|
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 ... |
6-852 |
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: 1583.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 6 SVAGIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHV 85
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 86 GFAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRA-NNLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSF 164
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKEkWPELVKRVIEKVKKKAKKRKVCPHCGAPQYKIKLEKPTTF 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 165 SEMSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILR 244
Cdd:cd02582 163 YEEKEEGEVKLTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIR 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 245 VTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSART 324
Cdd:cd02582 243 INQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSART 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 325 VISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVaNLEELATALEPG 404
Cdd:cd02582 323 VISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRRIRLRYV-NREELAERLEPG 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 405 YVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVEN 484
Cdd:cd02582 402 WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQE 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 485 NIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRGPIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVT 564
Cdd:cd02582 482 HILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEG 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 565 KSSF-------------TNTEVVVKNGQLISGVIDKGSVGVEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGF 631
Cdd:cd02582 562 KAKVcsgcseckdedcpNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGF 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 632 SFAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSS 711
Cdd:cd02582 642 TIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNN 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 712 AFIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRD 791
Cdd:cd02582 722 AVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGRE 801
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1286913233 792 GLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGEDGVDPAKSDHGK 852
Cdd:cd02582 802 GLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDS-RGNIIQFKYGEDGVDPAKSDHGK 861
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
7-866 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 1465.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 7 VAGIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVG 86
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHVG 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 87 FAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRANNLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSFSE 166
Cdd:PRK08566 89 FAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKFEKPTTFYE 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 167 MSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVT 246
Cdd:PRK08566 169 ERKEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRIN 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 247 QRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVI 326
Cdd:PRK08566 249 QRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVI 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 327 SPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLkFVANLEELATALEPGYV 406
Cdd:PRK08566 329 SPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKL-TDKNKEELAEKLEPGWI 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 407 VERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNI 486
Cdd:PRK08566 408 VERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHI 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 487 ISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRG-PIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVTK 565
Cdd:PRK08566 488 LSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDElPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFK 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 566 SSF-------------TNTEVVVKNGQLISGVIDKGSVGVEKaNSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFS 632
Cdd:PRK08566 568 AKIcsgcdeckkedceHDAYVVIKNGKLLEGVIDKKAIGAEQ-GSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFT 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 633 FAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSA 712
Cdd:PRK08566 647 TGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPA 726
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 713 FIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDG 792
Cdd:PRK08566 727 VIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREG 806
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1286913233 793 LVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGEDGVDPAKSDHGKAVTVSNIVNSVLAS 866
Cdd:PRK08566 807 LVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDT-RGNIVQFKYGEDGVDPMKSDHGKPVDVDRIIERVLGK 879
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
7-860 |
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: 1310.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 7 VAGIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVG 86
Cdd:TIGR02390 4 IGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVHVG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 87 FAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRAN-NLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSFS 165
Cdd:TIGR02390 84 FAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEgGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKPTYFY 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 166 EMSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRV 245
Cdd:TIGR02390 164 EEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRI 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 246 TQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTV 325
Cdd:TIGR02390 244 NQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 326 ISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVaNLEELATALEPGY 405
Cdd:TIGR02390 324 ISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDE-NKEELAERLEPGW 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 406 VVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENN 485
Cdd:TIGR02390 403 VVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEH 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 486 IISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRGPIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVTK 565
Cdd:TIGR02390 483 ILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEGR 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 566 SSF-------------TNTEVVVKNGQLISGVIDKGSVGVEKAnSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFS 632
Cdd:TIGR02390 563 AKIcsgsdackkeecpHDAYVVIKNGKLLKGVIDKKAIGAEKG-KILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFT 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 633 FAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSA 712
Cdd:TIGR02390 642 TGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHA 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 713 FIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDG 792
Cdd:TIGR02390 722 VIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREG 801
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1286913233 793 LVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGEDGVDPAKSDHGKAVTVSNIV 860
Cdd:TIGR02390 802 LVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDT-RGNLIQFKYGEDGVDPMKSDHGKPVDVKKIF 868
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
874-1252 |
3.14e-173 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 517.48 E-value: 3.14e-173
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 874 SQEYIEQKLQQASDKLNKKIIEELRAELRKTNPPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTF 953
Cdd:PRK04309 3 SEETLEEKLEDASLELPQKLKEELREKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 954 HFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLD 1033
Cdd:PRK04309 83 HYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDLANMTIIIELD 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1034 AKSLEEHGVTKRDIEKAL-KGVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEYVIRTE 1112
Cdd:PRK04309 163 EEMLEDRGLTVDDVKEAIeKKKGGEVEIEGNTLIISPKEPSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEGDEYVIYTE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1113 GSNLREVMEVPGVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGV 1192
Cdd:PRK04309 243 GSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGV 322
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1193 VKLKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLMSHEK 1252
Cdd:PRK04309 323 SGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
205-507 |
6.19e-164 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 489.34 E-value: 6.19e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 205 EWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEavGV 284
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 285 VPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTL 364
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 365 VRNGSdkyPGARYIIRpdGKRVRLKFvANLEELATALEPGYVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLR 444
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKL-AKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIR 232
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1286913233 445 LNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLY 507
Cdd:smart00663 233 LNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
892-1248 |
4.70e-160 |
|
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: 482.14 E-value: 4.70e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 892 KIIEELRAELRKTNPPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLI 971
Cdd:cd06528 2 LLKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 972 EIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLDAKSLEEHGVTKRDIEKAL 1051
Cdd:cd06528 82 EIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKAI 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1052 ---KGVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEYVIRTEGSNLREVMEVPGVDWR 1128
Cdd:cd06528 162 eklKKGKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEEDEYVIYTEGSNLKAVLKVEGVDPT 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1129 RIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARAAYEIS 1208
Cdd:cd06528 242 RTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVT 321
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 1286913233 1209 VQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLM 1248
Cdd:cd06528 322 VKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTM 361
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
889-1248 |
1.40e-146 |
|
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: 447.19 E-value: 1.40e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 889 LNKKIIEELRAELRKTN-PPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGL 967
Cdd:TIGR02389 2 LPEKLLKELEETVKKREiSDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 968 PRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLDAKSLEEHGVTKRDI 1047
Cdd:TIGR02389 82 PRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDEEQLKERGITVDDV 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1048 EKALK----GVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEYVIRTEGSNLREVMEVP 1123
Cdd:TIGR02389 162 EKAIKkaklGKVIEIDMDNNTITIKPGNPSLKELRKLKEKIKNLHIKGIKGIKRVVIRKEGDEYVIYTEGSNLKEVLKLE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1124 GVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARA 1203
Cdd:TIGR02389 242 GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARA 321
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1286913233 1204 AYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLM 1248
Cdd:TIGR02389 322 AFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
7-313 |
2.44e-101 |
|
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: 324.63 E-value: 2.44e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 7 VAGIRFGILSPDLIRKMSVAEIISPDTYDEDGL-PIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHV 85
Cdd:pfam04997 4 IKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLkPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFHI 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 86 GFAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRANNLpfKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSFS 165
Cdd:pfam04997 84 GFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLENL--KMGAKAILELCKKKDLCEHCGGKNGVCGSQQPVSRK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 166 E-------MSESGSTK----LNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDD 234
Cdd:pfam04997 162 EglklkaaIKKSKEEEekeiLNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDD 241
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1286913233 235 LTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNL 313
Cdd:pfam04997 242 LTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
776-1200 |
1.12e-100 |
|
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: 330.08 E-value: 1.12e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 776 GLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTADeGRIIQFAYGEDGVDPAKSDHGKAVT 855
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSG-GEIVQFLYGEDGLDPLKIEKQGRFT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 856 -----------------VSNIVNSVLASAYSGKPASQEY------IEQKLQQASDKLNKKIIEELRAELRKTNP---PAE 909
Cdd:pfam04998 80 iefsdlkledkfkndllDDLLLLSEFSLSYKKEILVRDSklgrdrLSKEAQERATLLFELLLKSGLESKRVRSEltcNSK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 910 AVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPL 989
Cdd:pfam04998 160 AFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 990 TPEYASNLAKARKLAKQIQHTTLGDLI------------SEVLVNYKRG-------TLEVQLDAKSLEEHGVTKRDIEKA 1050
Cdd:pfam04998 240 FDEVGRELEKAKKVYGAIEKVTLGSVVesgeilydpdpfNTPIISDVKGvvkffdiIDEVTNEEEIDPETGLLILVIRLL 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1051 L---------------KGVGAEYDEEKRVISVKLDEEGLMDIAR--------------------------VRERISSIKV 1089
Cdd:pfam04998 320 KilnksikkvvkseviPRSIRNKVDEGRDIAIGEITAFIIKISKkirqdtgglrrvdelfmeedpklailVASLLGNITL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1090 KGIRRIKKATV-----FKEKDEYVIRTEGSNLREVMEVPG-VDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQG 1163
Cdd:pfam04998 400 RGIPGIKRILVneddkGKVEPDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQG 479
|
490 500 510
....*....|....*....|....*....|....*..
gi 1286913233 1164 LDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVL 1200
Cdd:pfam04998 480 IYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-1125 |
6.58e-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: 295.92 E-value: 6.58e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1 MSTAASVAGIRFGILSPDLIRKMSVAEIISPDTYD-------EDGLPIPTsvmdpRLGTlepgqrCKT----CGN----T 65
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSYGEVKKPETINyrtfkpeRDGLFCER-----IFGP------CKDyecyCGKykrmV 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 66 YLG--CP----------------GHfgrIELPVPVIHVGFAKTIYE----LLKSTCRSCGRIL----------------- 106
Cdd:COG0086 70 YKGvvCEkcgvevtlskvrrermGH---IELAMPVFHIWGLKSLPSriglLLDMSLRDLERVLyfesyvvidpgdtplek 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 107 ---LPEDDCKKYHAELERlrannlPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSfsemsesgstKLNPSTVRAR 183
Cdd:COG0086 147 gqlLTEDEYREILEEYGD------EFVAKMGAEAIKDLLGRIDLEKESEELREELKETTS----------EQKRKKLIKR 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 184 LEripdadlVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLThklvDIL-RVT---QRLRENIRAGSPS 259
Cdd:COG0086 211 LK-------VVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLN----DLYrRVInrnNRLKRLLELKAPD 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 260 PVIEELSDLLQYHVTTYFNNEAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGV 339
Cdd:COG0086 280 IIVRNEKRMLQEAVDALFDNGRRGR-AVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGL 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 340 PLEIAMQLtvaerVTPWnleKMRTLVRNGSDKypgaryIIRPDGKRVRLKfvanLEELATALEpgYVVERHLqdgdiVLF 419
Cdd:COG0086 359 PKKMALEL-----FKPF---IYRKLEERGLAT------TIKSAKKMVERE----EPEVWDILE--EVIKEHP-----VLL 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 420 NRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVI 499
Cdd:COG0086 414 NRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPS 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 500 RDFLTSLYLLTRD------ETKLTKS----ELAMLLAAIKYRGPIPPPAVKDPEPMWT------GKQVFSLLLPKDFNHV 563
Cdd:COG0086 494 QDMVLGLYYLTREregakgEGMIFADpeevLRAYENGAVDLHARIKVRITEDGEQVGKivettvGRYLVNEILPQEVPFY 573
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 564 TKssftntevvvkngqlisgVIDKGSVGVekansILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQ 643
Cdd:COG0086 574 NQ------------------VINKKHIEV-----IIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKE 630
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 644 ihsdIQQIFKKSETEFSKLLAQYQTGeveippGMTAEQAFEAdVLKILSEARDSAGKLIRARVSQNSSAFIMAKTGARGt 723
Cdd:COG0086 631 ----KQEIFEEANKEVKEIEKQYAEG------LITEPERYNK-VIDGWTKASLETESFLMAAFSSQNTTYMMADSGARG- 698
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 724 mlNLDQMIAVVGQqsvrrervhRGyrkrvlsffkqddLSPRARG-----FVYNSFVSGLDPLEFFFHAVGGRDGLVDTAV 798
Cdd:COG0086 699 --SADQLRQLAGM---------RG-------------LMAKPSGniietPIGSNFREGLGVLEYFISTHGARKGLADTAL 754
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 799 RTQQSGYMQRRLINALEALYIDYD--GTVRTADEGRIIQfayGEDGVDPAKSDHGKAVTVSNIVNsvlasaysgkPASQE 876
Cdd:COG0086 755 KTADSGYLTRRLVDVAQDVIVTEEdcGTDRGITVTAIKE---GGEVIEPLKERILGRVAAEDVVD----------PGTGE 821
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 877 YIEQKLQQASDKLNKKIIEELRAELRKTNPPAEAVDKIVeeVVSKYNASLA-----EPGDAVGVVTAQSIGEPGTQLTLR 951
Cdd:COG0086 822 VLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGV--CAKCYGRDLArghlvNIGEAVGVIAAQSIGEPGTQLTMR 899
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 952 TFHFAGVGEQSIlkglprlIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQ 1031
Cdd:COG0086 900 TFHIGGAASRAA-------EESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELVIVDDGGRREEEYKVPYGGVLVVV 972
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1032 LDAKS----LEEHGVTKRDIEKALKGVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEY 1107
Cdd:COG0086 973 GGGVVvgggIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGL 1052
|
1210
....*....|....*...
gi 1286913233 1108 VIRTEGSNLREVMEVPGV 1125
Cdd:COG0086 1053 SLLLGGTDAAAAGVIIGG 1070
|
|
| |
|
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 ... |
6-852 |
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: 1583.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 6 SVAGIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHV 85
Cdd:cd02582 3 RIKGIKFGLLSPEEIRKMSVVEIITPDTYDEDGYPIEGGLMDPRLGVIEPGLRCKTCGNTAGECPGHFGHIELARPVIHV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 86 GFAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRA-NNLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSF 164
Cdd:cd02582 83 GFAKHIYDLLRATCRSCGRILLPEEEIEKYLERIRRLKEkWPELVKRVIEKVKKKAKKRKVCPHCGAPQYKIKLEKPTTF 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 165 SEMSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILR 244
Cdd:cd02582 163 YEEKEEGEVKLTPSEIRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIR 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 245 VTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSART 324
Cdd:cd02582 243 INQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSART 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 325 VISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVaNLEELATALEPG 404
Cdd:cd02582 323 VISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPDGRRIRLRYV-NREELAERLEPG 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 405 YVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVEN 484
Cdd:cd02582 402 WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQE 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 485 NIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRGPIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVT 564
Cdd:cd02582 482 HILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEG 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 565 KSSF-------------TNTEVVVKNGQLISGVIDKGSVGVEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGF 631
Cdd:cd02582 562 KAKVcsgcseckdedcpNDGYVVIKNGKLLEGVIDKKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGF 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 632 SFAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSS 711
Cdd:cd02582 642 TIGIDDEDIPEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNN 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 712 AFIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRD 791
Cdd:cd02582 722 AVIMARTGARGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGRE 801
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1286913233 792 GLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGEDGVDPAKSDHGK 852
Cdd:cd02582 802 GLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDS-RGNIIQFKYGEDGVDPAKSDHGK 861
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
7-866 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 1465.85 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 7 VAGIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVG 86
Cdd:PRK08566 9 IGSIKFGLLSPEEIRKMSVTKIITADTYDDDGYPIDGGLMDPRLGVIDPGLRCKTCGGRAGECPGHFGHIELARPVIHVG 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 87 FAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRANNLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSFSE 166
Cdd:PRK08566 89 FAKLIYKLLRATCRECGRLKLTEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHCGEKQYKIKFEKPTTFYE 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 167 MSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVT 246
Cdd:PRK08566 169 ERKEGLVKLTPSDIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRIN 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 247 QRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVI 326
Cdd:PRK08566 249 QRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVI 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 327 SPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLkFVANLEELATALEPGYV 406
Cdd:PRK08566 329 SPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDGRRIKL-TDKNKEELAEKLEPGWI 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 407 VERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNI 486
Cdd:PRK08566 408 VERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHI 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 487 ISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRG-PIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVTK 565
Cdd:PRK08566 488 LSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGIDElPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFK 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 566 SSF-------------TNTEVVVKNGQLISGVIDKGSVGVEKaNSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFS 632
Cdd:PRK08566 568 AKIcsgcdeckkedceHDAYVVIKNGKLLEGVIDKKAIGAEQ-GSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFT 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 633 FAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSA 712
Cdd:PRK08566 647 TGIDDEDIPEEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPA 726
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 713 FIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDG 792
Cdd:PRK08566 727 VIMARTGARGSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREG 806
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1286913233 793 LVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGEDGVDPAKSDHGKAVTVSNIVNSVLAS 866
Cdd:PRK08566 807 LVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDT-RGNIVQFKYGEDGVDPMKSDHGKPVDVDRIIERVLGK 879
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
9-1252 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 1338.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 9 GIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVGFA 88
Cdd:PRK14977 11 GIIFGLISPADARKIGFAEITAPEAYDEDGLPVQGGLLDGRLGTIEPGQKCLTCGNLAANCPGHFGHIELAEPVIHIAFI 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 89 KTIYELLKSTCRSCGRILLPEDD------CKKYHAELERLRANNLP---FKNLIYKIKQKAMNTQVCPHCGEKQLKLELE 159
Cdd:PRK14977 91 DNIKDLLNSTCHKCAKLKLPQEDlnvfklIEEAHAAARDIPEKRIDdeiIEEVRDQVKVYAKKAKECPHCGAPQHELEFE 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 160 KPTSFSEMSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKL 239
Cdd:PRK14977 171 EPTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHIL 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 240 VDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHR-SGRILKTLAQRLKGKEGRFRLNLSGKRV 318
Cdd:PRK14977 251 VDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKgSGRPLKSLFQRLKGKEGRFRGNLIGKRV 330
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 319 DFSARTVISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVAN----- 393
Cdd:PRK14977 331 DFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAIRKGDGTKIRLDFLEDkgkda 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 394 LEELATALEPGYVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQ 473
Cdd:PRK14977 411 LREAAEQLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDAR 490
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 474 TEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRGPIPPPAVKD-PEPMWTGKQVF 552
Cdd:PRK14977 491 AEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDPLPEPAIKTkDGPAWTGKQLF 570
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 553 SLLLPKDFNHVTKSSFT--------------NTEVVVKNGQLISGVIDKGSVG--VEKANSILHRLARDYGSDVARQFLD 616
Cdd:PRK14977 571 SLFLPKDFNFEGIAKWSagkageakdpsclgDGYVLIKEGELISGVIDDNIIGalVEEPESLIDRIAKDYGEAVAIEFLN 650
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 617 NVVRLANTFIELKGFSFAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQT--------GEVEIPPGMTAEQAFEADVL 688
Cdd:PRK14977 651 KILIIAKKEILHYGFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKItrkitiykGKEELLRGMKEEEALEADIV 730
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 689 KILSEARDSAGKLIRARVSQNSSAFIMAKTGARGTMLNLDQMIAVVGQQSVRRE--------RVHRGYRKRVLSFFKQDD 760
Cdd:PRK14977 731 NELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKTRigfvltggRLHEGYKDRALSHFQEGD 810
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 761 LSPRARGFVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGE 840
Cdd:PRK14977 811 DNPDAHGFVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDP-HGHIIQFKFGE 889
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 841 DGVDPAKSDHGKAVTVSNIVNSVLASAySGKPASQEYIEQKLQQASDKLNKKIIEELRAELRKTNPPAEAVDKIVEEVVS 920
Cdd:PRK14977 890 DGIDPQKLDHGEAFNLERIIEKQKIED-RGKGASKDEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELEAICAEGKE 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 921 KYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKA 1000
Cdd:PRK14977 969 GFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPTMDIYLDDECKEDIEKA 1048
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1001 RKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLDAKSLEEHGVTKR---DIEKAL-KGVGAEYDEEKRVISVKLDEEG--- 1073
Cdd:PRK14977 1049 IEIARNLKELKVRALIADSAIDNANEIKLIKPDKRALENGCIPMErfaEIEAALaKGKKFEMELEDDLIILDLVEAAdrd 1128
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1074 --LMDIARVRERISSIKVKGIRRIKKATV----FKEKDEYVIRTEGSNLREVMEVPGVDWRRIKTNDIYEIAEVFGIEAA 1147
Cdd:PRK14977 1129 kpLATLIAIRNKILDKPVKGVPDIERAWVelveKDGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCFEIAGTLGIEAA 1208
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1148 RNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIG------RHGVVKLKSSVLARAAYEISVQTLLEAAARGEV 1221
Cdd:PRK14977 1209 RNAIFNELASILEDQGLEVDNRYIMLVADIMCSRGTIEAIGlqaagvRHGFAGEKDSPLAKAAFEITTHTIAHAALGGEI 1288
|
1290 1300 1310
....*....|....*....|....*....|.
gi 1286913233 1222 DSLKGNVERILIGREIQVGTGMVTLLMSHEK 1252
Cdd:PRK14977 1289 EKIKGILDALIMGQNIPIGSGKVDLLMDFSG 1319
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
7-860 |
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: 1310.86 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 7 VAGIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVG 86
Cdd:TIGR02390 4 IGSIKFGLLSPEEIRKMSVVEVVTADTYDDDGYPIEGGLMDPRLGVIEPGLRCKTCGGKVGECPGHFGHIELARPVVHVG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 87 FAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRAN-NLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSFS 165
Cdd:TIGR02390 84 FAKEIYKILRATCRKCGRITLTEEEIEQYLEKINKLKEEgGDLASTLIEKIVKEAAKRMKCPHCGEEQKKIKFEKPTYFY 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 166 EMSESGSTKLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRV 245
Cdd:TIGR02390 164 EEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRI 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 246 TQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTV 325
Cdd:TIGR02390 244 NQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTV 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 326 ISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVaNLEELATALEPGY 405
Cdd:TIGR02390 324 ISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRPDGRRIKIRDE-NKEELAERLEPGW 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 406 VVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENN 485
Cdd:TIGR02390 403 VVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARELMLVEEH 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 486 IISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAIKYRGPIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVTK 565
Cdd:TIGR02390 483 ILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKPKEYWTGKQIFSAFLPEDLNFEGR 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 566 SSF-------------TNTEVVVKNGQLISGVIDKGSVGVEKAnSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFS 632
Cdd:TIGR02390 563 AKIcsgsdackkeecpHDAYVVIKNGKLLKGVIDKKAIGAEKG-KILHRIVREYGPEAARRFLDSVTRLFIRFITLRGFT 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 633 FAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSA 712
Cdd:TIGR02390 642 TGIDDIDIPKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHA 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 713 FIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDG 792
Cdd:TIGR02390 722 VIMARTGARGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREG 801
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1286913233 793 LVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTAdEGRIIQFAYGEDGVDPAKSDHGKAVTVSNIV 860
Cdd:TIGR02390 802 LVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDT-RGNLIQFKYGEDGVDPMKSDHGKPVDVKKIF 868
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
9-822 |
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: 967.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 9 GIRFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVGFA 88
Cdd:cd02733 2 RVQFGILSPDEIRAMSVAEIEHPETYENGGGPKLGGLNDPRMGTIDRNSRCQTCGGDMKECPGHFGHIELAKPVFHIGFL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 89 KTIYELLKSTCRscgRILLPEDdckkyhaelerlrannlpfknlIYKIkqkamntqvcphcgekqlklelekptsfsems 168
Cdd:cd02733 82 TKILKILRCVCK---RELSAER----------------------VLEI-------------------------------- 104
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 169 esgstklnpstvrarLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQR 248
Cdd:cd02733 105 ---------------FKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSARSEDDLTHKLADIIKANNQ 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 249 LRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISP 328
Cdd:cd02733 170 LKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITP 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 329 DPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVANLEELatALEPGYVVE 408
Cdd:cd02733 250 DPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERIDLRYLKKASDL--HLQYGYIVE 327
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 409 RHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIIS 488
Cdd:cd02733 328 RHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVS 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 489 PRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAAI-KYRGPIPPPAVKDPEPMWTGKQVFSLLLPKDFNHVTKSS 567
Cdd:cd02733 408 PQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLMWLpDWDGKIPQPAILKPKPLWTGKQIFSLIIPKINNLIRSSS 487
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 568 FTN----------TEVVVKNGQLISGVIDKGSVGvEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDD 637
Cdd:cd02733 488 HHDgdkkwispgdTKVIIENGELLSGILCKKTVG-ASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGD 566
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 638 LYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSAFIMAK 717
Cdd:cd02733 567 TIADKETMKKIQETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVT 646
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 718 TGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDGLVDTA 797
Cdd:cd02733 647 AGSKGSFINISQIIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTA 726
|
810 820
....*....|....*....|....*
gi 1286913233 798 VRTQQSGYMQRRLINALEALYIDYD 822
Cdd:cd02733 727 VKTAETGYIQRRLVKAMEDVMVKYD 751
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
15-826 |
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: 951.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 15 LSPDLIRKMSVAEIISPDTYD-EDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVGFAKTIYE 93
Cdd:cd02583 1 LSPEDIIRLSEVEVTNRNLYDiETRKPLPYGVLDPRLGTSDKDGICETCGLNLADCVGHFGYIKLELPVFHIGYFKAIIN 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 94 LLKSTCRSCGRILLPEDDCKKYHAELERLRANNLPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELekptsfsemsesgst 173
Cdd:cd02583 81 ILQCICKTCSRVLLPEEEKRKFLKRLRRPNLDNLQKKALKKKILEKCKKVRKCPHCGLLKKAQED--------------- 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 174 kLNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRS-EDDLTHKLVDILRVTQRLREN 252
Cdd:cd02583 146 -LNPLKVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEKSGTnEDDLTVKLSEIIFLNDVIKKH 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 253 IRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNI 332
Cdd:cd02583 225 LEKGAKTQKIMEDWDFLQLQCALYINSELPGL-PLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNL 303
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 333 RINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVANLEELATALEPGYVVERHLQ 412
Cdd:cd02583 304 RIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIKRDGGKKKFLKYGNRRKIARELKIGDIVERHLE 383
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 413 DGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYG 492
Cdd:cd02583 384 DGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNG 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 493 APIIGVIRDFLTSLYLLTRDETKLTKSELA-----MLLAAIKYRgpIPPPAVKDPEPMWTGKQVFSLLL-PKDFNHVTKS 566
Cdd:cd02583 464 EPLIAATQDFLTASYLLTSKDVFFDRAQFCqlcsyMLDGEIKID--LPPPAILKPVELWTGKQIFSLLLrPNKKSPVLVN 541
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 567 ------SFTNTE---------VVVKNGQLISGVIDKGSVGVEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGF 631
Cdd:cd02583 542 leakekSYTKKSpdmcpndgyVVIRNSELLCGRLDKSTLGSGSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNRGF 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 632 SFAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSS 711
Cdd:cd02583 622 SIGIDDVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNS 701
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 712 AFIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRD 791
Cdd:cd02583 702 PLIMALCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGRE 781
|
810 820 830
....*....|....*....|....*....|....*
gi 1286913233 792 GLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVR 826
Cdd:cd02583 782 GLVDTAVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
11-822 |
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: 610.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 11 RFGILSPDLIRKMSVAEIISPDTYDEDGLPIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVGFAKT 90
Cdd:cd01435 1 SFSFYSAEEIRKLSVKEITNPVTFDSLGHPVPGGLYDPALGPLDKDDICSTCGLNYLNCPGHFGHIELPLPVYNPLFFDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 91 IYELLKSTCRSCGRILLPEDDCKKYHAELERLRannlpfknliykikqkamntqvcphCGEKQLKLELEKPtsfsemses 170
Cdd:cd01435 81 LYKLLRGSCFYCHRFRISKWEVKLFVAKLKLLD-------------------------KGLLVEAAELDFG--------- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 171 gstklnpstvrarleripdadlvlldinpqtsrPEWMVLTVLPVPPVYVRPSITLeSGYRSEDDLTHKLVDILRVTQRLR 250
Cdd:cd01435 127 ---------------------------------YDMFFLDVLLVPPNRFRPPSFL-GDKVFENPQNVLLSKILKDNQQIR 172
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 251 ENIRAG------------SPSPVIEELSDL---LQYHVTTYFNNEAVGVVPAKHRSGriLKtlaQRLKGKEGRFRLNLSG 315
Cdd:cd01435 173 DLLASMrqaesqskldliSGKTNSEKLINAwlqLQSAVNELFDSTKAPKSGKKSPPG--IK---QLLEKKEGLFRMNMMG 247
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 316 KRVDFSARTVISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKF----- 390
Cdd:cd01435 248 KRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGPDVYPGANAIEDEDGRLILLSAlseer 327
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 391 ---VANLEELATALE----PGYVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLP-YKTLRLNPAVCTPYNADFDGDEM 462
Cdd:cd01435 328 rkaLAKLLLLLSSAKlllnGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLPgEKTLRLHYANCKSYNADFDGDEM 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 463 NLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLAA---------IKYRGP 533
Cdd:cd01435 408 NLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTREEYQQLVYAalrplftsdKDGRIK 487
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 534 IPPPAVKDPEPMWTGKQVFSLLL-------PKDFNHVTKSSFTN-------------TEVVVKNGQLISGVIDKGSVGvE 593
Cdd:cd01435 488 LLPPAILKPKPLWTGKQVISTILknlipgnAPLLNLSGKKKTKKkvgggkwgggseeSQVIIRNGELLTGVLDKSQFG-A 566
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 594 KANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQIHSDIQQIFKKSETEFSKLLAQYqtgevei 673
Cdd:cd01435 567 SAYGLVHAVYELYGGETAGKLLSALGRLFTAYLQMRGFTCGIEDLLLTPKADEKRRKILRKAKKLGLEAAAEF------- 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 674 ppgmtaeqaFEADVLKILSEARDSA--GKLIRARVSQNSSAfiMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGYRKR 751
Cdd:cd01435 640 ---------LGLKLNKVTSSIIKAClpKGLLKPFPENNLQL--MVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGK 708
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1286913233 752 VLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYIDYD 822
Cdd:cd01435 709 TLPSFPPYDTSPRAGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
15-822 |
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: 573.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 15 LSPDLIRKMSVAEIISPDTYDEDGLPIPTS-VMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHVGFAKTIYE 93
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGgKYDPRLGSIDRCEKCGTCGTGLNDCPGHFGHIELAKPVFHVGFIKKVPS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 94 LLKstcrscgrillpeddckkyhaelerlrannlpfknliykikqkamntqvcphcgekqlklelekptsfsemsesgst 173
Cdd:cd00399 81 FLG----------------------------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 174 klnpstvrarleripdadlvlldinpqtsrPEWMVLTVLPVPPVYVRPSItlesgyrseddlthklvdilrvtqrlreni 253
Cdd:cd00399 84 ------------------------------PEWMILTCLPVPPPCLRPSV------------------------------ 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 254 ragspspVIEELSDLLQYHVTTYFNNEAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIR 333
Cdd:cd00399 104 -------IIEERWRLLQEHVDTYLDNGIAGQ-PQTQKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLR 175
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 334 INEVGVPLEIAMQLtvaervtpwnlekmrtlvrngsdkypgaryiirpdgkrvrlkfvanleelatalepgyvverhlqD 413
Cdd:cd00399 176 LDQVGVPKSIALTL-----------------------------------------------------------------D 190
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 414 GDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGA 493
Cdd:cd00399 191 GDPVLFNRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGE 270
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 494 PIIGVIRDFLTSLYLLTRdetkltkselamllaaikyrgpipppavkdpepmwtGKQVFSLLLPkdfnhvtkssftntev 573
Cdd:cd00399 271 PLIGLSQDTLLGAYLLTL------------------------------------GKQIVSAALP---------------- 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 574 vvkngqlisgvidkgsvgvekaNSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQIHSDIQQIFK 653
Cdd:cd00399 299 ----------------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIDDGVIPEEKTELIE 356
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 654 KSETEFSKLLAQYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRA---RVSQNSSAFIMAKTGARGTMLNLDQM 730
Cdd:cd00399 357 EAKKKVDEVEEAFQAGLLTAQEGMTLEESLEDNILDFLNEARDKAGSAASVnldLVSKFNSIYVMAMSGAKGSFINIRQM 436
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 731 IAVVGQQSVRRERVHRGYRKRVLSFFKQDDLSPRARGFVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRL 810
Cdd:cd00399 437 SACVGQQSVEGKRIPRGFSDRTLPHFSKDDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRL 516
|
810
....*....|..
gi 1286913233 811 INALEALYIDYD 822
Cdd:cd00399 517 VKALEDLVVHYD 528
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
874-1252 |
3.14e-173 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 517.48 E-value: 3.14e-173
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 874 SQEYIEQKLQQASDKLNKKIIEELRAELRKTNPPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTF 953
Cdd:PRK04309 3 SEETLEEKLEDASLELPQKLKEELREKLEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTF 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 954 HFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLD 1033
Cdd:PRK04309 83 HYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIYLKDEYAYDREKAEEVARKIEATTLENLAKDISVDLANMTIIIELD 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1034 AKSLEEHGVTKRDIEKAL-KGVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEYVIRTE 1112
Cdd:PRK04309 163 EEMLEDRGLTVDDVKEAIeKKKGGEVEIEGNTLIISPKEPSYRELRKLAEKIRNIKIKGIKGIKRVIIRKEGDEYVIYTE 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1113 GSNLREVMEVPGVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGV 1192
Cdd:PRK04309 243 GSNLKEVLKVEGVDATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGRHGV 322
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1193 VKLKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLMSHEK 1252
Cdd:PRK04309 323 SGEKASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVELTMDPPL 382
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
205-507 |
6.19e-164 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 489.34 E-value: 6.19e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 205 EWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEavGV 284
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GL 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 285 VPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTL 364
Cdd:smart00663 79 PRANQKSGRPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 365 VRNGSdkyPGARYIIRpdGKRVRLKFvANLEELATALEPGYVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLR 444
Cdd:smart00663 159 VRNGP---NGAKYIIR--GKKTNLKL-AKKSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIR 232
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1286913233 445 LNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLY 507
Cdd:smart00663 233 LNPLVCSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
892-1248 |
4.70e-160 |
|
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: 482.14 E-value: 4.70e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 892 KIIEELRAELRKTNPPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLI 971
Cdd:cd06528 2 LLKEKLEEVLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLI 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 972 EIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLDAKSLEEHGVTKRDIEKAL 1051
Cdd:cd06528 82 EIVDARKEPSTPTMTIYLEEEYKYDREKAEEVARKIEETTLENLAEDISIDLFNMRITIELDEEMLEDRGITVDDVLKAI 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1052 ---KGVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEYVIRTEGSNLREVMEVPGVDWR 1128
Cdd:cd06528 162 eklKKGKVGEEGDVTLIVLKAEEPSIKELRKLAEKILNTKIKGIKGIKRVIVRKEEDEYVIYTEGSNLKAVLKVEGVDPT 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1129 RIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARAAYEIS 1208
Cdd:cd06528 242 RTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIGRHGIAGEKPSVLARAAFEVT 321
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 1286913233 1209 VQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLM 1248
Cdd:cd06528 322 VKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDVELTM 361
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
889-1248 |
1.40e-146 |
|
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: 447.19 E-value: 1.40e-146
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 889 LNKKIIEELRAELRKTN-PPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGL 967
Cdd:TIGR02389 2 LPEKLLKELEETVKKREiSDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 968 PRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLDAKSLEEHGVTKRDI 1047
Cdd:TIGR02389 82 PRLIEIVDARKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVAKDISIDLADMTVIIELDEEQLKERGITVDDV 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1048 EKALK----GVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEYVIRTEGSNLREVMEVP 1123
Cdd:TIGR02389 162 EKAIKkaklGKVIEIDMDNNTITIKPGNPSLKELRKLKEKIKNLHIKGIKGIKRVVIRKEGDEYVIYTEGSNLKEVLKLE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1124 GVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARA 1203
Cdd:TIGR02389 242 GVDKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIGRHGISGEKASVLARA 321
|
330 340 350 360
....*....|....*....|....*....|....*....|....*
gi 1286913233 1204 AYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLM 1248
Cdd:TIGR02389 322 AFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDVDLVM 366
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
888-1252 |
8.14e-117 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 373.76 E-value: 8.14e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 888 KLNKKIIEELRAELRKTNPPAEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGL 967
Cdd:PRK14897 140 RLPPSVIEEIAKAMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGL 219
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 968 PRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDlISEVLVNYKRGTLEVQLDAKSLEEHGVTKRDI 1047
Cdd:PRK14897 220 PRLIEIVDARKKPSTPTMTIYLKKDYREDEEKVREVAKKIENTTLID-VADIITDIAEMSVVVELDEEKMKERLIEYDDI 298
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1048 EKALKGVGAEYDEEKRV-ISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDE--YVIRTEGSNLREVMEVPG 1124
Cdd:PRK14897 299 LAAISKLTFKTVEIDDGiIRLKPQQPSFKKLYLLAEKVKSLTIKGIKGIKRAIARKENDErrWVIYTQGSNLKDVLEIDE 378
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1125 VDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARAA 1204
Cdd:PRK14897 379 VDPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHGISGEKSSVLARAA 458
|
330 340 350 360
....*....|....*....|....*....|....*....|....*...
gi 1286913233 1205 YEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLMSHEK 1252
Cdd:PRK14897 459 FEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLVYKGRK 506
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
19-826 |
5.92e-109 |
|
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: 360.18 E-value: 5.92e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 19 LIRKMSVAEIISPdtydedglpipTSVMDPRLGTLEPGQRCKTCGNTYLG-CPGHFGRIELPVPVIHVGFAKTIYELLKS 97
Cdd:cd10506 5 DIEKISVSEIKAP-----------NQVTNPRLGLPNESGQCTTCGAKDNKkCEGHFGVIKLPVTIYHPYFISEVAQILNK 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 98 TCRSCGRIllpeddcKKyhaELERLRANNLP--FKNLIYKIKQkamntqvcPHcgekqlklelekptsfsemsESGSTKL 175
Cdd:cd10506 74 ICPGCKSI-------KQ---KKKKPPRETLPpdYWDFIPKDGQ--------QE--------------------ESCVTKN 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 176 NPSTVRARLERIP-DADLVLldINPQTSRPEWMVLTVLPVPPVYVRpsiTLESGYRSEDdlthklvdilrvtqrlrenir 254
Cdd:cd10506 116 LPILSLAQVKKILkEIDPKL--IAKGLPRQEGLFLKCLPVPPNCHR---VTEFTHGFST--------------------- 169
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 255 aGSPSPVIEELSDLLQYHVTTYFNNEAvgvvPAKHRSG-RILKTLaqrlkgkegrfrlnLSGKRVDFSARTVISPDPNIR 333
Cdd:cd10506 170 -GSRLIFDERTRAYKKLVDFIGTANES----AASKKSGlKWMKDL--------------LLGKRSGHSFRSVVVGDPYLE 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 334 INEVGVPLEIAMQLTVAERVTPWNLEKMRTLVrngsDKYPGARYII--RPDGKRVRLKFVanleelaTALEPGYVVERHL 411
Cdd:cd10506 231 LNEIGIPCEIAERLTVSERVSSWNRERLQEYC----DLTLLLKGVIgvRRNGRLVGVRSH-------NTLQIGDVIHRPL 299
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 412 QDGDIVLFNRQPSLHRMSIMAHYVRVLPYK-TLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPR 490
Cdd:cd10506 300 VDGDVVLVNRPPSIHQHSLIALSVKVLPTNsVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQ 379
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 491 YGAPIIGVIRDFLTSLYLLTRDETKLTKSE---LAMLLAAIkyrgPIPPPAVKDP---EPMWTGKQVFSLLLPKDFNhvt 564
Cdd:cd10506 380 SGQNLLSLTQDSLLAAHLMTERGVFLDKAQmqqLQMLCPSQ----LPPPAIIKSPpsnGPLWTGKQLFQMLLPTDLD--- 452
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 565 kSSFTNTEVVVKNGQLISGViDKGSVGVEKaNSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVP--- 641
Cdd:cd10506 453 -YSFPSNLVFISDGELISSS-GGSSWLRDS-EGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSsds 529
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 642 -------DQIHSDIQQifkKSETEFSKLLA-------QYQTGEVEIPPGMTAEQAFEADVLKILSEARDSAGK------- 700
Cdd:cd10506 530 ysrqkmiEEISLGLRE---AEIACNIKQLLvdsrkdfLSGSGEENDVSSDVERVIYERQKSAALSQASVSAFKqvfrdiq 606
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 701 -LIRARVSQNSSAFIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRgyRKRVLS---FFKQDDL------------SPR 764
Cdd:cd10506 607 nLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVKLSYR--IPRQLScaaWNSQKSPrviekdgsecteSYI 684
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1286913233 765 ARGFVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTqqSGYMQRRLINALEALYIDYDGTVR 826
Cdd:cd10506 685 PYGVVESSFLDGLNPLECFVHSITSRDSSFSSNADL--PGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
10-1243 |
7.17e-104 |
|
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: 355.90 E-value: 7.17e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 10 IRFGILSPDLIRKMSVAEIISPDTYDEDGL-PIPTSVMDPRL-GTLE--------------PGQRCKTCGNTYLgcpgHF 73
Cdd:TIGR02386 2 IKISIASPDTIRNWSYGEVKKPETINYRTLkPEKDGLFCEKIfGPTKdwecycgkykkiryKGVVCERCGVEVT----ES 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 74 -------GRIELPVPVIHVGFAKT----IYELLKSTCRSCGRILLPED-----------------DCKKYHAELER---- 121
Cdd:TIGR02386 78 kvrrermGHIELAAPVAHIWYFKGlpsrIGLLLDITAKELESVLYFENyvvldpgdtkldkkevlDETEYREVLKRygdg 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 122 LRA-----------NNLPFKNLIYKIKQKAMNTQvcphcgekqlklelekptsfsemSESGSTKLnpstVRaRLEripda 190
Cdd:TIGR02386 158 FRAgmgaeaikellEKIDLDKEIEELKIQLRESK-----------------------SDQKRKKL----LK-RLE----- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 191 dlVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQ 270
Cdd:TIGR02386 205 --IVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQ 282
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 271 YHVTTYFNNEAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtva 350
Cdd:TIGR02386 283 EAVDALFDNGRRGK-PVVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALEL--- 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 351 erVTPWnleKMRTLVRNGsdkypgaryiIRPDGKRVRLKFVANLEELATALEpgYVVERHlqdgdIVLFNRQPSLHRMSI 430
Cdd:TIGR02386 359 --FKPF---IIKRLIDRE----------LAANIKSAKKMIEQEDPEVWDVLE--DVIKEH-----PVLLNRAPTLHRLGI 416
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 431 MAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLT 510
Cdd:TIGR02386 417 QAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLT 496
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 511 RD------ETKLTKSELAMLLA----AIKYRGPIpppAVK-DPEPMWT--GKQVFSLLLPKDFNHVTKssftnTEVVVKn 577
Cdd:TIGR02386 497 TEkpgakgEGKIFSNVDEAIRAydngKVHLHALI---GVRtSGEILETtvGRVIFNEILPEGFPYIND-----NEPLSK- 567
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 578 gQLISGVIDkgsvgvekansilhRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQihsdIQQIFKKSET 657
Cdd:TIGR02386 568 -KEISSLID--------------LLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDE----KYEILKEADK 628
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 658 EFSKLLAQYQTGEVeippgmTAEQAFEAdVLKILSEARDSAGKLIRARVSQNS----SAFIMAKTGARGTMLNLDQMIAV 733
Cdd:TIGR02386 629 EVAKIQKFYNKGLI------TDEERYRK-VVSIWSETKDKVTDAMMKLLKKDTykfnPIFMMADSGARGNISQFRQLAGM 701
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 734 vgqqsvrrervhRGyrkrvLSFFKQDDLSPRArgfVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINA 813
Cdd:TIGR02386 702 ------------RG-----LMAKPSGDIIELP---IKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDV 761
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 814 LEALYIDYD--GTVRTADEGRIIQfayGEDGVDPAKSDhgkavtvsNIVNSVLAsaysgKPASQEYIEQKLQQASDKLNK 891
Cdd:TIGR02386 762 AQDVVVREEdcGTEEGIEVEAIVE---GKDEIIESLKD--------RIVGRYSA-----EDVYDPDTGKLIAEANTLITE 825
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 892 KIIEELRaelrktnppAEAVDKIVEEVV----SKY------------NASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHF 955
Cdd:TIGR02386 826 EIAEKIE---------NSGIEKVKVRSVltceSEHgvcqkcygrdlaTGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHT 896
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 956 AGVGEQS--ILKGLPRLIEIVDARrtpttpimyiplTPEYASNLAKArklakqiqhttlgDLISEVLVNYKRGTLEVQLD 1033
Cdd:TIGR02386 897 GGVAGASgdITQGLPRVKELFEAR------------TPKDKAVIAEV-------------DGTVEIIEDIVKNKRVVVIK 951
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1034 AKSLEEHGVTkrdiekalkgvgAEYDEEKRVI---SVKLDE---EGLMDIARVrerissIKVKGIRRIKkatvfkekdEY 1107
Cdd:TIGR02386 952 DENDEEKKYT------------IPFGAQLRVKdgdSVSAGDkltEGSIDPHDL------LRIKGIQAVQ---------EY 1004
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1108 VIRtegsNLREVMEVPGVD-------------WRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLl 1174
Cdd:TIGR02386 1005 LVK----EVQKVYRLQGVEindkhievivrqmLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQLL- 1079
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1286913233 1175 admmtvsgsvkqigrhGVVK--LKS-SVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGM 1243
Cdd:TIGR02386 1080 ----------------GITKasLNTeSFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGL 1135
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
7-313 |
2.44e-101 |
|
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: 324.63 E-value: 2.44e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 7 VAGIRFGILSPDLIRKMSVAEIISPDTYDEDGL-PIPTSVMDPRLGTLEPGQRCKTCGNTYLGCPGHFGRIELPVPVIHV 85
Cdd:pfam04997 4 IKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLkPEEGGLLDERMGTIDKDYECETCGKKKKDCPGHFGHIELAKPVFHI 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 86 GFAKTIYELLKSTCRSCGRILLPEDDCKKYHAELERLRANNLpfKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSFS 165
Cdd:pfam04997 84 GFFKKTLKILECVCKYCSKLLLDPGKPKLFNKDKKRLGLENL--KMGAKAILELCKKKDLCEHCGGKNGVCGSQQPVSRK 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 166 E-------MSESGSTK----LNPSTVRARLERIPDADLVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDD 234
Cdd:pfam04997 162 EglklkaaIKKSKEEEekeiLNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDD 241
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1286913233 235 LTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAVGVVPAKHRSGRILKTLAQRLKGKEGRFRLNL 313
Cdd:pfam04997 242 LTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
776-1200 |
1.12e-100 |
|
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: 330.08 E-value: 1.12e-100
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 776 GLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYIDYDGTVRTADeGRIIQFAYGEDGVDPAKSDHGKAVT 855
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSG-GEIVQFLYGEDGLDPLKIEKQGRFT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 856 -----------------VSNIVNSVLASAYSGKPASQEY------IEQKLQQASDKLNKKIIEELRAELRKTNP---PAE 909
Cdd:pfam04998 80 iefsdlkledkfkndllDDLLLLSEFSLSYKKEILVRDSklgrdrLSKEAQERATLLFELLLKSGLESKRVRSEltcNSK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 910 AVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPL 989
Cdd:pfam04998 160 AFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVSKNIKSPSLTVYL 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 990 TPEYASNLAKARKLAKQIQHTTLGDLI------------SEVLVNYKRG-------TLEVQLDAKSLEEHGVTKRDIEKA 1050
Cdd:pfam04998 240 FDEVGRELEKAKKVYGAIEKVTLGSVVesgeilydpdpfNTPIISDVKGvvkffdiIDEVTNEEEIDPETGLLILVIRLL 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1051 L---------------KGVGAEYDEEKRVISVKLDEEGLMDIAR--------------------------VRERISSIKV 1089
Cdd:pfam04998 320 KilnksikkvvkseviPRSIRNKVDEGRDIAIGEITAFIIKISKkirqdtgglrrvdelfmeedpklailVASLLGNITL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1090 KGIRRIKKATV-----FKEKDEYVIRTEGSNLREVMEVPG-VDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQG 1163
Cdd:pfam04998 400 RGIPGIKRILVneddkGKVEPDWVLETEGVNLLRVLLVPGfVDAGRILSNDIHEILEILGIEAARNALLNEIRNVYRFQG 479
|
490 500 510
....*....|....*....|....*....|....*..
gi 1286913233 1164 LDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVL 1200
Cdd:pfam04998 480 IYINDRHLELIADQMTRKGYIMAIGRHGINKAELSAL 516
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
946-1254 |
1.28e-96 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 329.16 E-value: 1.28e-96
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 946 TQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKR 1025
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAKKIESLTLGDVATSIAIDLWT 620
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1026 GTLEVQLDAKSLEEHGVTKRDIEKALKG-VGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKE- 1103
Cdd:PRK14898 621 QSIKVELDEETLADRGLTIESVEEAIEKkLGVKIDRKGTVLYLKPKTPSYKALRKRIPKIKNIVLKGIPGIERVLVKKEe 700
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1104 ---KDEYVIRTEGSNLREVMEVPGVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTV 1180
Cdd:PRK14898 701 henDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTA 780
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1286913233 1181 SGSVKQIGRHGVVKLKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMVTLLMSHEKGE 1254
Cdd:PRK14898 781 DGEVKPIGRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDLRIDREYEE 854
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
315-482 |
4.92e-93 |
|
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: 295.75 E-value: 4.92e-93
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 315 GKRVDFSARTVISPDPNIRINEVGVPLEIAMQLTVAERVTPWNLEKMRTLVRNGSDKYPGARYIIRPDGKRVRLKFVAnl 394
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQK-- 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 395 EELATALEPGYVVERHLQDGDIVLFNRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQT 474
Cdd:pfam00623 79 RRLDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARA 158
|
....*...
gi 1286913233 475 EARELLVV 482
Cdd:pfam00623 159 EAEELMLV 166
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
921-1244 |
1.07e-84 |
|
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: 277.95 E-value: 1.07e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 921 KYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIPLTPEYasNLAKA 1000
Cdd:cd02736 1 KYMRAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTPIITAKLENDR--DEKSA 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1001 RKLAKQIQHTTLGDLISEVLVNYKRGT--LEVQLDAKSLEEHGVTKRDIekalkgvgaeydeekrvisvkldeegLMDIA 1078
Cdd:cd02736 79 RIVKGRIEKTYLGEVASYIEEVYSPDDcyILIKLDKKIIEKLQLSKSNL--------------------------YFLLQ 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1079 RVRERISSIKVKGIRRIKKATVFKEKDE--YVIRTEGSNLREVMEVPGVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAK 1156
Cdd:cd02736 133 SLKRKLPDVVVSGIPEVKRAVINKDKKKgkYKLLVEGYGLRAVMNTPGVIGTRTTSNHIMEVEKVLGIEAARSTIINEIQ 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1157 AVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGRE 1236
Cdd:cd02736 213 YTMKSHGMSIDPRHIMLLADLMTFKGEVLGITRFGIAKMKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKP 292
|
....*...
gi 1286913233 1237 IQVGTGMV 1244
Cdd:cd02736 293 MPIGTGLF 300
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
909-1247 |
8.67e-84 |
|
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: 279.86 E-value: 8.67e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 909 EAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARRTPTTPIMYIP 988
Cdd:cd02584 6 EAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTPSLTVY 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 989 LTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRG--------------------------------TLEVQLDAKS 1036
Cdd:cd02584 86 LEPGFAKDEEKAKKIQSRLEHTTLKDVTAATEIYYDPDpqntvieedkefvesyfefpdedveqdrlspwLLRIELDRKK 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1037 LEEHGVTKRDIEKALKG--------VGAEYDEEK-----RVISVKLDEEGLMDIARVRERI-----SSIKVKGIRRIKKA 1098
Cdd:cd02584 166 MTDKKLSMEQIAKKIKEefkddlnvIFSDDNAEKlviriRIINDDEEKEEDSEDDVFLKKIesnmlSDMTLKGIEGIRKV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1099 TV--------------FKEKDEYVIRTEGSNLREVMEVPGVDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGL 1164
Cdd:cd02584 246 FIreenkkkvdietgeFKKREEWVLETDGVNLREVLSHPGVDPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGS 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1165 DVDIRHLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGMV 1244
Cdd:cd02584 326 YVNYRHLALLCDVMTQRGHLMAITRHGINRQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGCF 405
|
...
gi 1286913233 1245 TLL 1247
Cdd:cd02584 406 DLL 408
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
203-978 |
1.70e-83 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 297.36 E-value: 1.70e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 203 RPEWMVLTVLPVPPVYVRPSITLESG----------YRseddlthklvdilRV---TQRLRENIRAGSPSPVIEELSDLL 269
Cdd:PRK00566 223 KPEWMILDVLPVIPPDLRPLVQLDGGrfatsdlndlYR-------------RVinrNNRLKRLLELGAPEIIVRNEKRML 289
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 270 QYHVTTYFNNEAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtv 349
Cdd:PRK00566 290 QEAVDALFDNGRRGR-PVTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALEL-- 366
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 350 aerVTPWnleKMRTLVRNG------SdkypgARYII---RPDGKRVrlkfvanLEElatalepgyVVERHLqdgdiVLFN 420
Cdd:PRK00566 367 ---FKPF---IMKKLVERGlattikS-----AKKMVereDPEVWDV-------LEE---------VIKEHP-----VLLN 414
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 421 RQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIR 500
Cdd:PRK00566 415 RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPANGKPIIVPSQ 494
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 501 DFLTSLYLLTRD------ETKLTKS----ELAM------LLAAIKYRgpipppaVKDPEPMWT--GKQVFSLLLPKDFnh 562
Cdd:PRK00566 495 DMVLGLYYLTREregakgEGMVFSSpeeaLRAYengevdLHARIKVR-------ITSKKLVETtvGRVIFNEILPEGL-- 565
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 563 vtksSFTNTEVVVKNGQlISGVIDkgsvgvekansilhRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPD 642
Cdd:PRK00566 566 ----PFINVNKPLKKKE-ISKIIN--------------EVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPP 626
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 643 QihsdIQQIFKKSETEFSKLLAQYQTGEVeippgmTAEQAFEAdVLKILSEARDSAGKLIRARVSQNS----SAFIMAKT 718
Cdd:PRK00566 627 E----KKEIIEEAEKEVAEIEKQYRRGLI------TDGERYNK-VIDIWSKATDEVAKAMMKNLSKDQesfnPIYMMADS 695
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 719 GARGTMLNLDQMIAVvgqqsvrrervhrgyrkrvlsffkqddlspraRGFVYN------------SFVSGLDPLEFFFHA 786
Cdd:PRK00566 696 GARGSASQIRQLAGM--------------------------------RGLMAKpsgeiietpiksNFREGLTVLEYFIST 743
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 787 VGGRDGLVDTAVRTQQSGYMQRRLI----------------NALEALYIDYDGTVRTADEGRIiqfaYG----EDGVDPa 846
Cdd:PRK00566 744 HGARKGLADTALKTADSGYLTRRLVdvaqdvivreddcgtdRGIEVTAIIEGGEVIEPLEERI----LGrvlaEDVVDP- 818
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 847 ksdhgkavtvsnIVNSVLASAysgkpasqeyieqklqqasdklNKKIIEELraelrktnppAEAVDKI-VEEVV------ 919
Cdd:PRK00566 819 ------------ETGEVIVPA----------------------GTLIDEEI----------ADKIEEAgIEEVKirsvlt 854
|
810 820 830 840 850 860 870
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1286913233 920 --SKY------------NASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVgeqSILKGLPRLIEIVDARR 978
Cdd:PRK00566 855 ceTRHgvcakcygrdlaTGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFEARK 924
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-1125 |
6.58e-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: 295.92 E-value: 6.58e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1 MSTAASVAGIRFGILSPDLIRKMSVAEIISPDTYD-------EDGLPIPTsvmdpRLGTlepgqrCKT----CGN----T 65
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSYGEVKKPETINyrtfkpeRDGLFCER-----IFGP------CKDyecyCGKykrmV 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 66 YLG--CP----------------GHfgrIELPVPVIHVGFAKTIYE----LLKSTCRSCGRIL----------------- 106
Cdd:COG0086 70 YKGvvCEkcgvevtlskvrrermGH---IELAMPVFHIWGLKSLPSriglLLDMSLRDLERVLyfesyvvidpgdtplek 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 107 ---LPEDDCKKYHAELERlrannlPFKNLIYKIKQKAMNTQVCPHCGEKQLKLELEKPTSfsemsesgstKLNPSTVRAR 183
Cdd:COG0086 147 gqlLTEDEYREILEEYGD------EFVAKMGAEAIKDLLGRIDLEKESEELREELKETTS----------EQKRKKLIKR 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 184 LEripdadlVLLDINPQTSRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLThklvDIL-RVT---QRLRENIRAGSPS 259
Cdd:COG0086 211 LK-------VVEAFRESGNRPEWMILDVLPVIPPDLRPLVPLDGGRFATSDLN----DLYrRVInrnNRLKRLLELKAPD 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 260 PVIEELSDLLQYHVTTYFNNEAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGV 339
Cdd:COG0086 280 IIVRNEKRMLQEAVDALFDNGRRGR-AVTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGL 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 340 PLEIAMQLtvaerVTPWnleKMRTLVRNGSDKypgaryIIRPDGKRVRLKfvanLEELATALEpgYVVERHLqdgdiVLF 419
Cdd:COG0086 359 PKKMALEL-----FKPF---IYRKLEERGLAT------TIKSAKKMVERE----EPEVWDILE--EVIKEHP-----VLL 413
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 420 NRQPSLHRMSIMAHYVRVLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVI 499
Cdd:COG0086 414 NRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPS 493
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 500 RDFLTSLYLLTRD------ETKLTKS----ELAMLLAAIKYRGPIPPPAVKDPEPMWT------GKQVFSLLLPKDFNHV 563
Cdd:COG0086 494 QDMVLGLYYLTREregakgEGMIFADpeevLRAYENGAVDLHARIKVRITEDGEQVGKivettvGRYLVNEILPQEVPFY 573
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 564 TKssftntevvvkngqlisgVIDKGSVGVekansILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQ 643
Cdd:COG0086 574 NQ------------------VINKKHIEV-----IIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKE 630
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 644 ihsdIQQIFKKSETEFSKLLAQYQTGeveippGMTAEQAFEAdVLKILSEARDSAGKLIRARVSQNSSAFIMAKTGARGt 723
Cdd:COG0086 631 ----KQEIFEEANKEVKEIEKQYAEG------LITEPERYNK-VIDGWTKASLETESFLMAAFSSQNTTYMMADSGARG- 698
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 724 mlNLDQMIAVVGQqsvrrervhRGyrkrvlsffkqddLSPRARG-----FVYNSFVSGLDPLEFFFHAVGGRDGLVDTAV 798
Cdd:COG0086 699 --SADQLRQLAGM---------RG-------------LMAKPSGniietPIGSNFREGLGVLEYFISTHGARKGLADTAL 754
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 799 RTQQSGYMQRRLINALEALYIDYD--GTVRTADEGRIIQfayGEDGVDPAKSDHGKAVTVSNIVNsvlasaysgkPASQE 876
Cdd:COG0086 755 KTADSGYLTRRLVDVAQDVIVTEEdcGTDRGITVTAIKE---GGEVIEPLKERILGRVAAEDVVD----------PGTGE 821
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 877 YIEQKLQQASDKLNKKIIEELRAELRKTNPPAEAVDKIVeeVVSKYNASLA-----EPGDAVGVVTAQSIGEPGTQLTLR 951
Cdd:COG0086 822 VLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGV--CAKCYGRDLArghlvNIGEAVGVIAAQSIGEPGTQLTMR 899
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 952 TFHFAGVGEQSIlkglprlIEIVDARRTPTTPIMYIPLTPEYASNLAKARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQ 1031
Cdd:COG0086 900 TFHIGGAASRAA-------EESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNSELVIVDDGGRREEEYKVPYGGVLVVV 972
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1032 LDAKS----LEEHGVTKRDIEKALKGVGAEYDEEKRVISVKLDEEGLMDIARVRERISSIKVKGIRRIKKATVFKEKDEY 1107
Cdd:COG0086 973 GGGVVvgggIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGL 1052
|
1210
....*....|....*...
gi 1286913233 1108 VIRTEGSNLREVMEVPGV 1125
Cdd:COG0086 1053 SLLLGGTDAAAAGVIIGG 1070
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
202-1243 |
4.76e-82 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 295.63 E-value: 4.76e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 202 SRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEA 281
Cdd:PRK14906 310 NDPADMILDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGR 389
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 282 VGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtvaerVTPWNLEKM 361
Cdd:PRK14906 390 RGR-PVTGPGNRPLKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALEL-----FKPFVMKRL 463
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 362 rtlvrngsdkypgaryiirpdgkrVRLKFVANLEELATALEPGY-----VVERHLQDgDIVLFNRQPSLHRMSIMAHYVR 436
Cdd:PRK14906 464 ------------------------VELEYAANIKAAKRAVDRGAsyvwdVLEEVIQD-HPVLLNRAPTLHRLGIQAFEPV 518
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 437 VLPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDET-- 514
Cdd:PRK14906 519 LVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDgf 598
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 515 ---KLTKSELAMLLAAIKYRGPIPPPA---VKDPEPM--------------------WTGKQVFSLLLPKDFnhvtksSF 568
Cdd:PRK14906 599 egeGRTFADFDDALNAYDARADLDLQAkivVRLSRDMtvrgsygdleetkagerietTVGRIIFNQVLPEDY------PY 672
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 569 TNTEVVVKN-GQLISGVIDKgsvgvekansilhrlardYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDqihsD 647
Cdd:PRK14906 673 LNYKMVKKDiGRLVNDCCNR------------------YSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPD----D 730
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 648 IQQIFKKSETEFSKLLAQYQTgeveippGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSAFIMAKTGARGTMLNL 727
Cdd:PRK14906 731 KPEILAEADEKVAAIDEDYED-------GFLSERERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQI 803
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 728 DQMIAVVGqqsvrrervhrgyrkrVLSFFKQD--DLSPRArgfvynSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGY 805
Cdd:PRK14906 804 RQLAGMRG----------------LMADMKGEiiDLPIKA------NFREGLSVLEYFISTHGARKGLVDTALRTADSGY 861
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 806 MQRRLINALEalyidyDGTVRTADEGRIIQFAYgeDGVDPAKSDHGKAV------TVSNIVNSVLASAySGKPASQEYIE 879
Cdd:PRK14906 862 LTRRLVDVAQ------DVIVREEDCGTDEGVTY--PLVKPKGDVDTNLIgrclleDVCDPNGEVLLSA-GDYIESMDDLK 932
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 880 QKLQQASDKLNKKIIEELRAElrktnppaeavdKIVEEVVSKYNASLAEP---GDAVGVVTAQSIGEPGTQLTLRTFHFA 956
Cdd:PRK14906 933 RLVEAGVTKVQIRTLMTCHAE------------YGVCQKCYGWDLATRRPvniGTAVGIIAAQSIGEPGTQLTMRTFHSG 1000
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 957 GVGEQSILKGLPRLIEIVDARRTPTTPIMyipltPEYAsnlakarklakqiqhttlgdlisevlvnykrGTLEVQLDAKs 1036
Cdd:PRK14906 1001 GVAGDDITQGLPRVAELFEARKPKGEAVL-----AEIS-------------------------------GTLQITGDKT- 1043
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1037 leehgvtkrdiEKALKGVGAEYDEEKRVISVKLD-EEGLMDIARVR--ERIS--SIKVKGIRRIKKAtvfkekdEYVIRT 1111
Cdd:PRK14906 1044 -----------EKTLTIHDQDGNSREYVVSARVQfMPGVEDGVEVRvgQQITrgSVNPHDLLRLTDP-------NTTLRY 1105
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1112 EGSNLREVMEVPGVDwrrikTNDIYeiAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRH- 1190
Cdd:PRK14906 1106 IVSQVQDVYVSQGVD-----INDKH--IEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPl 1178
|
1050 1060 1070 1080 1090
....*....|....*....|....*....|....*....|....*....|....*...
gi 1286913233 1191 --GVVKLKSSV---LARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGM 1243
Cdd:PRK14906 1179 llGITKASLATdswLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGL 1236
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
203-813 |
1.82e-80 |
|
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: 278.25 E-value: 1.82e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 203 RPEWMVLTVLPVPPVYVRPSITLESG-YRSED--DLTHKLvdILRvTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNN 279
Cdd:cd01609 138 RPEWMILTVLPVIPPDLRPMVQLDGGrFATSDlnDLYRRV--INR-NNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDN 214
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 280 EAVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtvaerVTPWnle 359
Cdd:cd01609 215 GRRGK-PVTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALEL-----FKPF--- 285
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 360 KMRTLVRNGSdkypgaRYIIRPDGKRVRlkfvANLEELATALEpgYVVERHLqdgdiVLFNRQPSLHRMSIMAHYVRVLP 439
Cdd:cd01609 286 VIRELIERGL------APNIKSAKKMIE----RKDPEVWDILE--EVIKGHP-----VLLNRAPTLHRLGIQAFEPVLIE 348
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 440 YKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKS 519
Cdd:cd01609 349 GKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASGKPIVTPSQDMVLGLYYLTKERKGDKGE 428
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 520 ELamllaaIKyrgpipppavkdpepmwT--GKQVFSLLLPKDFNHVTKssftntevvvkngqlisgVIDKGsvgveKANS 597
Cdd:cd01609 429 GI------IE-----------------TtvGRVIFNEILPEGLPFINK------------------TLKKK-----VLKK 462
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 598 ILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDqihsDIQQIFKKSETEFSKLLAQYQTGEVeippgm 677
Cdd:cd01609 463 LINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPP----EKKEIIKEAEEKVKEIEKQYEKGLL------ 532
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 678 TAEQAFEAdVLKILSEARDSAGKLIRARVSQ--NSSAFIMAKTGARGTMLNLDQMIAVVGQQSvrrervhrgyrkrvlsf 755
Cdd:cd01609 533 TEEERYNK-VIEIWTEVTEKVADAMMKNLDKdpFNPIYMMADSGARGSKSQIRQLAGMRGLMA----------------- 594
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1286913233 756 fkqddlSPRARGF---VYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINA 813
Cdd:cd01609 595 ------KPSGKIIelpIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDV 649
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
202-962 |
5.49e-79 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 287.59 E-value: 5.49e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 202 SRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNN-- 279
Cdd:PRK09603 1621 NRPEWMMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNgr 1700
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 280 EAVGVVPAKHRSgriLKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtvaerVTPWNLE 359
Cdd:PRK09603 1701 STNAVKGANKRP---LKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALEL-----FKPHLLS 1772
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 360 KMRTlvrngsdkyPGARYIIRPDGKRVRLKFVANLEELATALEpGYVVerhlqdgdivLFNRQPSLHRMSIMAHYVRVLP 439
Cdd:PRK09603 1773 KLEE---------RGYATTLKQAKRMIEQKSNEVWECLQEITE-GYPV----------LLNRAPTLHKQSIQAFHPKLID 1832
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 440 YKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLT------RDE 513
Cdd:PRK09603 1833 GKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSleksgvKGE 1912
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 514 TKLTKS--ELAMLLAAIKYRGPIPPPAVKDPEPMWT--GKQVFSLLLPkDFNHVtksSFTNTEVVVKN-GQLISGVIDKG 588
Cdd:PRK09603 1913 HKLFSSvnEIITAIDTKELDIHAKIRVLDQGNIIATsaGRMIIKSILP-DFIPT---DLWNRPMKKKDiGVLVDYVHKVG 1988
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 589 SVGvekansilhrlardygsdVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDqihsDIQQIFKKSETEFSKLLAQYQT 668
Cdd:PRK09603 1989 GIG------------------ITATFLDNLKTLGFRYATKAGISISMEDIITPK----DKQKMVEKAKVEVKKIQQQYDQ 2046
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 669 geveippGMTAEQAFEADVLKILSEARDSAGKLIRARVSQN----SSAFIMAKTGARGTMLNLDQMIAVVGQQSvrrerv 744
Cdd:PRK09603 2047 -------GLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDkegfNSIYMMADSGARGSAAQIRQLSAMRGLMT------ 2113
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 745 hrgyrkrvlsffKQDDL---SPrargfVYNSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINALEALYIDY 821
Cdd:PRK09603 2114 ------------KPDGSiieTP-----IISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVS 2176
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 822 D--GTvrtaDEG-RIIQFAYGEDGVDPAKSDHGKAVTVSNIVNsvlasaysgkPASQEYIEQKLQQASDKLNKKIIEelr 898
Cdd:PRK09603 2177 DdcGT----HEGiEITDIAVGSELIEPLEERIFGRVLLEDVID----------PITNEILLYADTLIDEEGAKKVVE--- 2239
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 899 AELRKTNPPAEAVDKIVEEVVSK-YNASLAE-----PGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQS 962
Cdd:PRK09603 2240 AGIKSITIRTPVTCKAPKGVCAKcYGLNLGEgkmsyPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
4-1244 |
3.58e-75 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 275.73 E-value: 3.58e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 4 AASVAGIRFGILSPDLIRKMSVAEI--ISPDTY-----DEDGLPIPtSVMDP------RLGTLEP----GQRCKTCGNTY 66
Cdd:PRK14844 1445 AQSFNEVSISIASPESIKRMSYGEIedVSTANYrtfkvEKGGLFCP-KIFGPvnddecLCGKYKKrrhrGRICEKCGVEV 1523
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 67 LGCP---GHFGRIELPVPVIHVGFAKT----IYELLKSTCRSCGRILLPED-----------------DCKKYHAELERL 122
Cdd:PRK14844 1524 TSSKvrrERMGHIELASPVAHIWFLKSlpsrIGALLDMSLRDIENILYSDNyividplvspfekgeiiSEKAYNEAKDSY 1603
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 123 RANNLPFKNLIYKIKQkaMNTQVCPHCGEKQLKLELEkptsfsemseSGSTKLNPSTVRARLEripdadlVLLDINPQTS 202
Cdd:PRK14844 1604 GIDSFVAMQGVEAIRE--LLTRLDLHEIRKDLRLELE----------SVASEIRRKKIIKRLR-------IVENFIKSGN 1664
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 203 RPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEAV 282
Cdd:PRK14844 1665 RPEWMILTTIPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRR 1744
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 283 GVVPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtvaerVTPWNLEKMr 362
Cdd:PRK14844 1745 NALVNKAGAVGYKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALEL-----FKPFVYSKL- 1818
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 363 tlvrngsdKYPGARYIIRPDGKRVRlkfvANLEELATALEPgyVVERHlqdgdIVLFNRQPSLHRMSIMAHYVRVLPYKT 442
Cdd:PRK14844 1819 --------KMYGMAPTIKFASKLIR----AEKPEVWDMLEE--VIKEH-----PVLLNRAPTLHRLGIQAFEPILIEGKA 1879
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 443 LRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDEtkLTKSELA 522
Cdd:PRK14844 1880 IQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTLQE--PKEDDLP 1957
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 523 MLLA-----------------AIKYR-------GPIPPPAVKDPepmwTGKQVFSLLLPKDFNhvtkssftntevvvKNG 578
Cdd:PRK14844 1958 SFGAfcevehslsdgtlhihsSIKYRmeyinssGETHYKTICTT----PGRLILWQIFPKHEN--------------LGF 2019
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 579 QLISGVIDkgsvgVEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQIHSDIQQifkkSETE 658
Cdd:PRK14844 2020 DLINQVLT-----VKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDH----ARGE 2090
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 659 FSKLLAQYQTGEVE--------IPPGMTAEQAFEADVLKILSeardsagklIRARVSQNSSAFIMAKTGARGTMlnlDQM 730
Cdd:PRK14844 2091 IKKFSMQYQDGLITrserynkvIDEWSKCTDMIANDMLKAIS---------IYDGNSKYNSVYMMVNSGARGST---SQM 2158
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 731 IAVVGQQSVRRERVHRGYRKRVLSFFKQddlsprargfvynsfvsGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRL 810
Cdd:PRK14844 2159 KQLAGMRGLMTKPSGEIIETPIISNFRE-----------------GLNVFEYFNSTHGARKGLADTALKTANSGYLTRRL 2221
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 811 INALE-ALYIDYDGTVRTadeGRIIQfaygedgvdpaksdhgKAVTVSNIVNSvLASAYSGKPASQEYIEQKLQQASDKL 889
Cdd:PRK14844 2222 VDVSQnCIVTKHDCKTKN---GLVVR----------------ATVEGSTIVAS-LESVVLGRTAANDIYNPVTKELLVKA 2281
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 890 NKKIIEElraELRKTNPPAEAVDKIVEEVVSK---------YNASLA-----EPGDAVGVVTAQSIGEPGTQLTLRTFHF 955
Cdd:PRK14844 2282 GELIDED---KVKQINIAGLDVVKIRSPLTCEispgvcslcYGRDLAtgkivSIGEAVGVIAAQSVGEPGTQLTMRTFHI 2358
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 956 AGV---GEQS--ILKGLPRLIE------IVD--ARRTPTTPIMYIPLTPEYASNLAK------ARKLAKQIQHTTLGDLI 1016
Cdd:PRK14844 2359 GGVmtrGVESsnIIASINAKIKlnnsniIIDknGNKIVISRSCEVVLIDSLGSEKLKhsvpygAKLYVDEGGSVKIGDKV 2438
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1017 SE------VLVNYKRGTLEVQ--LDAKSL-----EEHGVTKRDIE--KALKGVG------AEYDEEKRVISVKLDEEG-- 1073
Cdd:PRK14844 2439 AEwdpytlPIITEKTGTVSYQdlKDGISItevmdESTGISSKVVKdwKLYSGGAnlrpriVLLDDNGKVMTLASGVEAcy 2518
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1074 ---------LMDIARV----------RERISSIKVKG----------IRRIKKATVFKEKDEYVIRTEGSNL--REVM-- 1120
Cdd:PRK14844 2519 fipigavlnVQDGQKVhagdvitrtpRESVKTRDITGglprvielfeARRPKEHAIVSEIDGYVAFSEKDRRgkRSILik 2598
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1121 ----EVPGVDW-----RRIKTN----------------DIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHL-LLL 1174
Cdd:PRK14844 2599 pvdeQISPVEYlvsrsKHVIVNegdfvrkgdllmdgdpDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLeVIL 2678
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1175 ADMM-----TVSGSVKQIGRHGVVKLK--------------------------------SSVLARAAYEISVQTLLEAAA 1217
Cdd:PRK14844 2679 KQMLqkveiTDPGDTMYLVGESIDKLEvdrendamsnsgkrpahylpilqgitrasletSSFISAASFQETTKVLTEAAF 2758
|
1450 1460
....*....|....*....|....*..
gi 1286913233 1218 RGEVDSLKGNVERILIGREIQVGTGMV 1244
Cdd:PRK14844 2759 CGKSDPLSGLKENVIVGRLIPAGTGLI 2785
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
921-1247 |
3.34e-71 |
|
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: 240.56 E-value: 3.34e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 921 KYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIV-DARRTPTTPIMYIPLTPEYasNLAK 999
Cdd:cd02735 1 KYMRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILmTASKNIKTPSMTLPLKNGK--SAER 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1000 ARKLAKQIQHTTLGDLISEVLVNYKRGTLEVQLdAKSLEEHgvtkrdiekalkgvgAEYdeekrVISVKLDEEGLMDIAR 1079
Cdd:cd02735 79 AETLKKRLSRVTLSDVVEKVEVTEILKTIERVF-KKLLGKW---------------CEV-----TIKLPLSSPKLLLLSI 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1080 VRERISSIKVKGIRRIKKATVFKEKDE----YVIRTEGSNLREVMEVPG-VDWRRIKTNDIYEIAEVFGIEAARNAIVEE 1154
Cdd:cd02735 138 VEKLARKAVIREIPGITRCFVVEEDKGgktkYLVITEGVNLAALWKFSDiLDVNRIYTNDIHAMLNTYGIEAARRAIVKE 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1155 AKAVLEDQGLDVDIRHLLLLADMMTVSGSVKQIGRHGVVKlKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIG 1234
Cdd:cd02735 218 ISNVFKVYGIAVDPRHLSLIADYMTFEGGYRPFNRIGMES-STSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVG 296
|
330
....*....|...
gi 1286913233 1235 REIQVGTGMVTLL 1247
Cdd:cd02735 297 KPVNGGTGLFDLL 309
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
203-510 |
1.86e-49 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 187.42 E-value: 1.86e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 203 RPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSD--LLQYHVTTYFNNE 280
Cdd:CHL00018 260 EPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSRSTPGELVMCQkkLLQEAVDALLDNG 339
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 281 AVGVvPAKHRSGRILKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtvaerVTPWNLek 360
Cdd:CHL00018 340 IRGQ-PMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL-----FQPFVI-- 411
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 361 mRTLVRNGSDKYPG-ARYIIRPDGKRVR--LKFVANleelatalepgyvverhlqdGDIVLFNRQPSLHRMSIMAHYVRV 437
Cdd:CHL00018 412 -RGLIRQHLASNIRaAKSKIREKEPIVWeiLQEVMQ--------------------GHPVLLNRAPTLHRLGIQAFQPIL 470
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1286913233 438 LPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLT 510
Cdd:CHL00018 471 VEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLT 543
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
202-518 |
3.48e-47 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 179.94 E-value: 3.48e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 202 SRPEWMVLTVLPVPPVYVRPSITLESGYRSEDDLTHKLVDILRVTQRLRENIRAGSPSPVIEELSDLLQYHVTTYFNNEA 281
Cdd:PRK02625 240 SRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGR 319
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 282 VG--VVPAKHRSgriLKTLAQRLKGKEGRFRLNLSGKRVDFSARTVISPDPNIRINEVGVPLEIAMQLtvaerVTPWNLE 359
Cdd:PRK02625 320 RGrtVVGANNRP---LKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIEL-----FQPFVIH 391
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 360 KmrtLVRNG--SDKYPGARYIIRPDgkrvrlkfvanlEELATALEPgyVVERHlqdgdIVLFNRQPSLHRMSIMAHYVRV 437
Cdd:PRK02625 392 R---LIRQGivNNIKAAKKLIQRAD------------PEVWQVLEE--VIEGH-----PVLLNRAPTLHRLGIQAFEPIL 449
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 438 LPYKTLRLNPAVCTPYNADFDGDEMNLHVPQSEEAQTEARELLVVENNIISPRYGAPIIGVIRDFLTSLYLLTRDETKLT 517
Cdd:PRK02625 450 VEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQ 529
|
.
gi 1286913233 518 K 518
Cdd:PRK02625 530 K 530
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
485-638 |
3.66e-43 |
|
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: 154.32 E-value: 3.66e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 485 NIISPRYGAPIIGVIRDFLTSLYLLTRDETKLTKSELAMLLaaikYRGPI-PPPAVKDP-EPMWTGKQVFSLLLPKDFNH 562
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLL----MYGIVlPHPAILKPiKPLWTGKQTFSRLLPNEINP 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 563 VTKS-------SFTNTEVVVKNGQLISGVIDKGSVGvEKANSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAV 635
Cdd:pfam04983 77 KGKPktneedlCENDSYVLINNGELISGVIDKKTVG-KSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKSGFSIGI 155
|
...
gi 1286913233 636 DDL 638
Cdd:pfam04983 156 DDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
930-1243 |
2.20e-42 |
|
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: 152.19 E-value: 2.20e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 930 GDAVGVVTAQSIGEPGTQLTLRTFHFAGVGEQSILKGLPRLIEIVDARrtpttpimyipltpeyasnlakarklakqiqh 1009
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA-------------------------------- 48
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1010 ttlgdlisevlvnykrgtlevqldaksleehgvtkrdiekalkgvgaeydeekrvisvkldeeglmdiarvrerissikv 1089
Cdd:cd00630 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1090 kgirrikkatvfkekdeyvirtegsnlrevmevpgvdwrriktnDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIR 1169
Cdd:cd00630 49 --------------------------------------------SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRR 84
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1286913233 1170 HLLLLADMMTVSGSVKQIGRHGVVKLKSSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTGM 1243
Cdd:cd00630 85 HIELIADVMTYSGGLRGVTRSGFRASKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
669-769 |
5.47e-30 |
|
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: 114.77 E-value: 5.47e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 669 GEVEIPPGMTAEQAFEADVLKILSEARDSAGKLIRARVSQNSSAFIMAKTGARGTMLNLDQMIAVVGQQSVRRERVHRGY 748
Cdd:pfam05000 8 GKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEGKRIPFGF 87
|
90 100
....*....|....*....|.
gi 1286913233 749 RKRVLSFFKQDDLSPRARGFV 769
Cdd:pfam05000 88 SGRTLPHFKKDDEGPESRGFV 108
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
584-958 |
1.10e-24 |
|
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: 112.25 E-value: 1.10e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 584 VIDKGSVgvekaNSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDQIhsdiQQIFKKSETEFSKLL 663
Cdd:TIGR02388 6 VVDKKAL-----KNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAK----QDLLEAAEKEIRATE 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 664 AQYQTGEVeippgmTAEQAFEaDVLKILSEARDSAGKLIRARVSQN---SSAFIMAKTGARGTMLNLDQMIAVVGQQSVR 740
Cdd:TIGR02388 77 ERYRRGEI------TEVERFQ-KVIDTWNGTNEELKDEVVNNFRQTdplNSVYMMAFSGARGNMSQVRQLVGMRGLMANP 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 741 RERVhrgyrkrvlsffkqDDLSPRArgfvynSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINalealyID 820
Cdd:TIGR02388 150 QGEI--------------IDLPIKT------NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVD------VS 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 821 YDGTVRTADEGRiiqfaygEDGVD-PAKSDHGKAVTVSN-IVNSVLASAYSGkpASQEYIEQKLQQASDKLNKKIIEELR 898
Cdd:TIGR02388 204 QDVIVREEDCGT-------ERSIVvRAMTEGDKKISLGDrLLGRLVAEDVLH--PEGEVIVPKNTAIDPDLAKTIETAGI 274
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1286913233 899 AELRKTNP-PAEAVDKIVEEVV--SKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGV 958
Cdd:TIGR02388 275 SEVVVRSPlTCEAARSVCRKCYgwSLAHAHLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 337
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
584-958 |
4.12e-21 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 100.46 E-value: 4.12e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 584 VIDKGSVGvekanSILHRLARDYGSDVARQFLDNVVRLANTFIELKGFSFAVDDLYVPDqihsDIQQIFKKSETEFSKLL 663
Cdd:PRK02597 7 VVDKKALK-----NLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPP----AKRDLLEQAEEEITATE 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 664 AQYQTGEVeippgmTAEQAFEaDVLKILSEARDSAGKLIRARVSQN---SSAFIMAKTGARGtmlNLDQMIAVVGQqsvr 740
Cdd:PRK02597 78 ERYRRGEI------TEVERFQ-KVIDTWNETNERLKDEVVKNFRQNdplNSVYMMAFSGARG---NMSQVRQLVGM---- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 741 rervhRGyrkrvLSFFKQD---DLSPRArgfvynSFVSGLDPLEFFFHAVGGRDGLVDTAVRTQQSGYMQRRLINaleal 817
Cdd:PRK02597 144 -----RG-----LMANPQGeiiDLPIKT------NFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVD----- 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 818 yIDYDGTVRTADEG--RIIQFAYGEDGvdpaksDHGKAVTVSNIVNSVLASAYSGkpASQEYIEQKLQQASDKLNKKIIE 895
Cdd:PRK02597 203 -VSQDVIVREEDCGttRGIVVEAMDDG------DRVLIPLGDRLLGRVLAEDVVD--PEGEVIAERNTAIDPDLAKKIEK 273
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 896 ELRAELRKTNP-PAEAVdkivEEVVSK-YNASLA-----EPGDAVGVVTAQSIGEPGTQLTLRTFHFAGV 958
Cdd:PRK02597 274 AGVEEVMVRSPlTCEAA----RSVCRKcYGWSLAhnhlvDLGEAVGIIAAQSIGEPGTQLTMRTFHTGGV 339
|
|
| RNAP_IV_NRPD1_C |
cd02737 |
Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain; Higher plants ... |
930-1242 |
1.30e-17 |
|
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: 86.32 E-value: 1.30e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 930 GDAVGVVTAQSIGEPGTQLTLRTFHfagvgeQSILKGLPRLIEIVDAR-RTPTTP-----IMYIPLTPEYASNLAKARKL 1003
Cdd:cd02737 1 GEPVGSLAATAISEPAYKALLDPPQ------SLESSPLELLKEVLECRsKSKSKEndrrvILSLHLCKCDHGFEYERAAL 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1004 AKQ--IQHTTLGDLISEVLVNYKRGTLEvqldakSLEEHGVTKRDIEKALKGVGAEYDEEKR------VISVKLDEEGLM 1075
Cdd:cd02737 75 EVKnhLERVTLEDLATTSMIKYSPQATE------AIVGEIGDQLNTKKKGKKKAIFSTSLKItkfspwVCHFHLDKECQK 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1076 D---------------------IARVRERIS----SIKVKGIRRIKKATVFKE---------------KDEYVI------ 1109
Cdd:cd02737 149 LsdgpcltfsvskevsksseelLDVLRDRIIpfllETVIKGDERIKSVNILWEdspstswvksvgkssRGELVLevtvee 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 1110 ---RTEGSNLREVMEVPG-----VDWRRIKTNDIYEIAEVFGIEAARNAIVEEAKAVLEDQGLDVDIRHLLLLADMMTVS 1181
Cdd:cd02737 229 sckKTRGNAWNVVMDACIpvmdlIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMTYS 308
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1286913233 1182 GSVKQIGRHGVVKLK-----SSVLARAAYEISVQTLLEAAARGEVDSLKGNVERILIGREIQVGTG 1242
Cdd:cd02737 309 GEFVGLNAKGYKAQRrslkiSAPFTEACFSSPIKCFLKAAKKGASDSLSGVLDACAWGKEAPVGTG 374
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
925-978 |
1.69e-17 |
|
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: 82.19 E-value: 1.69e-17
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1286913233 925 SLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGVGeQSILKGLPRLIEIVDARR 978
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVA-TDITQGLPRVEELFEARK 53
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
788-958 |
8.20e-17 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 86.53 E-value: 8.20e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 788 GGRDGLVDTAVRTQQSGYMQRRLINALEalyidyDGTVRTADEGRIIQFAygedgVDPAKSDHGKAVTVSNIVNSVLA-S 866
Cdd:CHL00117 184 GARKGVVDTAVRTADAGYLTRRLVEVVQ------HIVVRETDCGTTRGIS-----VSPRNGMMIERILIQTLIGRVLAdD 252
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 867 AYSGKpasqEYIEQKLQQASDKLNKKIIEelraeLRKTN-----P-----------------PAeavdkiveevvskyNA 924
Cdd:CHL00117 253 IYIGS----RCIATRNQDIGIGLANRFIT-----FRAQPisirsPltcrstswicqlcygwsLA--------------HG 309
|
170 180 190
....*....|....*....|....*....|....
gi 1286913233 925 SLAEPGDAVGVVTAQSIGEPGTQLTLRTFHFAGV 958
Cdd:CHL00117 310 DLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
887-973 |
2.07e-10 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 65.30 E-value: 2.07e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1286913233 887 DKLNKKIIEELRAELRKTNppaEAVDKIVEEVVSKYNASLAEPGDAVGVVTAQSIGEPGTQLTLRTfhfagvGEQSILK- 965
Cdd:PRK14898 17 RSLKDELFEKLSKRDGVTE---EMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSLPY------DEKIIVKe 87
|
....*....
gi 1286913233 966 -GLPRLIEI 973
Cdd:PRK14898 88 gGETRVTEI 96
|
|
| KH_I_FMR1_FXR_rpt2 |
cd22426 |
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental ... |
1099-1160 |
4.33e-03 |
|
second type I K homology (KH) RNA-binding domain found in a family of fragile X mental retardation protein (FMR1) and fragile X related (FXR) proteins; The FMR1/FXR family includes FMR1 (also known as FMRP) and its two homologues, fragile X related 1 (FXR1) and 2 (FXR2). They are involved in translational regulation, particularly in neuronal cells and play an important role in the regulation of glutamate-mediated neuronal activity and plasticity. Each of these three proteins can form heteromers with the others, and each can also form homomers. Lack of expression of FMR1 results in mental retardation and macroorchidism. FXR1 and FXR2 may play important roles in the function of FMR1 and in the pathogenesis of the Fragile X Mental Retardation Syndrome. Members of this family contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.
Pssm-ID: 411854 [Multi-domain] Cd Length: 63 Bit Score: 36.74 E-value: 4.33e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1286913233 1099 TVFKEKDEYVIRTEGSNLREVMEVPGVdwRRIktnDIYEIAEVFGIEAARNAIVEEAKAVLE 1160
Cdd:cd22426 7 KVDPDLIGLAIGSHGSNIQQARKIPGV--ESI---DVDEEDGTFRIYGETPEAVEKARALLE 63
|
|
| |
