|
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 ... |
18-855 |
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: 1227.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 18 NEVQFEIFKERQIKSYAVCLVEHAKSYERGR-PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGV 96
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYENGGgPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 97 FDLVLQVLKCVCKtcgalllntreqdvhkklqhmtglnrlrqvakmaeakcrvststeddmgidgfdsapfnggsgmgpg 176
Cdd:cd02733 81 LTKILKILRCVCK------------------------------------------------------------------- 93
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 177 atrgcgasqprvsrfygiyptlvikavheeqdAEWHADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVR 256
Cdd:cd02733 94 --------------------------------RELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 257 PAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKES-DVQAAIDRSRALLQEHVATYFNNASTYYKPTKVNDTKKLKSLTE 334
Cdd:cd02733 142 PSVVMdGSARSEDDLTHKLADIIKANNQLKRQEQNgAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQ 221
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 335 RLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARRTV--YPSANYIHH 412
Cdd:cd02733 222 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPneYPGAKYIIR 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 413 PNGTITKLALLRDRSKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEM 492
Cdd:cd02733 302 DDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEM 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 493 NLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSVALWLDLW--QLPIPAILK 570
Cdd:cd02733 382 NLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWdgKIPQPAILK 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 571 PRPLWTGKQVFSLILPEVNHPA-----TPQDRPPFPHNDSVVMIRRGQLLCGPITKSIVGAAPGSLIHVIFNEHGSDEVA 645
Cdd:cd02733 462 PKPLWTGKQIFSLIIPKINNLIrssshHDGDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAAR 541
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 646 RFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLNRKAGMTLLQSFEADVNSALN 725
Cdd:cd02733 542 DFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILN 621
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 726 KCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMANRG 805
Cdd:cd02733 622 KARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENS 701
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|
gi 1115875379 806 YVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855
Cdd:cd02733 702 YLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
10-883 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 786.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 10 SQMELQKVNEVQFEIFKERQIKSYAVCLVEHAKSY-ERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELA 88
Cdd:PRK08566 2 MMMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 89 EPVFNIGVFDLVLQVLKCVCKTCGALLLntREQDVHKKLQHMTGLNRLRQVAK--MAEAKCRVSTSTEddmgidgfdsAP 166
Cdd:PRK08566 82 RPVIHVGFAKLIYKLLRATCRECGRLKL--TEEEIEEYLEKLERLKEWGSLADdlIKEVKKEAAKRMV----------CP 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 167 FnggsgmgpgatrgCGASQPRVsRFygIYPTlvikAVHEEQDAEWH---ADKVRQVLDRVSDDDARLMGFDPQRCHPRDL 243
Cdd:PRK08566 150 H-------------CGEKQYKI-KF--EKPT----TFYEERKEGLVkltPSDIRERLEKIPDEDLELLGINPEVARPEWM 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 244 VLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKPT 321
Cdd:PRK08566 210 VLTVLPVPPVTVRPSITLeTGQRSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVTTYFDNEIPGIPPA 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 322 KVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARR 401
Cdd:PRK08566 290 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLN 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 402 --TVYPSANYIHHPNGTITKLaLLRDRSKV--TLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 477
Cdd:PRK08566 370 gpEKHPGANYVIRPDGRRIKL-TDKNKEELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 478 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSV--A 555
Cdd:PRK08566 449 AVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLlrA 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 556 LWLDLWQLPIPAILKPRPLWTGKQVFSLILPE----------VNHPATPQDRPPFphNDSVVMIRRGQLLCGPITKSIVG 625
Cdd:PRK08566 529 AGIDELPEPEPAIENGKPYWTGKQIFSLFLPKdlnlefkakiCSGCDECKKEDCE--HDAYVVIKNGKLLEGVIDKKAIG 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 626 AAPGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLN 705
Cdd:PRK08566 607 AEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELE 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 706 RKAGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRT 785
Cdd:PRK08566 687 PLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRT 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 786 LPHFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDEL 865
Cdd:PRK08566 767 LPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNI 846
|
890
....*....|....*...
gi 1115875379 866 IQFMYGEDGLDGARIEGG 883
Cdd:PRK08566 847 VQFKYGEDGVDPMKSDHG 864
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
14-884 |
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: 758.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 14 LQKVNEVQFEIFKERQIKSYAVCLVEHAKSYER-GRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVF 92
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDdGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 93 NIGVFDLVLQVLKCVCKTCGALLLNTREQDvhkklQHMTGLNRLRQVAKMAEakcrvSTSTEDdmgidgfdsapfnggsg 172
Cdd:TIGR02390 81 HVGFAKEIYKILRATCRKCGRITLTEEEIE-----QYLEKINKLKEEGGDLA-----STLIEK----------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 173 MGPGATRG-----CGASQPRV-----SRFYGIYPTLVIKAVHEEqdaewhadkVRQVLDRVSDDDARLMGFDPQRCHPRD 242
Cdd:TIGR02390 134 IVKEAAKRmkcphCGEEQKKIkfekpTYFYEEGKEGDVKLTPSE---------IRERLEKIPDEDAELLGINPKVARPEW 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 243 LVLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKP 320
Cdd:TIGR02390 205 MVLTVLPVPPVTVRPSITLeTGERSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVATYFDNELPGIPP 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 321 TKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFAR 400
Cdd:TIGR02390 285 ARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVL 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 401 R--TVYPSANYIHHPNGTITKLALL-RDRSKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 477
Cdd:TIGR02390 365 NgpDSWPGANYVIRPDGRRIKIRDEnKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNL 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 478 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSVALW 557
Cdd:TIGR02390 445 AVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGV 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 558 LDLW-QLPIPAILKPRPLWTGKQVFSLILPE---------VNHPATPQDRPPFPHnDSVVMIRRGQLLCGPITKSIVGAA 627
Cdd:TIGR02390 525 AGYFgDPPEPAIEKPKEYWTGKQIFSAFLPEdlnfegrakICSGSDACKKEECPH-DAYVVIKNGKLLKGVIDKKAIGAE 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 628 PGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLNRK 707
Cdd:TIGR02390 604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 708 AGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLP 787
Cdd:TIGR02390 684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 788 HFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDELIQ 867
Cdd:TIGR02390 764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843
|
890
....*....|....*..
gi 1115875379 868 FMYGEDGLDGARIEGGQ 884
Cdd:TIGR02390 844 FKYGEDGVDPMKSDHGK 860
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
809-1422 |
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: 584.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 809 GLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDELIQFMYGEDGLDGARIEGGQLFPL 888
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 889 PFRDDKEMEDTYKYEYDVDGTFSGKVGGNYMDPHVRKMLradpqnvrklqeeyeqltadrewsrkmldledrdklklnlp 968
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSK----------------------------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 969 vnpgrliqnarstmgkrsqvsnlspitiidhvrklqedlmklfpsyhrggdgYIRNTLSRERIESALTLFNVHLRQLLAS 1048
Cdd:pfam04998 120 ----------------------------------------------------LGRDRLSKEAQERATLLFELLLKSGLES 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1049 KRVLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVS 1128
Cdd:pfam04998 148 KRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVS 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1129 RNQKHASMTVSLFPPY-DEKRNAQKAQHLIEYCTLESITRRIQFIYDPDPRHTVVEADRDILELEWNVMDESDAELRIQE 1207
Cdd:pfam04998 228 KNIKSPSLTVYLFDEVgRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1208 VVAGSPWVVRLELDVDM---------VTDKALDMKDVKQAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLK 1278
Cdd:pfam04998 308 ETGLLILVIRLLKILNKsikkvvkseVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDELFMEEDPKLA 387
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1279 REIPALLARVHLRGIPGVRRALLKDTTEFTVDQAtgkmsgnkiWAIDTDGTALRRAFIgvvgedGKNIINAVKTSSNKVP 1358
Cdd:pfam04998 388 ILVASLLGNITLRGIPGIKRILVNEDDKGKVEPD---------WVLETEGVNLLRVLL------VPGFVDAGRILSNDIH 452
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1115875379 1359 EVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSGP 1422
Cdd:pfam04998 453 EILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
242-537 |
1.15e-147 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 455.83 E-value: 1.15e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 242 DLVLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKE-SDVQAAIDRSRALLQEHVATYFNNASTyyK 319
Cdd:smart00663 2 WMILTVLPVPPPCLRPSVQLdGGRFAEDDLTHLLRDIIKRNNRLKRLLElGAPSIIIRNEKRLLQEAVDTLIDNEGL--P 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 320 PTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFA 399
Cdd:smart00663 80 RANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 400 RRTVyPSANYIHhpNGTITKLALLRD-RSKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLS 478
Cdd:smart00663 160 RNGP-NGAKYII--RGKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPL 236
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1115875379 479 CTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSY 537
Cdd:smart00663 237 VCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1055-1472 |
1.85e-140 |
|
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: 441.26 E-value: 1.85e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1055 YKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHA 1134
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1135 SMTVSLFPPYD-EKRNAQKAQHLIEYCTLESITRRIQFIYDPDPRHTVVEADRDILELEWNVMDESDAELRIqevvagSP 1213
Cdd:cd02584 81 SLTVYLEPGFAkDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRL------SP 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1214 WVVRLELDVDMVTDKALDMKDVKQAI---LRVDESYIIETGMANN--VRQRTIRMRSRYNEGADSIPKLKREIPALLARV 1288
Cdd:cd02584 155 WLLRIELDRKKMTDKKLSMEQIAKKIkeeFKDDLNVIFSDDNAEKlvIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDM 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1289 HLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALRRafigVVGEDGkniINAVKTSSNKVPEVCSLLGIEA 1368
Cdd:cd02584 235 TLKGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLRE----VLSHPG---VDPTRTTSNDIVEIFEVLGIEA 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1369 ARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTsGPLMRCSFEETVKVLMAAASFGECDPVR 1448
Cdd:cd02584 308 ARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDT-GPLMRCSFEETVDILLEAAAFGETDDLK 386
|
410 420
....*....|....*....|....
gi 1115875379 1449 GVSANLVLGNQARVGTGLFDLVLN 1472
Cdd:cd02584 387 GVSENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-347 |
1.56e-138 |
|
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: 432.10 E-value: 1.56e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 14 LQKVNEVQFEIFKERQIKSYAVCLVEHAKSYERG--RPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPV 91
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGslKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 92 FNIGVFDLVLQVLKCVCKTCGALLLNTREQDVHKKLQHMTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFdsapfnggs 171
Cdd:pfam04997 81 FHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKNGV--------- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 172 gmgpgatrgCGASQPrVSRFYGIYPTLVIKAVHE-EQDAEWHADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPV 250
Cdd:pfam04997 152 ---------CGSQQP-VSRKEGLKLKAAIKKSKEeEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPV 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 251 PPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKPTKVNDTKK 328
Cdd:pfam04997 222 PPPCIRPSVQLdGGRRAEDDLTHKLRDIIKRNNRLKKLLELGApSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRP 301
|
330
....*....|....*....
gi 1115875379 329 LKSLTERLKGKYGRLRGNL 347
Cdd:pfam04997 302 LKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1051-1471 |
1.75e-66 |
|
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: 229.94 E-value: 1.75e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1051 VLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRN 1130
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1131 QKHASMTVSLFPPYdeKRNAQKAQHL---IEYCTLESITRRIqfiydpdprhtvveadrdilelEWNVMDEsdaelriqe 1207
Cdd:TIGR02389 94 PSTPSMTIYLEDEY--EKDREKAEEVakkIEATKLEDVAKDI----------------------SIDLADM--------- 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1208 vvagspwVVRLELDVDMVTDKALDMKDVKQAILRVDESYIIETGMANNvrqrTIRMrsryNEGADSIPKLKREIPALLAr 1287
Cdd:TIGR02389 141 -------TVIIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDNN----TITI----KPGNPSLKELRKLKEKIKN- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1288 VHLRGIPGVRRALLKdtteftvdqatgkmSGNKIWAIDTDGTALRrafiGVVGEDGkniINAVKTSSNKVPEVCSLLGIE 1367
Cdd:TIGR02389 205 LHIKGIKGIKRVVIR--------------KEGDEYVIYTEGSNLK----EVLKLEG---VDKTRTTTNDIHEIAEVLGIE 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1368 AARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSgPLMRCSFEETVKVLMAAASFGECDPV 1447
Cdd:TIGR02389 264 AARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKAS-VLARAAFEVTVKHLLDAAIRGEVDEL 342
|
410 420
....*....|....*....|....
gi 1115875379 1448 RGVSANLVLGNQARVGTGLFDLVL 1471
Cdd:TIGR02389 343 KGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1029-1471 |
3.49e-61 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 215.09 E-value: 3.49e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1029 ERIESALTLFNVHLRQLLASKrvLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1108
Cdd:PRK04309 9 EKLEDASLELPQKLKEELREK--LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1109 ISSKNVTLGVPRLLELLNVSRNQKHASMTVSLFPPYdeKRNAQKAQHL---IEYCTLESITRRIqfiydpdprhtvvead 1185
Cdd:PRK04309 87 VAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEY--AYDREKAEEVarkIEATTLENLAKDI---------------- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1186 rdilelEWNVMDESdaelriqevvagspwvVRLELDVDMVTDKALDMKDVKQAIlrvDESYIIETGMANNVRQRTIRMRS 1265
Cdd:PRK04309 149 ------SVDLANMT----------------IIIELDEEMLEDRGLTVDDVKEAI---EKKKGGEVEIEGNTLIISPKEPS 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1266 rYNEGADSIPKLKReipallarVHLRGIPGVRRALL-KDTTEftvdqatgkmsgnkiWAIDTDGTALRrafiGVVGEDGk 1344
Cdd:PRK04309 204 -YRELRKLAEKIRN--------IKIKGIKGIKRVIIrKEGDE---------------YVIYTEGSNLK----EVLKVEG- 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1345 niINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSgPLM 1424
Cdd:PRK04309 255 --VDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKAS-VLA 331
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 1115875379 1425 RCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGLFDLVL 1471
Cdd:PRK04309 332 RAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTM 378
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
239-850 |
3.11e-53 |
|
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: 205.39 E-value: 3.11e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 239 HPRDLVLTVLPVPPPQVRPAISFGGLR---SDdeLTHQIMSIVKRNNQLRRDKESDVQAAIDRS-RALLQEHVATYFNNa 314
Cdd:COG0086 223 RPEWMILDVLPVIPPDLRPLVPLDGGRfatSD--LNDLYRRVINRNNRLKRLLELKAPDIIVRNeKRMLQEAVDALFDN- 299
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 315 STYYKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervNTVNKKR 394
Cdd:COG0086 300 GRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP---FIYRKLE 376
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 395 LTEFARrtvypsanyihhpngTITKLALLRDRskVTLNIGDVVERhVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFR 474
Cdd:COG0086 377 ERGLAT---------------TIKSAKKMVER--EEPEVWDILEE-VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQ 438
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 475 LNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFL---DKYF- 550
Cdd:COG0086 439 LHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTREREGAkgeGMIFa 518
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 551 -VQSVALWLDLWQLPIPAILKPRPLWTGKQVFSL--------ILPEVnhpaTPQDrppfphndsVVMIRRgqllcgPITK 621
Cdd:COG0086 519 dPEEVLRAYENGAVDLHARIKVRITEDGEQVGKIvettvgryLVNEI----LPQE---------VPFYNQ------VINK 579
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 622 SIVGAapgsLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADsdtlRQMNDVLVKTRRNVEKI------ 695
Cdd:COG0086 580 KHIEV----IIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVP----KEKQEIFEEANKEVKEIekqyae 651
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 696 GAAANNRTLNRkagmtllqsfeadVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVG-QQNVAG 774
Cdd:COG0086 652 GLITEPERYNK-------------VIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSG 718
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 775 SRI--PFG--FRrrtlphfmlddygetsrgmanrgyvEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDV 850
Cdd:COG0086 719 NIIetPIGsnFR-------------------------EGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDV 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 ... |
18-855 |
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: 1227.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 18 NEVQFEIFKERQIKSYAVCLVEHAKSYERGR-PVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGV 96
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYENGGgPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 97 FDLVLQVLKCVCKtcgalllntreqdvhkklqhmtglnrlrqvakmaeakcrvststeddmgidgfdsapfnggsgmgpg 176
Cdd:cd02733 81 LTKILKILRCVCK------------------------------------------------------------------- 93
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 177 atrgcgasqprvsrfygiyptlvikavheeqdAEWHADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVR 256
Cdd:cd02733 94 --------------------------------RELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 257 PAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKES-DVQAAIDRSRALLQEHVATYFNNASTYYKPTKVNDTKKLKSLTE 334
Cdd:cd02733 142 PSVVMdGSARSEDDLTHKLADIIKANNQLKRQEQNgAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQ 221
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 335 RLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARRTV--YPSANYIHH 412
Cdd:cd02733 222 RLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPneYPGAKYIIR 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 413 PNGTITKLALLRDRSKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEM 492
Cdd:cd02733 302 DDGERIDLRYLKKASDLHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEM 381
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 493 NLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSVALWLDLW--QLPIPAILK 570
Cdd:cd02733 382 NLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLPDWdgKIPQPAILK 461
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 571 PRPLWTGKQVFSLILPEVNHPA-----TPQDRPPFPHNDSVVMIRRGQLLCGPITKSIVGAAPGSLIHVIFNEHGSDEVA 645
Cdd:cd02733 462 PKPLWTGKQIFSLIIPKINNLIrssshHDGDKKWISPGDTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAAR 541
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 646 RFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLNRKAGMTLLQSFEADVNSALN 725
Cdd:cd02733 542 DFIGNIQRVVNNWLLHNGFSIGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILN 621
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 726 KCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMANRG 805
Cdd:cd02733 622 KARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENS 701
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|
gi 1115875379 806 YVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD 855
Cdd:cd02733 702 YLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
16-883 |
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: 821.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 16 KVNEVQFEIFKERQIKSYAVCLVEHAKSY-ERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNI 94
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYdEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 95 GVFDLVLQVLKCVCKTCGALLLNTREQD-VHKKLQHMTGLNRLRQVAKMAEAKCRVSTSTEddmgidgfdsAPFnggsgm 173
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLPEEEIEkYLERIRRLKEKWPELVKRVIEKVKKKAKKRKV----------CPH------ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 174 gpgatrgCGASQPRVsRFygIYPTlvikAVHEEQDAEWH---ADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPV 250
Cdd:cd02582 147 -------CGAPQYKI-KL--EKPT----TFYEEKEEGEVkltPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPV 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 251 PPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKPTKVNDTKK 328
Cdd:cd02582 213 PPVTVRPSITLeTGERSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRP 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 329 LKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARR--TVYPS 406
Cdd:cd02582 293 LKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNgpDKWPG 372
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 407 ANYIHHPNGTITKLALLrDRSKV--TLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYN 484
Cdd:cd02582 373 ANYVIRPDGRRIRLRYV-NREELaeRLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYN 451
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 485 ADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSVALWLDLWQ-L 563
Cdd:cd02582 452 ADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGlL 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 564 PIPAILKPRPLWTGKQVFSLILPE---------VNHPATPQDRPPFPHnDSVVMIRRGQLLCGPITKSIVGA-APGSLIH 633
Cdd:cd02582 532 PEPAILEPKPLWTGKQLFSLFLPKdlnfegkakVCSGCSECKDEDCPN-DGYVVIKNGKLLEGVIDKKAIGAeQPGSLLH 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 634 VIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLNRKAGMTLL 713
Cdd:cd02582 611 RIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLE 690
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 714 QSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDD 793
Cdd:cd02582 691 ETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGD 770
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 794 YGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDELIQFMYGED 873
Cdd:cd02582 771 LGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGED 850
|
890
....*....|
gi 1115875379 874 GLDGARIEGG 883
Cdd:cd02582 851 GVDPAKSDHG 860
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
10-883 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 786.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 10 SQMELQKVNEVQFEIFKERQIKSYAVCLVEHAKSY-ERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELA 88
Cdd:PRK08566 2 MMMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYdDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELA 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 89 EPVFNIGVFDLVLQVLKCVCKTCGALLLntREQDVHKKLQHMTGLNRLRQVAK--MAEAKCRVSTSTEddmgidgfdsAP 166
Cdd:PRK08566 82 RPVIHVGFAKLIYKLLRATCRECGRLKL--TEEEIEEYLEKLERLKEWGSLADdlIKEVKKEAAKRMV----------CP 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 167 FnggsgmgpgatrgCGASQPRVsRFygIYPTlvikAVHEEQDAEWH---ADKVRQVLDRVSDDDARLMGFDPQRCHPRDL 243
Cdd:PRK08566 150 H-------------CGEKQYKI-KF--EKPT----TFYEERKEGLVkltPSDIRERLEKIPDEDLELLGINPEVARPEWM 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 244 VLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKPT 321
Cdd:PRK08566 210 VLTVLPVPPVTVRPSITLeTGQRSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVTTYFDNEIPGIPPA 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 322 KVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARR 401
Cdd:PRK08566 290 RHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLN 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 402 --TVYPSANYIHHPNGTITKLaLLRDRSKV--TLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 477
Cdd:PRK08566 370 gpEKHPGANYVIRPDGRRIKL-TDKNKEELaeKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNL 448
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 478 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSV--A 555
Cdd:PRK08566 449 AVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLlrA 528
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 556 LWLDLWQLPIPAILKPRPLWTGKQVFSLILPE----------VNHPATPQDRPPFphNDSVVMIRRGQLLCGPITKSIVG 625
Cdd:PRK08566 529 AGIDELPEPEPAIENGKPYWTGKQIFSLFLPKdlnlefkakiCSGCDECKKEDCE--HDAYVVIKNGKLLEGVIDKKAIG 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 626 AAPGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLN 705
Cdd:PRK08566 607 AEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELE 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 706 RKAGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRT 785
Cdd:PRK08566 687 PLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRT 766
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 786 LPHFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDEL 865
Cdd:PRK08566 767 LPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNI 846
|
890
....*....|....*...
gi 1115875379 866 IQFMYGEDGLDGARIEGG 883
Cdd:PRK08566 847 VQFKYGEDGVDPMKSDHG 864
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
29-859 |
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: 767.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 29 QIKSYAVCLVEHAKSY--ERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVLQVLKC 106
Cdd:cd02583 5 DIIRLSEVEVTNRNLYdiETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIINILQC 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 107 VCKTCGALLLNTREQDVHKKLQHMTGLNRLRQVA--KMAEAKCRvststeddmgidgfdsapfnggsgmgpgATRGCgas 184
Cdd:cd02583 85 ICKTCSRVLLPEEEKRKFLKRLRRPNLDNLQKKAlkKKILEKCK----------------------------KVRKC--- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 185 qPRVSRfygiyptlvIKAVHEEQDAEwhadKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPVPPPQVRP--AISFG 262
Cdd:cd02583 134 -PHCGL---------LKKAQEDLNPL----KVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPsvVMDEK 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 263 GLRSDDELTHQIMSIVKRNNQLRRDKESDVQA-AIDRSRALLQEHVATYFNnASTYYKPTKVNDTKKLKSLTERLKGKYG 341
Cdd:cd02583 200 SGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTqKIMEDWDFLQLQCALYIN-SELPGLPLSMQPKKPIRGFCQRLKGKQG 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 342 RLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARR--TVYPSANYIHHPNGTITK 419
Cdd:cd02583 279 RFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNgpDVHPGANFVIKRDGGKKK 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 420 LALLRDRSKV--TLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVP 497
Cdd:cd02583 359 FLKYGNRRKIarELKIGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVP 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 498 QSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDK-YFVQSVALWLD---LWQLPIPAILKPRP 573
Cdd:cd02583 439 QTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRaQFCQLCSYMLDgeiKIDLPPPAILKPVE 518
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 574 LWTGKQVFSLIL--------------PEVNHPATPQDRPPfphNDSVVMIRRGQLLCGPITKSIVGA-APGSLIHVIFNE 638
Cdd:cd02583 519 LWTGKQIFSLLLrpnkkspvlvnleaKEKSYTKKSPDMCP---NDGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRD 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 639 HGSDEVARFINGVQRVTTFFLLNFGFSVGVQDtVADSDTLRQMNDVLVKT--RRNVEKIgAAANNRTLNRKAGMTLLQSF 716
Cdd:cd02583 596 YGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDD-VTPSKELLKKKEELVDNgyAKCDEYI-KQYKKGKLELQPGCTAEQTL 673
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 717 EADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDdyge 796
Cdd:cd02583 674 EAKISGELSKIREDAGKACLKELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRN---- 749
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1115875379 797 tSRGMANRGYVE-----GLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVR 859
Cdd:cd02583 750 -SKTPAAKGFVAnsfysGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
14-884 |
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: 758.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 14 LQKVNEVQFEIFKERQIKSYAVCLVEHAKSYER-GRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVF 92
Cdd:TIGR02390 1 PKKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDdGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 93 NIGVFDLVLQVLKCVCKTCGALLLNTREQDvhkklQHMTGLNRLRQVAKMAEakcrvSTSTEDdmgidgfdsapfnggsg 172
Cdd:TIGR02390 81 HVGFAKEIYKILRATCRKCGRITLTEEEIE-----QYLEKINKLKEEGGDLA-----STLIEK----------------- 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 173 MGPGATRG-----CGASQPRV-----SRFYGIYPTLVIKAVHEEqdaewhadkVRQVLDRVSDDDARLMGFDPQRCHPRD 242
Cdd:TIGR02390 134 IVKEAAKRmkcphCGEEQKKIkfekpTYFYEEGKEGDVKLTPSE---------IRERLEKIPDEDAELLGINPKVARPEW 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 243 LVLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKP 320
Cdd:TIGR02390 205 MVLTVLPVPPVTVRPSITLeTGERSEDDLTHKLVDIIRINQRLKENIEAGApQLIIEDLWELLQYHVATYFDNELPGIPP 284
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 321 TKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFAR 400
Cdd:TIGR02390 285 ARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVL 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 401 R--TVYPSANYIHHPNGTITKLALL-RDRSKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 477
Cdd:TIGR02390 365 NgpDSWPGANYVIRPDGRRIKIRDEnKEELAERLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNL 444
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 478 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSVALW 557
Cdd:TIGR02390 445 AVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGV 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 558 LDLW-QLPIPAILKPRPLWTGKQVFSLILPE---------VNHPATPQDRPPFPHnDSVVMIRRGQLLCGPITKSIVGAA 627
Cdd:TIGR02390 525 AGYFgDPPEPAIEKPKEYWTGKQIFSAFLPEdlnfegrakICSGSDACKKEECPH-DAYVVIKNGKLLKGVIDKKAIGAE 603
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 628 PGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDVLVKTRRNVEKIGAAANNRTLNRK 707
Cdd:TIGR02390 604 KGKILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPL 683
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 708 AGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLP 787
Cdd:TIGR02390 684 PGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLP 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 788 HFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDELIQ 867
Cdd:TIGR02390 764 HFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQ 843
|
890
....*....|....*..
gi 1115875379 868 FMYGEDGLDGARIEGGQ 884
Cdd:TIGR02390 844 FKYGEDGVDPMKSDHGK 860
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
12-1474 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 749.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 12 MELQKV---NEVQFEIFKERQIKSYAVCLVEHAKSY-ERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIEL 87
Cdd:PRK14977 1 EEILAVkaiDGIIFGLISPADARKIGFAEITAPEAYdEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 88 AEPVFNIGVFDLVLQVLKCVCKTCGALLLNTREQDVHKKLQHMTGLNRLRQVAKMAEAKCRvSTSTEDDMGIDGFDSAPF 167
Cdd:PRK14977 81 AEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDEIIE-EVRDQVKVYAKKAKECPH 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 168 nggsgmgpgatrgCGASQPRVSRfygIYPTLVIKAVHEEQDAEWhADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTV 247
Cdd:PRK14977 160 -------------CGAPQHELEF---EEPTIFIEKTEIEEHRLL-PIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQA 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 248 LPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKE-----SDVQAAIDrsraLLQEHVATYFNNASTYYKPT 321
Cdd:PRK14977 223 FLVPPLTARPSIILeTGERSEDDLTHILVDIIKANQKLKESKDagappLIVEDEVD----HLQYHTSTFFDNATAGIPQA 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 322 KVNDTKK-LKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFAR 400
Cdd:PRK14977 299 HHKGSGRpLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVI 378
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 401 R--TVYPSANYIHHPNGTITKLALLRDRSKV-------TLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYN 471
Cdd:PRK14977 379 NgpDEFPGANAIRKGDGTKIRLDFLEDKGKDalreaaeQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGA 458
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 472 TFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFV 551
Cdd:PRK14977 459 TFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEA 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 552 QSVALWLDLWQ-LPIPAI-LKPRPLWTGKQVFSLILP-EVNHPATP--------QDRPPFPHNDSVVMIRRGQLLCGPIT 620
Cdd:PRK14977 539 SNIAMLAGITDpLPEPAIkTKDGPAWTGKQLFSLFLPkDFNFEGIAkwsagkagEAKDPSCLGDGYVLIKEGELISGVID 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 621 KSIVGA---APGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNDV----------LVK 687
Cdd:PRK14977 619 DNIIGAlveEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDiqgmkdevsdLID 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 688 TRRNVEKIGAAANNRTLNRkaGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFV 767
Cdd:PRK14977 699 QRKITRKITIYKGKEELLR--GMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGAL 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 768 GQQNV--------AGSRIPFGFRRRTLPHFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYL 839
Cdd:PRK14977 777 GQQKRktrigfvlTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYF 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 840 QRKLIKALEDVHAAYDGTVRNANDELIQFMYGEDGLdgarieggqlfplpfrddkemedtykyeydvdgtfsgkvggnym 919
Cdd:PRK14977 857 QRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGI-------------------------------------------- 892
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 920 dphvrkmlraDPQnvrklqeeyeqltadrewsrkmldledrdKLKLNLPVNPGRLIqnarstmgkRSQVsnlspitIIDH 999
Cdd:PRK14977 893 ----------DPQ-----------------------------KLDHGEAFNLERII---------EKQK-------IEDR 917
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1000 VRKLQEDLMKlfpsyhrggdgyirnTLSRERIESaltlFNVHLRQLLASkrVLKEYKLNDRAFEYLLKEIRTKYHQSLTT 1079
Cdd:PRK14977 918 GKGASKDEIE---------------ELAKEYTKT----FNANLPKLLAD--AIHGAELKEDELEAICAEGKEGFEKAKVE 976
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1080 PGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHASMTVSLfppydeKRNAQKAqhliey 1159
Cdd:PRK14977 977 PGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYL------DDECKED------ 1044
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1160 ctlesitrriqfiydpdpRHTVVEADRDILelewnvmdesdaELRIQEVVAgspwvvrlELDVDMVTDKALDMKDVK--- 1236
Cdd:PRK14977 1045 ------------------IEKAIEIARNLK------------ELKVRALIA--------DSAIDNANEIKLIKPDKRale 1086
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1237 ------QAILRVDESyiIETGMANNVRQRTIRMRSRYNEGADSIPKLK--REIPALLARVHLRGIPGVRRALLKdtteft 1308
Cdd:PRK14977 1087 ngcipmERFAEIEAA--LAKGKKFEMELEDDLIILDLVEAADRDKPLAtlIAIRNKILDKPVKGVPDIERAWVE------ 1158
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1309 vdqaTGKMSGNKIWAIDTDGTALrRAFIGVVGEDGKNIInavktsSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNI 1388
Cdd:PRK14977 1159 ----LVEKDGRDEWIIQTSGSNL-AAVLEMKCIDIANTI------TNDCFEIAGTLGIEAARNAIFNELASILEDQGLEV 1227
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1389 NYRHYTILVDTICQHGYLMAV------SRSGInRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARV 1462
Cdd:PRK14977 1228 DNRYIMLVADIMCSRGTIEAIglqaagVRHGF-AGEKDSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPI 1306
|
1530
....*....|..
gi 1115875379 1463 GTGLFDLVLNMA 1474
Cdd:PRK14977 1307 GSGKVDLLMDFS 1318
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
809-1422 |
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: 584.70 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 809 GLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDELIQFMYGEDGLDGARIEGGQLFPL 888
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 889 PFRDDKEMEDTYKYEYDVDGTFSGKVGGNYMDPHVRKMLradpqnvrklqeeyeqltadrewsrkmldledrdklklnlp 968
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRDSK----------------------------------------- 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 969 vnpgrliqnarstmgkrsqvsnlspitiidhvrklqedlmklfpsyhrggdgYIRNTLSRERIESALTLFNVHLRQLLAS 1048
Cdd:pfam04998 120 ----------------------------------------------------LGRDRLSKEAQERATLLFELLLKSGLES 147
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1049 KRVLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVS 1128
Cdd:pfam04998 148 KRVRSELTCNSKAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVS 227
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1129 RNQKHASMTVSLFPPY-DEKRNAQKAQHLIEYCTLESITRRIQFIYDPDPRHTVVEADRDILELEWNVMDESDAELRIQE 1207
Cdd:pfam04998 228 KNIKSPSLTVYLFDEVgRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1208 VVAGSPWVVRLELDVDM---------VTDKALDMKDVKQAILRVDESYIIETGMANNVRQRTIRMRSRYNEGADSIPKLK 1278
Cdd:pfam04998 308 ETGLLILVIRLLKILNKsikkvvkseVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRVDELFMEEDPKLA 387
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1279 REIPALLARVHLRGIPGVRRALLKDTTEFTVDQAtgkmsgnkiWAIDTDGTALRRAFIgvvgedGKNIINAVKTSSNKVP 1358
Cdd:pfam04998 388 ILVASLLGNITLRGIPGIKRILVNEDDKGKVEPD---------WVLETEGVNLLRVLL------VPGFVDAGRILSNDIH 452
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1115875379 1359 EVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSGP 1422
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 ... |
21-855 |
5.92e-180 |
|
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: 561.81 E-value: 5.92e-180
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 21 QFEIFKERQIKSYAVCLVEHAKSY-ERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDL 99
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFdSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 100 VLQVLKCVCKTCGALLLNTREqdVHKKLQHMtglnRLRQVAKMAEAKcrvststEDDMGIDGFdsapfnggsgmgpgatr 179
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWE--VKLFVAKL----KLLDKGLLVEAA-------ELDFGYDMF----------------- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 180 gcgasqprvsrfygiyptlvikavheeqdaewhadkvrqvldrvsdddarlmgFdpqrchprdlvLTVLPVPPPQVRPAI 259
Cdd:cd01435 131 -----------------------------------------------------F-----------LDVLLVPPNRFRPPS 146
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 260 SFGGLRSDDELThQIMS-IVKRNNQLR-------RDKESDVQAAIDRSRAL---------LQEHVATYFNnaSTYYKPTK 322
Cdd:cd01435 147 FLGDKVFENPQN-VLLSkILKDNQQIRdllasmrQAESQSKLDLISGKTNSeklinawlqLQSAVNELFD--STKAPKSG 223
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 323 VNDTKKLKSLTERlkgKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARR- 401
Cdd:cd01435 224 KKSPPGIKQLLEK---KEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINg 300
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 402 -TVYPSANYIHHPNGTITKLALLRDRSKV--------------TLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVR 466
Cdd:cd01435 301 pDVYPGANAIEDEDGRLILLSALSEERRKalaklllllssaklLLNGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVR 380
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 467 VL-NYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTF 545
Cdd:cd01435 381 VLpGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTF 460
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 546 LDK-YFVQSV--ALWLDL-------WQLPIPAILKPRPLWTGKQVFSLIL----PEVNHPATPQDRPPFPH--------- 602
Cdd:cd01435 461 FTReEYQQLVyaALRPLFtsdkdgrIKLLPPAILKPKPLWTGKQVISTILknliPGNAPLLNLSGKKKTKKkvgggkwgg 540
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 603 --NDSVVMIRRGQLLCGPITKSIVGAAPGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTV--ADSDTL 678
Cdd:cd01435 541 gsEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLltPKADEK 620
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 679 RQmndvlvKTRRNVEKIGAAANNRTLNRKagmtllqsfeadvnsaLNKCREEAAKKALSNVRRT----NSFKVMIEAGSK 754
Cdd:cd01435 621 RR------KILRKAKKLGLEAAAEFLGLK----------------LNKVTSSIIKACLPKGLLKpfpeNNLQLMVQSGAK 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 755 GTDLNICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMldDYGETSRgmANrGYV-----EGLKPHEFFFHTMAGREGLIDT 829
Cdd:cd01435 679 GSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFP--PYDTSPR--AG-GFItdrflTGIRPQEYFFHCMAGREGLIDT 753
|
890 900
....*....|....*....|....*.
gi 1115875379 830 AVKTSDTGYLQRKLIKALEDVHAAYD 855
Cdd:cd01435 754 AVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
242-537 |
1.15e-147 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 455.83 E-value: 1.15e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 242 DLVLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKE-SDVQAAIDRSRALLQEHVATYFNNASTyyK 319
Cdd:smart00663 2 WMILTVLPVPPPCLRPSVQLdGGRFAEDDLTHLLRDIIKRNNRLKRLLElGAPSIIIRNEKRLLQEAVDTLIDNEGL--P 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 320 PTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFA 399
Cdd:smart00663 80 RANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLV 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 400 RRTVyPSANYIHhpNGTITKLALLRD-RSKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLS 478
Cdd:smart00663 160 RNGP-NGAKYII--RGKKTNLKLAKKsKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPL 236
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*....
gi 1115875379 479 CTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSY 537
Cdd:smart00663 237 VCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
43-855 |
1.73e-147 |
|
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: 464.98 E-value: 1.73e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 43 SYERGRPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPVFNIGVFDLVlqvlkcvcktcgalllntreqd 122
Cdd:cd00399 21 DNRTLKAERGGKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKV---------------------- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 123 vhkklqhmtglnrlrqvakmaeakcrvststeddmgidgfdsapfnggsgmgpgatrgcgasqprvsrfygiyptlvika 202
Cdd:cd00399 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 203 vheeqdaewhadkvrqvldrvsdddarlmgfdPQRCHPRDLVLTVLPVPPPQVRPAISFgglrsddelthqimsivkrnn 282
Cdd:cd00399 79 --------------------------------PSFLGPEWMILTCLPVPPPCLRPSVII--------------------- 105
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 283 qlrrdkesdvqaaIDRSRaLLQEHVATYFNNASTYYKPTKVNDtKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITG 362
Cdd:cd00399 106 -------------EERWR-LLQEHVDTYLDNGIAGQPQTQKSG-RPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISP 170
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 363 DPNIDVDEVGVPFSVAMTLtfpervntvnkkrltefarrtvypsanyihhpngtitklallrdrskvtlnigdvverhvi 442
Cdd:cd00399 171 DPNLRLDQVGVPKSIALTL------------------------------------------------------------- 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 443 NGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKS 522
Cdd:cd00399 190 DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNG 269
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 523 APCMGIVQDSLLGSYRLTdkdtfldkyfvqsvalwldlwqlpipailkprplwTGKQVFSLILPEvnhpatpqdrppfph 602
Cdd:cd00399 270 EPLIGLSQDTLLGAYLLT-----------------------------------LGKQIVSAALPG--------------- 299
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 603 ndsvvmirrgqllcgpitksivgaapgSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMN 682
Cdd:cd00399 300 ---------------------------GLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKT 352
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 683 DVLVKTRRNVEKIGAAANNRTLNRKAGMTLLQSFEADVNSALNKCREEAAKKALSNVRRT---NSFKVMIEAGSKGTDLN 759
Cdd:cd00399 353 ELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLNEARDKAGSAASVNLDLVskfNSIYVMAMSGAKGSFIN 432
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 760 ICQIAVFVGQQNVAGSRIPFGFRRRTLPHFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYL 839
Cdd:cd00399 433 IRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYL 512
|
810
....*....|....*.
gi 1115875379 840 QRKLIKALEDVHAAYD 855
Cdd:cd00399 513 QRRLVKALEDLVVHYD 528
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1055-1472 |
1.85e-140 |
|
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: 441.26 E-value: 1.85e-140
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1055 YKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHA 1134
Cdd:cd02584 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTP 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1135 SMTVSLFPPYD-EKRNAQKAQHLIEYCTLESITRRIQFIYDPDPRHTVVEADRDILELEWNVMDESDAELRIqevvagSP 1213
Cdd:cd02584 81 SLTVYLEPGFAkDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDPQNTVIEEDKEFVESYFEFPDEDVEQDRL------SP 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1214 WVVRLELDVDMVTDKALDMKDVKQAI---LRVDESYIIETGMANN--VRQRTIRMRSRYNEGADSIPKLKREIPALLARV 1288
Cdd:cd02584 155 WLLRIELDRKKMTDKKLSMEQIAKKIkeeFKDDLNVIFSDDNAEKlvIRIRIINDDEEKEEDSEDDVFLKKIESNMLSDM 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1289 HLRGIPGVRRALLKDTTEFTVDQATGKMSGNKIWAIDTDGTALRRafigVVGEDGkniINAVKTSSNKVPEVCSLLGIEA 1368
Cdd:cd02584 235 TLKGIEGIRKVFIREENKKKVDIETGEFKKREEWVLETDGVNLRE----VLSHPG---VDPTRTTSNDIVEIFEVLGIEA 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1369 ARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTsGPLMRCSFEETVKVLMAAASFGECDPVR 1448
Cdd:cd02584 308 ARKALLKELRNVISFDGSYVNYRHLALLCDVMTQRGHLMAITRHGINRQDT-GPLMRCSFEETVDILLEAAAFGETDDLK 386
|
410 420
....*....|....*....|....
gi 1115875379 1449 GVSANLVLGNQARVGTGLFDLVLN 1472
Cdd:cd02584 387 GVSENIMLGQLAPIGTGCFDLLLD 410
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-347 |
1.56e-138 |
|
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: 432.10 E-value: 1.56e-138
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 14 LQKVNEVQFEIFKERQIKSYAVCLVEHAKSYERG--RPVRGGINDLRMGTTDFEFACETCHRKHPECPGHFGYIELAEPV 91
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGslKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 92 FNIGVFDLVLQVLKCVCKTCGALLLNTREQDVHKKLQHMTGLNRLRQVAKMAEAKCRVSTSTEDDMGIDGFdsapfnggs 171
Cdd:pfam04997 81 FHIGFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLENLKMGAKAILELCKKKDLCEHCGGKNGV--------- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 172 gmgpgatrgCGASQPrVSRFYGIYPTLVIKAVHE-EQDAEWHADKVRQVLDRVSDDDARLMGFDPQRCHPRDLVLTVLPV 250
Cdd:pfam04997 152 ---------CGSQQP-VSRKEGLKLKAAIKKSKEeEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPV 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 251 PPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDV-QAAIDRSRALLQEHVATYFNNASTYYKPTKVNDTKK 328
Cdd:pfam04997 222 PPPCIRPSVQLdGGRRAEDDLTHKLRDIIKRNNRLKKLLELGApSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRP 301
|
330
....*....|....*....
gi 1115875379 329 LKSLTERLKGKYGRLRGNL 347
Cdd:pfam04997 302 LKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
54-859 |
9.49e-96 |
|
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: 327.44 E-value: 9.49e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 54 INDLRMGTTDFEFACETCHRKHP-ECPGHFGYIELAEPVFNIGVFDLVLQVLKCVCKTCGalllntreqdvhkklqhmtg 132
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCGAKDNkKCEGHFGVIKLPVTIYHPYFISEVAQILNKICPGCK-------------------- 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 133 lnRLRQVAKMAEAKcrvststedDMGIDGFDSAPfnggsgmgpgatrgcGASQPRVSRFYGIYPTLVikavheeqdaewH 212
Cdd:cd10506 80 --SIKQKKKKPPRE---------TLPPDYWDFIP---------------KDGQQEESCVTKNLPILS------------L 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 213 AdKVRQVLDRVsdDDARLMGFDPQrchPRDLVLTVLPVPPPQVR-PAISFGglrsddeltHQIMSivkrnnqlrrdkesd 291
Cdd:cd10506 122 A-QVKKILKEI--DPKLIAKGLPR---QEGLFLKCLPVPPNCHRvTEFTHG---------FSTGS--------------- 171
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 292 VQAAIDRSRALLQEHVATYfnnastyykptkvndTKKLKSLTERLKGKYgrLRGNLMGKRVDFSARTVITGDPNIDVDEV 371
Cdd:cd10506 172 RLIFDERTRAYKKLVDFIG---------------TANESAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEI 234
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 372 GVPFSVAMTLTFPERVNTVNKKRLTEFARRTvyPSANY-IHHPNGTItklaLLRDRSKVTLNIGDVVERHVINGDVVLFN 450
Cdd:cd10506 235 GIPCEIAERLTVSERVSSWNRERLQEYCDLT--LLLKGvIGVRRNGR----LVGVRSHNTLQIGDVIHRPLVDGDVVLVN 308
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 451 RQPTLHRMSMMGHRVRVLNYN-TFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIV 529
Cdd:cd10506 309 RPPSIHQHSLIALSVKVLPTNsVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLT 388
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 530 QDSLLGSYRLTDKDTFLDKYFVQSVALWLdLWQLPIPAILK--PR--PLWTGKQVFSLILPevnhpatPQDRPPFPHNDs 605
Cdd:cd10506 389 QDSLLAAHLMTERGVFLDKAQMQQLQMLC-PSQLPPPAIIKspPSngPLWTGKQLFQMLLP-------TDLDYSFPSNL- 459
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 606 vVMIRRGQLLCGPITKSIVGAAPGSLIHVIFnEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQD--TVADSDTLRQMND 683
Cdd:cd10506 460 -VFISDGELISSSGGSSWLRDSEGNLFSILV-KHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDlyLSSDSYSRQKMIE 537
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 684 -----------------VLVKTRRNVekigaAANNRTLNRKAGMTLLQSFEADVNSALNKCREEAAKKALSNVRRT---- 742
Cdd:cd10506 538 eislglreaeiacnikqLLVDSRKDF-----LSGSGEENDVSSDVERVIYERQKSAALSQASVSAFKQVFRDIQNLvyky 612
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 743 ----NSFKVMIEAGSKGTDLNICQIAVFVGQQNVAGsRIPFGFRR---------RTLPHFMLDDYGETSRGMANRGYVE- 808
Cdd:cd10506 613 askdNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLV-KLSYRIPRqlscaawnsQKSPRVIEKDGSECTESYIPYGVVEs 691
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*
gi 1115875379 809 ----GLKPHEFFFHTMAGREGLIDTAVKTSDTgyLQRKLIKALEDVHAAYDGTVR 859
Cdd:cd10506 692 sfldGLNPLECFVHSITSRDSSFSSNADLPGT--LFRKLMFFMRDIYVAYDGTVR 744
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
349-512 |
1.03e-91 |
|
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: 294.21 E-value: 1.03e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 349 GKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFARR--TVYPSANYIHHPNGTITKLALLRDR 426
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENgpNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 427 SKVTLNIGDVVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAEL 506
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 1115875379 507 IEMMMV 512
Cdd:pfam00623 161 EELMLV 166
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
1051-1471 |
1.75e-66 |
|
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: 229.94 E-value: 1.75e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1051 VLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRN 1130
Cdd:TIGR02389 14 VKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARKT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1131 QKHASMTVSLFPPYdeKRNAQKAQHL---IEYCTLESITRRIqfiydpdprhtvveadrdilelEWNVMDEsdaelriqe 1207
Cdd:TIGR02389 94 PSTPSMTIYLEDEY--EKDREKAEEVakkIEATKLEDVAKDI----------------------SIDLADM--------- 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1208 vvagspwVVRLELDVDMVTDKALDMKDVKQAILRVDESYIIETGMANNvrqrTIRMrsryNEGADSIPKLKREIPALLAr 1287
Cdd:TIGR02389 141 -------TVIIELDEEQLKERGITVDDVEKAIKKAKLGKVIEIDMDNN----TITI----KPGNPSLKELRKLKEKIKN- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1288 VHLRGIPGVRRALLKdtteftvdqatgkmSGNKIWAIDTDGTALRrafiGVVGEDGkniINAVKTSSNKVPEVCSLLGIE 1367
Cdd:TIGR02389 205 LHIKGIKGIKRVVIR--------------KEGDEYVIYTEGSNLK----EVLKLEG---VDKTRTTTNDIHEIAEVLGIE 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1368 AARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSgPLMRCSFEETVKVLMAAASFGECDPV 1447
Cdd:TIGR02389 264 AARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKAS-VLARAAFEVTVKHLLDAAIRGEVDEL 342
|
410 420
....*....|....*....|....
gi 1115875379 1448 RGVSANLVLGNQARVGTGLFDLVL 1471
Cdd:TIGR02389 343 KGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
200-1136 |
3.24e-66 |
|
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: 246.50 E-value: 3.24e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 200 IKAVHEEQDAEWHADKVRQVLdRVSDDDARLM----------GFDPQRCHPRDLVLTVLPVPPPQVRPAISFGGLR---S 266
Cdd:TIGR02386 167 IKELLEKIDLDKEIEELKIQL-RESKSDQKRKkllkrleiveAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRfatS 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 267 DdeLTHQIMSIVKRNNQLRRDKESDVQAAIDRS-RALLQEHVATYFNNaSTYYKPTKVNDTKKLKSLTERLKGKYGRLRG 345
Cdd:TIGR02386 246 D--LNDLYRRVINRNNRLKRLLELGAPEIIVRNeKRMLQEAVDALFDN-GRRGKPVVGKNNRPLKSLSDMLKGKQGRFRQ 322
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 346 NLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVntvnkKRLTEfarrtvYPSAnyihhPNGTITKLALLRD 425
Cdd:TIGR02386 323 NLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFII-----KRLID------RELA-----ANIKSAKKMIEQE 386
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 426 RSKVTlnigDVVERhVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAE 505
Cdd:TIGR02386 387 DPEVW----DVLED-VIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAE 461
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 506 LIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT--------DKDTFLDkyfVQSVALWLDLWQLPIPAILKPRP---- 573
Cdd:TIGR02386 462 ARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTtekpgakgEGKIFSN---VDEAIRAYDNGKVHLHALIGVRTsgei 538
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 574 LWT--GKQVFSLILPEvNHPATpqdrppfphNDSvvmirrgqllcGPITKSIVgaapGSLIHVIFNEHGSDEVARFINGV 651
Cdd:TIGR02386 539 LETtvGRVIFNEILPE-GFPYI---------NDN-----------EPLSKKEI----SSLIDLLYEVHGIEETAEMLDKI 593
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 652 QRVTTFFLLNFGFSVGVQDTVadsdTLRQMNDVLVKTRRNVEKIgaaannRTLNRKAGMTLLQSFEADV---NSALNKCR 728
Cdd:TIGR02386 594 KALGFKYATKSGTTISASDIV----VPDEKYEILKEADKEVAKI------QKFYNKGLITDEERYRKVVsiwSETKDKVT 663
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 729 EEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAvfvgqqnvagsripfGFRrrtlpHFMLDDYGETSRGMANRGYVE 808
Cdd:TIGR02386 664 DAMMKLLKKDTYKFNPIFMMADSGARGNISQFRQLA---------------GMR-----GLMAKPSGDIIELPIKSSFRE 723
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 809 GLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYD----------GTVRNANDELIQFMYGedgldga 878
Cdd:TIGR02386 724 GLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEdcgteegievEAIVEGKDEIIESLKD------- 796
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 879 RIEGGQLFplpfrddkemEDTYkyeydvdgtfsgkvggnymdphvrkmlraDPQNVRKLQEEYEQLTADrewsrkmldle 958
Cdd:TIGR02386 797 RIVGRYSA----------EDVY-----------------------------DPDTGKLIAEANTLITEE----------- 826
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 959 drdklklnlpvnpgrliqnarstmgKRSQVSNLSpitiIDHVrklqedlmklfpsyhrggdgyirntlsreRIESALTlf 1038
Cdd:TIGR02386 827 -------------------------IAEKIENSG----IEKV-----------------------------KVRSVLT-- 846
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1039 nvhlrqlLASKR--VLKEYKLNdrAFEYLLKEIrtkyhqslttpGENIGAIAAQSCGEPATQMTLNTFHNAGISS--KNV 1114
Cdd:TIGR02386 847 -------CESEHgvCQKCYGRD--LATGKLVEI-----------GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGasGDI 906
|
970 980
....*....|....*....|..
gi 1115875379 1115 TLGVPRLLELLNVSRNQKHASM 1136
Cdd:TIGR02386 907 TQGLPRVKELFEARTPKDKAVI 928
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
1051-1473 |
2.33e-65 |
|
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: 226.36 E-value: 2.33e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1051 VLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRN 1130
Cdd:cd06528 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1131 QKHASMTVSLFPPYDEKR-NAQKAQHLIEYCTLESITRRIqfiydpdprhtvveadrdilelEWNVMDESdaelriqevv 1209
Cdd:cd06528 90 PSTPTMTIYLEEEYKYDReKAEEVARKIEETTLENLAEDI----------------------SIDLFNMR---------- 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1210 agspwvVRLELDVDMVTDKALDMKDVKQAILRVDESYIIETGmanNVRQRTIRmrsrynEGADSIPKLKREIPALLaRVH 1289
Cdd:cd06528 138 ------ITIELDEEMLEDRGITVDDVLKAIEKLKKGKVGEEG---DVTLIVLK------AEEPSIKELRKLAEKIL-NTK 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1290 LRGIPGVRRALL-KDTTEftvdqatgkmsgnkiWAIDTDGTALRrafiGVVGEDGkniINAVKTSSNKVPEVCSLLGIEA 1368
Cdd:cd06528 202 IKGIKGIKRVIVrKEEDE---------------YVIYTEGSNLK----AVLKVEG---VDPTRTTTNNIHEIEEVLGIEA 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1369 ARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSgPLMRCSFEETVKVLMAAASFGECDPVR 1448
Cdd:cd06528 260 ARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPS-VLARAAFEVTVKHLLDAAVRGEVDELR 338
|
410 420
....*....|....*....|....*
gi 1115875379 1449 GVSANLVLGNQARVGTGLFDLVLNM 1473
Cdd:cd06528 339 GVIENIIVGQPIPLGTGDVELTMDP 363
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
1029-1471 |
3.49e-61 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 215.09 E-value: 3.49e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1029 ERIESALTLFNVHLRQLLASKrvLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAG 1108
Cdd:PRK04309 9 EKLEDASLELPQKLKEELREK--LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1109 ISSKNVTLGVPRLLELLNVSRNQKHASMTVSLFPPYdeKRNAQKAQHL---IEYCTLESITRRIqfiydpdprhtvvead 1185
Cdd:PRK04309 87 VAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEY--AYDREKAEEVarkIEATTLENLAKDI---------------- 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1186 rdilelEWNVMDESdaelriqevvagspwvVRLELDVDMVTDKALDMKDVKQAIlrvDESYIIETGMANNVRQRTIRMRS 1265
Cdd:PRK04309 149 ------SVDLANMT----------------IIIELDEEMLEDRGLTVDDVKEAI---EKKKGGEVEIEGNTLIISPKEPS 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1266 rYNEGADSIPKLKReipallarVHLRGIPGVRRALL-KDTTEftvdqatgkmsgnkiWAIDTDGTALRrafiGVVGEDGk 1344
Cdd:PRK04309 204 -YRELRKLAEKIRN--------IKIKGIKGIKRVIIrKEGDE---------------YVIYTEGSNLK----EVLKVEG- 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1345 niINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSDTSgPLM 1424
Cdd:PRK04309 255 --VDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGVSGEKAS-VLA 331
|
410 420 430 440
....*....|....*....|....*....|....*....|....*..
gi 1115875379 1425 RCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGLFDLVL 1471
Cdd:PRK04309 332 RAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTM 378
|
|
| RNA_pol_Rpb1_6 |
pfam04992 |
RNA polymerase Rpb1, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
875-1076 |
7.26e-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: 7.26e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 875 LDGARIEGgQLFPLPFRDDKEMEDTYKYeyDVDGTFSGKVGgNYMDPHVRKMLRADPQNVRKLQEEYEQLTADREWSRKM 954
Cdd:pfam04992 1 LDGAFIEK-QKIDTLKLSDAAFEKRYRL--DVMDEKSGFLP-GYLEEGVIKEIAGDPEVQQLLDEEYEQLLEDRELLREI 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 955 LDLEDRDKLKlNLPVNPGRLIQNARSTMG-KRSQVSNLSPITIIDHVRKLQEDLMKLfpsyhRGGDGyirntLSRERIES 1033
Cdd:pfam04992 77 IFPTGDSKVP-QLPVNIQRIIQNAQKIFHiDDRKPSDLHPIYVIEGVRELLDRLVVV-----RGDDP-----LSKEAQEN 145
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 1115875379 1034 ALTLFNVHLRQLLASKRVLKEYKLNDRAFEYLLKEIRTKYHQS 1076
Cdd:pfam04992 146 ATLLFKILLRSRLASKRVLEEYRLNKEAFDWVLGEIESRFLQA 188
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
239-850 |
1.10e-56 |
|
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: 210.07 E-value: 1.10e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 239 HPRDLVLTVLPVPPPQVRPAISFGGLR---SD-DELTHQImsiVKRNNQLRRDKESDVQAAIDRS-RALLQEHVATYFNN 313
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGGRfatSDlNDLYRRV---INRNNRLKKLLELGAPEIIVRNeKRMLQEAVDALIDN 214
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 314 ASTYyKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFP-------ER 386
Cdd:cd01609 215 GRRG-KPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPfvireliER 293
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 387 VNTVNKKRltefARRtvypsanyihhpngtitklaLLRDRSKVtlnIGDVVErHVINGDVVLFNRQPTLHRMSMMGHRVR 466
Cdd:cd01609 294 GLAPNIKS----AKK--------------------MIERKDPE---VWDILE-EVIKGHPVLLNRAPTLHRLGIQAFEPV 345
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 467 VLNYNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT--DKDT 544
Cdd:cd01609 346 LIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTkeRKGD 425
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 545 FLDKYFVQSValwldlwqlpipailkprplwtGKQVFSLILPEvnhpatpqdRPPFPHNdsvvmirrgqllcgPITKSIV 624
Cdd:cd01609 426 KGEGIIETTV----------------------GRVIFNEILPE---------GLPFINK--------------TLKKKVL 460
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 625 gaapGSLIHVIFNEHGSDEVARFINGVQrvttffllNFGF--------SVGVQDTVADSDTlrqmNDVLVKTRRNVEKIg 696
Cdd:cd01609 461 ----KKLINECYDRYGLEETAELLDDIK--------ELGFkyatrsgiSISIDDIVVPPEK----KEIIKEAEEKVKEI- 523
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 697 aaannrtlNRKAGMTLLQSFEAD--VNSALNKCREEAAKKALSNVR--RTNSFKVMIEAGSKGTDLNICQIAVFVG-QQN 771
Cdd:cd01609 524 --------EKQYEKGLLTEEERYnkVIEIWTEVTEKVADAMMKNLDkdPFNPIYMMADSGARGSKSQIRQLAGMRGlMAK 595
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 772 VAGSRIPF----GFRrrtlphfmlddygetsrgmanrgyvEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKAL 847
Cdd:cd01609 596 PSGKIIELpiksNFR-------------------------EGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVA 650
|
...
gi 1115875379 848 EDV 850
Cdd:cd01609 651 QDV 653
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1072-1467 |
4.90e-55 |
|
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: 194.36 E-value: 4.90e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1072 KYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHASMTVSLFPPYDEKRnAQ 1151
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLENDRDEKS-AR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1152 KAQHLIEYCTLESITRRIQFIYDPDprhtvveadrdilelewnvmdesDAELRIQevvagspwvvrleldvdmvtdkaLD 1231
Cdd:cd02736 80 IVKGRIEKTYLGEVASYIEEVYSPD-----------------------DCYILIK-----------------------LD 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1232 MKDVKQAILRVDESYiietgmannvrqrtIRMRSrynegadsipkLKReipaLLARVHLRGIPGVRRALLKDttEFTVDQ 1311
Cdd:cd02736 114 KKIIEKLQLSKSNLY--------------FLLQS-----------LKR----KLPDVVVSGIPEVKRAVINK--DKKKGK 162
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1312 ATGKMSGNKIwaidtdgtalrRAFIGVVGEDGKniinavKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYR 1391
Cdd:cd02736 163 YKLLVEGYGL-----------RAVMNTPGVIGT------RTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPR 225
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1115875379 1392 HYTILVDTICQHGYLMAVSRSGINRSDTSgPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGLF 1467
Cdd:cd02736 226 HIMLLADLMTFKGEVLGITRFGIAKMKES-VLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
240-1134 |
1.75e-54 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 210.50 E-value: 1.75e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 240 PRDLVLTVLPVPPPQVRPAISFGGLR-SDDELTHQIMSIVKRNNQLRRDKESDVQAAI-DRSRALLQEHVATYFNNASTY 317
Cdd:PRK14906 312 PADMILDVIPVIPPDLRPMVQLDGGRfATSDLNDLYRRVINRNNRLKRLLDLGAPEIIvNNEKRMLQEAVDSLFDNGRRG 391
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 318 yKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVntvnkKRLTE 397
Cdd:PRK14906 392 -RPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVM-----KRLVE 465
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 398 F--------ARRTVYPSANYIHhpngtitklallrdrskvtlnigDVVERhVINGDVVLFNRQPTLHRMSMMGHRVRVLN 469
Cdd:PRK14906 466 LeyaanikaAKRAVDRGASYVW-----------------------DVLEE-VIQDHPVLLNRAPTLHRLGIQAFEPVLVE 521
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 470 YNTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT-DKD----- 543
Cdd:PRK14906 522 GKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTtERDgfege 601
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 544 -----TFLDKYFVQSVALWLDLWQ---LPIPAILKPRPLW---------------TGKQVFSLILPEvnhpatpqDRPpf 600
Cdd:PRK14906 602 grtfaDFDDALNAYDARADLDLQAkivVRLSRDMTVRGSYgdleetkageriettVGRIIFNQVLPE--------DYP-- 671
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 601 phndsvvmirrgqLLCGPITKSIVGAapgsLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTlrq 680
Cdd:PRK14906 672 -------------YLNYKMVKKDIGR----LVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDK--- 731
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 681 mndvlvktrrnvEKIGAAANNRT--LNRKAGMTLLQSFE--ADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGt 756
Cdd:PRK14906 732 ------------PEILAEADEKVaaIDEDYEDGFLSERErhKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARG- 798
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 757 dlNICQIavfvgqQNVAGSRipfgfrrrtlpHFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDT 836
Cdd:PRK14906 799 --NIKQI------RQLAGMR-----------GLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADS 859
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 837 GYLQRKLIKALEDVhaaydgTVRNandeliqfmygedgLDGARIEGgqlFPLPFRDDKEmedtykyeyDVDGTFSGkvgg 916
Cdd:PRK14906 860 GYLTRRLVDVAQDV------IVRE--------------EDCGTDEG---VTYPLVKPKG---------DVDTNLIG---- 903
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 917 nymdphvrkmlradpqnvrklqeeyeqltadrewsrkmldledrdklklnlpvnpgrliqnarstmgkrsqvsnlspiti 996
Cdd:PRK14906 --------------------------------------------------------------------------------
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 997 idhvRKLQEDLMKLFPSYHRGGDGYIRNTLSRERIESAlTLFNVHLRQLLASKrvlKEYKLNDRAFEYLLKEIRTkyhqs 1076
Cdd:PRK14906 904 ----RCLLEDVCDPNGEVLLSAGDYIESMDDLKRLVEA-GVTKVQIRTLMTCH---AEYGVCQKCYGWDLATRRP----- 970
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*...
gi 1115875379 1077 lTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHA 1134
Cdd:PRK14906 971 -VNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEARKPKGEA 1027
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
239-850 |
3.11e-53 |
|
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: 205.39 E-value: 3.11e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 239 HPRDLVLTVLPVPPPQVRPAISFGGLR---SDdeLTHQIMSIVKRNNQLRRDKESDVQAAIDRS-RALLQEHVATYFNNa 314
Cdd:COG0086 223 RPEWMILDVLPVIPPDLRPLVPLDGGRfatSD--LNDLYRRVINRNNRLKRLLELKAPDIIVRNeKRMLQEAVDALFDN- 299
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 315 STYYKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervNTVNKKR 394
Cdd:COG0086 300 GRRGRAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKP---FIYRKLE 376
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 395 LTEFARrtvypsanyihhpngTITKLALLRDRskVTLNIGDVVERhVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFR 474
Cdd:COG0086 377 ERGLAT---------------TIKSAKKMVER--EEPEVWDILEE-VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQ 438
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 475 LNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFL---DKYF- 550
Cdd:COG0086 439 LHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTREREGAkgeGMIFa 518
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 551 -VQSVALWLDLWQLPIPAILKPRPLWTGKQVFSL--------ILPEVnhpaTPQDrppfphndsVVMIRRgqllcgPITK 621
Cdd:COG0086 519 dPEEVLRAYENGAVDLHARIKVRITEDGEQVGKIvettvgryLVNEI----LPQE---------VPFYNQ------VINK 579
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 622 SIVGAapgsLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADsdtlRQMNDVLVKTRRNVEKI------ 695
Cdd:COG0086 580 KHIEV----IIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVP----KEKQEIFEEANKEVKEIekqyae 651
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 696 GAAANNRTLNRkagmtllqsfeadVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVG-QQNVAG 774
Cdd:COG0086 652 GLITEPERYNK-------------VIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGlMAKPSG 718
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 775 SRI--PFG--FRrrtlphfmlddygetsrgmanrgyvEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDV 850
Cdd:COG0086 719 NIIetPIGsnFR-------------------------EGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDV 773
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
515-671 |
3.31e-53 |
|
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: 183.60 E-value: 3.31e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 515 NFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFLDKYFVQSVALWLDLwqLPIPAILKP-RPLWTGKQVFSLILP-EVNHPA 592
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLMYGIV--LPHPAILKPiKPLWTGKQTFSRLLPnEINPKG 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 593 TPQDRPP-FPHNDSVVMIRRGQLLCGPITKSIVGAAPGSLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDT 671
Cdd:pfam04983 79 KPKTNEEdLCENDSYVLINNGELISGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
240-1113 |
2.71e-51 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 200.92 E-value: 2.71e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 240 PRDLVLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKESDVQAAIDRS-RALLQEHVATYFNNASTY 317
Cdd:PRK09603 1623 PEWMMLTVLPVLPPDLRPLVALdGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNeKRMLQEAVDVLFDNGRST 1702
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 318 yKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKrlte 397
Cdd:PRK09603 1703 -NAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEER---- 1777
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 398 farrtvypsanyihhpnGTITKLAllRDRSKVTLNIGDVVE--RHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRL 475
Cdd:PRK09603 1778 -----------------GYATTLK--QAKRMIEQKSNEVWEclQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQL 1838
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 476 NLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLTDKDTFL---DKYF-- 550
Cdd:PRK09603 1839 HPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVkgeHKLFss 1918
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 551 VQSVALWLDLWQLPIPAILKP----RPLWT--GKQVFSLILPEVnhpaTPQDrppfphndsvvmirrgqLLCGPITKSIV 624
Cdd:PRK09603 1919 VNEIITAIDTKELDIHAKIRVldqgNIIATsaGRMIIKSILPDF----IPTD-----------------LWNRPMKKKDI 1977
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 625 GAapgsLIHVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNdvlvKTRRNVEKIGAAANNRTL 704
Cdd:PRK09603 1978 GV----LVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVE----KAKVEVKKIQQQYDQGLL 2049
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 705 NRKAGMTLLQSFEADVNSALNKcreEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGqqnvagsripfgfrrr 784
Cdd:PRK09603 2050 TDQERYNKIIDTWTEVNDKMSK---EMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSAMRG---------------- 2110
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 785 tlphFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDVHAAYDGTVRNANDE 864
Cdd:PRK09603 2111 ----LMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIE 2186
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 865 LIQFMYGEDGLDgarieggqlfPLPFRddkemedtykyeydvdgTFSGKVGGNYMDPHVRKMLradpqnvrklqeeyeql 944
Cdd:PRK09603 2187 ITDIAVGSELIE----------PLEER-----------------IFGRVLLEDVIDPITNEIL----------------- 2222
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 945 tadrewsrkmldledrdklklnlpVNPGRLIQnarSTMGKRSQVSNLSPITIIDHVrklqedlmklfpsyhrggdgyirn 1024
Cdd:PRK09603 2223 ------------------------LYADTLID---EEGAKKVVEAGIKSITIRTPV------------------------ 2251
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1025 TLSRERIESAltlfnvhlrqllaskrvlKEYKLNdrafeylLKEIRtkyhqsLTTPGENIGAIAAQSCGEPATQMTLNTF 1104
Cdd:PRK09603 2252 TCKAPKGVCA------------------KCYGLN-------LGEGK------MSYPGEAVGVVAAQSIGEPGTQLTLRTF 2300
|
....*....
gi 1115875379 1105 HNAGISSKN 1113
Cdd:PRK09603 2301 HVGGTASRS 2309
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
1050-1470 |
4.74e-51 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 189.63 E-value: 4.74e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1050 RVLKEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVSR 1129
Cdd:PRK14897 151 KAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1130 NQKHASMTVSLFPPYDEkrNAQKAQHLIEycTLESItrriqfiydpdprhtvveadrdilelewNVMDESDAELRIQEVV 1209
Cdd:PRK14897 231 KPSTPTMTIYLKKDYRE--DEEKVREVAK--KIENT----------------------------TLIDVADIITDIAEMS 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1210 agspwvVRLELDVDMVTDKALDMKDVKQAILRVDesyiIETGMANNVRqrtirMRSRYNEgaDSIPKLkREIPALLARVH 1289
Cdd:PRK14897 279 ------VVVELDEEKMKERLIEYDDILAAISKLT----FKTVEIDDGI-----IRLKPQQ--PSFKKL-YLLAEKVKSLT 340
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1290 LRGIPGVRRALLKdtteftvdqatgKMSGNKIWAIDTDGTALRrafiGVVGEDGkniINAVKTSSNKVPEVCSLLGIEAA 1369
Cdd:PRK14897 341 IKGIKGIKRAIAR------------KENDERRWVIYTQGSNLK----DVLEIDE---VDPTRTYTNDIIEIATVLGIEAA 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1370 RSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINrSDTSGPLMRCSFEETVKVLMAAASFGECDPVRG 1449
Cdd:PRK14897 402 RNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGIS-GEKSSVLARAAFEITGKHLLRAGILGEVDKLAG 480
|
410 420
....*....|....*....|.
gi 1115875379 1450 VSANLVLGNQARVGTGLFDLV 1470
Cdd:PRK14897 481 VAENIIVGQPITLGTGAVSLV 501
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1072-1470 |
1.15e-48 |
|
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: 176.23 E-value: 1.15e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1072 KYHQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLE-LLNVSRNQKHASMTVSLFPPYDEKRna 1150
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREiLMTASKNIKTPSMTLPLKNGKSAER-- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1151 qkaqhlieyctLESITRRIQFIYDPDprhtVVEadrDILELEWNVMDESDAELRIQEvvagspW-VVRLELDVDMVtdka 1229
Cdd:cd02735 79 -----------AETLKKRLSRVTLSD----VVE---KVEVTEILKTIERVFKKLLGK------WcEVTIKLPLSSP---- 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1230 ldmkdvkqailRVDESYIIETGMANNVrqrtirmrsrynegadsipklkreipallarvhLRGIPGVRRALLKDTTEFTV 1309
Cdd:cd02735 131 -----------KLLLLSIVEKLARKAV---------------------------------IREIPGITRCFVVEEDKGGK 166
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1310 DQATGKMSGNkiwaidtdgtaLRRAFIgvvgeDGKNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNIN 1389
Cdd:cd02735 167 TKYLVITEGV-----------NLAALW-----KFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFKVYGIAVD 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1390 YRHYTILVDTICQHGYLMAVSRSGInRSDTSgPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGLFDL 1469
Cdd:cd02735 231 PRHLSLIADYMTFEGGYRPFNRIGM-ESSTS-PLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTGLFDL 308
|
.
gi 1115875379 1470 V 1470
Cdd:cd02735 309 L 309
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
240-1466 |
2.97e-47 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 187.52 E-value: 2.97e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 240 PRDLVLTVLPVPPPQVRPAISF-GGLRSDDELTHQIMSIVKRNNQLRRDKE-SDVQAAIDRSRALLQEHVATYFNNASTY 317
Cdd:PRK14844 1666 PEWMILTTIPILPPDLRPLVSLeSGRPAVSDLNHHYRTIINRNNRLRKLLSlNPPEIMIRNEKRMLQEAVDSLFDNSRRN 1745
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 318 YKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervntvnkkrlTE 397
Cdd:PRK14844 1746 ALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKP-----------FV 1814
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 398 FARRTVYPSANYIHHPNGTITKlallrDRSKVTLNIGDVVERHvingdVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 477
Cdd:PRK14844 1815 YSKLKMYGMAPTIKFASKLIRA-----EKPEVWDMLEEVIKEH-----PVLLNRAPTLHRLGIQAFEPILIEGKAIQLHP 1884
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 478 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT-----DKDTFLDKYFVQ 552
Cdd:PRK14844 1885 LVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTlqepkEDDLPSFGAFCE 1964
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 553 sVALWLDLWQLPIPAILKPRPLWTGKQVFSLILPEVNHPATPQDRPPFPHNDSVVMIRRGQLLcgpITKSIVgaapgSLI 632
Cdd:PRK14844 1965 -VEHSLSDGTLHIHSSIKYRMEYINSSGETHYKTICTTPGRLILWQIFPKHENLGFDLINQVL---TVKEIT-----SIV 2035
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 633 HVIFNEHGSDEVARFINGVQRVTTFFLLNFGFSVGVQDTVADSDTLRQMNdvlvKTRRNVEKIGAAANNRTLNRKAGMTl 712
Cdd:PRK14844 2036 DLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVD----HARGEIKKFSMQYQDGLITRSERYN- 2110
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 713 lqsfeaDVNSALNKCREEAAKKALSNV------RRTNSFKVMIEAGSKGTDLNICQIAVFVGqqnvagsripfgfrrrtl 786
Cdd:PRK14844 2111 ------KVIDEWSKCTDMIANDMLKAIsiydgnSKYNSVYMMVNSGARGSTSQMKQLAGMRG------------------ 2166
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 787 phFMLDDYGETSRGMANRGYVEGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALED-VHAAYDGTVRNAndeL 865
Cdd:PRK14844 2167 --LMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNcIVTKHDCKTKNG---L 2241
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 866 IQfmygedgldGARIEGGQLFPlpfrddkemedtykyeyDVDGTFSGKVGGNymdphvrkmlradpqnvrklqEEYEQLT 945
Cdd:PRK14844 2242 VV---------RATVEGSTIVA-----------------SLESVVLGRTAAN---------------------DIYNPVT 2274
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 946 adREWSRKMLDLEDRDKLKlnlpvnpgrliqnarstmgkrsQVSnlspITIIDHVRklqedlmklfpsyhrggdgyIRNT 1025
Cdd:PRK14844 2275 --KELLVKAGELIDEDKVK----------------------QIN----IAGLDVVK--------------------IRSP 2306
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1026 LSRERIESALTLfnVHLRQLLASKrvlkeyklndrafeyllkeirtkyhqsLTTPGENIGAIAAQSCGEPATQMTLNTFH 1105
Cdd:PRK14844 2307 LTCEISPGVCSL--CYGRDLATGK---------------------------IVSIGEAVGVIAAQSVGEPGTQLTMRTFH 2357
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1106 -----NAGISSKNVTLGVPRLLELLN----VSRNQKHASMTVSLFPPYDEKRNAQKAQHLIEY----CTLESITRRIQ-- 1170
Cdd:PRK14844 2358 iggvmTRGVESSNIIASINAKIKLNNsniiIDKNGNKIVISRSCEVVLIDSLGSEKLKHSVPYgaklYVDEGGSVKIGdk 2437
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1171 -FIYDPDPRHTVVEADRDILELEWN-------VMDESDA-------ELRIQEVVAG-SPWVVRLEldvdmvtdkalDMKD 1234
Cdd:PRK14844 2438 vAEWDPYTLPIITEKTGTVSYQDLKdgisiteVMDESTGisskvvkDWKLYSGGANlRPRIVLLD-----------DNGK 2506
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1235 VKQAILRVDESYIIETGMANNVRQ-----------RTIRMRSRYNEGADSIPKLKREIPALLARVH--LRGIPGV----- 1296
Cdd:PRK14844 2507 VMTLASGVEACYFIPIGAVLNVQDgqkvhagdvitRTPRESVKTRDITGGLPRVIELFEARRPKEHaiVSEIDGYvafse 2586
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1297 -----RRALLKDTTEFTVDQATGKMSGNKiWAIDTDGTALRRafiGVVGEDGKNIINavktssnkvpEVCSLLGIEAARS 1371
Cdd:PRK14844 2587 kdrrgKRSILIKPVDEQISPVEYLVSRSK-HVIVNEGDFVRK---GDLLMDGDPDLH----------DILRVLGLEALAH 2652
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1372 KMLTELREAYLAYGLNINYRHYTILVDTICQH---------GYLM--------------AVSRS------------GINR 1416
Cdd:PRK14844 2653 YMISEIQQVYRLQGVRIDNKHLEVILKQMLQKveitdpgdtMYLVgesidklevdrendAMSNSgkrpahylpilqGITR 2732
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
gi 1115875379 1417 S--DTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGL 1466
Cdd:PRK14844 2733 AslETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
244-859 |
1.51e-37 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 154.84 E-value: 1.51e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 244 VLTVLPVPPPQVRPAISFGGLR---SD-DELTHQImsiVKRNNQLRRDKESDVQAAIDRS--RaLLQEHVATYFNNASty 317
Cdd:PRK00566 228 ILDVLPVIPPDLRPLVQLDGGRfatSDlNDLYRRV---INRNNRLKRLLELGAPEIIVRNekR-MLQEAVDALFDNGR-- 301
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 318 yKPTKVNDTKK--LKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFP-------ER-- 386
Cdd:PRK00566 302 -RGRPVTGPNNrpLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPfimkklvERgl 380
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 387 VNTV-NKKRLTEFARRTVYpsanyihhpngtitklallrdrskvtlnigDVVErHVINGDVVLFNRQPTLHRMSMMGhrv 465
Cdd:PRK00566 381 ATTIkSAKKMVEREDPEVW------------------------------DVLE-EVIKEHPVLLNRAPTLHRLGIQA--- 426
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 466 rvlnyntF----------RLN-LSCtTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPcmgIV---QD 531
Cdd:PRK00566 427 -------FepvliegkaiQLHpLVC-TAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKP---IIvpsQD 495
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 532 SLLGSYRLT-DKDTFLD--KYF--VQSVALWLDLWQLPIPAILKPRP-----LWT--GKQVFSLILPEVnhpatpqdrPP 599
Cdd:PRK00566 496 MVLGLYYLTrEREGAKGegMVFssPEEALRAYENGEVDLHARIKVRItskklVETtvGRVIFNEILPEG---------LP 566
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 600 FphndsvvmirrgQLLCGPITKSIVGAapgsLIHVIFNEHGSDEVARFINGvqrvttffLLNFGF--------SVGVQDT 671
Cdd:PRK00566 567 F------------INVNKPLKKKEISK----IINEVYRRYGLKETVIFLDK--------IKDLGFkyatrsgiSIGIDDI 622
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 672 VadsdTLRQMNDVLVKTRRNVEKI------GAAANNRTLNRkagmtllqsfeadVNSALNKCREEAAKKALSNVRRT--- 742
Cdd:PRK00566 623 V----IPPEKKEIIEEAEKEVAEIekqyrrGLITDGERYNK-------------VIDIWSKATDEVAKAMMKNLSKDqes 685
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 743 -NSFKVMIEAGSKGTDLNICQIAvfvGqqnvagsripfgfrrrtlphfMlddygetsRG-MAN-RG----------YVEG 809
Cdd:PRK00566 686 fNPIYMMADSGARGSASQIRQLA---G---------------------M--------RGlMAKpSGeiietpiksnFREG 733
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|
gi 1115875379 810 LKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIkaleDVhaAYDGTVR 859
Cdd:PRK00566 734 LTVLEYFISTHGARKGLADTALKTADSGYLTRRLV----DV--AQDVIVR 777
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1097-1469 |
1.20e-36 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 150.81 E-value: 1.20e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1097 TQMTLNTFHNAGISSKNVTLGVPRLLELLNVSRNQKHASMTVSLFPPYdeKRNAQKAQHL---IEYCTLESITRRIQFiy 1173
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEY--ATDREKAEEVakkIESLTLGDVATSIAI-- 616
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1174 DPDPRHTVVEADRDILELEWNVMDESDAelriqevvagspwVVRLELDVDMvtdkaldmkDVKQAILRVDesyiIETGMA 1253
Cdd:PRK14898 617 DLWTQSIKVELDEETLADRGLTIESVEE-------------AIEKKLGVKI---------DRKGTVLYLK----PKTPSY 670
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1254 NNVRQRtirmrsrynegadsIPKLKReipallarVHLRGIPGVRRALLKDTteftvdqatgKMSGNKIWAIDTDGTALRR 1333
Cdd:PRK14898 671 KALRKR--------------IPKIKN--------IVLKGIPGIERVLVKKE----------EHENDEEYVLYTQGSNLRE 718
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1334 AFiGVVGEDgkniinAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSG 1413
Cdd:PRK14898 719 VF-KIEGVD------TSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIGRHG 791
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....*.
gi 1115875379 1414 INRSDTSgPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGLFDL 1469
Cdd:PRK14898 792 VAGEKGS-VLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDL 846
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
243-540 |
1.90e-36 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 148.51 E-value: 1.90e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 243 LVLTVLPVPPPQVRPAISFGGLR---SD-DELtHQImsIVKRNNQLRRDKESDVQAAIDRSRA---LLQEHVATYFNNaS 315
Cdd:CHL00018 264 MVLCLLPVLPPELRPIIQLDGGKlmsSDlNEL-YRR--VIYRNNTLTDLLTTSRSTPGELVMCqkkLLQEAVDALLDN-G 339
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 316 TYYKPTKVNDTKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPervntvnkkrl 395
Cdd:CHL00018 340 IRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELFQP----------- 408
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 396 teFARRtvypsaNYIHHPNGTITKLA--LLRDRSKVTLNIgdvvERHVINGDVVLFNRQPTLHRmsmmghrvrvLNYNTF 473
Cdd:CHL00018 409 --FVIR------GLIRQHLASNIRAAksKIREKEPIVWEI----LQEVMQGHPVLLNRAPTLHR----------LGIQAF 466
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 474 ----------RLN-LSCTTpYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSP----NKSAPCmgivQDSLLGSYR 538
Cdd:CHL00018 467 qpilvegraiCLHpLVCKG-FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPaigdPISVPS----QDMLLGLYV 541
|
..
gi 1115875379 539 LT 540
Cdd:CHL00018 542 LT 543
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
240-540 |
3.39e-35 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 144.12 E-value: 3.39e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 240 PRDLVLTVLPVPPPQVRPAISFGGLR-SDDELTHQIMSIVKRNNQLRRDKESDVQAAIDRS-RALLQEHVATYFNNASTY 317
Cdd:PRK02625 242 PEWMVLDVIPVIPPDLRPMVQLDGGRfATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNeKRMLQEAVDALIDNGRRG 321
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 318 YKPTKVNDtKKLKSLTERLKGKYGRLRGNLMGKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTe 397
Cdd:PRK02625 322 RTVVGANN-RPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIV- 399
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 398 farrtvypsaNYIHHPNGTItklallrdrSKVTLNIGDVVErHVINGDVVLFNRQPTLHRMSMMGHRVRVLNYNTFRLNL 477
Cdd:PRK02625 400 ----------NNIKAAKKLI---------QRADPEVWQVLE-EVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHP 459
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1115875379 478 SCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMVPKNFVSPNKSAPCMGIVQDSLLGSYRLT 540
Cdd:PRK02625 460 LVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLT 522
|
|
| RNA_pol_Rpb1_7 |
pfam04990 |
RNA polymerase Rpb1, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1160-1291 |
6.43e-33 |
|
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: 124.57 E-value: 6.43e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1160 CTLESITRRIQFIYDPDPRHTVVEADRDILELEWNVMDESDAELRIQevvagSPWVVRLELDVDMVTDKALDMKDVKQAI 1239
Cdd:pfam04990 1 TTLRSVTAATEIYYDPDPRNTVIEEDREFVESYFEIPDEDVEDLDRQ-----SPWLLRIELDRKKMLDKGLTMEDVAEKI 75
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1115875379 1240 LRVDESYIIETGMANNVRQRTIRMRSRY---------NEGADSIPKLKREIPALLARVHLR 1291
Cdd:pfam04990 76 KEEFGNDLFVIFSDDNAEKLVIRIRIINdekekdeeqEDKAEDDVFLKRLEANMLDSLTLR 136
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
695-800 |
1.17e-32 |
|
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: 122.86 E-value: 1.17e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 695 IGAAANNRTLNRKAGMTLLQSFEADVNSALNKCREEAAKKALSNVRRTNSFKVMIEAGSKGTDLNICQIAVFVGQQNVAG 774
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*.
gi 1115875379 775 SRIPFGFRRRTLPHFMLDDYGETSRG 800
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRG 106
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1344-1466 |
4.44e-27 |
|
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: 109.04 E-value: 4.44e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1344 KNIINAVKTSsnkvpEVCSLLGIEAARSKMLTELREAYLAYGLNINYRHYTILVDTICQHGYLMAVSRSGINRSdTSGPL 1423
Cdd:cd00630 42 KEILNAASIH-----EMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRAS-KTSPL 115
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 1115875379 1424 MRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGL 1466
Cdd:cd00630 116 MRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1081-1128 |
5.18e-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: 5.18e-18
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 1115875379 1081 GENIGAIAAQSCGEPATQMTLNTFHNAGISSKNVTLGVPRLLELLNVS 1128
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1081-1125 |
3.65e-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: 64.47 E-value: 3.65e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 1115875379 1081 GENIGAIAAQSCGEPATQMTLNTFHNAGISSkNVTLGVPRLLELL 1125
Cdd:cd02655 6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEELF 49
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1074-1114 |
1.01e-06 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 53.85 E-value: 1.01e-06
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 1115875379 1074 HQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNV 1114
Cdd:PRK02597 304 HNHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1074-1109 |
1.06e-06 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 53.79 E-value: 1.06e-06
10 20 30
....*....|....*....|....*....|....*.
gi 1115875379 1074 HQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGI 1109
Cdd:CHL00117 308 HGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
1306-1469 |
2.35e-06 |
|
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: 52.04 E-value: 2.35e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1306 EFTVDQATGKMSGNkIWaidtdgTALRRAFIGVVgedgkNIINAVKTSSNKVPEVCSLLGIEAARSKMLTELREAYLAYG 1385
Cdd:cd02737 223 EVTVEESCKKTRGN-AW------NVVMDACIPVM-----DLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTG 290
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1386 LNInYRHYTILV-DTICQHGYLMAVSRSG----INRSDTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQA 1460
Cdd:cd02737 291 KSV-LREHLLLVaDSMTYSGEFVGLNAKGykaqRRSLKISAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEA 369
|
170
....*....|
gi 1115875379 1461 RVGTG-LFDL 1469
Cdd:cd02737 370 PVGTGsKFEI 379
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1074-1114 |
2.35e-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: 52.93 E-value: 2.35e-06
10 20 30 40
....*....|....*....|....*....|....*....|.
gi 1115875379 1074 HQSLTTPGENIGAIAAQSCGEPATQMTLNTFHNAGISSKNV 1114
Cdd:TIGR02388 302 HAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1053-1101 |
1.79e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 46.42 E-value: 1.79e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 1115875379 1053 KEYKLNDRAFEYLLKEIRTKYHQSLTTPGENIGAIAAQSCGEPATQMTL 1101
Cdd:PRK14898 29 KRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
1349-1466 |
2.61e-04 |
|
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: 44.06 E-value: 2.61e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1115875379 1349 AVKTSSNKVPEVCSLlGIEAARSKMLTELREAYLAYGLNINYRHYTILV-------------DTICQHGYLMAVSRS--- 1412
Cdd:cd02655 51 ARKINPHDLLRIKFL-GPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVrqmtskvkiidpgDSGFLPGELVDLNEFeee 129
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1115875379 1413 -------------------GINRS--DTSGPLMRCSFEETVKVLMAAASFGECDPVRGVSANLVLGNQARVGTGL 1466
Cdd:cd02655 130 nkrllllgkkpakyepvllGITKAslNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
823-850 |
4.68e-04 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 45.32 E-value: 4.68e-04
10 20
....*....|....*....|....*...
gi 1115875379 823 REGLIDTAVKTSDTGYLQRKLIKALEDV 850
Cdd:CHL00117 186 RKGVVDTAVRTADAGYLTRRLVEVVQHI 213
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
808-850 |
4.96e-04 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 44.99 E-value: 4.96e-04
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1115875379 808 EGLKPHEFFFHTMAGREGLIDTAVKTSDTGYLQRKLIKALEDV 850
Cdd:PRK02597 165 EGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDV 207
|
|
| |
