSNLAAVLEMKCIDIANTITNDCFEia 1200
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1397 -KWDVEALNERLIAEGKTPVAWKPL------------LM--------------GVTKSALST-KSWLSAASFQNTTHVLT 1448
Cdd:PRK14977 1201 gTLGIEAARNAIFNELASILEDQGLevdnryimlvadIMcsrgtieaiglqaaGVRHGFAGEkDSPLAKAAFEITTHTIA 1280
|
1130 1140 1150
....*....|....*....|....*....|
gi 78101264 1449 EAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:PRK14977 1281 HAALGGEIEKIKGILDALIMGQNIPIGSGK 1310
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
2-162 |
2.04e-78 |
|
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: 283.97 E-value: 2.04e-78
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 2 KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT 81
Cdd:COG0086 4 VEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 82 KSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAilngvPVEKRQLLTDEEYREL 161
Cdd:COG0086 84 LSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDT-----PLEKGQLLTEDEYREI 158
|
.
gi 78101264 162 R 162
Cdd:COG0086 159 L 159
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
7-164 |
6.59e-77 |
|
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: 279.24 E-value: 6.59e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 7 KVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVR 86
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 87 RYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPkgailNGVPVEKRQLLTDEEYREL--RYG 164
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDP-----GDTKLDKKEVLDETEYREVlkRYG 155
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1251-1477 |
2.08e-68 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 254.15 E-value: 2.08e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1251 DITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETE-EKLSVFV-ESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRG 1328
Cdd:PRK02597 978 DIIQGLPRIEELLEARKPKESCILAKKPGTVQIKYGDdESVDVKViESDGTITEYPILPGQNVMVSDGQQVDAGEPLTDG 1057
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1329 AIDPHQLLEA----------------KGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEG 1392
Cdd:PRK02597 1058 PINPHELLEIffedlrdrkglyeaalEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPG 1137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1393 QVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLI 1472
Cdd:PRK02597 1138 ELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLI 1217
|
....*
gi 78101264 1473 PAGTG 1477
Cdd:PRK02597 1218 PAGTG 1222
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1175-1477 |
2.68e-64 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 240.52 E-value: 2.68e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1175 IKAAEAGEIQEVpvrspltcQTRYGVcqkcygydLSMARP--VSIGeAVGIVAAQSIGEPGTQLTMRTFHTggvAGAADI 1252
Cdd:TIGR02388 918 VKAEESGEIEEV--------ASDYVI--------LRIGRPyrVSPG-AVLHIEDGDLVQRGDNLALLVFER---AKTGDI 977
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1253 TQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSV---FVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGA 1329
Cdd:TIGR02388 978 VQGLPRIEELLEARKPKEACILAKRPGVVQVKYGTDDESVsikVIERDGTISEYPLLPGQNIMVSDGQQVTGGEPLTDGP 1057
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1330 IDPHQLLE----------------AKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQ 1393
Cdd:TIGR02388 1058 INPHDILDvffsyykdqdglyeaaQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGE 1137
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1394 VLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIP 1473
Cdd:TIGR02388 1138 LVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIP 1217
|
....
gi 78101264 1474 AGTG 1477
Cdd:TIGR02388 1218 AGTG 1221
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-129 |
1.03e-60 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 221.70 E-value: 1.03e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1 MKKEVRKVRIALASPEKIRSWSY---------GEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFE-- 69
Cdd:CHL00018 3 DRYKHQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGDEke 82
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 78101264 70 -GKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYF 129
Cdd:CHL00018 83 dPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYC 143
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1246-1477 |
1.18e-60 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 230.97 E-value: 1.18e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1246 VAGAADITQGLPRVIELFEARRPKAK--AVISEIDGVVRIEET---EEKLsVFVESEGFSKEYKLPKEARLLVKDGDYVE 1320
Cdd:PRK09603 2637 TVKSRDITGGLPRVSELFEARKPKPKdvAILSEVDGIVSFGKPirnKEHI-IVTSKDGRSMDYFVDKGKQILVHADEFVH 2715
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1321 AGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDV 1400
Cdd:PRK09603 2716 AGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLF 2795
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 78101264 1401 EALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Cdd:PRK09603 2796 KEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
3-161 |
2.58e-60 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 229.81 E-value: 2.58e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEG-KVCERCGVEVT 81
Cdd:PRK09603 1394 KDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDiGTCEKCGVAIT 1473
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 82 KSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNG---VPVEKRQLLTDEEY 158
Cdd:PRK09603 1474 HSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNegtKLVMKYDILNEEQY 1553
|
...
gi 78101264 159 REL 161
Cdd:PRK09603 1554 QNI 1556
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
8-161 |
6.96e-59 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 215.38 E-value: 6.96e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 8 VRIALASPEKIRSWS---------YGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGV 78
Cdd:PRK02625 12 VKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCERCGV 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 79 EVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKgailNGVPVEKRQLLTDEEY 158
Cdd:PRK02625 92 EVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPG----NHKNLKYKQLLTEDQW 167
|
...
gi 78101264 159 REL 161
Cdd:PRK02625 168 LEI 170
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
1064-1387 |
1.59e-57 |
|
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: 208.36 E-value: 1.59e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1064 GLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYIS-VPLFQPDEVTRSLRLRKRA---- 1138
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEiVQFLYGEDGLDPLKIEKQGrfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1139 -DIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVP-------------------VRSPLTCQTRY 1198
Cdd:pfam04998 81 eFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGRDRLSKEAQeratllfelllksgleskrVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1199 GVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRV------------------- 1259
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVA-SKNVTLGVPRLkeiinvsknikspsltvyl 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1260 -----------------------------IELFEARRPKAKAVISEIDGVVR---------------------------- 1282
Cdd:pfam04998 240 fdevgrelekakkvygaiekvtlgsvvesGEILYDPDPFNTPIISDVKGVVKffdiidevtneeeidpetgllilvirll 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1283 ------------------------------------------------------------IEETEEKLSVFVESEGFSKE 1302
Cdd:pfam04998 320 kilnksikkvvkseviprsirnkvdegrdiaigeitafiikiskkirqdtgglrrvdelfMEEDPKLAILVASLLGNITL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1303 YKLPKEARLLVKDGDYVE---------AGQPLTR-----GAID--------PHQLLEAKGPEAVERYLVEEIQKVYRAQG 1360
Cdd:pfam04998 400 RGIPGIKRILVNEDDKGKvepdwvletEGVNLLRvllvpGFVDagrilsndIHEILEILGIEAARNALLNEIRNVYRFQG 479
|
490 500
....*....|....*....|....*..
gi 78101264 1361 VKLHDKHIEIVVRQMMKYVEVTDPGDS 1387
Cdd:pfam04998 480 IYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
502-1099 |
2.07e-56 |
|
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: 211.64 E-value: 2.07e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 502 FLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGrfATSDLNDL---YRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAV 578
Cdd:cd02583 168 MNPLAGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQC 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 579 DALLDNGRRGAPVTNPGSdRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP--- 655
Cdd:cd02583 246 ALYINSELPGLPLSMQPK-KPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPerv 324
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 656 -----------------------FLLKKMEEKGIapNVKAA-RRMLERQRDIKDEVWDALEEvihGKVVLLNRAPTLHRL 711
Cdd:cd02583 325 trynieklrklvlngpdvhpganFVIKRDGGKKK--FLKYGnRRKIARELKIGDIVERHLED---GDIVLFNRQPSLHRL 399
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 712 GIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYY 791
Cdd:cd02583 400 SIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYL 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 792 ITQvrKEKkgagleFATPEEA-------LAAHERGEVALNAPIKVAgretsvgRL---KYVFanpdEALLavahgIVDLQ 861
Cdd:cd02583 480 LTS--KDV------FFDRAQFcqlcsymLDGEIKIDLPPPAILKPV-------ELwtgKQIF----SLLL-----RPNKK 535
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 862 DVVTVRYMGKrletspGRILFARIVAEAVEDEKVAW---ELI--QLDvpqeKNSL----KDLVYQAFLRL--------GM 924
Cdd:cd02583 536 SPVLVNLEAK------EKSYTKKSPDMCPNDGYVVIrnsELLcgRLD----KSTLgsgsKNSLFYVLLRDygpeaaaaAM 605
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 925 EKTARLldALKY---YGFtfsttsgiTIGIDDaVIP-----EEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQIlqlw 996
Cdd:cd02583 606 NRLAKL--SSRWlsnRGF--------SIGIDD-VTPskellKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAE---- 670
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 997 tETTE--------KVTQAVFKN-FEENYPFN-PLyVMAQSGARGNP-----------QQI----RQLCGL--RGL--MQK 1047
Cdd:cd02583 671 -QTLEakisgelsKIREDAGKAcLKELHKSNsPL-IMALCGSKGSNinisqmiacvgQQIisgkRIPNGFedRTLphFPR 748
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*.
gi 78101264 1048 ----PSGETFevpVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLV 1099
Cdd:cd02583 749 nsktPAAKGF---VANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLM 801
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1218-1478 |
3.51e-54 |
|
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: 186.47 E-value: 3.51e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1218 GEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIELFEARrpkakaviseidgvvrieeteeklsvfvese 1297
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVA-SMNVTLGLPRLKEILNAA------------------------------- 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1298 gfskeyklpkearllvkdgdyveagqpltrgaiDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMK 1377
Cdd:cd00630 49 ---------------------------------SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTY 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1378 YVEVtdpgdsrllegqvlekwdvealnerliaegktpvawkpllMGVTKSAL--STKSWLSAASFQNTTHVLTEAAIAGK 1455
Cdd:cd00630 96 SGGL----------------------------------------RGVTRSGFraSKTSPLMRASFEKTTKHLLDAAAAGE 135
|
250 260
....*....|....*....|...
gi 78101264 1456 KDELIGLKENVILGRLIPAGTGS 1478
Cdd:cd00630 136 KDELEGVSENIILGRPAPLGTGS 158
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
498-618 |
1.09e-52 |
|
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: 188.27 E-value: 1.09e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 498 VVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEA 577
Cdd:pfam04997 200 EILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEH 279
|
90 100 110 120
....*....|....*....|....*....|....*....|.
gi 78101264 578 VDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNL 618
Cdd:pfam04997 280 VATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-214 |
1.04e-50 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 198.31 E-value: 1.04e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 7 KVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVR 86
Cdd:PRK14844 1450 EVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSKVR 1529
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 87 RYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAilngvPVEKRQLLTDEEYRELRygkq 166
Cdd:PRK14844 1530 RERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVS-----PFEKGEIISEKAYNEAK---- 1600
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 78101264 167 ETYplppGVDALVkdgeeVVKGQELAPGVVSRLDgvaLYRFPRRVRVE 214
Cdd:PRK14844 1601 DSY----GIDSFV-----AMQGVEAIRELLTRLD---LHEIRKDLRLE 1636
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1251-1508 |
1.98e-50 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 196.70 E-value: 1.98e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1251 DITQGLPRVIELFEARrpkakavisEIDGV-VRIEETEEKLSvfvesEGFSKEYKLP----KEARL-LVKdgdyveagqp 1324
Cdd:CHL00117 1130 DITQGLPKVEQLLEAR---------SIDSIsMNLEKRLEGWN-----ERITRILGIPwgflIGAELsIAQ---------- 1185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1325 ltrgaidphqlleakgpeaVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDS-RLLEGQVLEKWDVEAL 1403
Cdd:CHL00117 1186 -------------------SQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSnVFLPGELIGLLRAERI 1246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1404 NERLiaegKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGsdFVRF 1483
Cdd:CHL00117 1247 NRAL----EEAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTG--FKGL 1320
|
250 260
....*....|....*....|....*
gi 78101264 1484 TQVVDQKTLKAIEEARKEAVEAKER 1508
Cdd:CHL00117 1321 VHRSKQHKNKNLEIKKKNLFEGEMR 1345
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
508-1108 |
2.60e-50 |
|
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: 191.98 E-value: 2.60e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 508 RPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRR 587
Cdd:cd02733 124 RPDWMILTVLPVPPPAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIP 203
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 588 GAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMAL-----ELFKPFLLKKME 662
Cdd:cd02733 204 GLPQATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLQ 283
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 663 E---KGIAPNVKA--------ARRMLERQRDIKD---EVWDALEE-VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQ 727
Cdd:cd02733 284 ElvrNGPNEYPGAkyiirddgERIDLRYLKKASDlhlQYGYIVERhLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFR 363
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 728 LHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKekkgagleFA 807
Cdd:cd02733 364 LNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDT--------FL 435
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 808 TPEEALA-----AHERGEVALNAPIK-------------------VAGRETSVGRLKYVFANPDEALLAVAHGIVdLQDV 863
Cdd:cd02733 436 EKDQVMNllmwlPDWDGKIPQPAILKpkplwtgkqifsliipkinNLIRSSSHHDGDKKWISPGDTKVIIENGEL-LSGI 514
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 864 VTVRYMGkrleTSPGrilfarivaeavedekvaweliqldvpqeknslkDLVYQAFLRLGMEKTARLLDA--------LK 935
Cdd:cd02733 515 LCKKTVG----ASSG----------------------------------GLIHVIWLEYGPEAARDFIGNiqrvvnnwLL 556
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 936 YYGFtfsttsgiTIGIDDAVIP----EEKKQYLEEADRKLLQIEQAYEMGFL------TDRERYD-QILQLWTETTEKVT 1004
Cdd:cd02733 557 HNGF--------SIGIGDTIADketmKKIQETIKKAKRDVIKLIEKAQNGELepqpgkTLRESFEnKVNRILNKARDKAG 628
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1005 QAVFKNFEEnypFNPLYVMAQSGARGNPQQIRQLCGLRGlmQK-------PSG----------------ET--FevpVRS 1059
Cdd:cd02733 629 KSAQKSLSE---DNNFKAMVTAGSKGSFINISQIIACVG--QQnvegkriPFGfrrrtlphfikddygpESrgF---VEN 700
|
650 660 670 680
....*....|....*....|....*....|....*....|....*....
gi 78101264 1060 SFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVR 1108
Cdd:cd02733 701 SYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVK 749
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
620-764 |
7.94e-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: 162.86 E-value: 7.94e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 620 GKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFL--------LKKMEEKG--IAP------NVKAARRMLERQ-RD 682
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpynikrLRQLVENGpnVYPganyiiRINGARRDLRYQkRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 683 IKDEVW--DALEE-VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEA 759
Cdd:pfam00623 81 LDKELEigDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 78101264 760 RIQML 764
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 ... |
503-1099 |
3.20e-41 |
|
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: 164.28 E-value: 3.20e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 503 LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFaTSDLNDLYRRLINRNNRLKKLLA-----QGAPEIIIRNEKRM---- 573
Cdd:cd01435 121 AELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLAsmrqaESQSKLDLISGKTNsekl 199
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 574 ------LQEAVDALLDN--GRRGAPVTNPGsdrpLRSltdILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLP 645
Cdd:cd01435 200 inawlqLQSAVNELFDStkAPKSGKKSPPG----IKQ---LLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIP 272
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 646 KRMALEL--------FKPFLLKKMEEKGiaPNV--KAA------------RRMLERQRDIKDEVWDALEE---------- 693
Cdd:cd01435 273 LVFAKKLtfpepvtpFNVEELRQAVING--PDVypGANaiededgrlillSALSEERRKALAKLLLLLSSaklllngpkk 350
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 694 ----VIHGKVVLLNRAPTLHRLGIQAFQ-PVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHN 768
Cdd:cd01435 351 vyrhLLDGDVVLLNRQPTLHKPSIMAHKvRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQ 430
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 769 LLSPASGEPLAkpsrdiilGL---YYITQVRKEKKGaglEFATPEEalaahergevalnapikvagretsvgrlkY---V 842
Cdd:cd01435 431 YLVPTDGKPLR--------GLiqdHVVSGVLLTSRD---TFFTREE-----------------------------YqqlV 470
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 843 FAnpdeALLAVAHGIVDLqDVVTV---------RYMGKRLETS---------PGRILFARIVAEAVEDEKVAW------- 897
Cdd:cd01435 471 YA----ALRPLFTSDKDG-RIKLLppailkpkpLWTGKQVISTilknlipgnAPLLNLSGKKKTKKKVGGGKWgggsees 545
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 898 -------ELIQ--LDVPQ---EKNSLKDLVYQAFlrlGMEKTARLLDA--------LKYYGFtfsttsgiTIGIDDAVIp 957
Cdd:cd01435 546 qviirngELLTgvLDKSQfgaSAYGLVHAVYELY---GGETAGKLLSAlgrlftayLQMRGF--------TCGIEDLLL- 613
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 958 eekkqyLEEADRKLLQI-EQAYEMGFLTDRERYDQILqlwTETTEKVTQAVF-KNFEENYPFNPLYVMAQSGARGNPQQI 1035
Cdd:cd01435 614 ------TPKADEKRRKIlRKAKKLGLEAAAEFLGLKL---NKVTSSIIKACLpKGLLKPFPENNLQLMVQSGAKGSMVNA 684
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1036 RQLCGLRG----------LMQK----PSGETFEVPVRS------SFREGLTVLEYFISSHGARKGGADTALRTADSGYLT 1095
Cdd:cd01435 685 SQISCLLGqqelegrrvpLMVSgktlPSFPPYDTSPRAggfitdRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQ 764
|
....
gi 78101264 1096 RKLV 1099
Cdd:cd01435 765 RCLI 768
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
2-160 |
6.41e-38 |
|
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: 145.51 E-value: 6.41e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 2 KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECA-CGKYKRqrfegkvceRCGVev 80
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 81 tksivrryRMGHIELATPAAHIWFVKdvpskigtlldLSATELEQVLYFSKYIVLDPkgailngvpvEKRQLLTDEEYRE 160
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDP----------GKPKLFNKDKKRL 120
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
13-113 |
2.10e-29 |
|
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: 124.85 E-value: 2.10e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 13 ASPEKIRSWSYGEVEKPETINYRTLKPERDGlfderifgpikdyecacgKYKRQRFEGKVCERCGVEVTKSIVRRYRMGH 92
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100
....*....|....*....|.
gi 78101264 93 IELATPAAHIWFVKDVPSKIG 113
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG 83
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
768-953 |
3.08e-25 |
|
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: 103.48 E-value: 3.08e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 768 NLLSPASGEPLAKPSRDIILGLYYITQVRKekkgagleFATPEEALAAHERGEVALNAPIKVAGREtsvgrlkyvfanpd 847
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDT--------FFDREEVMQLLMYGIVLPHPAILKPIKP-------------- 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 848 eallavahgivdlqdvvtvRYMGKrleTSPGRILFARIV----------AEAVEDEKVAW---ELIQ--LDVPQEKNSLK 912
Cdd:pfam04983 59 -------------------LWTGK---QTFSRLLPNEINpkgkpktneeDLCENDSYVLInngELISgvIDKKTVGKSLG 116
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 78101264 913 DLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDD 953
Cdd:pfam04983 117 SLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDD 157
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1215-1478 |
2.28e-24 |
|
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: 106.57 E-value: 2.28e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1215 VSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIELFEAR-------------------RPKAKAVIS 1275
Cdd:cd06528 37 IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVA-EINVTLGLPRLIEIVDARkepstptmtiyleeeykydREKAEEVAR 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1276 EI-----------------DGVVRIEETEEKLS--------------------VFVESEG----FSKEYKLPKEARLLV- 1313
Cdd:cd06528 116 KIeettlenlaedisidlfNMRITIELDEEMLEdrgitvddvlkaieklkkgkVGEEGDVtlivLKAEEPSIKELRKLAe 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1314 -------------------KDGD----YVEA---GQPLTRGAIDP--------HQLLEAKGPEAVERYLVEEIQKVYRAQ 1359
Cdd:cd06528 196 kilntkikgikgikrvivrKEEDeyviYTEGsnlKAVLKVEGVDPtrtttnniHEIEEVLGIEAARNAIINEIKRTLEEQ 275
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1360 GVKLHDKHIeIVVRQMMKYvevtdpgdsrllEGQVlekwdvealneRLIaeGKTPVAwkpllmgVTKsalstKSWLSAAS 1439
Cdd:cd06528 276 GLDVDIRHI-MLVADIMTY------------DGEV-----------RQI--GRHGIA-------GEK-----PSVLARAA 317
|
330 340 350
....*....|....*....|....*....|....*....
gi 78101264 1440 FQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:cd06528 318 FEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGD 356
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1207-1478 |
1.73e-23 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 104.36 E-value: 1.73e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1207 YDLSMARPvsiGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIELFEAR-------------------R 1267
Cdd:TIGR02389 36 YLRSLIDP---GEAVGIVAAQSIGEPGTQMTMRTFHYAGVA-ELNVTLGLPRLIEIVDARktpstpsmtiyledeyekdR 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1268 PKAKAVISEI-----------------DGVVRIEETEEKLsvfvESEGFSKEYKLPKEARL-LVKDGDYVEAGQPLTRGA 1329
Cdd:TIGR02389 112 EKAEEVAKKIeatkledvakdisidlaDMTVIIELDEEQL----KERGITVDDVEKAIKKAkLGKVIEIDMDNNTITIKP 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1330 IDP-----HQLLEA------KGPEAVERYLVEE-------------IQKVYRAQGV--------KLHDKH----IE---- 1369
Cdd:TIGR02389 188 GNPslkelRKLKEKiknlhiKGIKGIKRVVIRKegdeyviytegsnLKEVLKLEGVdktrtttnDIHEIAevlgIEaarn 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1370 IVVRQMMkyvevtdpgdsRLLEGQVLekwDVEALNERLIAEGKTpvaWKPLLMGVTKSALSTK--SWLSAASFQNTTHVL 1447
Cdd:TIGR02389 268 AIIEEIK-----------RTLEEQGL---DVDIRHLMLVADLMT---WDGEVRQIGRHGISGEkaSVLARAAFEVTVKHL 330
|
330 340 350
....*....|....*....|....*....|.
gi 78101264 1448 TEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:TIGR02389 331 LDAAIRGEVDELKGVIENIIVGQPIPLGTGD 361
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1218-1478 |
1.96e-23 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 104.16 E-value: 1.96e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1218 GEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIELFEAR-------------------RPKAKAVISEI- 1277
Cdd:PRK04309 59 GEAVGVVAAQSIGEPGTQMTMRTFHYAGVA-EINVTLGLPRLIEIVDARkepstpmmtiylkdeyaydREKAEEVARKIe 137
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1278 ----------------DGVVRIEETEEKLS------------------VFVESEG----FSKEYKLPKEARLLV------ 1313
Cdd:PRK04309 138 attlenlakdisvdlaNMTIIIELDEEMLEdrgltvddvkeaiekkkgGEVEIEGntliISPKEPSYRELRKLAekirni 217
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1314 --------------KDGD----YVEaGQPL-----------TR-GAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKL 1363
Cdd:PRK04309 218 kikgikgikrviirKEGDeyviYTE-GSNLkevlkvegvdaTRtTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDV 296
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1364 HDKHIeIVVRQMMKYvevtdpgdsrllEGQVlekwdvealneRLIaeGKtpvawkpllMGVT--KSalstkSWLSAASFQ 1441
Cdd:PRK04309 297 DIRHI-MLVADMMTW------------DGEV-----------RQI--GR---------HGVSgeKA-----SVLARAAFE 336
|
330 340 350
....*....|....*....|....*....|....*..
gi 78101264 1442 NTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:PRK04309 337 VTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGD 373
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1207-1478 |
2.98e-20 |
|
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: 93.05 E-value: 2.98e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1207 YDLSMARPvsiGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIE----------------------LFE 1264
Cdd:cd02736 2 YMRAKVEP---GTAVGAIAAQSIGEPGTQMTLKTFHFAGVA-SMNITLGVPRIKEiinasknistpiitaklendrdEKS 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1265 ARRPKA-------KAVISEIDGV-------VRIE---ETEEKLSVFVES-----------------EGFS-------KEY 1303
Cdd:cd02736 78 ARIVKGriektylGEVASYIEEVyspddcyILIKldkKIIEKLQLSKSNlyfllqslkrklpdvvvSGIPevkraviNKD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1304 KLPKEARLLVKDGDYVEAgqpLTRGAIDP------H--QLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIeIVVRQM 1375
Cdd:cd02736 158 KKKGKYKLLVEGYGLRAV---MNTPGVIGtrttsnHimEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHI-MLLADL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1376 MKYvevtdpgdsrllEGQVLekwdvealnerliaegktpvawkpllmGVTKSALS--TKSWLSAASFQNTTHVLTEAAIA 1453
Cdd:cd02736 234 MTF------------KGEVL---------------------------GITRFGIAkmKESVLMLASFEKTTDHLFNAALH 274
|
330 340
....*....|....*....|....*
gi 78101264 1454 GKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:cd02736 275 GRKDSIEGVSECIIMGKPMPIGTGL 299
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
601-1107 |
4.98e-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: 96.70 E-value: 4.98e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 601 RSLTDILSGKQG--RFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKP--------------FLLKKMEEK 664
Cdd:cd10506 191 TANESAASKKSGlkWMKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVServsswnrerlqeyCDLTLLLKG 270
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 665 GI----APNVKAARRMLERQ------RDIKDevwdaleevihGKVVLLNRAPTLHRLGIQAFQPVLVEGQS-IQLHPLVC 733
Cdd:cd10506 271 VIgvrrNGRLVGVRSHNTLQigdvihRPLVD-----------GDVVLVNRPPSIHQHSLIALSVKVLPTNSvVSINPLCC 339
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 734 EAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQvrkekKGAGLEFATPE--E 811
Cdd:cd10506 340 SPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTE-----RGVFLDKAQMQqlQ 414
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 812 ALAAHERGEValnAPIKVAGRETSVGRLKYVF--ANPDEALLAVAHGIVDLQDvvtvrymGKRLETSpgrilfarivaea 889
Cdd:cd10506 415 MLCPSQLPPP---AIIKSPPSNGPLWTGKQLFqmLLPTDLDYSFPSNLVFISD-------GELISSS------------- 471
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 890 vedEKVAWELIQldvpqeknslKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIP---EEKKQYLEE 966
Cdd:cd10506 472 ---GGSSWLRDS----------EGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSsdsYSRQKMIEE 538
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 967 ADRKLLQIEQA---------------------YEMGFLTDRERYD-QILQLWTETTEKVTQAVFKNFE-----ENYPFNP 1019
Cdd:cd10506 539 ISLGLREAEIAcnikqllvdsrkdflsgsgeeNDVSSDVERVIYErQKSAALSQASVSAFKQVFRDIQnlvykYASKDNS 618
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1020 LYVMAQSGARGNPQQIRQLCGLRGL----------------------------MQKPSGETFEVP-----VRSSFREGLT 1066
Cdd:cd10506 619 LLAMIKAGSKGSLLKLVQQSGCLGLqlslvklsyriprqlscaawnsqksprvIEKDGSECTESYipygvVESSFLDGLN 698
|
570 580 590 600
....*....|....*....|....*....|....*....|...
gi 78101264 1067 VLEYFISSHGARkggaDTALRT-AD-SGYLTRKLVDVTHEIVV 1107
Cdd:cd10506 699 PLECFVHSITSR----DSSFSSnADlPGTLFRKLMFFMRDIYV 737
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1215-1478 |
8.55e-20 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 94.88 E-value: 8.55e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1215 VSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIELFEARR-------------------PKAKAVIS 1275
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVA-EMNVTLGLPRLIEIVDARKkpstptmtiylkkdyredeEKVREVAK 257
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1276 EIDG-----VVRIEETEEKLSVFVE-SEGFSKEYKLPKE---ARLLVKDGDYVEAGQPLTRgaIDPHQ-------LLEak 1339
Cdd:PRK14897 258 KIENttlidVADIITDIAEMSVVVElDEEKMKERLIEYDdilAAISKLTFKTVEIDDGIIR--LKPQQpsfkklyLLA-- 333
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1340 gpEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQ---MMKYVEVTDPGDSRLLEGQVLEKWDV---EALNERLIAEGKT 1413
Cdd:PRK14897 334 --EKVKSLTIKGIKGIKRAIARKENDERRWVIYTQgsnLKDVLEIDEVDPTRTYTNDIIEIATVlgiEAARNAIIHEAKR 411
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1414 PVAWKPL------LM---------------GVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLI 1472
Cdd:PRK14897 412 TLQEQGLnvdirhIMlvadmmtfdgsvkaiGRHGISGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPI 491
|
....*.
gi 78101264 1473 PAGTGS 1478
Cdd:PRK14897 492 TLGTGA 497
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
983-1062 |
1.09e-16 |
|
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: 77.02 E-value: 1.09e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 983 LTDRERYDQILQLWTETTEKVTQAVFKNFEEN-------------YPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQK-- 1047
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKardpagniaskslDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVeg 80
|
90 100
....*....|....*....|....*...
gi 78101264 1048 ------------PSGETF-EVPVRSSFR 1062
Cdd:pfam05000 81 kripfgfsgrtlPHFKKDdEGPESRGFV 108
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1207-1478 |
1.22e-15 |
|
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: 79.54 E-value: 1.22e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1207 YDLSMARPvsiGEAVGIVAAQSIGEPGTQLTMRTFHTGGVaGAADITQGLPRVIELF----------------------- 1263
Cdd:cd02735 2 YMRSLVEP---GEAVGLLAAQSIGEPSTQMTLNTFHFAGR-GEMNVTLGIPRLREILmtaskniktpsmtlplkngksae 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1264 -------EARRPKAKAVISEIDgVVRIEETEEK------------------------LSVFVESEGFS---KEYKLPKEA 1309
Cdd:cd02735 78 raetlkkRLSRVTLSDVVEKVE-VTEILKTIERvfkkllgkwcevtiklplsspkllLLSIVEKLARKaviREIPGITRC 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1310 RLLVKDGDYVEAGQPLTRGAI-------------------DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEI 1370
Cdd:cd02735 157 FVVEEDKGGKTKYLVITEGVNlaalwkfsdildvnriytnDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1371 VvrqmmkyvevtdpGDSRLLEGqvlekwDVEALNeRliaegktpvawkpllMGVTKSAlstkSWLSAASFQNTTHVLTEA 1450
Cdd:cd02735 237 I-------------ADYMTFEG------GYRPFN-R---------------IGMESST----SPLQKMSFETTLAFLKKA 277
|
330 340
....*....|....*....|....*...
gi 78101264 1451 AIAGKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:cd02735 278 TLNGDIDNLSSPSSRLVVGKPVNGGTGL 305
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1207-1478 |
1.85e-14 |
|
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: 77.25 E-value: 1.85e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1207 YDLSMARPvsiGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAgAADITQGLPRVIEL-------------------FEARR 1267
Cdd:cd02584 19 FNRSLVHP---GEMVGTIAAQSIGEPATQMTLNTFHFAGVS-AKNVTLGVPRLKEIinvakniktpsltvylepgFAKDE 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1268 PKAKAVISEI----------------DGVVR---IEETEEKLSVFVESEGF----------------------------- 1299
Cdd:cd02584 95 EKAKKIQSRLehttlkdvtaateiyyDPDPQntvIEEDKEFVESYFEFPDEdveqdrlspwllrieldrkkmtdkklsme 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1300 ------SKEYKLPKEA------------RLLVKDGDYVEAGQP-----LTRGAIDPHQLLEAKGPEAVERYLVEE--IQK 1354
Cdd:cd02584 175 qiakkiKEEFKDDLNVifsddnaeklviRIRIINDDEEKEEDSeddvfLKKIESNMLSDMTLKGIEGIRKVFIREenKKK 254
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1355 VYRAQGVklHDKHIEIVV-------RQMMKYVEVtDPgdSRLLEGQVLEKWDV---EALNERLIAEGKTPVAW------- 1417
Cdd:cd02584 255 VDIETGE--FKKREEWVLetdgvnlREVLSHPGV-DP--TRTTSNDIVEIFEVlgiEAARKALLKELRNVISFdgsyvny 329
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 78101264 1418 ------------KPLLMGVT-----KSALSTkswLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGS 1478
Cdd:cd02584 330 rhlallcdvmtqRGHLMAITrhginRQDTGP---LMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1346-1477 |
5.57e-12 |
|
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: 70.96 E-value: 5.57e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1346 RYLVEEI--QKV--YRAQgvkLHDKHIEIVVRQM---------------MKYVEV---TDPGDSRLLEGQVL--EKWD-V 1400
Cdd:COG0086 559 RYLVNEIlpQEVpfYNQV---INKKHIEVIIRQMyrrcglketvifldrLKKLGFkyaTRAGISIGLDDMVVpkEKQEiF 635
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1401 EALNERLI------AEGKT--PVAWKPLLMGVTKSALSTKSWLSAA-SFQNTTHVLTEAAIAGKKDELIGL--------- 1462
Cdd:COG0086 636 EEANKEVKeiekqyAEGLItePERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmak 715
|
170
....*....|....*....
gi 78101264 1463 -KENVI---LGRLIPAGTG 1477
Cdd:COG0086 716 pSGNIIetpIGSNFREGLG 734
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1201-1477 |
1.36e-11 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 69.54 E-value: 1.36e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1201 CQKCYGYDLSMARPVSIGEAVGIVaaqsigepgTQLTMRTFHTGGVAgAADITQGLPRVIELFEAR-------------- 1266
Cdd:PRK14898 517 CDKKYVYDISVEGLETFTTADGVV---------THNTMRTFHYAGVA-EINVTLGLPRMIEIVDARkepstpimtvhlkg 586
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1267 -----RPKAKAVISEIDGV-----------------VRIEETEEKLS---VFVES--EGFSKEYKLPKEarllvKDGDYV 1319
Cdd:PRK14898 587 eyatdREKAEEVAKKIESLtlgdvatsiaidlwtqsIKVELDEETLAdrgLTIESveEAIEKKLGVKID-----RKGTVL 661
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1320 EAGqPLTRGAIDPHQLLEA------KGPEAVERYLVEEIQK------VYRAQGVKLhdkhieivvRQMMKyVEVTDPgdS 1387
Cdd:PRK14898 662 YLK-PKTPSYKALRKRIPKiknivlKGIPGIERVLVKKEEHendeeyVLYTQGSNL---------REVFK-IEGVDT--S 728
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 1388 RLLEGQVLEKWDV---EALNERLIAEGKTPVAWKPL------LM---------GVTKS------ALSTKSWLSAASFQNT 1443
Cdd:PRK14898 729 RTTTNNIIEIQEVlgiEAARNAIINEMMNTLEQQGLevdirhLMlvadimtadGEVKPigrhgvAGEKGSVLARAAFEET 808
|
330 340 350
....*....|....*....|....*....|....
gi 78101264 1444 THVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
Cdd:PRK14898 809 VKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1186-1248 |
7.17e-08 |
|
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: 57.48 E-value: 7.17e-08
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 78101264 1186 VPVRSPLTCQTRYGVC--QKCYGYDLsmARPVSIG---EAVGI------VAAQSIGEpgTQLTMRTFHTGGVAG 1248
Cdd:COG0086 40 KPERDGLFCERIFGPCkdYECYCGKY--KRMVYKGvvcEKCGVevtlskVRRERMGH--IELAMPVFHIWGLKS 109
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
3-108 |
1.03e-03 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 43.86 E-value: 1.03e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 3 KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLkPERDGLFDERIfGPIKdyecacgkyKRQRfegkvCERCGvEVTK 82
Cdd:PRK14977 7 KAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIE---------PGQK-----CLTCG-NLAA 69
|
90 100
....*....|....*....|....*.
gi 78101264 83 SIVRRYrmGHIELATPAAHIWFVKDV 108
Cdd:PRK14977 70 NCPGHF--GHIELAEPVIHIAFIDNI 93
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1219-1238 |
1.27e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.34 E-value: 1.27e-03
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
2-108 |
3.42e-03 |
|
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: 42.23 E-value: 3.42e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 78101264 2 KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLkPERDGLFDERiFGPIKdyecacgkykrqrfEGKVCERCGvevt 81
Cdd:cd02582 1 PKRIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGY-PIEGGLMDPR-LGVIE--------------PGLRCKTCG---- 60
|
90 100 110
....*....|....*....|....*....|..
gi 78101264 82 ksivRRYR-----MGHIELATPAAHIWFVKDV 108
Cdd:cd02582 61 ----NTAGecpghFGHIELARPVIHVGFAKHI 88
|
|
| |
