|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
19-832 |
0e+00 |
|
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: 1187.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 19 EVQFEVFKEAQIKAYAKCIIEHAKSYEHGQ-PVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIFNINVF 97
Cdd:cd02733 2 RVQFGILSPDEIRAMSVAEIEHPETYENGGgPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGFL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 98 DVVLIALKCVCKYcgallmdtndpsemkkiahlqglnrlrmvaklcgsvckrskdiqgcegkgrqprigrfagiypglqi 177
Cdd:cd02733 82 TKILKILRCVCKR------------------------------------------------------------------- 94
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 178 kvtqeeqdyVWHAENARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAF-GSAKSDDELTHQIMSIVK 256
Cdd:cd02733 95 ---------ELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMdGSARSEDDLTHKLADIIK 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 257 RNIQLRKDKESGVKAAV-DRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSART 335
Cdd:cd02733 166 ANNQLKRQEQNGAPAHIiEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSART 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 336 VITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKLALVKDRNAVHLDVGDV 413
Cdd:cd02733 246 VITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNgpNEYPGAKYIIRDDGERIDLRYLKKASDLHLQYGYI 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 414 VERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNF 493
Cdd:cd02733 326 VERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQI 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 494 VSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDKYFIQSVALWLDLWE--LPIPAILKPRPLWTGKQIFSLILPEVNHPASP 571
Cdd:cd02733 406 VSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDgkIPQPAILKPKPLWTGKQIFSLIIPKINNLIRS 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 572 Y-----DKPPFPHNDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEVAKFINGVQRITTYFNYCFAFSVGVQ 646
Cdd:cd02733 486 SshhdgDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIG 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 647 DTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMI 726
Cdd:cd02733 566 DTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNFKAMV 645
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 727 EAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDT 806
Cdd:cd02733 646 TAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDT 725
|
810 820
....*....|....*....|....*.
gi 1706887638 807 AVKTSDTGYLQRKLVKALEDVHASYD 832
Cdd:cd02733 726 AVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
10-856 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 745.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 10 SQMPLQKVHEVQFEVFKEAQIKAYAKCIIEHAKSY-EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELA 88
Cdd:PRK08566 2 MMMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 89 EPIFNINVFDVVLIALKCVCKYCGALLMDTNDPSE-MKKIAHLQGLNRLrmVAKLCGSVCKRSKDIQGCegkgrqPRIGr 167
Cdd:PRK08566 82 RPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEyLEKLERLKEWGSL--ADDLIKEVKKEAAKRMVC------PHCG- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 168 fagiYPGLQIKVTQ-----EEQDYVWH---AENARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAFG 239
Cdd:PRK08566 153 ----EKQYKIKFEKpttfyEERKEGLVkltPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLE 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 240 SA-KSDDELTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKY 317
Cdd:PRK08566 229 TGqRSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKE 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 318 GRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVT 395
Cdd:PRK08566 309 GRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNgpEKHPGANYVIRPDGRRI 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 396 KLaLVKDRNAV--HLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHV 473
Cdd:PRK08566 389 KL-TDKNKEELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 474 PQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDK---YFIQSVALwLDLWELPIPAILKPRP 550
Cdd:PRK08566 468 PQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKeeaLDLLRAAG-IDELPEPEPAIENGKP 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 551 LWTGKQIFSLILPE---------VNHPASPYDKPPFPHnDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEV 621
Cdd:PRK08566 547 YWTGKQIFSLFLPKdlnlefkakICSGCDECKKEDCEH-DAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERA 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 622 AKFINGVQRITTYFNYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSAL 701
Cdd:PRK08566 626 RRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVL 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 702 NKCREEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATR 781
Cdd:PRK08566 706 GKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRS 785
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1706887638 782 GYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGAR 856
Cdd:PRK08566 786 SYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMK 860
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
14-862 |
0e+00 |
|
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.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 735.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 14 LQKVHEVQFEVFKEAQIKAYAKCIIEHAKSY-EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIF 92
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVEVVTADTYdDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 93 NINVFDVVLIALKCVCKYCGALLMdtndpSEMKKIAHLQGLNRLR----MVAK-LCGSVCKRSKDIQGCEGKGRQPRIGR 167
Cdd:TIGR02390 81 HVGFAKEIYKILRATCRKCGRITL-----TEEEIEQYLEKINKLKeeggDLAStLIEKIVKEAAKRMKCPHCGEEQKKIK 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 168 FAGIY------PGLQIKVTQEEqdyvwhaenARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAFGSA 241
Cdd:TIGR02390 156 FEKPTyfyeegKEGDVKLTPSE---------IRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETG 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 242 -KSDDELTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGR 319
Cdd:TIGR02390 227 eRSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGR 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 320 LRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKL 397
Cdd:TIGR02390 307 FRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNgpDSWPGANYVIRPDGRRIKI 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 398 ALV-KDRNAVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQS 476
Cdd:TIGR02390 387 RDEnKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQT 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 477 LLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDK---YFIQSVALWLDlwELPIPAILKPRPLWT 553
Cdd:TIGR02390 467 EEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKeevQTILGVAGYFG--DPPEPAIEKPKEYWT 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 554 GKQIFSLILPE---------VNHPASPYDKPPFPHnDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEVAKF 624
Cdd:TIGR02390 545 GKQIFSAFLPEdlnfegrakICSGSDACKKEECPH-DAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRF 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 625 INGVQRITTYFNYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSALNKC 704
Cdd:TIGR02390 624 LDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKA 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 705 REEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATRGYV 784
Cdd:TIGR02390 704 RDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFK 783
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1706887638 785 EGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGARIEGNQA 862
Cdd:TIGR02390 784 KGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHGKP 861
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
786-1396 |
0e+00 |
|
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: 572.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 786 GLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGARIEGNQAFPI 865
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 866 PHMTNSEMADKYRYEYNDEGSFSENMGGHYMDPFVRDSLLRDpqsvlklqeefeqlmkdramsrlvidmedknklkmnlp 945
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGR-------------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 946 vnvarliqnarttmgkrsqvsnlnpitvinrvrelqedlaqlfpsyhkdyngrfaNVLSQQRVERALTLFGIHLRQILGS 1025
Cdd:pfam04998 123 -------------------------------------------------------DRLSKEAQERATLLFELLLKSGLES 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1026 KRVLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVS 1105
Cdd:pfam04998 148 KRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVS 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1106 KNQRNASVAVCLIREY-QKRNKAQEAQQFIEYCTLANITTTVQIIYDPDPRNTVVAEDEEMIRWEQAVMNEEDEEPDAEQ 1184
Cdd:pfam04998 228 KNIKSPSLTVYLFDEVgRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1185 PPSPFIARLILDNDL------------FNDKRLNMKDVKSAIRQVDDTYMVQANMENDGQRIVRLRPRKCTGADSVPALT 1252
Cdd:pfam04998 308 ETGLLILVIRLLKILnksikkvvksevIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDELFMEEDPKLA 387
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1253 KAVAQLLQSVHLRGIPGIKKTLLKEGNTFRVDPEtggiknessWMVDTEGTALQRifvgVVNNEGknIIDFSKTSSNKIP 1332
Cdd:pfam04998 388 ILVASLLGNITLRGIPGIKRILVNEDDKGKVEPD---------WVLETEGVNLLR----VLLVPG--FVDAGRILSNDIH 452
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1706887638 1333 EVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSGP 1396
Cdd:pfam04998 453 EILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1032-1446 |
2.89e-155 |
|
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: 479.78 E-value: 2.89e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1032 YKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKNQRNA 1111
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1112 SVAVCLIREYQKR-NKAQEAQQFIEYCTLANITTTVQIIYDPDPRNTVVAEDEEMIRweqaVMNEEDEEPDAEQPPSPFI 1190
Cdd:cd02584 81 SLTVYLEPGFAKDeEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVE----SYFEFPDEDVEQDRLSPWL 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1191 ARLILDNDLFNDKRLNMKDVKSAIRQV-DDTYMVQANMENDGQRIVRLR-----PRKCTGADSVPALTKAVAQLLQSVHL 1264
Cdd:cd02584 157 LRIELDRKKMTDKKLSMEQIAKKIKEEfKDDLNVIFSDDNAEKLVIRIRiinddEEKEEDSEDDVFLKKIESNMLSDMTL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1265 RGIPGIKKTLLKEGNTFRVDPETGGIKNESSWMVDTEGTALQRIFvgvvNNEGkniIDFSKTSSNKIPEVVTVLGIEAAR 1344
Cdd:cd02584 237 KGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVL----SHPG---VDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1345 RKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETsGPLMRCSFEETVKVLMTAAAFGEKDPVRGV 1424
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDT-GPLMRCSFEETVDILLEAAAFGETDDLKGV 388
|
410 420
....*....|....*....|..
gi 1706887638 1425 SASLVLGNQARIGTGLFDLLLD 1446
Cdd:cd02584 389 SENIMLGQLAPIGTGCFDLLLD 410
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
219-514 |
1.45e-148 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 456.98 E-value: 1.45e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 219 DLILTVLPIPPPQVRPAVAF-GSAKSDDELTHQIMSIVKRNIQLRKDKESG-VKAAVDRSRALLQEHVATFFNNASTYYK 296
Cdd:smart00663 2 WMILTVLPVPPPCLRPSVQLdGGRFAEDDLTHLLRDIIKRNNRLKRLLELGaPSIIIRNEKRLLQEAVDTLIDNEGLPRA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 297 PAKVGdtKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFV 376
Cdd:smart00663 82 NQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 377 QRTTyPSANYIIRpnGNVTKLALVKD-RNAVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLS 455
Cdd:smart00663 160 RNGP-NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPL 236
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1706887638 456 CTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSY 514
Cdd:smart00663 237 VCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-324 |
4.83e-136 |
|
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: 424.01 E-value: 4.83e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 14 LQKVHEVQFEVFKEAQIKAYAKCIIEHAKSYEHG--QPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPI 91
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGslKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 92 FNINVFDVVLIALKCVCKYCGALLMDTNDPSEMKKIAHLQGLNRLRMVAKLCGSVCKRSKDIQGCEGK----GRQPRIGR 167
Cdd:pfam04997 81 FHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKngvcGSQQPVSR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 168 FAGIYPGLQIKVTQE-EQDYVWHAENARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAF-GSAKSDD 245
Cdd:pfam04997 161 KEGLKLKAAIKKSKEeEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLdGGRRAED 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 246 ELTHQIMSIVKRNIQLRKDKESGVKA-AVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNL 324
Cdd:pfam04997 241 DLTHKLRDIIKRNNRLKKLLELGAPShIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1028-1446 |
2.92e-69 |
|
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: 238.03 E-value: 2.92e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1028 VLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKN 1107
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1108 QRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITTTVQIiydpDPRNTVVaedeemirweqavmneedeepdaeqpp 1186
Cdd:TIGR02389 94 PSTPSMTIYLEDEYEKdREKAEEVAKKIEATKLEDVAKDISI----DLADMTV--------------------------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1187 spfiaRLILDNDLFNDKRLNMKDVKSAIRQVDDTYMVQANMENDgqrIVRLRPrkctGADSVPALTKAVAQLLQsVHLRG 1266
Cdd:TIGR02389 143 -----IIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDNN---TITIKP----GNPSLKELRKLKEKIKN-LHIKG 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1267 IPGIKKTLLKEGNtfrvdpetggikneSSWMVDTEGTALQrifvGVVNNEGkniIDFSKTSSNKIPEVVTVLGIEAARRK 1346
Cdd:TIGR02389 210 IKGIKRVVIRKEG--------------DEYVIYTEGSNLK----EVLKLEG---VDKTRTTTNDIHEIAEVLGIEAARNA 268
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1347 LLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSgPLMRCSFEETVKVLMTAAAFGEKDPVRGVSA 1426
Cdd:TIGR02389 269 IIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKAS-VLARAAFEVTVKHLLDAAIRGEVDELKGVIE 347
|
410 420
....*....|....*....|
gi 1706887638 1427 SLVLGNQARIGTGLFDLLLD 1446
Cdd:TIGR02389 348 NIIVGQPIPLGTGDVDLVMD 367
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1005-1450 |
1.82e-65 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 227.42 E-value: 1.82e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1005 QQRVERALTLFGIHLRQILGSKrvLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNA 1084
Cdd:PRK04309 8 EEKLEDASLELPQKLKEELREK--LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1085 GISSKNVTLGVPRLLELLNVSKNQRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITTTVQIiydpDPRNTVVaede 1163
Cdd:PRK04309 86 GVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYdREKAEEVARKIEATTLENLAKDISV----DLANMTI---- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1164 emirweqavmneedeepdaeqppspfiaRLILDNDLFNDKRLNMKDVKSAIRqvdDTYMVQANMENDgqrIVRLRPRKct 1243
Cdd:PRK04309 158 ----------------------------IIELDEEMLEDRGLTVDDVKEAIE---KKKGGEVEIEGN---TLIISPKE-- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1244 gaDSVPALTKAVAQLLQsVHLRGIPGIKKTLL-KEGNtfrvdpetggiknesSWMVDTEGTALQrifvGVVNNEGkniID 1322
Cdd:PRK04309 202 --PSYRELRKLAEKIRN-IKIKGIKGIKRVIIrKEGD---------------EYVIYTEGSNLK----EVLKVEG---VD 256
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1323 FSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSgPLMRCSF 1402
Cdd:PRK04309 257 ATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKAS-VLARAAF 335
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 1706887638 1403 EETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLFDLLLDMSKL 1450
Cdd:PRK04309 336 EVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPLR 383
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
206-827 |
7.64e-54 |
|
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: 207.32 E-value: 7.64e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 206 LIMGFDPRFCHPRDLILTVLPIPPPQVRPAVA-----FgsAKSDdeLTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRAL 279
Cdd:COG0086 213 VVEAFRESGNRPEWMILDVLPVIPPDLRPLVPldggrF--ATSD--LNDLYRRVINRNNRLKRLLELKApDIIVRNEKRM 288
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 280 LQEHVATFFNNaSTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLT 359
Cdd:COG0086 289 LQEAVDALFDN-GRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELF 367
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 360 FPervNVINKKRLTEFVqrTTYPSANYIIrpngnvtklalvkDRnaVHLDVGDVVERhVIDGDVVLFNRQPTLHRMSMMG 439
Cdd:COG0086 368 KP---FIYRKLEERGLA--TTIKSAKKMV-------------ER--EEPEVWDILEE-VIKEHPVLLNRAPTLHRLGIQA 426
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 440 HRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDK 519
Cdd:COG0086 427 FEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTRE 506
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 520 DTFV---DKYF--IQSVALWLDLWELPIPAILKPRPLWTGKQ------------IFSLILPEVnhpASPYDKppfPHNDK 582
Cdd:COG0086 507 REGAkgeGMIFadPEEVLRAYENGAVDLHARIKVRITEDGEQvgkivettvgryLVNEILPQE---VPFYNQ---VINKK 580
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 583 KImiqrgqllvgaitkgvvgaapGSLIHVIFNERGSDEVAKFINGVQRITtyFNYCF--AFSVGVQDTVADATtlKEmnN 660
Cdd:COG0086 581 HI---------------------EVIIRQMYRRCGLKETVIFLDRLKKLG--FKYATraGISIGLDDMVVPKE--KQ--E 633
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 661 VLHKTRQSVEKIGAAANNGKLTRKAgmsllqSFEAdVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQI 740
Cdd:COG0086 634 IFEEANKEVKEIEKQYAEGLITEPE------RYNK-VIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQL 706
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 741 avfvgqqnvAGSRipfgfrrrtlpHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKL 820
Cdd:COG0086 707 ---------AGMR-----------GLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRL 766
|
....*..
gi 1706887638 821 VKALEDV 827
Cdd:COG0086 767 VDVAQDV 773
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
19-832 |
0e+00 |
|
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: 1187.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 19 EVQFEVFKEAQIKAYAKCIIEHAKSYEHGQ-PVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIFNINVF 97
Cdd:cd02733 2 RVQFGILSPDEIRAMSVAEIEHPETYENGGgPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGFL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 98 DVVLIALKCVCKYcgallmdtndpsemkkiahlqglnrlrmvaklcgsvckrskdiqgcegkgrqprigrfagiypglqi 177
Cdd:cd02733 82 TKILKILRCVCKR------------------------------------------------------------------- 94
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 178 kvtqeeqdyVWHAENARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAF-GSAKSDDELTHQIMSIVK 256
Cdd:cd02733 95 ---------ELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMdGSARSEDDLTHKLADIIK 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 257 RNIQLRKDKESGVKAAV-DRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSART 335
Cdd:cd02733 166 ANNQLKRQEQNGAPAHIiEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSART 245
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 336 VITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKLALVKDRNAVHLDVGDV 413
Cdd:cd02733 246 VITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNgpNEYPGAKYIIRDDGERIDLRYLKKASDLHLQYGYI 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 414 VERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNF 493
Cdd:cd02733 326 VERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQI 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 494 VSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDKYFIQSVALWLDLWE--LPIPAILKPRPLWTGKQIFSLILPEVNHPASP 571
Cdd:cd02733 406 VSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWDgkIPQPAILKPKPLWTGKQIFSLIIPKINNLIRS 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 572 Y-----DKPPFPHNDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEVAKFINGVQRITTYFNYCFAFSVGVQ 646
Cdd:cd02733 486 SshhdgDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIG 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 647 DTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMI 726
Cdd:cd02733 566 DTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNFKAMV 645
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 727 EAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDT 806
Cdd:cd02733 646 TAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDT 725
|
810 820
....*....|....*....|....*.
gi 1706887638 807 AVKTSDTGYLQRKLVKALEDVHASYD 832
Cdd:cd02733 726 AVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
16-860 |
0e+00 |
|
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: 787.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 16 KVHEVQFEVFKEAQIKAYAKCIIEHAKSY-EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIFNI 94
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYdEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 95 NVFDVVLIALKCVCKYCGALLMDTNDPSEMKKIAHLQGLNRLRMVAKLCGSVCKRSKDIQGCEGKG-RQPRIgRFagIYP 173
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKEKWPELVKRVIEKVKKKAKKRKVCPHCGaPQYKI-KL--EKP 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 174 GLQIKVTQEEQDYVWHAEnARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAFGSA-KSDDELTHQIM 252
Cdd:cd02582 160 TTFYEEKEEGEVKLTPSE-IRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLETGeRSEDDLTHKLV 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 253 SIVKRNIQLRKDKESGV-KAAVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDF 331
Cdd:cd02582 239 DIIRINQRLKENIEAGApQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNF 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 332 SARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKLALV-KDRNAVHL 408
Cdd:cd02582 319 SARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNgpDKWPGANYVIRPDGRRIRLRYVnREELAERL 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 409 DVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMM 488
Cdd:cd02582 399 EPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELML 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 489 VPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDK---YFIQSVALWLDLWelPIPAILKPRPLWTGKQIFSLILPE- 564
Cdd:cd02582 479 VQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKeeaLQLLSAAGYDGLL--PEPAILEPKPLWTGKQLFSLFLPKd 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 565 --------VNHPASPYDKPPFPHnDKKIMIQRGQLLVGAITKGVVGA-APGSLIHVIFNERGSDEVAKFINGVQRITTYF 635
Cdd:cd02582 557 lnfegkakVCSGCSECKDEDCPN-DGYVVIKNGKLLEGVIDKKAIGAeQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRF 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 636 NYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSALNKCREEAAKKALSN 715
Cdd:cd02582 636 IELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKY 715
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 716 VRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATRGYVEGLQPHEFYFH 795
Cdd:cd02582 716 LDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFH 795
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1706887638 796 TMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGARIEGN 860
Cdd:cd02582 796 AMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSDHG 860
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
45-836 |
0e+00 |
|
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: 751.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 45 EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIFNINVFDVVLIALKCVCKYCGALLMdtndpSEM 124
Cdd:cd02583 23 ETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIINILQCICKTCSRVLL-----PEE 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 125 KKIAHLQGLNR-------LRMVAKLCGSVCKRSKdiqGCegkgrqPRIGRfagiypglqIKVTQEEQD--YVWHaenarq 195
Cdd:cd02583 98 EKRKFLKRLRRpnldnlqKKALKKKILEKCKKVR---KC------PHCGL---------LKKAQEDLNplKVLN------ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 196 VLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVA--FGSAKSDDELTHQIMSIVKRNIQLRKDKESGVKA-A 272
Cdd:cd02583 154 LFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPSVVmdEKSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTqK 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 273 VDRSRALLQEHVATFFNnASTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPF 352
Cdd:cd02583 234 IMEDWDFLQLQCALYIN-SELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPE 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 353 SVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKLALVKDRNAVH--LDVGDVVERHVIDGDVVLFNR 428
Cdd:cd02583 313 HVAKILTYPERVTRYNIEKLRKLVLNgpDVHPGANFVIKRDGGKKKFLKYGNRRKIAreLKIGDIVERHLEDGDIVLFNR 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 429 QPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQD 508
Cdd:cd02583 393 QPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQD 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 509 SLLGSYRLTDKDTFVDK-YFIQSVALWLD---LWELPIPAILKPRPLWTGKQIFSLIL-PevnHPASPY----------- 572
Cdd:cd02583 473 FLTASYLLTSKDVFFDRaQFCQLCSYMLDgeiKIDLPPPAILKPVELWTGKQIFSLLLrP---NKKSPVlvnleakeksy 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 573 --DKPPFPHNDKKIMIQRGQLLVGAITKGVVGA-APGSLIHVIFNERGSDEVAKFINGVQRITTYF--NYcfAFSVGVQD 647
Cdd:cd02583 550 tkKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWlsNR--GFSIGIDD 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 648 TVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIE 727
Cdd:cd02583 628 VTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMAL 707
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 728 AGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDdygetSRGMATRGYVE-----GLQPHEFYFHTMAGREG 802
Cdd:cd02583 708 CGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRN-----SKTPAAKGFVAnsfysGLTPTEFFFHTMSGREG 782
|
810 820 830
....*....|....*....|....*....|....
gi 1706887638 803 LIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVR 836
Cdd:cd02583 783 LVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
10-856 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 745.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 10 SQMPLQKVHEVQFEVFKEAQIKAYAKCIIEHAKSY-EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELA 88
Cdd:PRK08566 2 MMMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 89 EPIFNINVFDVVLIALKCVCKYCGALLMDTNDPSE-MKKIAHLQGLNRLrmVAKLCGSVCKRSKDIQGCegkgrqPRIGr 167
Cdd:PRK08566 82 RPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEyLEKLERLKEWGSL--ADDLIKEVKKEAAKRMVC------PHCG- 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 168 fagiYPGLQIKVTQ-----EEQDYVWH---AENARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAFG 239
Cdd:PRK08566 153 ----EKQYKIKFEKpttfyEERKEGLVkltPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLE 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 240 SA-KSDDELTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKY 317
Cdd:PRK08566 229 TGqRSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKE 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 318 GRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVT 395
Cdd:PRK08566 309 GRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNgpEKHPGANYVIRPDGRRI 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 396 KLaLVKDRNAV--HLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHV 473
Cdd:PRK08566 389 KL-TDKNKEELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHV 467
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 474 PQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDK---YFIQSVALwLDLWELPIPAILKPRP 550
Cdd:PRK08566 468 PQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKeeaLDLLRAAG-IDELPEPEPAIENGKP 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 551 LWTGKQIFSLILPE---------VNHPASPYDKPPFPHnDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEV 621
Cdd:PRK08566 547 YWTGKQIFSLFLPKdlnlefkakICSGCDECKKEDCEH-DAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERA 625
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 622 AKFINGVQRITTYFNYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSAL 701
Cdd:PRK08566 626 RRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVL 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 702 NKCREEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATR 781
Cdd:PRK08566 706 GKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRS 785
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1706887638 782 GYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGAR 856
Cdd:PRK08566 786 SYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMK 860
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
12-1449 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 744.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 12 MPLQKVHEVQFEVFKEAQIKAYAKCIIEHAKSY-EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEP 90
Cdd:PRK14977 4 LAVKAIDGIIFGLISPADARKIGFAEITAPEAYdEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEP 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 91 IFNINVFDVVLIALKCVCKYCGALLMDTNDPSEMKKIAHLQGLNRL--------RMVAKLCGSVCKRSKDIQGCEGKGRQ 162
Cdd:PRK14977 84 VIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDipekriddEIIEEVRDQVKVYAKKAKECPHCGAP 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 163 PRIGRFAGIYpgLQIKVTQEEQDYVWHAEnARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAFGSA- 241
Cdd:PRK14977 164 QHELEFEEPT--IFIEKTEIEEHRLLPIE-IRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGe 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 242 KSDDELTHQIMSIVKRNIQLRKDKESGVKAAVDRSRA-LLQEHVATFFNNASTYYKPA-KVGDTKKLKSLTERLKGKYGR 319
Cdd:PRK14977 241 RSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVdHLQYHTSTFFDNATAGIPQAhHKGSGRPLKSLFQRLKGKEGR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 320 LRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKL 397
Cdd:PRK14977 321 FRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINgpDEFPGANAIRKGDGTKIRL 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 398 ALVKDRN-------AVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMN 470
Cdd:PRK14977 401 DFLEDKGkdalreaAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMN 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 471 LHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDKYFIQSVALWLDLWE-LPIPAI-LKP 548
Cdd:PRK14977 481 LHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDpLPEPAIkTKD 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 549 RPLWTGKQIFSLILP-EVNHPASPYD--------KPPFPHNDKKIMIQRGQLLVGAITKGVVGA---APGSLIHVIFNER 616
Cdd:PRK14977 561 GPAWTGKQLFSLFLPkDFNFEGIAKWsagkageaKDPSCLGDGYVLIKEGELISGVIDDNIIGAlveEPESLIDRIAKDY 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 617 GSDEVAKFINGVQRITTYFNYCFAFSVGVQDTVA----------DATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRkaG 686
Cdd:PRK14977 641 GEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIpdeakqeiedDIQGMKDEVSDLIDQRKITRKITIYKGKEELLR--G 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 687 MSLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNV--------AGSRIPFGF 758
Cdd:PRK14977 719 MKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRktrigfvlTGGRLHEGY 798
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 759 RRRTLPHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNA 838
Cdd:PRK14977 799 KDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDP 878
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 839 NQELIQLAYGEDGLDGARIEGNQAFPIphmtnSEMADKYRYEYNDEGSfsenmgghymdpfvrdsllrdpqsvlkLQEEF 918
Cdd:PRK14977 879 HGHIIQFKFGEDGIDPQKLDHGEAFNL-----ERIIEKQKIEDRGKGA---------------------------SKDEI 926
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 919 EQLMKdramsrlvidmEDKNKLKMNLPVNVARLIQNARttmgkrsqvsnlnpitvinrvreLQEDlaqlfpsyhkdyngr 998
Cdd:PRK14977 927 EELAK-----------EYTKTFNANLPKLLADAIHGAE-----------------------LKED--------------- 957
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 999 fanvlsqqrveraltlfgihlrqilGSKRVLKEYKLNdkafeyllkeirtkYQQSLITPGEIIGAIAAQSCGEPATQMTL 1078
Cdd:PRK14977 958 -------------------------ELEAICAEGKEG--------------FEKAKVEPGQAIGIISAQSIAEPGTQMTL 998
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1079 NTFHNAGISSKNVTLGVPRLLELLNVSKNQRNASVAVCLIREYQK-RNKAQEAQqfieyctlanitttvqiiydpdpRNT 1157
Cdd:PRK14977 999 RTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEdIEKAIEIA-----------------------RNL 1055
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1158 VVAEDEEMIrweqavmneEDEEPDAeqppSPFIARLILDNDLFNDKRLNMKDVKSAIRQVDDTymVQANMENDGQRIVrL 1237
Cdd:PRK14977 1056 KELKVRALI---------ADSAIDN----ANEIKLIKPDKRALENGCIPMERFAEIEAALAKG--KKFEMELEDDLII-L 1119
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1238 RPRKCTGADSVPALTKAVAQLLQSVHLRGIPGIKktllkegntfRVDPETGGIKNESSWMVDTEGTALQRIFvgvvnneG 1317
Cdd:PRK14977 1120 DLVEAADRDKPLATLIAIRNKILDKPVKGVPDIE----------RAWVELVEKDGRDEWIIQTSGSNLAAVL-------E 1182
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1318 KNIIDFSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAV------SRTGInRS 1391
Cdd:PRK14977 1183 MKCIDIANTITNDCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIglqaagVRHGF-AG 1261
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*...
gi 1706887638 1392 ETSGPLMRCSFEETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLFDLLLDMSK 1449
Cdd:PRK14977 1262 EKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKVDLLMDFSG 1319
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
14-862 |
0e+00 |
|
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.
Pssm-ID: 274106 [Multi-domain] Cd Length: 868 Bit Score: 735.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 14 LQKVHEVQFEVFKEAQIKAYAKCIIEHAKSY-EHGQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIF 92
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVEVVTADTYdDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 93 NINVFDVVLIALKCVCKYCGALLMdtndpSEMKKIAHLQGLNRLR----MVAK-LCGSVCKRSKDIQGCEGKGRQPRIGR 167
Cdd:TIGR02390 81 HVGFAKEIYKILRATCRKCGRITL-----TEEEIEQYLEKINKLKeeggDLAStLIEKIVKEAAKRMKCPHCGEEQKKIK 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 168 FAGIY------PGLQIKVTQEEqdyvwhaenARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAFGSA 241
Cdd:TIGR02390 156 FEKPTyfyeegKEGDVKLTPSE---------IRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETG 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 242 -KSDDELTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGR 319
Cdd:TIGR02390 227 eRSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGR 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 320 LRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKL 397
Cdd:TIGR02390 307 FRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNgpDSWPGANYVIRPDGRRIKI 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 398 ALV-KDRNAVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQS 476
Cdd:TIGR02390 387 RDEnKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQT 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 477 LLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDK---YFIQSVALWLDlwELPIPAILKPRPLWT 553
Cdd:TIGR02390 467 EEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKeevQTILGVAGYFG--DPPEPAIEKPKEYWT 544
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 554 GKQIFSLILPE---------VNHPASPYDKPPFPHnDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEVAKF 624
Cdd:TIGR02390 545 GKQIFSAFLPEdlnfegrakICSGSDACKKEECPH-DAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRF 623
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 625 INGVQRITTYFNYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSLLQSFEADVNSALNKC 704
Cdd:TIGR02390 624 LDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKA 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 705 REEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMATRGYV 784
Cdd:TIGR02390 704 RDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFK 783
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1706887638 785 EGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGARIEGNQA 862
Cdd:TIGR02390 784 KGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHGKP 861
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
786-1396 |
0e+00 |
|
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: 572.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 786 GLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNANQELIQLAYGEDGLDGARIEGNQAFPI 865
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 866 PHMTNSEMADKYRYEYNDEGSFSENMGGHYMDPFVRDSLLRDpqsvlklqeefeqlmkdramsrlvidmedknklkmnlp 945
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSKLGR-------------------------------------- 122
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 946 vnvarliqnarttmgkrsqvsnlnpitvinrvrelqedlaqlfpsyhkdyngrfaNVLSQQRVERALTLFGIHLRQILGS 1025
Cdd:pfam04998 123 -------------------------------------------------------DRLSKEAQERATLLFELLLKSGLES 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1026 KRVLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVS 1105
Cdd:pfam04998 148 KRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVS 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1106 KNQRNASVAVCLIREY-QKRNKAQEAQQFIEYCTLANITTTVQIIYDPDPRNTVVAEDEEMIRWEQAVMNEEDEEPDAEQ 1184
Cdd:pfam04998 228 KNIKSPSLTVYLFDEVgRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1185 PPSPFIARLILDNDL------------FNDKRLNMKDVKSAIRQVDDTYMVQANMENDGQRIVRLRPRKCTGADSVPALT 1252
Cdd:pfam04998 308 ETGLLILVIRLLKILnksikkvvksevIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDELFMEEDPKLA 387
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1253 KAVAQLLQSVHLRGIPGIKKTLLKEGNTFRVDPEtggiknessWMVDTEGTALQRifvgVVNNEGknIIDFSKTSSNKIP 1332
Cdd:pfam04998 388 ILVASLLGNITLRGIPGIKRILVNEDDKGKVEPD---------WVLETEGVNLLR----VLLVPG--FVDAGRILSNDIH 452
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1706887638 1333 EVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSGP 1396
Cdd:pfam04998 453 EILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
21-832 |
3.32e-172 |
|
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: 539.08 E-value: 3.32e-172
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 21 QFEVFKEAQIKAYAKCIIEHAKSYEH-GQPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIFNINVFDV 99
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSlGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 100 VLIALKCVCKYCgallmdtndpsemkkiahlqglNRLRMvaklcgsvckrskdiqgcegkgrqprigrfagiypglqikv 179
Cdd:cd01435 81 LYKLLRGSCFYC----------------------HRFRI----------------------------------------- 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 180 tqeEQDYVWHAENARQVLDRVSDSDALIMGFDPR--FchprdliLTVLPIPPPQVRPAVAFGSAKSDDELThQIMS-IVK 256
Cdd:cd01435 98 ---SKWEVKLFVAKLKLLDKGLLVEAAELDFGYDmfF-------LDVLLVPPNRFRPPSFLGDKVFENPQN-VLLSkILK 166
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 257 RNIQLRK-----------DKESGVKAAVDRSRAL-----LQEHVATFFNnaSTYYKPAKVGDTKKLKSLTERlkgKYGRL 320
Cdd:cd01435 167 DNQQIRDllasmrqaesqSKLDLISGKTNSEKLInawlqLQSAVNELFD--STKAPKSGKKSPPGIKQLLEK---KEGLF 241
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 321 RGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKLA 398
Cdd:cd01435 242 RMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINgpDVYPGANAIEDEDGRLILLS 321
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 399 L--VKDRNAV------------HLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVL-NYNTFRLNLSCTTPYNAD 463
Cdd:cd01435 322 AlsEERRKALaklllllssaklLLNGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLpGEKTLRLHYANCKSYNAD 401
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 464 FDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDK-YFIQSV--ALWLDL--- 537
Cdd:cd01435 402 FDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTReEYQQLVyaALRPLFtsd 481
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 538 ----WELPIPAILKPRPLWTGKQIFSLILPEVNHPASPYD----------KPPFPHNDK-----KIMIQRGQLLVGAITK 598
Cdd:cd01435 482 kdgrIKLLPPAILKPKPLWTGKQVISTILKNLIPGNAPLLnlsgkkktkkKVGGGKWGGgseesQVIIRNGELLTGVLDK 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 599 GVVGAAPGSLIHVIFNERGSDEVAKFINGVQRITTYFNYCFAFSVGVQDTVADattlKEMNnvlHKTRQSVEKIgaaann 678
Cdd:cd01435 562 SQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLT----PKAD---EKRRKILRKA------ 628
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 679 gkltRKAGMSLLQSFeadVNSALNKCREEAAKKALSNVRRT----NSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRI 754
Cdd:cd01435 629 ----KKLGLEAAAEF---LGLKLNKVTSSIIKACLPKGLLKpfpeNNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRV 701
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1706887638 755 PFGFRRRTLPHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYD 832
Cdd:cd01435 702 PLMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1032-1446 |
2.89e-155 |
|
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: 479.78 E-value: 2.89e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1032 YKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKNQRNA 1111
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1112 SVAVCLIREYQKR-NKAQEAQQFIEYCTLANITTTVQIIYDPDPRNTVVAEDEEMIRweqaVMNEEDEEPDAEQPPSPFI 1190
Cdd:cd02584 81 SLTVYLEPGFAKDeEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVE----SYFEFPDEDVEQDRLSPWL 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1191 ARLILDNDLFNDKRLNMKDVKSAIRQV-DDTYMVQANMENDGQRIVRLR-----PRKCTGADSVPALTKAVAQLLQSVHL 1264
Cdd:cd02584 157 LRIELDRKKMTDKKLSMEQIAKKIKEEfKDDLNVIFSDDNAEKLVIRIRiinddEEKEEDSEDDVFLKKIESNMLSDMTL 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1265 RGIPGIKKTLLKEGNTFRVDPETGGIKNESSWMVDTEGTALQRIFvgvvNNEGkniIDFSKTSSNKIPEVVTVLGIEAAR 1344
Cdd:cd02584 237 KGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLREVL----SHPG---VDPTRTTSNDIVEIFEVLGIEAAR 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1345 RKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETsGPLMRCSFEETVKVLMTAAAFGEKDPVRGV 1424
Cdd:cd02584 310 KALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDT-GPLMRCSFEETVDILLEAAAFGETDDLKGV 388
|
410 420
....*....|....*....|..
gi 1706887638 1425 SASLVLGNQARIGTGLFDLLLD 1446
Cdd:cd02584 389 SENIMLGQLAPIGTGCFDLLLD 410
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
219-514 |
1.45e-148 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 456.98 E-value: 1.45e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 219 DLILTVLPIPPPQVRPAVAF-GSAKSDDELTHQIMSIVKRNIQLRKDKESG-VKAAVDRSRALLQEHVATFFNNASTYYK 296
Cdd:smart00663 2 WMILTVLPVPPPCLRPSVQLdGGRFAEDDLTHLLRDIIKRNNRLKRLLELGaPSIIIRNEKRLLQEAVDTLIDNEGLPRA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 297 PAKVGdtKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFV 376
Cdd:smart00663 82 NQKSG--RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 377 QRTTyPSANYIIRpnGNVTKLALVKD-RNAVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLS 455
Cdd:smart00663 160 RNGP-NGAKYIIR--GKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPL 236
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1706887638 456 CTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSY 514
Cdd:smart00663 237 VCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
49-832 |
1.99e-148 |
|
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: 466.14 E-value: 1.99e-148
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 49 PVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPIFNINVFDVVlialkcvckycgallmdtndpsemkkia 128
Cdd:cd00399 27 AERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKV---------------------------- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 129 hlqglnrlrmvaklcgsvckrskdiqgcegkgrqprigrfagiypglqikvtqeeqdyvwhaenarqvldrvsdsdalim 208
Cdd:cd00399 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 209 gfdPRFCHPRDLILTVLPIPPPQVRPAVAFGSAKSddelthqimsivkrniqlrkdkesgvkaavdrsraLLQEHVATFF 288
Cdd:cd00399 79 ---PSFLGPEWMILTCLPVPPPCLRPSVIIEERWR-----------------------------------LLQEHVDTYL 120
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 289 NNaSTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLtfpervnvin 368
Cdd:cd00399 121 DN-GIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL---------- 189
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 369 kkrltefvqrttypsanyiirpngnvtklalvkdrnavhldvgdvverhviDGDVVLFNRQPTLHRMSMMGHRVRVLNYN 448
Cdd:cd00399 190 ---------------------------------------------------DGDPVLFNRQPSLHKLSIMAHRVRVLPGS 218
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 449 TFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTdkdtfvdkyfi 528
Cdd:cd00399 219 TFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDTLLGAYLLT----------- 287
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 529 qsvalwldlwelpipailkprplwTGKQIFSLILPEvnhpaspydkppfphndkkimiqrgqllvgaitkgvvgaapgSL 608
Cdd:cd00399 288 ------------------------LGKQIVSAALPG------------------------------------------GL 301
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 609 IHVIFNERGSDEVAKFINGVQRITTYFNYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMS 688
Cdd:cd00399 302 LHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMT 381
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 689 LLQSFEADVNSALNKCREEAAKKALSNVRRT---NSFKVMIEAGSKGSDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPH 765
Cdd:cd00399 382 LEESLEDNILDFLNEARDKAGSAASVNLDLVskfNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPH 461
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1706887638 766 FMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYD 832
Cdd:cd00399 462 FSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-324 |
4.83e-136 |
|
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: 424.01 E-value: 4.83e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 14 LQKVHEVQFEVFKEAQIKAYAKCIIEHAKSYEHG--QPVRGGINDLRMGTTDFEYSCETCGLKHPECPGHFGYVELAEPI 91
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGslKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 92 FNINVFDVVLIALKCVCKYCGALLMDTNDPSEMKKIAHLQGLNRLRMVAKLCGSVCKRSKDIQGCEGK----GRQPRIGR 167
Cdd:pfam04997 81 FHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKngvcGSQQPVSR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 168 FAGIYPGLQIKVTQE-EQDYVWHAENARQVLDRVSDSDALIMGFDPRFCHPRDLILTVLPIPPPQVRPAVAF-GSAKSDD 245
Cdd:pfam04997 161 KEGLKLKAAIKKSKEeEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLdGGRRAED 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 246 ELTHQIMSIVKRNIQLRKDKESGVKA-AVDRSRALLQEHVATFFNNASTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNL 324
Cdd:pfam04997 241 DLTHKLRDIIKRNNRLKKLLELGAPShIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
54-836 |
4.27e-94 |
|
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: 322.43 E-value: 4.27e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 54 INDLRMGTTDFEYSCETCGLKHP-ECPGHFGYVELAEPIFNinvfdvvlialkcvckycgallmdtndPSEMKKIAhlqg 132
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCGAKDNkKCEGHFGVIKLPVTIYH---------------------------PYFISEVA---- 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 133 lnrlRMVAKLCGSvCKRSKdiqgcEGKGRQPRigrfAGIYPGLQIKVTQEEQDYVWHA------ENARQVLDRVSDSD-A 205
Cdd:cd10506 69 ----QILNKICPG-CKSIK-----QKKKKPPR----ETLPPDYWDFIPKDGQQEESCVtknlpiLSLAQVKKILKEIDpK 134
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 206 LIMGFDPRfchPRDLILTVLPIPPPQVRPAvafgsaksddELTHQiMSIVKRNIqlrKDkesgvkaavDRSRALLQehva 285
Cdd:cd10506 135 LIAKGLPR---QEGLFLKCLPVPPNCHRVT----------EFTHG-FSTGSRLI---FD---------ERTRAYKK---- 184
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 286 tffnnastyykpaKVGDTKKLKS--LTERLKGKYgrLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPER 363
Cdd:cd10506 185 -------------LVDFIGTANEsaASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSER 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 364 VNVINKKRLTEFVQRTTYPSANYIIRPNGNvtklaLVKDRNAVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVR 443
Cdd:cd10506 250 VSSWNRERLQEYCDLTLLLKGVIGVRRNGR-----LVGVRSHNTLQIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSVK 324
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 444 VLNYN-TFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTF 522
Cdd:cd10506 325 VLPTNsVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGVF 404
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 523 VDKYFIQSVALWLdLWELPIPAILK--PR--PLWTGKQIFSLILPevnhPASPYDkppFPHNDkkIMIQRGQLLVGAITK 598
Cdd:cd10506 405 LDKAQMQQLQMLC-PSQLPPPAIIKspPSngPLWTGKQLFQMLLP----TDLDYS---FPSNL--VFISDGELISSSGGS 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 599 GVVGAAPGSLIHVIFnERGSDEVAKFINGVQRITTYFNYCFAFSVGVQD------TVADATTLKEMNNVLHKTRQ----- 667
Cdd:cd10506 475 SWLRDSEGNLFSILV-KHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDlylssdSYSRQKMIEEISLGLREAEIacnik 553
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 668 -----SVEKIGAAANNGKLTRKAGMSLlqSFEADVNSALNKCREEAAKKALSNVRRT--------NSFKVMIEAGSKGSD 734
Cdd:cd10506 554 qllvdSRKDFLSGSGEENDVSSDVERV--IYERQKSAALSQASVSAFKQVFRDIQNLvykyaskdNSLLAMIKAGSKGSL 631
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 735 LNICQIAVFVGQQNVAGsRIPFGFRR---------RTLPHFMLDDYGETSRGMATRGYVE-----GLQPHEFYFHTMAGR 800
Cdd:cd10506 632 LKLVQQSGCLGLQLSLV-KLSYRIPRqlscaawnsQKSPRVIEKDGSECTESYIPYGVVEssfldGLNPLECFVHSITSR 710
|
810 820 830
....*....|....*....|....*....|....*.
gi 1706887638 801 EGLIDTAVKTSDTgyLQRKLVKALEDVHASYDGTVR 836
Cdd:cd10506 711 DSSFSSNADLPGT--LFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
326-489 |
7.92e-92 |
|
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: 294.60 E-value: 7.92e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 326 GKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKRLTEFVQR--TTYPSANYIIRPNGNVTKLALVKDR 403
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENgpNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 404 NAVHLDVGDVVERHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAEL 483
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 1706887638 484 IEMMMV 489
Cdd:pfam00623 161 EELMLV 166
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1028-1447 |
4.30e-70 |
|
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: 240.23 E-value: 4.30e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1028 VLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKN 1107
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1108 QRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITTTVQIiydpDPRNTVVaedeemirweqavmneedeepdaeqpp 1186
Cdd:cd06528 90 PSTPTMTIYLEEEYKYdREKAEEVARKIEETTLENLAEDISI----DLFNMRI--------------------------- 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1187 spfiaRLILDNDLFNDKRLNMKDVKSAIRQVddtyMVQANMENDGQRIVRLRPRKctgaDSVPALTKAVAQLLQsVHLRG 1266
Cdd:cd06528 139 -----TIELDEEMLEDRGITVDDVLKAIEKL----KKGKVGEEGDVTLIVLKAEE----PSIKELRKLAEKILN-TKIKG 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1267 IPGIKKTLLKegntfrvdpetggiKNESSWMVDTEGTALQrifvGVVNNEGkniIDFSKTSSNKIPEVVTVLGIEAARRK 1346
Cdd:cd06528 205 IKGIKRVIVR--------------KEEDEYVIYTEGSNLK----AVLKVEG---VDPTRTTTNNIHEIEEVLGIEAARNA 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1347 LLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINrSETSGPLMRCSFEETVKVLMTAAAFGEKDPVRGVSA 1426
Cdd:cd06528 264 IINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIA-GEKPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIE 342
|
410 420
....*....|....*....|.
gi 1706887638 1427 SLVLGNQARIGTGLFDLLLDM 1447
Cdd:cd06528 343 NIIVGQPIPLGTGDVELTMDP 363
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1028-1446 |
2.92e-69 |
|
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: 238.03 E-value: 2.92e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1028 VLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKN 1107
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1108 QRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITTTVQIiydpDPRNTVVaedeemirweqavmneedeepdaeqpp 1186
Cdd:TIGR02389 94 PSTPSMTIYLEDEYEKdREKAEEVAKKIEATKLEDVAKDISI----DLADMTV--------------------------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1187 spfiaRLILDNDLFNDKRLNMKDVKSAIRQVDDTYMVQANMENDgqrIVRLRPrkctGADSVPALTKAVAQLLQsVHLRG 1266
Cdd:TIGR02389 143 -----IIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDNN---TITIKP----GNPSLKELRKLKEKIKN-LHIKG 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1267 IPGIKKTLLKEGNtfrvdpetggikneSSWMVDTEGTALQrifvGVVNNEGkniIDFSKTSSNKIPEVVTVLGIEAARRK 1346
Cdd:TIGR02389 210 IKGIKRVVIRKEG--------------DEYVIYTEGSNLK----EVLKLEG---VDKTRTTTNDIHEIAEVLGIEAARNA 268
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1347 LLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSgPLMRCSFEETVKVLMTAAAFGEKDPVRGVSA 1426
Cdd:TIGR02389 269 IIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKAS-VLARAAFEVTVKHLLDAAIRGEVDELKGVIE 347
|
410 420
....*....|....*....|
gi 1706887638 1427 SLVLGNQARIGTGLFDLLLD 1446
Cdd:TIGR02389 348 NIIVGQPIPLGTGDVDLVMD 367
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
216-1440 |
7.93e-68 |
|
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: 251.51 E-value: 7.93e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 216 HPRDLILTVLPIPPPQVRPAVAFGSAK---SDdeLTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRALLQEHVATFFNNa 291
Cdd:TIGR02386 215 RPEWMVLDVIPVIPPELRPMVQLDGGRfatSD--LNDLYRRVINRNNRLKRLLELGApEIIVRNEKRMLQEAVDALFDN- 291
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 292 STYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervNVInkKR 371
Cdd:TIGR02386 292 GRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKP---FII--KR 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 372 LTEFVQRTTYPSANYIIRPNGNvtklalvkdrnavhlDVGDVVERhVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFR 451
Cdd:TIGR02386 367 LIDRELAANIKSAKKMIEQEDP---------------EVWDVLED-VIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIR 430
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 452 LNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDK---DTFVDKYF- 527
Cdd:TIGR02386 431 LHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEkpgAKGEGKIFs 510
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 528 -IQSVALWLDLWELPIPAILKPRP----LWT--GKQIFSLILPEvNHpasPYDKPPFPHNDKKImiqrgqllvgaitkgv 600
Cdd:TIGR02386 511 nVDEAIRAYDNGKVHLHALIGVRTsgeiLETtvGRVIFNEILPE-GF---PYINDNEPLSKKEI---------------- 570
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 601 vgaapGSLIHVIFNERGSDEVAKFINGVQRITTYFNYCFAFSVGVQDTVadatTLKEMNNVLHKTRQSVEKIGAAANNGK 680
Cdd:TIGR02386 571 -----SSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIV----VPDEKYEILKEADKEVAKIQKFYNKGL 641
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 681 LTRKAGMSLLQSFEADVNSALNkcrEEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAvfvgqqnvagsripfGFRr 760
Cdd:TIGR02386 642 ITDEERYRKVVSIWSETKDKVT---DAMMKLLKKDTYKFNPIFMMADSGARGNISQFRQLA---------------GMR- 702
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 761 rtlpHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVhasydgTVRNAnq 840
Cdd:TIGR02386 703 ----GLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDV------VVREE-- 770
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 841 eliqlaygedglDGARIEGnqaFPIPHMTNSEmadkyryeyndegsfsenmgghymdpfvrdsllrdpqsvlklQEEFEQ 920
Cdd:TIGR02386 771 ------------DCGTEEG---IEVEAIVEGK------------------------------------------DEIIES 793
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 921 LmKDRAMSRLVI-DMEDKNKLKMNLPVNvarliqnarttmgkrsqvsnlnpiTVINrvrelqEDLAQLFpsyhkdyngrf 999
Cdd:TIGR02386 794 L-KDRIVGRYSAeDVYDPDTGKLIAEAN------------------------TLIT------EEIAEKI----------- 831
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1000 anvlsqqrveRALTLFGIHLRQILGSKRvlkEYKLNDKAFEyllkeiRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLN 1079
Cdd:TIGR02386 832 ----------ENSGIEKVKVRSVLTCES---EHGVCQKCYG------RDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMR 892
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1080 TFHNAGISS--KNVTLGVPRLLELLNVSknqrnasvavclireyQKRNKAqeaqqfieycTLANITTTVQIIYDpdprnt 1157
Cdd:TIGR02386 893 TFHTGGVAGasGDITQGLPRVKELFEAR----------------TPKDKA----------VIAEVDGTVEIIED------ 940
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1158 vvaedeemIRWEQAVMNEEDEEPDAEQPPSPFIARLIldndlfndkrlnmkdVKsairqvddtymvqanmenDGQRIvrl 1237
Cdd:TIGR02386 941 --------IVKNKRVVVIKDENDEEKKYTIPFGAQLR---------------VK------------------DGDSV--- 976
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1238 rprkctgadsvpaltkavaqllqsvhlrgIPGIKktlLKEGNtfrVDPEtggiknesswmvdtegtalqrifvgvvnneg 1317
Cdd:TIGR02386 977 -----------------------------SAGDK---LTEGS---IDPH------------------------------- 990
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1318 kniidfsktssnkipEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQR-------------------- 1377
Cdd:TIGR02386 991 ---------------DLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKvritdsgdsnllpgelidih 1055
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1378 ------------GYLMAVSR---TGINR--SETSGPLMRCSFEETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGL 1440
Cdd:TIGR02386 1056 efneenrklleqGKKPASAIpqlLGITKasLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGL 1135
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1005-1450 |
1.82e-65 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 227.42 E-value: 1.82e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1005 QQRVERALTLFGIHLRQILGSKrvLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNA 1084
Cdd:PRK04309 8 EEKLEDASLELPQKLKEELREK--LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYA 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1085 GISSKNVTLGVPRLLELLNVSKNQRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITTTVQIiydpDPRNTVVaede 1163
Cdd:PRK04309 86 GVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYdREKAEEVARKIEATTLENLAKDISV----DLANMTI---- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1164 emirweqavmneedeepdaeqppspfiaRLILDNDLFNDKRLNMKDVKSAIRqvdDTYMVQANMENDgqrIVRLRPRKct 1243
Cdd:PRK04309 158 ----------------------------IIELDEEMLEDRGLTVDDVKEAIE---KKKGGEVEIEGN---TLIISPKE-- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1244 gaDSVPALTKAVAQLLQsVHLRGIPGIKKTLL-KEGNtfrvdpetggiknesSWMVDTEGTALQrifvGVVNNEGkniID 1322
Cdd:PRK04309 202 --PSYRELRKLAEKIRN-IKIKGIKGIKRVIIrKEGD---------------EYVIYTEGSNLK----EVLKVEG---VD 256
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1323 FSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSETSgPLMRCSF 1402
Cdd:PRK04309 257 ATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKAS-VLARAAF 335
|
410 420 430 440
....*....|....*....|....*....|....*....|....*...
gi 1706887638 1403 EETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLFDLLLDMSKL 1450
Cdd:PRK04309 336 EVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPLR 383
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
216-827 |
2.63e-61 |
|
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: 223.55 E-value: 2.63e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 216 HPRDLILTVLPIPPPQVRPAVA-----FgsAKSD-DELTHQImsiVKRNIQLRKDKESGVKAAVDRS-RALLQEHVATFF 288
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQldggrF--ATSDlNDLYRRV---INRNNRLKKLLELGAPEIIVRNeKRMLQEAVDALI 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 289 NNASTYyKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTL--TFpervnV 366
Cdd:cd01609 213 DNGRRG-KPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELfkPF-----V 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 367 InkKRLTEFVQRTTYPSANYIIRPNGNVtklalvkdrnavhldVGDVVErHVIDGDVVLFNRQPTLHRMSMMGHRVRVLN 446
Cdd:cd01609 287 I--RELIERGLAPNIKSAKKMIERKDPE---------------VWDILE-EVIKGHPVLLNRAPTLHRLGIQAFEPVLIE 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 447 YNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT--DKDTFVD 524
Cdd:cd01609 349 GKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTkeRKGDKGE 428
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 525 KYFIQSValwldlwelpipailkprplwtGKQIFSLILPEvnhpaspydKPPFPHNdkkimiqrgqllvgAITKGVVgaa 604
Cdd:cd01609 429 GIIETTV----------------------GRVIFNEILPE---------GLPFINK--------------TLKKKVL--- 460
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 605 pGSLIHVIFNERGSDEVAKFINgvqRITTY-FNYcfAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTR 683
Cdd:cd01609 461 -KKLINECYDRYGLEETAELLD---DIKELgFKY--ATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYEKGLLTE 534
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 684 KagmsllQSFEAdVNSALNKCREEAAKKALSNVR--RTNSFKVMIEAGSKGSDLNICQIAvfvgqqnvagsripfGFRrr 761
Cdd:cd01609 535 E------ERYNK-VIEIWTEVTEKVADAMMKNLDkdPFNPIYMMADSGARGSKSQIRQLA---------------GMR-- 590
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1706887638 762 tlpHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDV 827
Cdd:cd01609 591 ---GLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDV 653
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
852-1053 |
6.94e-61 |
|
RNA polymerase Rpb1, domain 6; 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 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module. This family appears to be specific to the largest subunit of RNA polymerase II.
Pssm-ID: 461511 Cd Length: 188 Bit Score: 206.97 E-value: 6.94e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 852 LDGARIEgNQAFPIPHMTNSEMADKYRYEYNDEGSfseNMGGHYMDPFVRDSLLRDPQSVLKLQEEFEQLMKDRAMSRLV 931
Cdd:pfam04992 1 LDGAFIE-KQKIDTLKLSDAAFEKRYRLDVMDEKS---GFLPGYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREI 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 932 IDMEDKNKLkMNLPVNVARLIQNARTTMG-KRSQVSNLNPITVINRVRELQEDLAQLfpsyhkdyngRFANVLSQQRVER 1010
Cdd:pfam04992 77 IFPTGDSKV-PQLPVNIQRIIQNAQKIFHiDDRKPSDLHPIYVIEGVRELLDRLVVV----------RGDDPLSKEAQEN 145
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1706887638 1011 ALTLFGIHLRQILGSKRVLKEYKLNDKAFEYLLKEIRTKYQQS 1053
Cdd:pfam04992 146 ATLLFKILLRSRLASKRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1049-1441 |
1.73e-60 |
|
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: 210.15 E-value: 1.73e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1049 KYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKNQRNASVAVCLIREYQKRnKAQ 1128
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLENDRDEK-SAR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1129 EAQQFIEYCTLANITTTVQIIYDPDprntvvaedeemirweqavmneedeepdaeqppSPFIaRLILDNDLFNDKRLNMK 1208
Cdd:cd02736 80 IVKGRIEKTYLGEVASYIEEVYSPD---------------------------------DCYI-LIKLDKKIIEKLQLSKS 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1209 DVKSAIRQVddtymvqanmendgqrivrlrprkctgadsvpaltkavAQLLQSVHLRGIPGIKKTLlkegntFRVDPETG 1288
Cdd:cd02736 126 NLYFLLQSL--------------------------------------KRKLPDVVVSGIPEVKRAV------INKDKKKG 161
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1289 GIKnesswmVDTEGTALQrifvGVVNNEGkniIDFSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYT 1368
Cdd:cd02736 162 KYK------LLVEGYGLR----AVMNTPG---VIGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIM 228
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1706887638 1369 ILVDTMCQRGYLMAVSRTGINRSETSgPLMRCSFEETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLF 1441
Cdd:cd02736 229 LLADLMTFKGEVLGITRFGIAKMKES-VLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
217-1114 |
2.16e-57 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 219.74 E-value: 2.16e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 217 PRDLILTVLPIPPPQVRPAVAF-GSAKSDDELTHQIMSIVKRNIQLRKDKESGVKAA-VDRSRALLQEHVATFFNNASTY 294
Cdd:PRK14906 312 PADMILDVIPVIPPDLRPMVQLdGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIiVNNEKRMLQEAVDSLFDNGRRG 391
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 295 yKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervnvINKKRLTE 374
Cdd:PRK14906 392 -RPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKP-----FVMKRLVE 465
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 375 fvqrttypsanyiIRPNGNVTKLALVKDRNAVHldVGDVVERhVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 454
Cdd:PRK14906 466 -------------LEYAANIKAAKRAVDRGASY--VWDVLEE-VIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHP 529
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 455 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT-DKD-------TFVDky 526
Cdd:PRK14906 530 LVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDgfegegrTFAD-- 607
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 527 FIQSVALWLDLWELPIPAILKPRplwtgkqifsliLPEVNHPASPYDKPPFPHNDKKIMIQRGQLLVGA--------ITK 598
Cdd:PRK14906 608 FDDALNAYDARADLDLQAKIVVR------------LSRDMTVRGSYGDLEETKAGERIETTVGRIIFNQvlpedypyLNY 675
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 599 GVVGAAPGSLIHVIFNERGSDEVAKFINGVQRitTYFNYcfAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANN 678
Cdd:PRK14906 676 KMVKKDIGRLVNDCCNRYSTAEVEPILDGIKK--TGFHY--ATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYED 751
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 679 GKLTRKagmsllqSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGsdlNICQIavfvgqQNVAGSRipfgf 758
Cdd:PRK14906 752 GFLSER-------ERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARG---NIKQI------RQLAGMR----- 810
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 759 rrrtlpHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVhasydgTVRNa 838
Cdd:PRK14906 811 ------GLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQDV------IVRE- 877
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 839 nqeliqlaygedgLDGARIEGnQAFPIphmtnsemadkyryeYNDEGSFSENMGGhymdpfvrdsllrdpqsvlklqeef 918
Cdd:PRK14906 878 -------------EDCGTDEG-VTYPL---------------VKPKGDVDTNLIG------------------------- 903
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 919 eqlmkdRAMSRLVIDMEDKNKLKMNLPVNVarliqnarttmgkrsqvsnlnpitvinrvrelQEDLAQLfpsyhkdyngr 998
Cdd:PRK14906 904 ------RCLLEDVCDPNGEVLLSAGDYIES--------------------------------MDDLKRL----------- 934
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 999 fanvlsqqrVERALTlfGIHLRQILGSKrvlKEYKLNDKAFEYLLKEIRTkyqqslITPGEIIGAIAAQSCGEPATQMTL 1078
Cdd:PRK14906 935 ---------VEAGVT--KVQIRTLMTCH---AEYGVCQKCYGWDLATRRP------VNIGTAVGIIAAQSIGEPGTQLTM 994
|
890 900 910
....*....|....*....|....*....|....*.
gi 1706887638 1079 NTFHNAGISSKNVTLGVPRLLELLNVSKNQRNASVA 1114
Cdd:PRK14906 995 RTFHSGGVAGDDITQGLPRVAELFEARKPKGEAVLA 1030
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1027-1444 |
6.89e-57 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 206.58 E-value: 6.89e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1027 RVLKEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSK 1106
Cdd:PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1107 NQRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITttvQIIYDPDPRNTVVAEDEEMIrweqavmneedeepdaeqp 1185
Cdd:PRK14897 231 KPSTPTMTIYLKKDYREdEEKVREVAKKIENTTLIDVA---DIITDIAEMSVVVELDEEKM------------------- 288
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1186 pspfiarlildndlfNDKRLNMKDVKSAIRQVDdtymVQANMENDGQriVRLRPRKctgaDSVPALTKaVAQLLQSVHLR 1265
Cdd:PRK14897 289 ---------------KERLIEYDDILAAISKLT----FKTVEIDDGI--IRLKPQQ----PSFKKLYL-LAEKVKSLTIK 342
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1266 GIPGIKKTLLKEGNtfrvdpetggikNESSWMVDTEGTALQrifvGVVNNEGkniIDFSKTSSNKIPEVVTVLGIEAARR 1345
Cdd:PRK14897 343 GIKGIKRAIARKEN------------DERRWVIYTQGSNLK----DVLEIDE---VDPTRTYTNDIIEIATVLGIEAARN 403
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1346 KLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINrSETSGPLMRCSFEETVKVLMTAAAFGEKDPVRGVS 1425
Cdd:PRK14897 404 AIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGIS-GEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVA 482
|
410
....*....|....*....
gi 1706887638 1426 ASLVLGNQARIGTGLFDLL 1444
Cdd:PRK14897 483 ENIIVGQPITLGTGAVSLV 501
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
217-1090 |
7.96e-56 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 215.56 E-value: 7.96e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 217 PRDLILTVLPIPPPQVRPAVAFGSAK---SD-DELTHQImsiVKRNIQLRKDKESGVKAAVDRS-RALLQEHVATFFNNA 291
Cdd:PRK09603 1623 PEWMMLTVLPVLPPDLRPLVALDGGKfavSDvNELYRRV---INRNQRLKRLMELGAPEIIVRNeKRMLQEAVDVLFDNG 1699
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 292 STYyKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVnvinkKR 371
Cdd:PRK09603 1700 RST-NAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLL-----SK 1773
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 372 LTEFVQRTTYPSANYIIRPNGNvtklalvkdrnavhldvgDVVE--RHVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNT 449
Cdd:PRK09603 1774 LEERGYATTLKQAKRMIEQKSN------------------EVWEclQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKA 1835
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 450 FRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFV---DKY 526
Cdd:PRK09603 1836 IQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVkgeHKL 1915
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 527 F--IQSVALWLDLWELPIPAILKP----RPLWT--GKQIFSLILPEVNhPASPYDKPPfphndKKIMIqrgqllvgaitk 598
Cdd:PRK09603 1916 FssVNEIITAIDTKELDIHAKIRVldqgNIIATsaGRMIIKSILPDFI-PTDLWNRPM-----KKKDI------------ 1977
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 599 gvvgaapGSLIHVIFNERGSDEVAKFINGVQRIttyfNYCFAFSVGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANN 678
Cdd:PRK09603 1978 -------GVLVDYVHKVGGIGITATFLDNLKTL----GFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQ 2046
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 679 GKLTRKAGMSLLQSFEADVNSALNKcreEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGqqnvagsripfgf 758
Cdd:PRK09603 2047 GLLTDQERYNKIIDTWTEVNDKMSK---EMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRG------------- 2110
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 759 rrrtlphFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDVHASYDGTVRNA 838
Cdd:PRK09603 2111 -------LMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHE 2183
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 839 NQELIQLAYGedgldgariegnqafpiphmtnSEMadkyrYEYNDEGSFSENMGGHYMDPFVRDSLLrdpqsvlklqeeF 918
Cdd:PRK09603 2184 GIEITDIAVG----------------------SEL-----IEPLEERIFGRVLLEDVIDPITNEILL------------Y 2224
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 919 EQLMKDRAMSRLVIDmedknklkmnlpVNVARLIqnARTtmgkrsqvsnlnPITVinrvrelqedlaqlfpsyhKDYNGR 998
Cdd:PRK09603 2225 ADTLIDEEGAKKVVE------------AGIKSIT--IRT------------PVTC-------------------KAPKGV 2259
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 999 FAnvlsqqrveraltlfgihlrqilgskrvlKEYKLNdkafeylLKEIRTKYqqslitPGEIIGAIAAQSCGEPATQMTL 1078
Cdd:PRK09603 2260 CA-----------------------------KCYGLN-------LGEGKMSY------PGEAVGVVAAQSIGEPGTQLTL 2297
|
890
....*....|..
gi 1706887638 1079 NTFHNAGISSKN 1090
Cdd:PRK09603 2298 RTFHVGGTASRS 2309
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
206-827 |
7.64e-54 |
|
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: 207.32 E-value: 7.64e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 206 LIMGFDPRFCHPRDLILTVLPIPPPQVRPAVA-----FgsAKSDdeLTHQIMSIVKRNIQLRKDKESGV-KAAVDRSRAL 279
Cdd:COG0086 213 VVEAFRESGNRPEWMILDVLPVIPPDLRPLVPldggrF--ATSD--LNDLYRRVINRNNRLKRLLELKApDIIVRNEKRM 288
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 280 LQEHVATFFNNaSTYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLT 359
Cdd:COG0086 289 LQEAVDALFDN-GRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELF 367
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 360 FPervNVINKKRLTEFVqrTTYPSANYIIrpngnvtklalvkDRnaVHLDVGDVVERhVIDGDVVLFNRQPTLHRMSMMG 439
Cdd:COG0086 368 KP---FIYRKLEERGLA--TTIKSAKKMV-------------ER--EEPEVWDILEE-VIKEHPVLLNRAPTLHRLGIQA 426
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 440 HRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDK 519
Cdd:COG0086 427 FEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTRE 506
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 520 DTFV---DKYF--IQSVALWLDLWELPIPAILKPRPLWTGKQ------------IFSLILPEVnhpASPYDKppfPHNDK 582
Cdd:COG0086 507 REGAkgeGMIFadPEEVLRAYENGAVDLHARIKVRITEDGEQvgkivettvgryLVNEILPQE---VPFYNQ---VINKK 580
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 583 KImiqrgqllvgaitkgvvgaapGSLIHVIFNERGSDEVAKFINGVQRITtyFNYCF--AFSVGVQDTVADATtlKEmnN 660
Cdd:COG0086 581 HI---------------------EVIIRQMYRRCGLKETVIFLDRLKKLG--FKYATraGISIGLDDMVVPKE--KQ--E 633
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 661 VLHKTRQSVEKIGAAANNGKLTRKAgmsllqSFEAdVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQI 740
Cdd:COG0086 634 IFEEANKEVKEIEKQYAEGLITEPE------RYNK-VIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQL 706
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 741 avfvgqqnvAGSRipfgfrrrtlpHFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKL 820
Cdd:COG0086 707 ---------AGMR-----------GLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRL 766
|
....*..
gi 1706887638 821 VKALEDV 827
Cdd:COG0086 767 VDVAQDV 773
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1049-1444 |
2.02e-52 |
|
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: 187.01 E-value: 2.02e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1049 KYQQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVsknqrnASvavclireyqkrnkaq 1128
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMT------AS---------------- 58
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1129 eaqqfieyctlANITTTVQIIYdpdPRNTVVAEDEEmirweqavmneedeepdaeqppspFIARLIldndlfndKRLNMK 1208
Cdd:cd02735 59 -----------KNIKTPSMTLP---LKNGKSAERAE------------------------TLKKRL--------SRVTLS 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1209 DVksaIRQVDDTYmVQANMENdgqRIVRLRPRKCTGADSVPA------LTKAVAQLLQSVHLRGIPGIKKTLLKEGNTFR 1282
Cdd:cd02735 93 DV---VEKVEVTE-ILKTIER---VFKKLLGKWCEVTIKLPLsspkllLLSIVEKLARKAVIREIPGITRCFVVEEDKGG 165
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1283 VDPEtggiknesswMVDTEGTALQRIFvgvvnnEGKNIIDFSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYGLNI 1362
Cdd:cd02735 166 KTKY----------LVITEGVNLAALW------KFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAV 229
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1363 NYRHYTILVDTMCQRGYLMAVSRTGInRSETSgPLMRCSFEETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLFD 1442
Cdd:cd02735 230 DPRHLSLIADYMTFEGGYRPFNRIGM-ESSTS-PLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFD 307
|
..
gi 1706887638 1443 LL 1444
Cdd:cd02735 308 LL 309
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
217-1451 |
9.80e-50 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 195.61 E-value: 9.80e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 217 PRDLILTVLPIPPPQVRPAVAFGSAK-SDDELTHQIMSIVKRNIQLRKDKESGVKAAVDRS-RALLQEHVATFFNNASTY 294
Cdd:PRK14844 1666 PEWMILTTIPILPPDLRPLVSLESGRpAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNeKRMLQEAVDSLFDNSRRN 1745
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 295 YKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervnvINKKRLTE 374
Cdd:PRK14844 1746 ALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----FVYSKLKM 1820
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 375 FVQRTTYPSANYIIRpngnvtklalvkdrnAVHLDVGDVVERhVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 454
Cdd:PRK14844 1821 YGMAPTIKFASKLIR---------------AEKPEVWDMLEE-VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHP 1884
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 455 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT----DKDTFVDKYFIQS 530
Cdd:PRK14844 1885 LVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTlqepKEDDLPSFGAFCE 1964
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 531 VALWLDLWELPIPAILKPRPLWTGKQIFSLILPEVNHPASPYDKPPFP-HNDKKIMIQRGQLLVGAITkgvvgaapgSLI 609
Cdd:PRK14844 1965 VEHSLSDGTLHIHSSIKYRMEYINSSGETHYKTICTTPGRLILWQIFPkHENLGFDLINQVLTVKEIT---------SIV 2035
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 610 HVIFNERGSDEVAKFINgvQRITTYFNYCfAFSvGVQDTVADATTLKEMNNVLHKTRQSVEKIGAAANNGKLTRKAGMSl 689
Cdd:PRK14844 2036 DLVYRNCGQSATVAFSD--KLMVLGFEYA-TFS-GVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYN- 2110
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 690 lqsfeaDVNSALNKCREEAAKKALSNV------RRTNSFKVMIEAGSKGSDLNICQIAVFVGqqnvagsripfgfrrrtl 763
Cdd:PRK14844 2111 ------KVIDEWSKCTDMIANDMLKAIsiydgnSKYNSVYMMVNSGARGSTSQMKQLAGMRG------------------ 2166
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 764 phFMLDDYGETSRGMATRGYVEGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALED-VHASYDGTVRNAnqeL 842
Cdd:PRK14844 2167 --LMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNcIVTKHDCKTKNG---L 2241
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 843 IQLAYGEDGLDGARIEGNQafpiphMTNSEMADKYryeyndegsfsenmgghymDPFVRDSLLRDPQSVlklqeefeqlm 922
Cdd:PRK14844 2242 VVRATVEGSTIVASLESVV------LGRTAANDIY-------------------NPVTKELLVKAGELI----------- 2285
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 923 kdramsrlvidmeDKNKLKMnlpVNVARLiqnarttmgkrSQVSNLNPITVinrvrELQEDLAQLfpSYHKDyngrfanv 1002
Cdd:PRK14844 2286 -------------DEDKVKQ---INIAGL-----------DVVKIRSPLTC-----EISPGVCSL--CYGRD-------- 2323
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1003 lsqqrveraltlfgihlrqiLGSKRVlkeyklndkafeyllkeirtkyqqslITPGEIIGAIAAQSCGEPATQMTLNTFH 1082
Cdd:PRK14844 2324 --------------------LATGKI--------------------------VSIGEAVGVIAAQSVGEPGTQLTMRTFH 2357
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1083 -----NAGISSKNVTLGVPRLLELLN----VSKNQR----NASVAVCLI----REYQKRNKAQEAQQFIEYCTLANITTT 1145
Cdd:PRK14844 2358 iggvmTRGVESSNIIASINAKIKLNNsniiIDKNGNkiviSRSCEVVLIdslgSEKLKHSVPYGAKLYVDEGGSVKIGDK 2437
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1146 VQiIYDP-------DPRNTVVAED-------EEMIRWEQAVMNEEDEEPDAEQPPSPFIARLILDNDlfNDKRLNMKD-V 1210
Cdd:PRK14844 2438 VA-EWDPytlpiitEKTGTVSYQDlkdgisiTEVMDESTGISSKVVKDWKLYSGGANLRPRIVLLDD--NGKVMTLASgV 2514
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1211 KS-------AIRQVDDTYMVQAnmendGQRIVRlRPRKCTGADSVPALTKAVAQLLQSVHLRGIPGIKKTllkEGNTFRV 1283
Cdd:PRK14844 2515 EAcyfipigAVLNVQDGQKVHA-----GDVITR-TPRESVKTRDITGGLPRVIELFEARRPKEHAIVSEI---DGYVAFS 2585
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1284 DPETGGIKNESSWMVDTEGTALQRIFV---GVVNNEGKNII--DFSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAY 1358
Cdd:PRK14844 2586 EKDRRGKRSILIKPVDEQISPVEYLVSrskHVIVNEGDFVRkgDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQ 2665
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1359 GLNINYRHYTILVDTMCQR---------GYLM--------------AVSRT------------GINRS--ETSGPLMRCS 1401
Cdd:PRK14844 2666 GVRIDNKHLEVILKQMLQKveitdpgdtMYLVgesidklevdrendAMSNSgkrpahylpilqGITRAslETSSFISAAS 2745
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1402 FEETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLFdllldMSKLQ 1451
Cdd:PRK14844 2746 FQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLI-----MNKVR 2790
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
492-648 |
3.71e-46 |
|
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 163.57 E-value: 3.71e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 492 NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFVDKYFIQSVALWLDlwELPIPAILKP-RPLWTGKQIFSLILP-EVNHPA 569
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGI--VLPHPAILKPiKPLWTGKQTFSRLLPnEINPKG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 570 SPYDKPP-FPHNDKKIMIQRGQLLVGAITKGVVGAAPGSLIHVIFNERGSDEVAKFINGVQRITTYFNYCFAFSVGVQDT 648
Cdd:pfam04983 79 KPKTNEEdLCENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1074-1446 |
5.71e-41 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 164.30 E-value: 5.71e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1074 TQMTLNTFHNAGISSKNVTLGVPRLLELLNVSKNQRNASVAVCLIREYQK-RNKAQEAQQFIEYCTLANITTTVQIIYdp 1152
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATdREKAEEVAKKIESLTLGDVATSIAIDL-- 618
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1153 dprntvvaedeemirWEQAVMNEedeepdaeqppspfiarliLDNDLFNDKRLNMKDVKSAIRQvddtyMVQANMENDGQ 1232
Cdd:PRK14898 619 ---------------WTQSIKVE-------------------LDEETLADRGLTIESVEEAIEK-----KLGVKIDRKGT 659
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1233 rIVRLRPRKctgaDSVPALTKAVAQLlQSVHLRGIPGIKKTLLKEGNTfrvdpetggiKNESSWMVDTEGTALQRIFvgv 1312
Cdd:PRK14898 660 -VLYLKPKT----PSYKALRKRIPKI-KNIVLKGIPGIERVLVKKEEH----------ENDEEYVLYTQGSNLREVF--- 720
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1313 vNNEGkniIDFSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRSE 1392
Cdd:PRK14898 721 -KIEG---VDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHGVAGEK 796
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 1706887638 1393 TSgPLMRCSFEETVKVLMTAAAFGEKDPVRGVSASLVLGNQARIGTGLFDLLLD 1446
Cdd:PRK14898 797 GS-VLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRID 849
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
221-827 |
6.47e-41 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 165.63 E-value: 6.47e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 221 ILTVLPIPPPQVRPAVA-----FgsAKSD-DELTHQImsiVKRNIQLRKDKESGvkaAVD-------RsraLLQEHVATF 287
Cdd:PRK00566 228 ILDVLPVIPPDLRPLVQldggrF--ATSDlNDLYRRV---INRNNRLKRLLELG---APEiivrnekR---MLQEAVDAL 296
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 288 FNNASTYyKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTL--TFpervn 365
Cdd:PRK00566 297 FDNGRRG-RPVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELfkPF----- 370
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 366 VInkKRLtefVQR---TTYPSANYII---RPngnvtklalvkdrnavhlDVGDVVErHVIDGDVVLFNRQPTLHRMSMMG 439
Cdd:PRK00566 371 IM--KKL---VERglaTTIKSAKKMVereDP------------------EVWDVLE-EVIKEHPVLLNRAPTLHRLGIQA 426
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 440 hrvrvlnyntF----------RLN-LSCtTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPcmgIV-- 506
Cdd:PRK00566 427 ----------FepvliegkaiQLHpLVC-TAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKP---IIvp 492
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 507 -QDSLLGSYRLT-DKDTFVD--KYF--IQSVALWLDLWELPIPAILKPRP-----LWT--GKQIFSLILPEvnhpASPYD 573
Cdd:PRK00566 493 sQDMVLGLYYLTrEREGAKGegMVFssPEEALRAYENGEVDLHARIKVRItskklVETtvGRVIFNEILPE----GLPFI 568
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 574 kppfphNDKKIMiqrgqllvgaiTKGVVGAapgsLIHVIFNERGSDEVAKFINGVQrittYFNYCFAFSVGVQDTVADAT 653
Cdd:PRK00566 569 ------NVNKPL-----------KKKEISK----IINEVYRRYGLKETVIFLDKIK----DLGFKYATRSGISIGIDDIV 623
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 654 TLKEMNNVLHKTRQSVEKIGAAANNGKLT-----RKagmsllqsfeadVNSALNKCREEAAKKALSNVRRT----NSFKV 724
Cdd:PRK00566 624 IPPEKKEIIEEAEKEVAEIEKQYRRGLITdgeryNK------------VIDIWSKATDEVAKAMMKNLSKDqesfNPIYM 691
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 725 MIEAGSKGSDLNICQIAvfvGqqnvagsripfgfrrrtlphfMlddygetsRG-MA-TRG----------YVEGLQPHEF 792
Cdd:PRK00566 692 MADSGARGSASQIRQLA---G---------------------M--------RGlMAkPSGeiietpiksnFREGLTVLEY 739
|
650 660 670
....*....|....*....|....*....|....*
gi 1706887638 793 YFHTMAGREGLIDTAVKTSDTGYLQRKLVkaleDV 827
Cdd:PRK00566 740 FISTHGARKGLADTALKTADSGYLTRRLV----DV 770
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
220-517 |
4.79e-36 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 147.36 E-value: 4.79e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 220 LILTVLPIPPPQVRPAVAFGS---AKSD-DELtHQImsIVKRNIQLRKDKESGVKAAVDRSRA---LLQEHVATFFNNaS 292
Cdd:CHL00018 264 MVLCLLPVLPPELRPIIQLDGgklMSSDlNEL-YRR--VIYRNNTLTDLLTTSRSTPGELVMCqkkLLQEAVDALLDN-G 339
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 293 TYYKPAKVGDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTL--TFPERvNVINKK 370
Cdd:CHL00018 340 IRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELfqPFVIR-GLIRQH 418
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 371 rlteFVQRTTypSANYIIRPNGNVTKLALvkdrnavhldvgdvveRHVIDGDVVLFNRQPTLHRmsmmghrvrvLNYNTF 450
Cdd:CHL00018 419 ----LASNIR--AAKSKIREKEPIVWEIL----------------QEVMQGHPVLLNRAPTLHR----------LGIQAF 466
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 451 ----------RLN-LSCTTpYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSP----NKSAPCmgivQDSLLGSYR 515
Cdd:CHL00018 467 qpilvegraiCLHpLVCKG-FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPaigdPISVPS----QDMLLGLYV 541
|
..
gi 1706887638 516 LT 517
Cdd:CHL00018 542 LT 543
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
672-777 |
1.97e-34 |
|
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: 127.87 E-value: 1.97e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 672 IGAAANNGKLTRKAGMSLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGSDLNICQIAVFVGQQNVAG 751
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*.
gi 1706887638 752 SRIPFGFRRRTLPHFMLDDYGETSRG 777
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRG 106
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1137-1265 |
8.95e-34 |
|
RNA polymerase Rpb1, domain 7; 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 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (pfam04561).
Pssm-ID: 461510 [Multi-domain] Cd Length: 136 Bit Score: 127.27 E-value: 8.95e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1137 CTLANITTTVQIIYDPDPRNTVVAEDEEMIRWEQAVmneEDEEPDAEQPPSPFIARLILDNDLFNDKRLNMKDVKSAIRQ 1216
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEI---PDEDVEDLDRQSPWLLRIELDRKKMLDKGLTMEDVAEKIKE 77
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1217 V--DDTyMVQANMENDGQRIVRLRPRK---------CTGADSVPALTKAVAQLLQSVHLR 1265
Cdd:pfam04990 78 EfgNDL-FVIFSDDNAEKLVIRIRIINdekekdeeqEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
217-517 |
5.97e-32 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 134.11 E-value: 5.97e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 217 PRDLILTVLPIPPPQVRPAVAFGS---AKSDdeLTHQIMSIVKRNIQLRKDKESGVKAAVDRS-RALLQEHVATFFNNAS 292
Cdd:PRK02625 242 PEWMVLDVIPVIPPDLRPMVQLDGgrfATSD--LNDLYRRVINRNNRLARLQEILAPEIIVRNeKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 293 TyyKPAKVG-DTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNVINKKR 371
Cdd:PRK02625 320 R--GRTVVGaNNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQG 397
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 372 LTEFVQrttypSANYIIRPNGNvtklalvkdrnavhlDVGDVVERhVIDGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFR 451
Cdd:PRK02625 398 IVNNIK-----AAKKLIQRADP---------------EVWQVLEE-VIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQ 456
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1706887638 452 LNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT 517
Cdd:PRK02625 457 LHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLT 522
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1331-1440 |
2.45e-30 |
|
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: 118.29 E-value: 2.45e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1331 IPEVVTVLGIEAARRKLLSELREAYLAYGLNINYRHYTILVDTMCQRGYLMAVSRTGINRsETSGPLMRCSFEETVKVLM 1410
Cdd:cd00630 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRA-SKTSPLMRASFEKTTKHLL 128
|
90 100 110
....*....|....*....|....*....|
gi 1706887638 1411 TAAAFGEKDPVRGVSASLVLGNQARIGTGL 1440
Cdd:cd00630 129 DAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1058-1105 |
4.50e-18 |
|
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: 82.85 E-value: 4.50e-18
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1706887638 1058 GEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVS 1105
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1053-1102 |
2.62e-11 |
|
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: 64.86 E-value: 2.62e-11
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1053 SLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSkNVTLGVPRLLELL 1102
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELF 49
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1058-1445 |
2.46e-10 |
|
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; 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 (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb 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. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Pssm-ID: 132724 [Multi-domain] Cd Length: 381 Bit Score: 64.36 E-value: 2.46e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1058 GEIIGAIAAQSCGEPATQMTLNTFHNAGISSknvtlgVPRLLELLNVSKNQRNASVAVCLI---------REYQKRNKAQ 1128
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQSLESSP------LELLKEVLECRSKSKSKENDRRVIlslhlckcdHGFEYERAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1129 EAQQFIEYCTLANITTTVQIIYDPDPRNTVVAEDEEMIRWEQAVMNEEdeEPDAEQPPSPFiarLILDNDLFNDKRLNMK 1208
Cdd:cd02737 75 EVKNHLERVTLEDLATTSMIKYSPQATEAIVGEIGDQLNTKKKGKKKA--IFSTSLKITKF---SPWVCHFHLDKECQKL 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1209 DVKSAIrqvddTYMVQANMENDGQRIVR-LRPRKCtgadsvPALTKAVaqllqsvhLRGIPGIKKT-LLKEGNTFRVDPE 1286
Cdd:cd02737 150 SDGPCL-----TFSVSKEVSKSSEELLDvLRDRII------PFLLETV--------IKGDERIKSVnILWEDSPSTSWVK 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1287 TGGIKNESSWMVD---TEGTALQRI-FVGVVNN---EGKNIIDFSKTSSNKIPEVVTVLGIEAARRKLLSELREAYLAYG 1359
Cdd:cd02737 211 SVGKSSRGELVLEvtvEESCKKTRGnAWNVVMDaciPVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTG 290
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1706887638 1360 LNInYRHYTILV-DTMCQRGYLMAVSRTG---INRSE-TSGPLMRCSFEETVKVLMTAAAFGEKDPVRGVSASLVLGNQA 1434
Cdd:cd02737 291 KSV-LREHLLLVaDSMTYSGEFVGLNAKGykaQRRSLkISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEA 369
|
410
....*....|..
gi 1706887638 1435 RIGTG-LFDLLL 1445
Cdd:cd02737 370 PVGTGsKFEILW 381
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1051-1086 |
5.36e-07 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 54.95 E-value: 5.36e-07
10 20 30
....*....|....*....|....*....|....*.
gi 1706887638 1051 QQSLITPGEIIGAIAAQSCGEPATQMTLNTFHNAGI 1086
Cdd:CHL00117 308 HGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1058-1091 |
1.32e-06 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 53.46 E-value: 1.32e-06
10 20 30
....*....|....*....|....*....|....
gi 1706887638 1058 GEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNV 1091
Cdd:PRK02597 311 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1054-1091 |
5.70e-06 |
|
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: 51.39 E-value: 5.70e-06
10 20 30
....*....|....*....|....*....|....*...
gi 1706887638 1054 LITPGEIIGAIAAQSCGEPATQMTLNTFHNAGISSKNV 1091
Cdd:TIGR02388 305 LVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1030-1078 |
2.60e-05 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 49.12 E-value: 2.60e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1706887638 1030 KEYKLNDKAFEYLLKEIRTKYQQSLITPGEIIGAIAAQSCGEPATQMTL 1078
Cdd:PRK14898 29 KRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
785-827 |
1.28e-04 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 46.91 E-value: 1.28e-04
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1706887638 785 EGLQPHEFYFHTMAGREGLIDTAVKTSDTGYLQRKLVKALEDV 827
Cdd:PRK02597 165 EGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDV 207
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
800-827 |
1.40e-04 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 46.86 E-value: 1.40e-04
10 20
....*....|....*....|....*...
gi 1706887638 800 REGLIDTAVKTSDTGYLQRKLVKALEDV 827
Cdd:CHL00117 186 RKGVVDTAVRTADAGYLTRRLVEVVQHI 213
|
|
| |
