|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
14-872 |
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: 1575.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 14 LDKILFGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIPH 93
Cdd:cd02582 4 IKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHVG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 94 YTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLRGKWPQLAKTFATMVVKEAAQATQCPHCGKPQYKVVYIRPFHFY 173
Cdd:cd02582 84 FAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKEKWPELVKRVIEKVKKKAKKRKVCPHCGAPQYKIKLEKPTTFY 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 174 EKKPEGDVKLTPSEIRERLEKTGSE-IEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQ 252
Cdd:cd02582 164 EEKEEGEVKLTPSEIRERLEKIPDEdLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRI 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 253 NEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTV 332
Cdd:cd02582 244 NQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 333 ISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKtSERKKYDLRFFkDYKKLAESLEPG 412
Cdd:cd02582 324 ISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIR-PDGRRIRLRYV-NREELAERLEPG 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 413 DIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEK 492
Cdd:cd02582 402 WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQE 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 493 HILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSVAGYKGDLPEPAILKPRPLWTGKQLASIFLPDDLNFKG 572
Cdd:cd02582 482 HILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEG 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 573 KSKTNAGDLACADELCLHDSYIVITNGKLLEGVLDKKAIGAEEPNNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGL 652
Cdd:cd02582 562 KAKVCSGCSECKDEDCPNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGF 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 653 TISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYRKGTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVASNNLDPFND 732
Cdd:cd02582 642 TIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNN 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 733 VFVMARTGARGSDVNISQMAAMLGQQAVRGKRIRRGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEVFFHAAAGRE 812
Cdd:cd02582 722 AVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGRE 801
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 813 GLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQLKYGEDGVDPMKTYHGK 872
Cdd:cd02582 802 GLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSDHGK 861
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
12-880 |
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: 1571.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 12 NLLDKILFGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLI 91
Cdd:TIGR02390 2 KKIGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 92 PHYTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLRGKWPQLAKTFATMVVKEAAQATQCPHCGKPQYKVVYIRPFH 171
Cdd:TIGR02390 82 VGFAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEGGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKPTY 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 172 FYEKKPEGDVKLTPSEIRERLEKTGSE-IEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIV 250
Cdd:TIGR02390 162 FYEEGKEGDVKLTPSEIRERLEKIPDEdAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDII 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 251 RQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSAR 330
Cdd:TIGR02390 242 RINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSAR 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 331 TVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKtSERKKYDLRFFKdYKKLAESLE 410
Cdd:TIGR02390 322 TVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIR-PDGRRIKIRDEN-KEELAERLE 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 411 PGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLV 490
Cdd:TIGR02390 400 PGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLV 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 491 EKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSVAGYKGDLPEPAILKPRPLWTGKQLASIFLPDDLNF 570
Cdd:TIGR02390 480 EEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNF 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 571 KGKSKTNAGDLACADELCLHDSYIVITNGKLLEGVLDKKAIGAEEPNnLLHIIALEYGNSKARQLLDSFYRMFIRMLELR 650
Cdd:TIGR02390 560 EGRAKICSGSDACKKEECPHDAYVVIKNGKLLKGVIDKKAIGAEKGK-ILHRIVREYGPEAARRFLDSVTRLFIRFITLR 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 651 GLTISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYRKGTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVASNNLDPF 730
Cdd:TIGR02390 639 GFTTGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPE 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 731 NDVFVMARTGARGSDVNISQMAAMLGQQAVRGKRIRRGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEVFFHAAAG 810
Cdd:TIGR02390 719 NHAVIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGG 798
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 811 REGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQLKYGEDGVDPMKTYHGKPVDVKRIV 880
Cdd:TIGR02390 799 REGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDHGKPVDVKKIF 868
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
6-889 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 1553.67 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 6 SEFREANLLDKILFGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIEL 85
Cdd:PRK08566 1 SMMMIPKRIGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIEL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 86 ARPVLIPHYTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLRgKWPQLAKTFATMVVKEAAQATQCPHCGKPQYKVV 165
Cdd:PRK08566 81 ARPVIHVGFAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLK-EWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 166 YIRPFHFYEKKPEGDVKLTPSEIRERLEKTGSE-IEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTH 244
Cdd:PRK08566 160 FEKPTTFYEERKEGLVKLTPSDIRERLEKIPDEdLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTH 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 245 ALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKR 324
Cdd:PRK08566 240 KLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 325 VNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKTsERKKYDLrFFKDYKK 404
Cdd:PRK08566 320 VNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRP-DGRRIKL-TDKNKEE 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 405 LAESLEPGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEA 484
Cdd:PRK08566 398 LAEKLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEA 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 485 REIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSVAGYKG-DLPEPAILKPRPLWTGKQLASIF 563
Cdd:PRK08566 478 RILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDElPEPEPAIENGKPYWTGKQIFSLF 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 564 LPDDLNFKGKSKTNAGDLACADELCLHDSYIVITNGKLLEGVLDKKAIGAEEpNNLLHIIALEYGNSKARQLLDSFYRMF 643
Cdd:PRK08566 558 LPKDLNLEFKAKICSGCDECKKEDCEHDAYVVIKNGKLLEGVIDKKAIGAEQ-GSILDRIVKEYGPERARRFLDSVTRLA 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 644 IRMLELRGLTISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYRKGTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVA 723
Cdd:PRK08566 637 IRFIMLRGFTTGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIA 716
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 724 SNNLDPFNDVFVMARTGARGSDVNISQMAAMLGQQAVRGKRIRRGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEV 803
Cdd:PRK08566 717 EKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEF 796
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 804 FFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQLKYGEDGVDPMKTYHGKPVDVKRIVQRV 883
Cdd:PRK08566 797 FFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHGKPVDVDRIIERV 876
|
....*.
gi 547222393 884 KTGKAN 889
Cdd:PRK08566 877 LGKEVE 882
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
14-884 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 961.02 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 14 LDKILFGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIPH 93
Cdd:PRK14977 9 IDGIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVIHIA 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 94 YTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLRGKW--------PQLAKTFATMVVKEAAQATQCPHCGKPQYKVV 165
Cdd:PRK14977 89 FIDNIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARdipekridDEIIEEVRDQVKVYAKKAKECPHCGAPQHELE 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 166 YIRPFHFYEKKPEGDVKLTPSEIRERLEKTGSE-IEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTH 244
Cdd:PRK14977 169 FEEPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDdLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTH 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 245 ALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRR-KRYLKTLAQRLKGKDGRIRGNLSGK 323
Cdd:PRK14977 249 ILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKGsGRPLKSLFQRLKGKEGRFRGNLIGK 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 324 RVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKtSERKKYDLRFFKD-- 401
Cdd:PRK14977 329 RVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRK-GDGTKIRLDFLEDkg 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 402 ---YKKLAESLEPGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLE 478
Cdd:PRK14977 408 kdaLREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIE 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 479 EAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSVAGYKGDLPEPAI-LKPRPLWTGK 557
Cdd:PRK14977 488 DARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIkTKDGPAWTGK 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 558 QLASIFLPDDLNFKGKSKTNAGDLA-CADELCLHDSYIVITNGKLLEGVLDKKAIGA--EEPNNLLHIIALEYGNSKARQ 634
Cdd:PRK14977 568 QLFSLFLPKDFNFEGIAKWSAGKAGeAKDPSCLGDGYVLIKEGELISGVIDDNIIGAlvEEPESLIDRIAKDYGEAVAIE 647
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 635 LLDSFYRMFIRMLELRGLTISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYR--------KGTLEPIPGRSLEESLEI 706
Cdd:PRK14977 648 FLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKitrkitiyKGKEELLRGMKEEEALEA 727
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 707 KIMEVLDELRKKVQEVASNNLDPFNDVFVMARTGARGSDVNISQMAAMLGQQAVR--------GKRIRRGFRNRVLAHFR 778
Cdd:PRK14977 728 DIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKtrigfvltGGRLHEGYKDRALSHFQ 807
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 779 ENDTEPEAWGFVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQLKY 858
Cdd:PRK14977 808 EGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKF 887
|
890 900
....*....|....*....|....*.
gi 547222393 859 GEDGVDPMKTYHGKPVDVKRIVQRVK 884
Cdd:PRK14977 888 GEDGIDPQKLDHGEAFNLERIIEKQK 913
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
15-843 |
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: 895.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 15 DKILFGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIPHY 94
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYENGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 95 TDYVYKILQatCrVCgRITLPEEKIKYyrlIFRRlrgkwpqlaktfatmvvkeaaqatqcphcgkpqykvvyirpfhfye 174
Cdd:cd02733 81 LTKILKILR--C-VC-KRELSAERVLE---IFKR---------------------------------------------- 107
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 175 kkpegdvkltpseIRErlektgSEIEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNE 254
Cdd:cd02733 108 -------------ISD------EDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARSEDDLTHKLADIIKANN 168
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 255 KLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVIS 334
Cdd:cd02733 169 QLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVIT 248
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 335 PDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKTSERkKYDLRFFKdyKKLAESLEPGDI 414
Cdd:cd02733 249 PDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGE-RIDLRYLK--KASDLHLQYGYI 325
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 415 VERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHI 494
Cdd:cd02733 326 VERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQI 405
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 495 LTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLS-VAGYKGDLPEPAILKPRPLWTGKQLASIFLPDDLNFKGK 573
Cdd:cd02733 406 VSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMwLPDWDGKIPQPAILKPKPLWTGKQIFSLIIPKINNLIRS 485
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 574 SKTNAGDlacADELCLHDSYIVITNGKLLEGVLDKKAIGAeEPNNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLT 653
Cdd:cd02733 486 SSHHDGD---KKWISPGDTKVIIENGELLSGILCKKTVGA-SSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFS 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 654 ISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYRKGTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVASNNLDPFNDV 733
Cdd:cd02733 562 IGIGDTIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNF 641
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 734 FVMARTGARGSDVNISQMAAMLGQQAVRGKRIRRGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEVFFHAAAGREG 813
Cdd:cd02733 642 KAMVTAGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREG 721
|
810 820 830
....*....|....*....|....*....|
gi 547222393 814 LVDTAVKTSQSGYMQRRLINALQDIVVTYD 843
Cdd:cd02733 722 LIDTAVKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
22-847 |
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: 890.36 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 22 LSPHEIRQLAKVTVVRGDLYEAD-GTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLipH--YTDYV 98
Cdd:cd02583 1 LSPEDIIRLSEVEVTNRNLYDIEtRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVF--HigYFKAI 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 99 YKILQATCRVCGRITLPEEKIKYYRLIFRRLRGKWPQLAKTFATmVVKEAAQATQCPHCGKPQYKVVYIRP---FHFYEK 175
Cdd:cd02583 79 INILQCICKTCSRVLLPEEEKRKFLKRLRRPNLDNLQKKALKKK-ILEKCKKVRKCPHCGLLKKAQEDLNPlkvLNLFKN 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 176 KPEGDvkltpseirerlektgseIEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRS-EDDLTHALAEIVRQNE 254
Cdd:cd02583 158 IPPED------------------VELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEKSGTnEDDLTVKLSEIIFLND 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 255 KLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARrLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVIS 334
Cdd:cd02583 220 VIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLP-LSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVIS 298
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 335 PDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKTSERKKYDLRFfKDYKKLAESLEPGDI 414
Cdd:cd02583 299 PDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIKRDGGKKKFLKY-GNRRKIARELKIGDI 377
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 415 VERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHI 494
Cdd:cd02583 378 VERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNL 457
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 495 LTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLS---VAGYKGDLPEPAILKPRPLWTGKQLASIFL------P 565
Cdd:cd02583 458 VTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCSymlDGEIKIDLPPPAILKPVELWTGKQIFSLLLrpnkksP 537
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 566 DDLNFKGKSKTNagdLACADELCLHDSYIVITNGKLLEGVLDKKAIGAEEPNNLLHIIALEYGNSKARQLLDSFYRMFIR 645
Cdd:cd02583 538 VLVNLEAKEKSY---TKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSGSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSR 614
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 646 MLELRGLTISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYRKGTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVASN 725
Cdd:cd02583 615 WLSNRGFSIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEAKISGELSKIREDAGKACLK 694
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 726 NLDPFNDVFVMARTGARGSDVNISQMAAMLGQQAVRGKRIRRGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEVFF 805
Cdd:cd02583 695 ELHKSNSPLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRNSKTPAAKGFVANSFYSGLTPTEFFF 774
|
810 820 830 840
....*....|....*....|....*....|....*....|..
gi 547222393 806 HAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVR 847
Cdd:cd02583 775 HTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
19-843 |
0e+00 |
|
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: 602.25 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 19 FGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIPHYTDYV 98
Cdd:cd01435 2 FSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDLL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 99 YKILQATCRVCGRITLPEEKIKYYRLIFRRLRgkwpqlaktfatmvvkeaaqatqcphCGKPQykvvyirpfhfyekkpe 178
Cdd:cd01435 82 YKLLRGSCFYCHRFRISKWEVKLFVAKLKLLD--------------------------KGLLV----------------- 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 179 gdvkltpseirerlektgsEIEILgvhpeRSRPEWMVATVLIVPPLAVRPSITLEtGLRSEDDLTHALAEIVRQNEKLRN 258
Cdd:cd01435 119 -------------------EAAEL-----DFGYDMFFLDVLLVPPNRFRPPSFLG-DKVFENPQNVLLSKILKDNQQIRD 173
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 259 VIV----------------TNAPETLIEeNWMVLQEMVAAYIDNELPgarrlthrrKRYLKTLA----QRLKGKDGRIRG 318
Cdd:cd01435 174 LLAsmrqaesqskldlisgKTNSEKLIN-AWLQLQSAVNELFDSTKA---------PKSGKKSPpgikQLLEKKEGLFRM 243
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 319 NLSGKRVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFV-----------YK 387
Cdd:cd01435 244 NMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGPDVYPGANAIededgrlillsAL 323
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 388 TSERKKYDLRFFKDYKKLAESLEPGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPG-KTFRLNLLVCPPYNADFD 466
Cdd:cd01435 324 SEERRKALAKLLLLLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLPGeKTLRLHYANCKSYNADFD 403
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 467 GDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSVA-------GYK 539
Cdd:cd01435 404 GDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTREEYQQLVYAAlrplftsDKD 483
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 540 GD--LPEPAILKPRPLWTGKQLASIFL---------PDDLNFKGKSKTNAGDLACADELClhDSYIVITNGKLLEGVLDK 608
Cdd:cd01435 484 GRikLLPPAILKPKPLWTGKQVISTILknlipgnapLLNLSGKKKTKKKVGGGKWGGGSE--ESQVIIRNGELLTGVLDK 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 609 KAIGAEePNNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDIDLPERAKQEIEELIREYKGRVYSIIEDYr 688
Cdd:cd01435 562 SQFGAS-AYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEF- 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 689 kgtlepipgrsleesLEIKIMEVLDELRKKvqEVASNNLDPF--NDVFVMARTGARGSDVNISQMAAMLGQQAVRGKRIR 766
Cdd:cd01435 640 ---------------LGLKLNKVTSSIIKA--CLPKGLLKPFpeNNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVP 702
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 547222393 767 RGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYD 843
Cdd:cd01435 703 LMVSGKTLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
22-843 |
0e+00 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 554.74 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 22 LSPHEIRQLAKVTVVRGDLYEADGTPVSGGLR-DPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIPHYTDYVYK 100
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGGKyDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 101 ILQatcrvcgritlpeekikyyrlifrrlrgkwpqlaktfatmvvkeaaqatqcphcgkpqykvvyirpfhfyekkpegd 180
Cdd:cd00399 81 FLG----------------------------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 181 vkltpseirerlektgseieilgvhpersrPEWMVATVLIVPPLAVRPSItletglrseddlthalaeivrqneklrnvi 260
Cdd:cd00399 84 ------------------------------PEWMILTCLPVPPPCLRPSV------------------------------ 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 261 vtnapetLIEENWMVLQEMVAAYIDNELPGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYIS 340
Cdd:cd00399 104 -------IIEERWRLLQEHVDTYLDNGIAG-QPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLR 175
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 341 INEVGVPEEIAKTLtiamrvtpynleearrfvlngpdkwpgalfvyktserkkydlrffkdykklaeslepgdiverhli 420
Cdd:cd00399 176 LDQVGVPKSIALTL------------------------------------------------------------------ 189
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 421 NGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYG 500
Cdd:cd00399 190 DGDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNG 269
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 501 GPIIGGRQDYVSGAYLLTVktrlftkeeverllsvagykgdlpepailkprplwtGKQLASIFLPddlnfkgksktnagd 580
Cdd:cd00399 270 EPLIGLSQDTLLGAYLLTL------------------------------------GKQIVSAALP--------------- 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 581 lacadelclhdsyivitngkllegvldkkaigaeepNNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDID 660
Cdd:cd00399 299 ------------------------------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVI 342
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 661 LPERAKQEIEELIREYKGRVYSIIEDYRKGTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVASNNLD---PFNDVFVMA 737
Cdd:cd00399 343 DDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLNEARDKAGSAASVNLDlvsKFNSIYVMA 422
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 738 RTGARGSDVNISQMAAMLGQQAVRGKRIRRGFRNRVLAHFRENDTEPEAWGFVRSSFRKGLRPTEVFFHAAAGREGLVDT 817
Cdd:cd00399 423 MSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDT 502
|
810 820
....*....|....*....|....*.
gi 547222393 818 AVKTSQSGYMQRRLINALQDIVVTYD 843
Cdd:cd00399 503 AVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
212-515 |
3.01e-162 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 475.09 E-value: 3.01e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 212 EWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNElpGA 291
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 292 RRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRF 371
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 372 VLNGPdkwPGALFVYKTserKKYDLRFfKDYKKLAESLEPGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTF 451
Cdd:smart00663 159 VRNGP---NGAKYIIRG---KKTNLKL-AKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTI 231
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 547222393 452 RLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAY 515
Cdd:smart00663 232 RLNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
210-841 |
1.33e-88 |
|
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: 295.58 E-value: 1.33e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 210 RPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKLRNVIVTNAPETLIE-ENWMvLQEMVAAYIDNEL 288
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRnEKRM-LQEAVDALIDNGR 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 289 PGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYISINEVGVPEEIAktltiamrvtpynLEEA 368
Cdd:cd01609 217 RG-KPVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMA-------------LELF 282
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 369 RRFVLngpdkwpgalfvyktserKKYDLRFF----KDYKKLAESLEPG--DIVErHLINGDIVLFNRQPSLHRMSIMGHI 442
Cdd:cd01609 283 KPFVI------------------RELIERGLapniKSAKKMIERKDPEvwDILE-EVIKGHPVLLNRAPTLHRLGIQAFE 343
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 443 VRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTvktr 522
Cdd:cd01609 344 PVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLT---- 419
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 523 lftkeeVERllsvagyKGDLPEpAILKPRPlwtGKQLASIFLPDDLNFKGKsktnagdlacadelclhdsyivitngkll 602
Cdd:cd01609 420 ------KER-------KGDKGE-GIIETTV---GRVIFNEILPEGLPFINK----------------------------- 453
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 603 egVLDKKAIGaeepnNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDIDLPERaKQEIeelIREYKGRVYS 682
Cdd:cd01609 454 --TLKKKVLK-----KLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPE-KKEI---IKEAEEKVKE 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 683 IIEDYRKGTLepipgrSLEESLE--IKI-MEVLDELRKKVQEVASNnlDPFNDVFVMARTGARGSDVNISQMAAMLGQQA 759
Cdd:cd01609 523 IEKQYEKGLL------TEEERYNkvIEIwTEVTEKVADAMMKNLDK--DPFNPIYMMADSGARGSKSQIRQLAGMRGLMA 594
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 760 -VRGKRIrrgfrnrvlahfrENdtePeawgfVRSSFRKGLRPTEvFFHAAAG-REGLVDTAVKTSQSGYMQRRLINALQD 837
Cdd:cd01609 595 kPSGKII-------------EL---P-----IKSNFREGLTVLE-YFISTHGaRKGLADTALKTADSGYLTRRLVDVAQD 652
|
....
gi 547222393 838 IVVT 841
Cdd:cd01609 653 VIVT 656
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
322-490 |
2.76e-88 |
|
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: 277.65 E-value: 2.76e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 322 GKRVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRFVLNGPDKWPGALFVYKtSERKKYDLRFfkD 401
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIR-INGARRDLRY--Q 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 402 YKKLAESLEPGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQ 481
Cdd:pfam00623 78 KRRLDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEAR 157
|
....*....
gi 547222393 482 AEAREIMLV 490
Cdd:pfam00623 158 AEAEELMLV 166
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
180-843 |
1.47e-87 |
|
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: 302.74 E-value: 1.47e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 180 DVKLTPSEIRERLEKTGSE---------IEIL-GVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEI 249
Cdd:TIGR02386 175 DLDKEIEELKIQLRESKSDqkrkkllkrLEIVeAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRV 254
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 250 VRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSA 329
Cdd:TIGR02386 255 INRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRG-KPVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSG 333
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 330 RTVISPDPYISINEVGVPEEIAKTL-------TIAMRVTPYNLEEARRFVLNGPDK-Wpgalfvyktserkkydlrffkd 401
Cdd:TIGR02386 334 RSVIVVGPELKMYQCGLPKKMALELfkpfiikRLIDRELAANIKSAKKMIEQEDPEvW---------------------- 391
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 402 ykklaeslepgDIVERhLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQ 481
Cdd:TIGR02386 392 -----------DVLED-VIKEHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQ 459
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 482 AEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVK-------TRLF-TKEEVERllsvAGYKGDLPEPAILKPRpl 553
Cdd:TIGR02386 460 AEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTEkpgakgeGKIFsNVDEAIR----AYDNGKVHLHALIGVR-- 533
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 554 wtgkqlasiflpddlnFKGKS-KTNAGDLACADELCLHDSYIVITNgkllegVLDKKAIGaeepnNLLHIIALEYGNSKA 632
Cdd:TIGR02386 534 ----------------TSGEIlETTVGRVIFNEILPEGFPYINDNE------PLSKKEIS-----SLIDLLYEVHGIEET 586
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 633 RQLLDSFYRMFIRMLELRGLTISLHDIDLPErakqEIEELIREYKGRVYSIIEDYRKGTLepipgrsLEESLEIKIMEVL 712
Cdd:TIGR02386 587 AEMLDKIKALGFKYATKSGTTISASDIVVPD----EKYEILKEADKEVAKIQKFYNKGLI-------TDEERYRKVVSIW 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 713 ----DELRKKVQEVASNNLDPFNDVFVMARTGARGSDVNISQMAAMlgqqavrgkrirRGFRNRVlahfrENDTEPEAwg 788
Cdd:TIGR02386 656 setkDKVTDAMMKLLKKDTYKFNPIFMMADSGARGNISQFRQLAGM------------RGLMAKP-----SGDIIELP-- 716
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*
gi 547222393 789 fVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYD 843
Cdd:TIGR02386 717 -IKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREE 770
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
52-847 |
1.03e-84 |
|
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: 287.38 E-value: 1.03e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 52 LRDPHFGAIEPGERCPVCG-NSREECPGHFGKIELARPVLIPHYTDYVYKILQATCRVCGRItlpEEKIKyyrlifRRLR 130
Cdd:cd10506 20 VTNPRLGLPNESGQCTTCGaKDNKKCEGHFGVIKLPVTIYHPYFISEVAQILNKICPGCKSI---KQKKK------KPPR 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 131 GKWPQlakTFATMVVKEAAQATQCPHCGKPQyKVVYIrpfhfyekkpegdVKLTPSEIRERLektgseieILGVHPersR 210
Cdd:cd10506 91 ETLPP---DYWDFIPKDGQQEESCVTKNLPI-LSLAQ-------------VKKILKEIDPKL--------IAKGLP---R 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 211 PEWMVATVLIVPPLAVRPSitletglrsedDLTHALAeivrqneklrnvivTNAPETLIEENWMVLQEMVAAYIDNELPG 290
Cdd:cd10506 143 QEGLFLKCLPVPPNCHRVT-----------EFTHGFS--------------TGSRLIFDERTRAYKKLVDFIGTANESAA 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 291 ARRLThrrKRYLKTLaqrlkgkdgrirgnLSGKRVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARR 370
Cdd:cd10506 198 SKKSG---LKWMKDL--------------LLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLQE 260
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 371 FVLNGPdkwpgaLFVYKTSERKKYDLRFFKDYKKLaeslEPGDIVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMP-GK 449
Cdd:cd10506 261 YCDLTL------LLKGVIGVRRNGRLVGVRSHNTL----QIGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSVKVLPtNS 330
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 450 TFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEV 529
Cdd:cd10506 331 VVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGVFLDKAQM 410
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 530 ERLLSVAGYKgdLPEPAILK--PR--PLWTGKQLASIFLPDDLNFKGksktnagdlacadelclhDSYIVITNGKLLEGV 605
Cdd:cd10506 411 QQLQMLCPSQ--LPPPAIIKspPSngPLWTGKQLFQMLLPTDLDYSF------------------PSNLVFISDGELISS 470
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 606 LDKKAIGAEEPNNLLHIIaLEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDI----DLPERAK--QEIEELIREYKGR 679
Cdd:cd10506 471 SGGSSWLRDSEGNLFSIL-VKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLylssDSYSRQKmiEEISLGLREAEIA 549
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 680 VY--SIIEDYRKGTL--------------EPIPGRS----LEESLEIKIMEVLDELRKKVQEVASNNldpfNDVFVMART 739
Cdd:cd10506 550 CNikQLLVDSRKDFLsgsgeendvssdveRVIYERQksaaLSQASVSAFKQVFRDIQNLVYKYASKD----NSLLAMIKA 625
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 740 GARGSDVNISQMAAMLGQQAVRGK---RIRR-----GFRNRVLAHFRENDTE-----PEAWGFVRSSFRKGLRPTEVFFH 806
Cdd:cd10506 626 GSKGSLLKLVQQSGCLGLQLSLVKlsyRIPRqlscaAWNSQKSPRVIEKDGSectesYIPYGVVESSFLDGLNPLECFVH 705
|
810 820 830 840
....*....|....*....|....*....|....*....|.
gi 547222393 807 AAAGREGLVDTAVKTsqSGYMQRRLINALQDIVVTYDGTVR 847
Cdd:cd10506 706 SITSRDSSFSSNADL--PGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
187-883 |
6.66e-83 |
|
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: 289.75 E-value: 6.66e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 187 EIRERLEKTGSE---------IEIL-GVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKL 256
Cdd:COG0086 190 ELREELKETTSEqkrkklikrLKVVeAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRL 269
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 257 RNVIVTNAPETLIE-ENWMvLQEMVAAYIDNELPGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISP 335
Cdd:COG0086 270 KRLLELKAPDIIVRnEKRM-LQEAVDALFDNGRRG-RAVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVV 347
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 336 DPYISINEVGVPEEIAktltiamrvtpynLEearrfvLNGPdkwpgalFVYKTSERKKYDlRFFKDYKKLAESLEPG--D 413
Cdd:COG0086 348 GPELKLHQCGLPKKMA-------------LE------LFKP-------FIYRKLEERGLA-TTIKSAKKMVEREEPEvwD 400
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 414 IVERhLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKH 493
Cdd:COG0086 401 ILEE-VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNN 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 494 ILTPRYGGPIIGGRQDYVSGAYLLTvKTRLFTK---------EEVERllsvAGYKGDLPEPAILKPRPLWTGKQLASIFl 564
Cdd:COG0086 480 ILSPANGKPIIVPSQDMVLGLYYLT-REREGAKgegmifadpEEVLR----AYENGAVDLHARIKVRITEDGEQVGKIV- 553
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 565 pddlnfkgksKTNAGDlacadelclhdsyiVITNGKLLEGV------LDKKAIGaeepnNLLHIIALEYGNSKARQLLDS 638
Cdd:COG0086 554 ----------ETTVGR--------------YLVNEILPQEVpfynqvINKKHIE-----VIIRQMYRRCGLKETVIFLDR 604
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 639 FYRMFIRMLELRGLTISLHDIDLPErAKQEIeelIREYKGRVYSIIEDYRKGtLEPIPGRSLeesleiKIMEVLDELRKK 718
Cdd:COG0086 605 LKKLGFKYATRAGISIGLDDMVVPK-EKQEI---FEEANKEVKEIEKQYAEG-LITEPERYN------KVIDGWTKASLE 673
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 719 VQEVASNNLDPFNDVFVMARTGARGSDVNISQMAAMLGQQA-VRGKRIrrgfrnrvlahfrENDtepeawgfVRSSFRKG 797
Cdd:COG0086 674 TESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGLMAkPSGNII-------------ETP--------IGSNFREG 732
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 798 LRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYD--GTVRdlyGNLIQ-LKYGEDGVDPMKtyhgkpv 874
Cdd:COG0086 733 LGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEdcGTDR---GITVTaIKEGGEVIEPLK------- 802
|
....*....
gi 547222393 875 dvKRIVQRV 883
Cdd:COG0086 803 --ERILGRV 809
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
15-320 |
5.41e-81 |
|
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: 264.15 E-value: 5.41e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 15 DKILFGVLSPHEIRQLAKVTVVRGDLYE-ADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVLIPH 93
Cdd:pfam04997 5 KEIQFGIASPEEIRKWSVGEVTKPETYNyGSLKPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFHIG 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 94 YTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLR-GKWPQLAKtfatMVVKEAAQATQCPHCGKPQ---------YK 163
Cdd:pfam04997 85 FFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGlENLKMGAK----AILELCKKKDLCEHCGGKNgvcgsqqpvSR 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 164 VVYIRPFHFYEKKP--EGDVKLTPSEIRERLEK-TGSEIEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSED 240
Cdd:pfam04997 161 KEGLKLKAAIKKSKeeEEKEILNPEKVLKIFKRiSDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAED 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 241 DLTHALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRGNL 320
Cdd:pfam04997 241 DLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
187-883 |
8.19e-77 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 272.33 E-value: 8.19e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 187 EIRERLEKTGSE---------IEILgvhpE---RS--RPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQ 252
Cdd:PRK00566 190 ELREELKETGSEqkrkkalkrLKVV----EafrKSgnKPEWMILDVLPVIPPDLRPLVQLDGGRFATSDLNDLYRRVINR 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 253 NEKLRNVIVTNAPETLIE-ENWMvLQEMVAAYIDNelpgARR---LTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYS 328
Cdd:PRK00566 266 NNRLKRLLELGAPEIIVRnEKRM-LQEAVDALFDN----GRRgrpVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYS 340
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 329 ARTVISPDPYISINEVGVPEEIAktltiamrvtpynLEearrfvLNGPdkwpgalFVYKTSERKKY--DLrffKDYKKLA 406
Cdd:PRK00566 341 GRSVIVVGPELKLHQCGLPKKMA-------------LE------LFKP-------FIMKKLVERGLatTI---KSAKKMV 391
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 407 ESLEPG--DIVErHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEA 484
Cdd:PRK00566 392 EREDPEvwDVLE-EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEA 470
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 485 REIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTV-------KTRLF-TKEEVERLLSvAGY-------KGDLPEPAILK 549
Cdd:PRK00566 471 RVLMLSSNNILSPANGKPIIVPSQDMVLGLYYLTReregakgEGMVFsSPEEALRAYE-NGEvdlhariKVRITSKKLVE 549
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 550 PRPlwtGKQLASIFLPDDLnfkgksktnagdlacadelclhdSYIVItngkllEGVLDKKAIGaeepnNLLHIIALEYGN 629
Cdd:PRK00566 550 TTV---GRVIFNEILPEGL-----------------------PFINV------NKPLKKKEIS-----KIINEVYRRYGL 592
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 630 SKARQLLDsfyrmfiRMLEL-------RGLTISLHDIDLPErAKQEIeelIREYKGRVYSIIEDYRKGTLepipgrSLEE 702
Cdd:PRK00566 593 KETVIFLD-------KIKDLgfkyatrSGISIGIDDIVIPP-EKKEI---IEEAEKEVAEIEKQYRRGLI------TDGE 655
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 703 --SLEIKI-MEVLDELRKKVQEVASNNLDPFNDVFVMARTGARGSDVNISQMAAMLGQQA-VRGKRIRRgfrnrvlahfr 778
Cdd:PRK00566 656 ryNKVIDIwSKATDEVAKAMMKNLSKDQESFNPIYMMADSGARGSASQIRQLAGMRGLMAkPSGEIIET----------- 724
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 779 endtePeawgfVRSSFRKGLRPTEVFF--HAAagREGLVDTAVKTSQSGYMQRRLINALQDIVVTYD--GTVRDLYgnLI 854
Cdd:PRK00566 725 -----P-----IKSNFREGLTVLEYFIstHGA--RKGLADTALKTADSGYLTRRLVDVAQDVIVREDdcGTDRGIE--VT 790
|
730 740
....*....|....*....|....*....
gi 547222393 855 QLKYGEDGVDPMKTyhgkpvdvkRIVQRV 883
Cdd:PRK00566 791 AIIEGGEVIEPLEE---------RILGRV 810
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
209-865 |
1.07e-73 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 264.81 E-value: 1.07e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 209 SRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNEL 288
Cdd:PRK14906 310 NDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGR 389
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 289 PGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYISINEVGVPEEIAktltiamrvtpynLEEA 368
Cdd:PRK14906 390 RG-RPVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMA-------------LELF 455
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 369 RRFVLngpdkwpgalfvyktseRKKYDLRFFKDYKKLAESLEPG-----DIVERhLINGDIVLFNRQPSLHRMSIMGHIV 443
Cdd:PRK14906 456 KPFVM-----------------KRLVELEYAANIKAAKRAVDRGasyvwDVLEE-VIQDHPVLLNRAPTLHRLGIQAFEP 517
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 444 RVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTV---- 519
Cdd:PRK14906 518 VLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTerdg 597
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 520 ---KTRLFTKEEVERLLSVAGYKGDLPEPAILKPRPLWTGKQLASIFlpDDLNFKGKSKTNAGDLACADelCLHDSYivi 596
Cdd:PRK14906 598 fegEGRTFADFDDALNAYDARADLDLQAKIVVRLSRDMTVRGSYGDL--EETKAGERIETTVGRIIFNQ--VLPEDY--- 670
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 597 tngKLLEGVLDKKAIGAeepnnLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDIDLPErakqEIEELIREY 676
Cdd:PRK14906 671 ---PYLNYKMVKKDIGR-----LVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPD----DKPEILAEA 738
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 677 KGRVYSIIEDYRKGTLEpipgrslEESLEIKIMEVLDELRKKVQEVASNNLDPFNDVFVMARTGARGSDVNISQMAAMLG 756
Cdd:PRK14906 739 DEKVAAIDEDYEDGFLS-------ERERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRG 811
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 757 QQA-VRGKRIRRGfrnrvlahfrendtepeawgfVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINAL 835
Cdd:PRK14906 812 LMAdMKGEIIDLP---------------------IKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVA 870
|
650 660 670 680
....*....|....*....|....*....|....*....|...
gi 547222393 836 QDIVV------TYDGTVRDLY-------GNLIQLKYGEDGVDP 865
Cdd:PRK14906 871 QDVIVreedcgTDEGVTYPLVkpkgdvdTNLIGRCLLEDVCDP 913
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
187-841 |
1.06e-64 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 237.98 E-value: 1.06e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 187 EIRERLEKTGSEIE----------ILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKL 256
Cdd:PRK14844 1632 DLRLELESVASEIRrkkiikrlriVENFIKSGNRPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRL 1711
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 257 RNVIVTNAPETLIEENWMVLQEMVAAYIDNelpgARRLTHRRKR----YLKTLAQRLKGKDGRIRGNLSGKRVNYSARTV 332
Cdd:PRK14844 1712 RKLLSLNPPEIMIRNEKRMLQEAVDSLFDN----SRRNALVNKAgavgYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSV 1787
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 333 ISPDPYISINEVGVPEEIAktltiamrvtpynLEEARRFVLNgpdkwpgALFVYKTSERKKYDLRFFKdykklAESLEPG 412
Cdd:PRK14844 1788 IVVGPTLKLNQCGLPKRMA-------------LELFKPFVYS-------KLKMYGMAPTIKFASKLIR-----AEKPEVW 1842
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 413 DIVERhLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEK 492
Cdd:PRK14844 1843 DMLEE-VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTN 1921
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 493 HILTPRYGGPIIGGRQDYVSGAYLLTVKTR-------LFTKEEVERLLSvagyKGDLPEPAILKPRPLWTGKQlasiflp 565
Cdd:PRK14844 1922 NVLSPSNGRPIIVPSKDIVLGIYYLTLQEPkeddlpsFGAFCEVEHSLS----DGTLHIHSSIKYRMEYINSS------- 1990
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 566 DDLNFKgKSKTNAGDLACADELCLHDSYivitNGKLLEGVLDKKAIgaeepNNLLHIIALEYGNSKARQLLDSFYRMFIR 645
Cdd:PRK14844 1991 GETHYK-TICTTPGRLILWQIFPKHENL----GFDLINQVLTVKEI-----TSIVDLVYRNCGQSATVAFSDKLMVLGFE 2060
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 646 MLELRGLTISLHDIDLPE-------RAKQEIEELIREYKGRVYSIIEDYRKgtlepipgrsleesleikimeVLDELRKK 718
Cdd:PRK14844 2061 YATFSGVSFSRCDMVIPEtkathvdHARGEIKKFSMQYQDGLITRSERYNK---------------------VIDEWSKC 2119
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 719 VQEVASNNL---------DPFNDVFVMARTGARGSDVNISQMAAMlgqqavrgkrirRGFRNRVLAHFRENDtepeawgf 789
Cdd:PRK14844 2120 TDMIANDMLkaisiydgnSKYNSVYMMVNSGARGSTSQMKQLAGM------------RGLMTKPSGEIIETP-------- 2179
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|..
gi 547222393 790 VRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVT 841
Cdd:PRK14844 2180 IISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVT 2231
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
209-883 |
5.57e-64 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 235.97 E-value: 5.57e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 209 SRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNEl 288
Cdd:PRK09603 1621 NRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNG- 1699
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 289 PGARRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYISINEVGVPEEIAKTLtiamrVTPY---NL 365
Cdd:PRK09603 1700 RSTNAVKGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALEL-----FKPHllsKL 1774
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 366 EEARrfvlngpdkwpgalfvYKTSerkkydlrfFKDYKKLAESlEPGDIVE--RHLINGDIVLFNRQPSLHRMSIMGHIV 443
Cdd:PRK09603 1775 EERG----------------YATT---------LKQAKRMIEQ-KSNEVWEclQEITEGYPVLLNRAPTLHKQSIQAFHP 1828
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 444 RVMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTVKT-- 521
Cdd:PRK09603 1829 KLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKsg 1908
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 522 -----RLFTK-EEVERLLSVAGYKGDLPEPAILKPRPLWT--GKQLASIFLPDdlnfkgksktnagdlacadelclhdsy 593
Cdd:PRK09603 1909 vkgehKLFSSvNEIITAIDTKELDIHAKIRVLDQGNIIATsaGRMIIKSILPD--------------------------- 1961
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 594 IVITNgkLLEGVLDKKAIGAeepnnLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDIDLPERAKQEIEELI 673
Cdd:PRK09603 1962 FIPTD--LWNRPMKKKDIGV-----LVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAK 2034
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 674 REYKgrvySIIEDYRKGTLEpipgrslEESLEIKIM----EVLDELRKKVQEVASNNLDPFNDVFVMARTGARGSDVNIS 749
Cdd:PRK09603 2035 VEVK----KIQQQYDQGLLT-------DQERYNKIIdtwtEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIR 2103
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 750 QMAAMLGQQAvrgkrirrgfrnrvlahfRENDTEPEAwgFVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQR 829
Cdd:PRK09603 2104 QLSAMRGLMT------------------KPDGSIIET--PIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTR 2163
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*.
gi 547222393 830 RLINALQDIVVTYD--GTVRDLygNLIQLKYGEDGVDPMKtyhgkpvdvKRIVQRV 883
Cdd:PRK09603 2164 KLIDVSQNVKVVSDdcGTHEGI--EITDIAVGSELIEPLE---------ERIFGRV 2208
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
493-659 |
6.74e-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: 181.29 E-value: 6.74e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 493 HILTPRYGGPIIGGRQDYVSGAYLLTVKTRLFTKEEVERLLSvagYKGDLPEPAILKP-RPLWTGKQLASIFLPDDLNFK 571
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLM---YGIVLPHPAILKPiKPLWTGKQTFSRLLPNEINPK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 572 GKSKTnagdlaCADELCLHDSYIVITNGKLLEGVLDKKAIGAeEPNNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRG 651
Cdd:pfam04983 78 GKPKT------NEEDLCENDSYVLINNGELISGVIDKKTVGK-SLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSG 150
|
....*...
gi 547222393 652 LTISLHDI 659
Cdd:pfam04983 151 FSIGIDDI 158
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
209-519 |
7.85e-49 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 183.80 E-value: 7.85e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 209 SRPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNEL 288
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 289 PGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYISINEVGVPEEIAKTLtiamrVTPYNLEE- 367
Cdd:PRK02625 320 RG-RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIEL-----FQPFVIHRl 393
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 368 ARRFVLNGpdkwpgalfvyktserkkydlrfFKDYKKLAESLEPG--DIVERhLINGDIVLFNRQPSLHRMSIMGHIVRV 445
Cdd:PRK02625 394 IRQGIVNN-----------------------IKAAKKLIQRADPEvwQVLEE-VIEGHPVLLNRAPTLHRLGIQAFEPIL 449
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 547222393 446 MPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTV 519
Cdd:PRK02625 450 VEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTA 523
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
210-519 |
1.02e-45 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 175.09 E-value: 1.02e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 210 RPEWMVATVLIVPPLAVRPSITLETGLRSEDDLTHALAEIVRQNEKLRN--VIVTNAPETLIEENWMVLQEMVAAYIDNE 287
Cdd:CHL00018 260 EPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDllTTSRSTPGELVMCQKKLLQEAVDALLDNG 339
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 288 LPGaRRLTHRRKRYLKTLAQRLKGKDGRIRGNLSGKRVNYSARTVISPDPYISINEVGVPEEIAktltiamrvtpynLEE 367
Cdd:CHL00018 340 IRG-QPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIA-------------IEL 405
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 368 ARRFVLNGPDKWPGAlfvyktserkkydlRFFKDYKKLAESLEPgdIVE---RHLINGDIVLFNRQPSLHRMSIMGHIVR 444
Cdd:CHL00018 406 FQPFVIRGLIRQHLA--------------SNIRAAKSKIREKEP--IVWeilQEVMQGHPVLLNRAPTLHRLGIQAFQPI 469
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 547222393 445 VMPGKTFRLNLLVCPPYNADFDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTV 519
Cdd:CHL00018 470 LVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTI 544
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
684-790 |
7.79e-41 |
|
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: 145.20 E-value: 7.79e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 684 IEDYRK-GTLEPIPGRSLEESLEIKIMEVLDELRKKVQEVASNNLDPFNDVFVMARTGARGSDVNISQMAAMLGQQAVRG 762
Cdd:pfam05000 1 ITDAERyGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 547222393 763 KRIRRGFRNRVLAHFRENDTEPEAWGFV 790
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
797-870 |
1.06e-31 |
|
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: 130.55 E-value: 1.06e-31
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 547222393 797 GLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQLKYGEDGVDPMKTYH 870
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEK 74
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
605-847 |
1.85e-14 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 78.11 E-value: 1.85e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 605 VLDKKAIGaeepnNLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDIDLPErAKQEI----EELIREYKGRv 680
Cdd:PRK02597 7 VVDKKALK-----NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPP-AKRDLleqaEEEITATEER- 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 681 ysiiedYRKGtlepipgrsleesleiKIMEVldELRKKV------------QEVASN--NLDPFNDVFVMARTGARGsdv 746
Cdd:PRK02597 80 ------YRRG----------------EITEV--ERFQKVidtwnetnerlkDEVVKNfrQNDPLNSVYMMAFSGARG--- 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 747 NISQMAAMLGqqaVRGkrirrgfrnrVLAhfrenDTEPEAWGF-VRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSG 825
Cdd:PRK02597 133 NMSQVRQLVG---MRG----------LMA-----NPQGEIIDLpIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSG 194
|
250 260
....*....|....*....|....
gi 547222393 826 YMQRRLINALQDIVVTYD--GTVR 847
Cdd:PRK02597 195 YLTRRLVDVSQDVIVREEdcGTTR 218
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
720-840 |
1.02e-13 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 75.75 E-value: 1.02e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 547222393 720 QEVASN--NLDPFNDVFVMARTGARGsdvNISQ---MAAMLGQQA-VRGKRIRRgfrnrvlahfrendtePeawgfVRSS 793
Cdd:CHL00117 113 QEMNPNfrMTDPLNPVYMMSFSGARG---NASQvhqLVGMRGLMSdPQGQIIDL----------------P-----IQSN 168
|
90 100 110 120
....*....|....*....|....*....|....*....|....*..
gi 547222393 794 FRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVV 840
Cdd:CHL00117 169 FREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVV 215
|
|
| |
