|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
1-809 |
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: 1119.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCfycskikllkkecksskiknardsrnrlnrvwslcktktlcgdktegsgcg 80
Cdd:cd02733 64 GHFGHIELAKPVFHIGFLTKILKILRCVC--------------------------------------------------- 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 81 nrqplikkeglnlvafmkddegKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRPSVIMDGIL 160
Cdd:cd02733 93 ----------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSA 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 161 RGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISARLKGKEGRV 240
Cdd:cd02733 151 RSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRI 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 241 RGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIREDGQRIDLR 320
Cdd:cd02733 231 RGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERIDLR 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 321 YNRSS---IIKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQ 397
Cdd:cd02733 311 YLKKAsdlHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLE 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 398 TMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLI-YKSRNTIKSIRPSIKRPIRLYTGKQ 476
Cdd:cd02733 391 TRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLmWLPDWDGKIPQPAILKPKPLWTGKQ 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 477 LYSINLPTLNYKRYSNIDGSFVSSFVSSnsfvssntntntntntntntntnnlntnnlntnlntnkmvvqffeyidrilN 556
Cdd:cd02733 471 IFSLIIPKINNLIRSSSHHDGDKKWISP---------------------------------------------------G 499
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 557 DSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGDTIADKYTMRKIV 636
Cdd:cd02733 500 DTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHN-GFSIGIGDTIADKETMKKIQ 578
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 637 ESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSKGSFINISQ 716
Cdd:cd02733 579 ETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQ 658
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 717 VTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRR 796
Cdd:cd02733 659 IIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR 738
|
810
....*....|...
gi 2313927249 797 LVKAMEDCKINYD 809
Cdd:cd02733 739 LVKAMEDVMVKYD 751
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
1-837 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 821.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLlkkecKSSKIKNARDSRNRLNR----VWSLCKT-KTLCGDKTE 75
Cdd:PRK08566 73 GHFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKL-----TEEEIEEYLEKLERLKEwgslADDLIKEvKKEAAKRMV 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 76 GSGCGNRQPLIKKEG-LNLVAFMKDDEGKLILSgeKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRPSV 154
Cdd:PRK08566 148 CPHCGEKQYKIKFEKpTTFYEERKEGLVKLTPS--DIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSI 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 155 IMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISARLK 234
Cdd:PRK08566 226 TLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLK 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 235 GKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIREDG 314
Cdd:PRK08566 306 GKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDG 385
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 315 QRIDLRY-NRSSI---IKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNL 390
Cdd:PRK08566 386 RRIKLTDkNKEELaekLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNL 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 391 HMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYKSR-NTIKSIRPSIKRPI 469
Cdd:PRK08566 466 HVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGiDELPEPEPAIENGK 545
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 470 RLYTGKQLYSINLP-TLNYKRYSNIdgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlnTNKMVVQFF 548
Cdd:PRK08566 546 PYWTGKQIFSLFLPkDLNLEFKAKI----------------------------------------------CSGCDECKK 579
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 549 EYIDrilNDSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGDTIAD 628
Cdd:PRK08566 580 EDCE---HDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLR-GFTTGIDDEDIP 655
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 629 KYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSK 708
Cdd:PRK08566 656 EEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGAR 735
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 709 GSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTA 788
Cdd:PRK08566 736 GSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTS 815
|
810 820 830 840
....*....|....*....|....*....|....*....|....*....
gi 2313927249 789 ETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEHN 837
Cdd:PRK08566 816 QSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHG 864
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
1-836 |
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: 781.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLlkkecKSSKIKNARDSRNRLNRVWSLcKTKTLCGD-------K 73
Cdd:TIGR02390 68 GHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITL-----TEEEIEQYLEKINKLKEEGGD-LASTLIEKivkeaakR 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 74 TEGSGCGNRQPLIKKEglNLVAFM-KDDEGKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRP 152
Cdd:TIGR02390 142 MKCPHCGEEQKKIKFE--KPTYFYeEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRP 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 153 SVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISAR 232
Cdd:TIGR02390 220 SITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQR 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 233 LKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIRE 312
Cdd:TIGR02390 300 LKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRP 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 313 DGQRIDLRY-NRSSI---IKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEM 388
Cdd:TIGR02390 380 DGRRIKIRDeNKEELaerLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEM 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 389 NLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYKSRNTIKSIRPSIKRP 468
Cdd:TIGR02390 460 NLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKP 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 469 IRLYTGKQLYSINLP-TLNYKRYSNIdgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlnTNKMVVQF 547
Cdd:TIGR02390 540 KEYWTGKQIFSAFLPeDLNFEGRAKI----------------------------------------------CSGSDACK 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 548 FEyidRILNDSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTyYSSFSCGIGDTIA 627
Cdd:TIGR02390 574 KE---ECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFIT-LRGFTTGIDDIDI 649
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 628 DKYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGS 707
Cdd:TIGR02390 650 PKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGA 729
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 708 KGSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKT 787
Cdd:TIGR02390 730 RGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRT 809
|
810 820 830 840
....*....|....*....|....*....|....*....|....*....
gi 2313927249 788 AETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEH 836
Cdd:TIGR02390 810 SQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDH 858
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
156-433 |
2.43e-151 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 449.28 E-value: 2.43e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 156 MDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEisGQPQAVQKSGRPLKSISARLKG 235
Cdd:smart00663 21 LDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GLPRANQKSGRPLKSLSQRLKG 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 236 KEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPfeyPGANYIIRedGQ 315
Cdd:smart00663 99 KEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP---NGAKYIIR--GK 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 316 RIDLRYNRSSII----KEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLH 391
Cdd:smart00663 174 KTNLKLAKKSKIanhlKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLH 253
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 2313927249 392 MPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVR 433
Cdd:smart00663 254 VPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-244 |
3.89e-97 |
|
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: 308.84 E-value: 3.89e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLLKKE----CKSSKIKNARDSRNRLNRVWSLCKTKTLC-GDKTE 75
Cdd:pfam04997 69 GHFGHIELAKPVFHIGFFKKTLKILECVCKYCSKLLLDPGKpklfNKDKKRLGLENLKMGAKAILELCKKKDLCeHCGGK 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 76 GSGCGNRQPLIKKEGLNLVAFMK---DDEGKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRP 152
Cdd:pfam04997 149 NGVCGSQQPVSRKEGLKLKAAIKkskEEEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRP 228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 153 SVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISAR 232
Cdd:pfam04997 229 SVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQR 308
|
250
....*....|..
gi 2313927249 233 LKGKEGRVRGNL 244
Cdd:pfam04997 309 LKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
763-974 |
6.78e-53 |
|
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: 193.72 E-value: 6.78e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 763 GLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEHNVIESF 842
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 843 ysfrGSRTMFGKRRVTLPLNFKRLILSEEMKNSGFVSEGR-ISECRVELLDFVGNLKFLTNKIFSKSStLADAIIYfmQP 921
Cdd:pfam04998 81 ----EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRdSKLGRDRLSKEAQERATLLFELLLKSG-LESKRVR--SE 153
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 2313927249 922 KFLSSLNLEGLRNlveEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:pfam04998 154 LTCNSKAFVCLLC---YGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTF 203
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
3-974 |
8.50e-52 |
|
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: 198.08 E-value: 8.50e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 3 FGHMELARPVFHIGFL----SKIK-------KILETVCFYCSKI-------KLLKKEcksskIKNARDSRNRLNRVwslc 64
Cdd:COG0086 92 MGHIELAMPVFHIWGLkslpSRIGllldmslRDLERVLYFESYVvidpgdtPLEKGQ-----LLTEDEYREILEEY---- 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 65 ktktlcGDK-TEGSGCGNRQPLIKKEGLNLVAFMKDDEGKLILSGEKVYSILKRIpdsDLEElGFNPSTSRPEWMvltvl 143
Cdd:COG0086 163 ------GDEfVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRL---KVVE-AFRESGNRPEWM----- 227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 144 lvppppvrpsvIMDGI------LR----------GEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATL 207
Cdd:COG0086 228 -----------ILDVLpvippdLRplvpldggrfATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDAL 296
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 208 MDNEISGQPqAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMihtfpekvnsf 287
Cdd:COG0086 297 FDNGRRGRA-VTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL----------- 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 288 nlekmeELVKkgPFeypganyIIRedgqRIDLRYNRSSIIKEGYTVERH----------MLDGDVVLFNRQPSLHKMSMM 357
Cdd:COG0086 365 ------ELFK--PF-------IYR----KLEERGLATTIKSAKKMVEREepevwdileeVIKEHPVLLNRAPTLHRLGIQ 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 358 AHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTS 437
Cdd:COG0086 426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTR 505
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 438 LD-------SFFSEREMMSLIYksRNTIKSIRPSIKRPIRLyTGKQLYSINLPTLNykRY--SNIdgsfvssfvssnsfv 508
Cdd:COG0086 506 ERegakgegMIFADPEEVLRAY--ENGAVDLHARIKVRITE-DGEQVGKIVETTVG--RYlvNEI--------------- 565
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 509 ssntntntntntntntntnnlntnnlntnlntnkmVVQFFEYIDRILNDSNIlivkgnlllgtldkksvgntqGGIIHVI 588
Cdd:COG0086 566 -----------------------------------LPQEVPFYNQVINKKHI---------------------EVIIRQM 589
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 589 KNDYGCDSTVKFFDGSQRMVNAYLTyYSSFSCGIGDTIADKYTMRKIVEsidlAKREVDTIIKSAREGRM---ERmagls 665
Cdd:COG0086 590 YRRCGLKETVIFLDRLKKLGFKYAT-RAGISIGLDDMVVPKEKQEIFEE----ANKEVKEIEKQYAEGLItepER----- 659
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 666 kfrtfESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSKGSFINISQVTACVGQQNVEGQRI---PFG--FRErtl 740
Cdd:COG0086 660 -----YNKVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIietPIGsnFRE--- 731
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 741 phfskfdygpgsrgfvensflsGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKIN-YDCSVRDGSgRV 819
Cdd:COG0086 732 ----------------------GLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTeEDCGTDRGI-TV 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 820 FQFLYGDDgfdatylehnVIESFYSFRGSRTmfgkrrvtlplnfkrliLSEEMKNSGfvsEGRISECRVELLDFVGNLKf 899
Cdd:COG0086 789 TAIKEGGE----------VIEPLKERILGRV-----------------AAEDVVDPG---TGEVLVPAGTLIDEEVAEI- 837
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2313927249 900 ltnkifsksstLADAIIYfmQPKFLSSLNLEGLRNLVEEIKREILRGIVCAN--EMVGTLASQSIGEPATQMTLNTF 974
Cdd:COG0086 838 -----------IEEAGID--SVKVRSVLTCETRGGVCAKCYGRDLARGHLVNigEAVGVIAAQSIGEPGTQLTMRTF 901
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
927-974 |
3.05e-16 |
|
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: 82.25 E-value: 3.05e-16
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 2313927249 927 LNLEGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:cd02584 3 LNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTF 50
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
930-974 |
6.84e-10 |
|
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: 61.99 E-value: 6.84e-10
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 2313927249 930 EGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:TIGR02389 23 EELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTF 67
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
697-974 |
9.63e-10 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 62.71 E-value: 9.63e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 697 NNVKQMVLAGSKGsfiNISQVTACVGQQ----NVEGQRIpfgfrerTLPhfskfdygpgsrgfVENSFLSGLTPEEFYFH 772
Cdd:PRK02597 120 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 773 TMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKI-NYDCsvrdGSGRvfqflygddgfdatyleHNVIESfysfrgsrtM 851
Cdd:PRK02597 176 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVrEEDC----GTTR-----------------GIVVEA---------M 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 852 FGKRRVTLPLN---FKRLILSEEMKNSGFVSEGRISECRVELldfvgnlkfltnkifskSSTLADAIIyfMQPKFLSSLN 928
Cdd:PRK02597 226 DDGDRVLIPLGdrlLGRVLAEDVVDPEGEVIAERNTAIDPDL-----------------AKKIEKAGV--EEVMVRSPLT 286
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2313927249 929 LEGLRNlveeikreilrgiVCAN---------------EMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK02597 287 CEAARS-------------VCRKcygwslahnhlvdlgEAVGIIAAQSIGEPGTQLTMRTF 334
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
1-809 |
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: 1119.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCfycskikllkkecksskiknardsrnrlnrvwslcktktlcgdktegsgcg 80
Cdd:cd02733 64 GHFGHIELAKPVFHIGFLTKILKILRCVC--------------------------------------------------- 92
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 81 nrqplikkeglnlvafmkddegKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRPSVIMDGIL 160
Cdd:cd02733 93 ----------------------KRELSAERVLEIFKRISDEDCRILGFDPKFSRPDWMILTVLPVPPPAVRPSVVMDGSA 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 161 RGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISARLKGKEGRV 240
Cdd:cd02733 151 RSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPQATQKSGRPLKSIRQRLKGKEGRI 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 241 RGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIREDGQRIDLR 320
Cdd:cd02733 231 RGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLTFPEIVTPFNIDRLQELVRNGPNEYPGAKYIIRDDGERIDLR 310
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 321 YNRSS---IIKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQ 397
Cdd:cd02733 311 YLKKAsdlHLQYGYIVERHLQDGDVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDGDEMNLHVPQSLE 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 398 TMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLI-YKSRNTIKSIRPSIKRPIRLYTGKQ 476
Cdd:cd02733 391 TRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLTKRDTFLEKDQVMNLLmWLPDWDGKIPQPAILKPKPLWTGKQ 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 477 LYSINLPTLNYKRYSNIDGSFVSSFVSSnsfvssntntntntntntntntnnlntnnlntnlntnkmvvqffeyidrilN 556
Cdd:cd02733 471 IFSLIIPKINNLIRSSSHHDGDKKWISP---------------------------------------------------G 499
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 557 DSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGDTIADKYTMRKIV 636
Cdd:cd02733 500 DTKVIIENGELLSGILCKKTVGASSGGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHN-GFSIGIGDTIADKETMKKIQ 578
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 637 ESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSKGSFINISQ 716
Cdd:cd02733 579 ETIKKAKRDVIKLIEKAQNGELEPQPGKTLRESFENKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQ 658
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 717 VTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRR 796
Cdd:cd02733 659 IIACVGQQNVEGKRIPFGFRRRTLPHFIKDDYGPESRGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRR 738
|
810
....*....|...
gi 2313927249 797 LVKAMEDCKINYD 809
Cdd:cd02733 739 LVKAMEDVMVKYD 751
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
1-837 |
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: 834.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKL-------LKKECKSSKIKNARDSRNRLNRVWSLCKTKTLCgdk 73
Cdd:cd02582 68 GHFGHIELARPVIHVGFAKHIYDLLRATCRSCGRILLpeeeiekYLERIRRLKEKWPELVKRVIEKVKKKAKKRKVC--- 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 74 tegSGCGNRQPLIKKEGLNLVAFMKDDEGKLILSGEkVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRPS 153
Cdd:cd02582 145 ---PHCGAPQYKIKLEKPTTFYEEKEEGEVKLTPSE-IRERLEKIPDEDLELLGIDPKTARPEWMVLTVLPVPPVTVRPS 220
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 154 VIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISARL 233
Cdd:cd02582 221 ITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRL 300
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 234 KGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIRED 313
Cdd:cd02582 301 KGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWNIEKMRKLVLNGPDKWPGANYVIRPD 380
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 314 GQRIDLRY-NRSSI---IKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMN 389
Cdd:cd02582 381 GRRIRLRYvNREELaerLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMN 460
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 390 LHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYKSRNTIKSIRPSIKRPI 469
Cdd:cd02582 461 LHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFTKEEALQLLSAAGYDGLLPEPAILEPK 540
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 470 RLYTGKQLYSINLP-TLNYKRYSNIDGSFVSSFVSSNsfvssntntntntntntntntnnlntnnlntnlntnkmvvqff 548
Cdd:cd02582 541 PLWTGKQLFSLFLPkDLNFEGKAKVCSGCSECKDEDC------------------------------------------- 577
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 549 eyidriLNDSNILIVKGNLLLGTLDKKSVGNTQGG-IIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGDTIA 627
Cdd:cd02582 578 ------PNDGYVVIKNGKLLEGVIDKKAIGAEQPGsLLHRIAKEYGNEVARRFLDSVTRLAIRFIELR-GFTIGIDDEDI 650
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 628 DKYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGS 707
Cdd:cd02582 651 PEEARKEIEEIIKEAEKKVYELIEQYKNGELEPLPGRTLEETLEMKIMQVLGKARDEAGKVASKYLDPFNNAVIMARTGA 730
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 708 KGSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKT 787
Cdd:cd02582 731 RGSMLNLTQMAACLGQQSVRGERINRGYRNRTLPHFKPGDLGPEARGFVRSSFRDGLSPTEFFFHAMGGREGLVDTAVRT 810
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|
gi 2313927249 788 AETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEHN 837
Cdd:cd02582 811 SQSGYMQRRLINALQDLYVEYDGTVRDSRGNIIQFKYGEDGVDPAKSDHG 860
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
1-837 |
0e+00 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 821.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLlkkecKSSKIKNARDSRNRLNR----VWSLCKT-KTLCGDKTE 75
Cdd:PRK08566 73 GHFGHIELARPVIHVGFAKLIYKLLRATCRECGRLKL-----TEEEIEEYLEKLERLKEwgslADDLIKEvKKEAAKRMV 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 76 GSGCGNRQPLIKKEG-LNLVAFMKDDEGKLILSgeKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRPSV 154
Cdd:PRK08566 148 CPHCGEKQYKIKFEKpTTFYEERKEGLVKLTPS--DIRERLEKIPDEDLELLGINPEVARPEWMVLTVLPVPPVTVRPSI 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 155 IMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISARLK 234
Cdd:PRK08566 226 TLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEIPGIPPARHRSGRPLKTLAQRLK 305
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 235 GKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIREDG 314
Cdd:PRK08566 306 GKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTEWNIEELREYVLNGPEKHPGANYVIRPDG 385
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 315 QRIDLRY-NRSSI---IKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNL 390
Cdd:PRK08566 386 RRIKLTDkNKEELaekLEPGWIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNL 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 391 HMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYKSR-NTIKSIRPSIKRPI 469
Cdd:PRK08566 466 HVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRKSTLFTKEEALDLLRAAGiDELPEPEPAIENGK 545
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 470 RLYTGKQLYSINLP-TLNYKRYSNIdgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlnTNKMVVQFF 548
Cdd:PRK08566 546 PYWTGKQIFSLFLPkDLNLEFKAKI----------------------------------------------CSGCDECKK 579
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 549 EYIDrilNDSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGDTIAD 628
Cdd:PRK08566 580 EDCE---HDAYVVIKNGKLLEGVIDKKAIGAEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIMLR-GFTTGIDDEDIP 655
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 629 KYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSK 708
Cdd:PRK08566 656 EEAKEEIDEIIEEAEKRVEELIEAYENGELEPLPGRTLEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGAR 735
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 709 GSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTA 788
Cdd:PRK08566 736 GSMLNLTQMAACVGQQSVRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTS 815
|
810 820 830 840
....*....|....*....|....*....|....*....|....*....
gi 2313927249 789 ETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEHN 837
Cdd:PRK08566 816 QSGYMQRRLINALQDLKVEYDGTVRDTRGNIVQFKYGEDGVDPMKSDHG 864
|
|
| RNA_pol_rpoA1 |
TIGR02390 |
DNA-directed RNA polymerase subunit A'; This family consists of the archaeal A' subunit of the ... |
1-836 |
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: 781.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLlkkecKSSKIKNARDSRNRLNRVWSLcKTKTLCGD-------K 73
Cdd:TIGR02390 68 GHFGHIELARPVVHVGFAKEIYKILRATCRKCGRITL-----TEEEIEQYLEKINKLKEEGGD-LASTLIEKivkeaakR 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 74 TEGSGCGNRQPLIKKEglNLVAFM-KDDEGKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRP 152
Cdd:TIGR02390 142 MKCPHCGEEQKKIKFE--KPTYFYeEGKEGDVKLTPSEIRERLEKIPDEDAELLGINPKVARPEWMVLTVLPVPPVTVRP 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 153 SVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISAR 232
Cdd:TIGR02390 220 SITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVATYFDNELPGIPPARHRSGRPLKTLAQR 299
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 233 LKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIRE 312
Cdd:TIGR02390 300 LKGKEGRFRGNLSGKRVNFSARTVISPDPNISINEVGVPEQIAKELTVPERVTPWNIDELREYVLNGPDSWPGANYVIRP 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 313 DGQRIDLRY-NRSSI---IKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEM 388
Cdd:TIGR02390 380 DGRRIKIRDeNKEELaerLEPGWVVERHLIDGDIVLFNRQPSLHRMSMMGHKVKVLPGKTFRLNLAVCPPYNADFDGDEM 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 389 NLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYKSRNTIKSIRPSIKRP 468
Cdd:TIGR02390 460 NLHVPQTEEARAEARELMLVEEHILTPRYGGPIIGGIHDYISGAYLLTHKSTLFTKEEVQTILGVAGYFGDPPEPAIEKP 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 469 IRLYTGKQLYSINLP-TLNYKRYSNIdgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlnTNKMVVQF 547
Cdd:TIGR02390 540 KEYWTGKQIFSAFLPeDLNFEGRAKI----------------------------------------------CSGSDACK 573
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 548 FEyidRILNDSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTyYSSFSCGIGDTIA 627
Cdd:TIGR02390 574 KE---ECPHDAYVVIKNGKLLKGVIDKKAIGAEKGKILHRIVREYGPEAARRFLDSVTRLFIRFIT-LRGFTTGIDDIDI 649
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 628 DKYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGS 707
Cdd:TIGR02390 650 PKEAKEEIEELIEKAEKRVDNLIERYRNGELEPLPGRTVEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGA 729
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 708 KGSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKT 787
Cdd:TIGR02390 730 RGSLLNITQMAAMVGQQSVRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAVRT 809
|
810 820 830 840
....*....|....*....|....*....|....*....|....*....
gi 2313927249 788 AETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEH 836
Cdd:TIGR02390 810 SQSGYMQRRLINALQDLYVEYDGTVRDTRGNLIQFKYGEDGVDPMKSDH 858
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
1-813 |
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: 708.93 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLLKKECKS--SKIKNARDSRNR----LNRVWSLCKTKTLCgdkt 74
Cdd:cd02583 58 GHFGYIKLELPVFHIGYFKAIINILQCICKTCSRVLLPEEEKRKflKRLRRPNLDNLQkkalKKKILEKCKKVRKC---- 133
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 75 egSGCGNRQplikkeglnlvaFMKDDEGKLilsgeKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRPSV 154
Cdd:cd02583 134 --PHCGLLK------------KAQEDLNPL-----KVLNLFKNIPPEDVELLLMNPLAGRPENLILTRIPVPPLCIRPSV 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 155 IMDG-ILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAvQKSGRPLKSISARL 233
Cdd:cd02583 195 VMDEkSGTNEDDLTVKLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLS-MQPKKPIRGFCQRL 273
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 234 KGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIRED 313
Cdd:cd02583 274 KGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPERVTRYNIEKLRKLVLNGPDVHPGANFVIKRD 353
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 314 GQ-RIDLRY-NRSSIIKE---GYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEM 388
Cdd:cd02583 354 GGkKKFLKYgNRRKIARElkiGDIVERHLEDGDIVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEM 433
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 389 NLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLI---YKSRNTIKSIRPSI 465
Cdd:cd02583 434 NLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSKDVFFDRAQFCQLCsymLDGEIKIDLPPPAI 513
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 466 KRPIRLYTGKQLYSINL-PTLNYKRYSNIDgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlntNKMV 544
Cdd:cd02583 514 LKPVELWTGKQIFSLLLrPNKKSPVLVNLE----------------------------------------------AKEK 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 545 VQFFEYIDRILNDSNILIVKGNLLLGTLDKKSVGN-TQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIG 623
Cdd:cd02583 548 SYTKKSPDMCPNDGYVVIRNSELLCGRLDKSTLGSgSKNSLFYVLLRDYGPEAAAAAMNRLAKLSSRWLSNR-GFSIGID 626
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 624 DTIADKYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMV 703
Cdd:cd02583 627 DVTPSKELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTAEQTLEAKISGELSKIREDAGKACLKELHKSNSPLIMA 706
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 704 LAGSKGSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDT 783
Cdd:cd02583 707 LCGSKGSNINISQMIACVGQQIISGKRIPNGFEDRTLPHFPRNSKTPAAKGFVANSFYSGLTPTEFFFHTMSGREGLVDT 786
|
810 820 830
....*....|....*....|....*....|
gi 2313927249 784 AIKTAETGYIQRRLVKAMEDCKINYDCSVR 813
Cdd:cd02583 787 AVKTAETGYMQRRLMKALEDLSVQYDGTVR 816
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
1-974 |
0e+00 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 650.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLLKKE---CKSSKIKNARDSRNRLNRV------WSLCKTKTLCG 71
Cdd:PRK14977 73 GHFGHIELAEPVIHIAFIDNIKDLLNSTCHKCAKLKLPQEDlnvFKLIEEAHAAARDIPEKRIddeiieEVRDQVKVYAK 152
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 72 DKTEGSGCGNRQ-PLIKKEGLNLVafMKDDEGKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPV 150
Cdd:PRK14977 153 KAKECPHCGAPQhELEFEEPTIFI--EKTEIEEHRLLPIEIRDIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVPPLTA 230
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 151 RPSVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQK-SGRPLKSI 229
Cdd:PRK14977 231 RPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAHHKgSGRPLKSL 310
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 230 SARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYI 309
Cdd:PRK14977 311 FQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNENNIEKMKELVINGPDEFPGANAI 390
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 310 IREDGQRIDLRY--NRSSI--------IKEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPY 379
Cdd:PRK14977 391 RKGDGTKIRLDFleDKGKDalreaaeqLEIGDIVERHLADGDIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAVCPPY 470
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 380 NADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYKSRNTIK 459
Cdd:PRK14977 471 NADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDALFDKNEASNIAMLAGITDP 550
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 460 SIRPSIK-RPIRLYTGKQLYSINLPT-LNYKRYSNIDGSFVSSFVSSNSfvssntntntntntntntntnnlntnnlntn 537
Cdd:PRK14977 551 LPEPAIKtKDGPAWTGKQLFSLFLPKdFNFEGIAKWSAGKAGEAKDPSC------------------------------- 599
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 538 lntnkmvvqffeyidriLNDSNILIVKGNLLLGTLDKKSVGNTQGG---IIHVIKNDYGCDSTVKFFDGSQRMVNAYLTY 614
Cdd:PRK14977 600 -----------------LGDGYVLIKEGELISGVIDDNIIGALVEEpesLIDRIAKDYGEAVAIEFLNKILIIAKKEILH 662
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 615 YsSFSCGIGDTIADKYTMRKIVESIDLAKREVDTIIKSAR--------EGRMERMAGLSKFRTFESKIILALNKARDVSG 686
Cdd:PRK14977 663 Y-GFSNGPGDLIIPDEAKQEIEDDIQGMKDEVSDLIDQRKitrkitiyKGKEELLRGMKEEEALEADIVNELDKARDKAG 741
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 687 KSAQECLASSNNVKQMVLAGSKGSFINISQVTACVGQQNVE--------GQRIPFGFRERTLPHFSKFDYGPGSRGFVEN 758
Cdd:PRK14977 742 SSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKRKtrigfvltGGRLHEGYKDRALSHFQEGDDNPDAHGFVKN 821
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 759 SFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEHNV 838
Cdd:PRK14977 822 NYREGLNAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIDPQKLDHGE 901
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 839 iesfysfrgsrtmfgkrrvtlPLNFKRLILSEEMKNSGF-VSEGRISECRVELLD-FVGNLKFLtnkifsksstLADAII 916
Cdd:PRK14977 902 ---------------------AFNLERIIEKQKIEDRGKgASKDEIEELAKEYTKtFNANLPKL----------LADAIH 950
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*...
gi 2313927249 917 YfmqpkflSSLNLEGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK14977 951 G-------AELKEDELEAICAEGKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRTF 1001
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
1-809 |
1.04e-167 |
|
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: 509.80 E-value: 1.04e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLLKKECKSSKIKnardsrnrlnrvwslcktktlcgdktegsgcg 80
Cdd:cd01435 61 GHFGHIELPLPVYNPLFFDLLYKLLRGSCFYCHRFRISKWEVKLFVAK-------------------------------- 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 81 nrqplikkegLNLVAFMKDDEGKLILSGEKVYsILKRIPDSdleelgfnPSTSRPEWMVltvllvppppvrpsvimdGIL 160
Cdd:cd01435 109 ----------LKLLDKGLLVEAAELDFGYDMF-FLDVLLVP--------PNRFRPPSFL------------------GDK 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 161 RGEDDLTHKLSDIVKANNNLRRYEREGA---------------PAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGrp 225
Cdd:cd01435 152 VFENPQNVLLSKILKDNQQIRDLLASMRqaesqskldlisgktNSEKLINAWLQLQSAVNELFDSTKAPKSGKKSPPG-- 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 226 lksISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPG 305
Cdd:cd01435 230 ---IKQLLEKKEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLTFPEPVTPFNVEELRQAVINGPDVYPG 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 306 ANYIIREDGQRIDLRYN----RSSIIK-------------EGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKL- 367
Cdd:cd01435 307 ANAIEDEDGRLILLSALseerRKALAKlllllssaklllnGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHKVRVLPGEk 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 368 TFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREM 447
Cdd:cd01435 387 TLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTSRDTFFTREEY 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 448 MSLIY---------KSRNTIKSIRPSIKRPIRLYTGKQLYSINLPTLNYKRYSNIDGSFVSSFVSSNSfvssntntntnt 518
Cdd:cd01435 467 QQLVYaalrplftsDKDGRIKLLPPAILKPKPLWTGKQVISTILKNLIPGNAPLLNLSGKKKTKKKVG------------ 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 519 ntntntntnnlntnnlntnlntnkmvvqfFEYIDRILNDSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTV 598
Cdd:cd01435 535 -----------------------------GGKWGGGSEESQVIIRNGELLTGVLDKSQFGASAYGLVHAVYELYGGETAG 585
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 599 KFFDGSQRMVNAYLTYYsSFSCGIGDTIadkytmrkIVESIDLAKREvdtIIKSAREgrmermAGLSKFRTFESkiiLAL 678
Cdd:cd01435 586 KLLSALGRLFTAYLQMR-GFTCGIEDLL--------LTPKADEKRRK---ILRKAKK------LGLEAAAEFLG---LKL 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 679 NKardVSGKSAQECLAS-------SNNVKQMVLAGSKGSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSKFDYGPG 751
Cdd:cd01435 645 NK---VTSSIIKACLPKgllkpfpENNLQLMVQSGAKGSMVNASQISCLLGQQELEGRRVPLMVSGKTLPSFPPYDTSPR 721
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*...
gi 2313927249 752 SRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKINYD 809
Cdd:cd01435 722 AGGFITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLIKHLEGLKVNYD 779
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
189-809 |
6.25e-156 |
|
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: 470.38 E-value: 6.25e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 189 PAHVVRDYEQLLQFHVATLMDNEISGQPQAvQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISEL 268
Cdd:cd00399 101 PSVIIEERWRLLQEHVDTYLDNGIAGQPQT-QKSGRPLRSLAQRLKGKEGRFRGNLMGKRVDFSGRSVISPDPNLRLDQV 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 269 GVPKRVAMIhtfpekvnsfnlekmeelvkkgpfeypganyiiredgqridlrynrssiikegytverhmLDGDVVLFNRQ 348
Cdd:cd00399 180 GVPKSIALT------------------------------------------------------------LDGDPVLFNRQ 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 349 PSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDT 428
Cdd:cd00399 200 PSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQDT 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 429 LIGVRRLTsldsffseremmsliyksrntiksirpsikrpirlyTGKQLYSINLPTlnykrysnidgsfvssfvssnsfv 508
Cdd:cd00399 280 LLGAYLLT------------------------------------LGKQIVSAALPG------------------------ 299
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 509 ssntntntntntntntntnnlntnnlntnlntnkmvvqffeyidrilndsnilivkgnlllgtldkksvgntqgGIIHVI 588
Cdd:cd00399 300 --------------------------------------------------------------------------GLLHTV 305
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 589 KNDYGCDSTVKFFDGSQRMVNAYLTYySSFSCGIGDTIADKYTMRKIVESIDLAKREVDTIIKSAREGRMERMAGLSKFR 668
Cdd:cd00399 306 TRELGPEKAAKLLSNLQRVGFVFLTT-SGFSVGIGDVIDDGVIPEEKTELIEEAKKKVDEVEEAFQAGLLTAQEGMTLEE 384
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 669 TFESKIILALNKARDVSGKSAQ---ECLASSNNVKQMVLAGSKGSFINISQVTACVGQQNVEGQRIPFGFRERTLPHFSK 745
Cdd:cd00399 385 SLEDNILDFLNEARDKAGSAASvnlDLVSKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIPRGFSDRTLPHFSK 464
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2313927249 746 FDYGPGSRGFVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKINYD 809
Cdd:cd00399 465 DDYSPEAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
156-433 |
2.43e-151 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 449.28 E-value: 2.43e-151
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 156 MDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEisGQPQAVQKSGRPLKSISARLKG 235
Cdd:smart00663 21 LDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNE--GLPRANQKSGRPLKSLSQRLKG 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 236 KEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPfeyPGANYIIRedGQ 315
Cdd:smart00663 99 KEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNIDKLRKLVRNGP---NGAKYIIR--GK 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 316 RIDLRYNRSSII----KEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLH 391
Cdd:smart00663 174 KTNLKLAKKSKIanhlKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCSPYNADFDGDEMNLH 253
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 2313927249 392 MPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVR 433
Cdd:smart00663 254 VPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
1-244 |
3.89e-97 |
|
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: 308.84 E-value: 3.89e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLLKKE----CKSSKIKNARDSRNRLNRVWSLCKTKTLC-GDKTE 75
Cdd:pfam04997 69 GHFGHIELAKPVFHIGFFKKTLKILECVCKYCSKLLLDPGKpklfNKDKKRLGLENLKMGAKAILELCKKKDLCeHCGGK 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 76 GSGCGNRQPLIKKEGLNLVAFMK---DDEGKLILSGEKVYSILKRIPDSDLEELGFNPSTSRPEWMVLTVLLVPPPPVRP 152
Cdd:pfam04997 149 NGVCGSQQPVSRKEGLKLKAAIKkskEEEEKEILNPEKVLKIFKRISDEDVEILGFNPSGSRPEWMILTVLPVPPPCIRP 228
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 153 SVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISAR 232
Cdd:pfam04997 229 SVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVATLFDNEIPGLPPALQKSKRPLKSISQR 308
|
250
....*....|..
gi 2313927249 233 LKGKEGRVRGNL 244
Cdd:pfam04997 309 LKGKEGRFRGNL 320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
246-406 |
1.53e-86 |
|
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: 274.56 E-value: 1.53e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 246 GKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEYPGANYIIREDGQRIDLRYNRSS 325
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIKRLRQLVENGPNVYPGANYIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 326 IIKE---GYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAEL 402
Cdd:pfam00623 81 LDKEleiGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....
gi 2313927249 403 KELA 406
Cdd:pfam00623 161 EELM 164
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
1-813 |
1.97e-67 |
|
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: 240.77 E-value: 1.97e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 1 GHFGHMELARPVFHIGFLSKIKKILETVCFYCSKIKLLKKecKSSKIKNARDSrnrlnrvWSLcktktLCGD-KTEGSGC 79
Cdd:cd10506 47 GHFGVIKLPVTIYHPYFISEVAQILNKICPGCKSIKQKKK--KPPRETLPPDY-------WDF-----IPKDgQQEESCV 112
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 80 GNRQPLIkkeglnlvafmkddegklilsgekVYSILKRIPDsdleelgfnpsTSRPEWmvltvllvppppvrpsvIMDGI 159
Cdd:cd10506 113 TKNLPIL------------------------SLAQVKKILK-----------EIDPKL-----------------IAKGL 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 160 LRGEDdltHKLSDIVKANNNLRryeregapahvVRDYEQLLQFHVATLMDNEISGQPQAVQKSGRPLKSISARLKGKEgR 239
Cdd:cd10506 141 PRQEG---LFLKCLPVPPNCHR-----------VTEFTHGFSTGSRLIFDERTRAYKKLVDFIGTANESAASKKSGLK-W 205
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 240 VRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKGPFEypgaNYiirEDGQRIDL 319
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLQEYCDLTLLL----KG---VIGVRRNG 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 320 RYNRSSIIKE---GYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKK-LTFRLNLSATTPYNADFDGDEMNLHMPQS 395
Cdd:cd10506 279 RLVGVRSHNTlqiGDVIHRPLVDGDVVLVNRPPSIHQHSLIALSVKVLPTnSVVSINPLCCSPFRGDFDGDCLHGYIPQS 358
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 396 YQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSL-IYKSRN-----TIKSirPSIKRPi 469
Cdd:cd10506 359 LQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGVFLDKAQMQQLqMLCPSQlpppaIIKS--PPSNGP- 435
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 470 rLYTGKQLYSINLPT-LNYKrysnidgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlntnkmvvqff 548
Cdd:cd10506 436 -LWTGKQLFQMLLPTdLDYS------------------------------------------------------------ 454
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 549 eyidrilNDSNILIVKGNLLLGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGD--TI 626
Cdd:cd10506 455 -------FPSNLVFISDGELISSSGGSSWLRDSEGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMR-GFSVSLSDlyLS 526
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 627 ADKYTMRKIVESIDLAKREV---------------DTIIKSAREGRM----ERMAGLSKF--RTFESKIILALNKARDVS 685
Cdd:cd10506 527 SDSYSRQKMIEEISLGLREAeiacnikqllvdsrkDFLSGSGEENDVssdvERVIYERQKsaALSQASVSAFKQVFRDIQ 606
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 686 gKSAQECLASSNNVKQMVLAGSKGSFINISQVTACVGQQNVEGQ---RIP-----FGFRERTLPHFSKFDY-----GPGS 752
Cdd:cd10506 607 -NLVYKYASKDNSLLAMIKAGSKGSLLKLVQQSGCLGLQLSLVKlsyRIPrqlscAAWNSQKSPRVIEKDGsecteSYIP 685
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2313927249 753 RGFVENSFLSGLTPEEFYFHTMGGREGLIDtaiKTAET-GYIQRRLVKAMEDCKINYDCSVR 813
Cdd:cd10506 686 YGVVESSFLDGLNPLECFVHSITSRDSSFS---SNADLpGTLFRKLMFFMRDIYVAYDGTVR 744
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
4-974 |
1.22e-56 |
|
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: 212.99 E-value: 1.22e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 4 GHMELARPVFHIGFL----SKIKKIL-------ETVCFYCSKIKLlkkecksSKIKNARDSRNRLNRVwSLCKTKTLCGD 72
Cdd:TIGR02386 85 GHIELAAPVAHIWYFkglpSRIGLLLditakelESVLYFENYVVL-------DPGDTKLDKKEVLDET-EYREVLKRYGD 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 73 KTE-GSGCGNRQPLIKKEGLNLVAFMKDDEGKLILSGEKVYSILKRipdsdLEEL-GFNPSTSRPEWMvltvllvppppv 150
Cdd:TIGR02386 157 GFRaGMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKR-----LEIVeAFKDSGNRPEWM------------ 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 151 rpsvIMDGI------------LRGEDDLTHKLSD----IVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISG 214
Cdd:TIGR02386 220 ----VLDVIpvippelrpmvqLDGGRFATSDLNDlyrrVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRG 295
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 215 QPqAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAM-------IHTFPEKVNSF 287
Cdd:TIGR02386 296 KP-VVGKNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALelfkpfiIKRLIDRELAA 374
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 288 NLEKMEELVKkgpfeypganyiiREDGQRIDLRYnrsSIIKEgytverhmldgDVVLFNRQPSLHKMSMMAHTVKVMKKL 367
Cdd:TIGR02386 375 NIKSAKKMIE-------------QEDPEVWDVLE---DVIKE-----------HPVLLNRAPTLHRLGIQAFEPVLVEGK 427
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 368 TFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTS-LDSFFSERE 446
Cdd:TIGR02386 428 AIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKPIVTPSQDMVLGLYYLTTeKPGAKGEGK 507
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 447 MMSLIYKSRNTIKSIRPSIKRPIRLYTGKQLysinLPTLNYKRYSNidgsfvssfvssnsfvssntntntntntntntnt 526
Cdd:TIGR02386 508 IFSNVDEAIRAYDNGKVHLHALIGVRTSGEI----LETTVGRVIFN---------------------------------- 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 527 nnlntnnlntnlntnkmvvqffeyidRILNDSNILIVKGNlllgTLDKKSVGNtqggIIHVIKNDYGCDSTVKFFDgsqR 606
Cdd:TIGR02386 550 --------------------------EILPEGFPYINDNE----PLSKKEISS----LIDLLYEVHGIEETAEMLD---K 592
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 607 MVNAYLTYYSSFSCGIGdtIADKYTMRKIVESIDLAKREVDTIIKSAREGRM---ERmaglskfrtfESKIILALNKARD 683
Cdd:TIGR02386 593 IKALGFKYATKSGTTIS--ASDIVVPDEKYEILKEADKEVAKIQKFYNKGLItdeER----------YRKVVSIWSETKD 660
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 684 VSGKSAQECLASS----NNVKQMVLAGSKGsfiNISQVTACVGQQ----NVEGQRIPfgfrertLPhfskfdygpgsrgf 755
Cdd:TIGR02386 661 KVTDAMMKLLKKDtykfNPIFMMADSGARG---NISQFRQLAGMRglmaKPSGDIIE-------LP-------------- 716
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 756 VENSFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKINY-DCSVRDG--SGRVFQflygddgfdat 832
Cdd:TIGR02386 717 IKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREeDCGTEEGieVEAIVE----------- 785
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 833 yLEHNVIESFYSFRGSRTMFgkRRVTLPLNFKRLILSEEMknsgfvsegrISEcrvELLDFVGNLKFLTNKIFSKsstla 912
Cdd:TIGR02386 786 -GKDEIIESLKDRIVGRYSA--EDVYDPDTGKLIAEANTL----------ITE---EIAEKIENSGIEKVKVRSV----- 844
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2313927249 913 daiiyfmqpkfLSSLNLEGL------RNLVEEIKREIlrgivcaNEMVGTLASQSIGEPATQMTLNTF 974
Cdd:TIGR02386 845 -----------LTCESEHGVcqkcygRDLATGKLVEI-------GEAVGVIAAQSIGEPGTQLTMRTF 894
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
763-974 |
6.78e-53 |
|
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: 193.72 E-value: 6.78e-53
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 763 GLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKINYDCSVRDGSGRVFQFLYGDDGFDATYLEHNVIESF 842
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 843 ysfrGSRTMFGKRRVTLPLNFKRLILSEEMKNSGFVSEGR-ISECRVELLDFVGNLKFLTNKIFSKSStLADAIIYfmQP 921
Cdd:pfam04998 81 ----EFSDLKLEDKFKNDLLDDLLLLSEFSLSYKKEILVRdSKLGRDRLSKEAQERATLLFELLLKSG-LESKRVR--SE 153
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|...
gi 2313927249 922 KFLSSLNLEGLRNlveEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:pfam04998 154 LTCNSKAFVCLLC---YGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTF 203
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
3-974 |
8.50e-52 |
|
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: 198.08 E-value: 8.50e-52
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 3 FGHMELARPVFHIGFL----SKIK-------KILETVCFYCSKI-------KLLKKEcksskIKNARDSRNRLNRVwslc 64
Cdd:COG0086 92 MGHIELAMPVFHIWGLkslpSRIGllldmslRDLERVLYFESYVvidpgdtPLEKGQ-----LLTEDEYREILEEY---- 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 65 ktktlcGDK-TEGSGCGNRQPLIKKEGLNLVAFMKDDEGKLILSGEKVYSILKRIpdsDLEElGFNPSTSRPEWMvltvl 143
Cdd:COG0086 163 ------GDEfVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRL---KVVE-AFRESGNRPEWM----- 227
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 144 lvppppvrpsvIMDGI------LR----------GEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATL 207
Cdd:COG0086 228 -----------ILDVLpvippdLRplvpldggrfATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDAL 296
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 208 MDNEISGQPqAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMihtfpekvnsf 287
Cdd:COG0086 297 FDNGRRGRA-VTGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMAL----------- 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 288 nlekmeELVKkgPFeypganyIIRedgqRIDLRYNRSSIIKEGYTVERH----------MLDGDVVLFNRQPSLHKMSMM 357
Cdd:COG0086 365 ------ELFK--PF-------IYR----KLEERGLATTIKSAKKMVEREepevwdileeVIKEHPVLLNRAPTLHRLGIQ 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 358 AHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTS 437
Cdd:COG0086 426 AFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPANGKPIIVPSQDMVLGLYYLTR 505
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 438 LD-------SFFSEREMMSLIYksRNTIKSIRPSIKRPIRLyTGKQLYSINLPTLNykRY--SNIdgsfvssfvssnsfv 508
Cdd:COG0086 506 ERegakgegMIFADPEEVLRAY--ENGAVDLHARIKVRITE-DGEQVGKIVETTVG--RYlvNEI--------------- 565
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 509 ssntntntntntntntntnnlntnnlntnlntnkmVVQFFEYIDRILNDSNIlivkgnlllgtldkksvgntqGGIIHVI 588
Cdd:COG0086 566 -----------------------------------LPQEVPFYNQVINKKHI---------------------EVIIRQM 589
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 589 KNDYGCDSTVKFFDGSQRMVNAYLTyYSSFSCGIGDTIADKYTMRKIVEsidlAKREVDTIIKSAREGRM---ERmagls 665
Cdd:COG0086 590 YRRCGLKETVIFLDRLKKLGFKYAT-RAGISIGLDDMVVPKEKQEIFEE----ANKEVKEIEKQYAEGLItepER----- 659
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 666 kfrtfESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSKGSFINISQVTACVGQQNVEGQRI---PFG--FRErtl 740
Cdd:COG0086 660 -----YNKVIDGWTKASLETESFLMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIietPIGsnFRE--- 731
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 741 phfskfdygpgsrgfvensflsGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKIN-YDCSVRDGSgRV 819
Cdd:COG0086 732 ----------------------GLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTeEDCGTDRGI-TV 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 820 FQFLYGDDgfdatylehnVIESFYSFRGSRTmfgkrrvtlplnfkrliLSEEMKNSGfvsEGRISECRVELLDFVGNLKf 899
Cdd:COG0086 789 TAIKEGGE----------VIEPLKERILGRV-----------------AAEDVVDPG---TGEVLVPAGTLIDEEVAEI- 837
|
970 980 990 1000 1010 1020 1030
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2313927249 900 ltnkifsksstLADAIIYfmQPKFLSSLNLEGLRNLVEEIKREILRGIVCAN--EMVGTLASQSIGEPATQMTLNTF 974
Cdd:COG0086 838 -----------IEEAGID--SVKVRSVLTCETRGGVCAKCYGRDLARGHLVNigEAVGVIAAQSIGEPGTQLTMRTF 901
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
4-974 |
2.64e-48 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 188.21 E-value: 2.64e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 4 GHMELARPVFHIGFLSKIK-----------KILETVCFYCSKIKLLKKEC----KSSKIKNARDSRNRlNRVWSLCKTKT 68
Cdd:PRK09603 1483 GHIELATPVAHIWYVNSLPsrigtllgvkmKDLERVLYYEAYIVKEPGEAaydnEGTKLVMKYDILNE-EQYQNISRRYE 1561
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 69 LCGDKTEGSGCGNRQPLikkEGLNLVAFMKD--DEGKLILSGEKVYSILKRIPDSDleelGFNPSTSRPEWMVLTVLLVP 146
Cdd:PRK09603 1562 DRGFVAQMGGEAIKDLL---EEIDLITLLQSlkEEVKDTNSDAKKKKLIKRLKVVE----SFLNSGNRPEWMMLTVLPVL 1634
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 147 PPPVRPSVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQpqAVQKSG-RP 225
Cdd:PRK09603 1635 PPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTN--AVKGANkRP 1712
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 226 LKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMihtfpEKVNSFNLEKMEElvkkgpfeyPG 305
Cdd:PRK09603 1713 LKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMAL-----ELFKPHLLSKLEE---------RG 1778
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 306 ANYIIREDGQRIDLRYNrssiikEGYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDG 385
Cdd:PRK09603 1779 YATTLKQAKRMIEQKSN------EVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDG 1852
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 386 DEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLtSLdsffsEREMMSLIYKSRNTIKSIRpsi 465
Cdd:PRK09603 1853 DQMAVHVPLSQEAIAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYL-SL-----EKSGVKGEHKLFSSVNEII--- 1923
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 466 krpIRLYTGKQLYSINLPTLNYKRYSNidgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnLNTNKMVv 545
Cdd:PRK09603 1924 ---TAIDTKELDIHAKIRVLDQGNIIA---------------------------------------------TSAGRMI- 1954
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 546 qffeyIDRILNDsnilIVKGNLLLGTLDKKSVGNTqggIIHVIKNDyGCDSTVKFFDGSQRMVNAYLTyyssfSCGIGDT 625
Cdd:PRK09603 1955 -----IKSILPD----FIPTDLWNRPMKKKDIGVL---VDYVHKVG-GIGITATFLDNLKTLGFRYAT-----KAGISIS 2016
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 626 IADKYTMRKIVESIDLAKREVDTIiksaregRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASS----NNVKQ 701
Cdd:PRK09603 2017 MEDIITPKDKQKMVEKAKVEVKKI-------QQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDkegfNSIYM 2089
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 702 MVLAGSKGSFINISQVTACVG-QQNVEGQRIpfgfrerTLPHFSKFDygpgsrgfvensflSGLTPEEFYFHTMGGREGL 780
Cdd:PRK09603 2090 MADSGARGSAAQIRQLSAMRGlMTKPDGSII-------ETPIISNFK--------------EGLNVLEYFNSTHGARKGL 2148
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 781 IDTAIKTAETGYIQRRLVKAMEDCKINY-DCSVRDGSgRVFQFLYGDDgfdatylehnVIESFysfrgSRTMFGKrrvtl 859
Cdd:PRK09603 2149 ADTALKTANAGYLTRKLIDVSQNVKVVSdDCGTHEGI-EITDIAVGSE----------LIEPL-----EERIFGR----- 2207
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 860 plnfkrlILSEEMKNSgfvsegrisecrvelldfvgnlkfLTNKIFSKSSTLADAiiyfmqpkflsslnlEGLRNLVEE- 938
Cdd:PRK09603 2208 -------VLLEDVIDP------------------------ITNEILLYADTLIDE---------------EGAKKVVEAg 2241
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*....
gi 2313927249 939 IKREILRGI--------VCAN---------------EMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK09603 2242 IKSITIRTPvtckapkgVCAKcyglnlgegkmsypgEAVGVVAAQSIGEPGTQLTLRTF 2300
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
118-807 |
1.49e-44 |
|
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: 171.93 E-value: 1.49e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 118 IPDSDLEEL------GFNPSTSRPEWMvltvllvppppvrpsvIMDGI------LR------GEDDLTHKLSD----IVK 175
Cdd:cd01609 116 LSPKDLERViyfvveSFRKSGNRPEWM----------------ILTVLpvippdLRpmvqldGGRFATSDLNDlyrrVIN 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 176 ANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPqAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARS 255
Cdd:cd01609 180 RNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKP-VTGANNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRS 258
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 256 VITPDSNISISELGVPKRVAMihtfpekvnsfNLEK---MEELVKKgpfeypGANYIIREDGQRIDlryNRSSIIkegYT 332
Cdd:cd01609 259 VIVVGPELKLHQCGLPKEMAL-----------ELFKpfvIRELIER------GLAPNIKSAKKMIE---RKDPEV---WD 315
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 333 VERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQI 412
Cdd:cd01609 316 ILEEVIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNI 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 413 VSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMmsliyksrntiksirpsikrpIRLYTGKQLYSINLPtlnykrysn 492
Cdd:cd01609 396 LSPASGKPIVTPSQDMVLGLYYLTKERKGDKGEGI---------------------IETTVGRVIFNEILP--------- 445
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 493 idgsfvssfvssnsfvssntntntntntntntntnnlntnnlntnlntnkmvvQFFEYIDRilndsnilivkgnlllgTL 572
Cdd:cd01609 446 -----------------------------------------------------EGLPFINK-----------------TL 455
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 573 DKKSVGNtqggIIHVIKNDYGCDSTVKFFDgsQRMVNAYltYYSSFSC---GIGD--TIADKytmRKIVESidlAKREVD 647
Cdd:cd01609 456 KKKVLKK----LINECYDRYGLEETAELLD--DIKELGF--KYATRSGisiSIDDivVPPEK---KEIIKE---AEEKVK 521
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 648 TIIKSAREGRM---ERmaglskfrtfESKIILALNKARD-VSGKSAQECLASSNN-VKQMVLAGSKGSFINISQVTACVG 722
Cdd:cd01609 522 EIEKQYEKGLLteeER----------YNKVIEIWTEVTEkVADAMMKNLDKDPFNpIYMMADSGARGSKSQIRQLAGMRG 591
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 723 -QQNVEGQRIPfgfrertLPhfskfdygpgsrgfVENSFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAM 801
Cdd:cd01609 592 lMAKPSGKIIE-------LP--------------IKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVA 650
|
....*.
gi 2313927249 802 EDCKIN 807
Cdd:cd01609 651 QDVIVT 656
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
156-974 |
5.64e-44 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 173.90 E-value: 5.64e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 156 MDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPqAVQKSGRPLKSISARLKG 235
Cdd:PRK14906 333 LDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRP-VTGPGNRPLKSLADMLKG 411
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 236 KEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMihtfpEKVNSFNLEKMEELVKkgpfeypGANyiIREDGQ 315
Cdd:PRK14906 412 KQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMAL-----ELFKPFVMKRLVELEY-------AAN--IKAAKR 477
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 316 RIDlryNRSSIIkegYTVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQS 395
Cdd:PRK14906 478 AVD---RGASYV---WDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLS 551
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 396 YQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLTSL-DSF------FSEREMMSLIYKSRNTIKSIRPSIKRP 468
Cdd:PRK14906 552 TQAQAEARVLMLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTErDGFegegrtFADFDDALNAYDARADLDLQAKIVVRL 631
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 469 IRLYTGKQlysinlptlNYKRYSNIDGSfvssfvssnsfvssntntntntntntntntnnlntnnlntnlntnkmvVQFF 548
Cdd:PRK14906 632 SRDMTVRG---------SYGDLEETKAG------------------------------------------------ERIE 654
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 549 EYIDRILNDsNILIVKGNLLLGTLDKKSVGNtqggIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTyyssfSCGIGDTIAD 628
Cdd:PRK14906 655 TTVGRIIFN-QVLPEDYPYLNYKMVKKDIGR----LVNDCCNRYSTAEVEPILDGIKKTGFHYAT-----RAGLTVSVYD 724
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 629 KYTMRKIVESIDLAKREVDTIIKSAREGRMERmaglskfRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSK 708
Cdd:PRK14906 725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSE-------RERHKQVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGAR 797
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 709 GSFINISQVTACVG-QQNVEGQRIpfgfrerTLPhfskfdygpgsrgfVENSFLSGLTPEEFYFHTMGGREGLIDTAIKT 787
Cdd:PRK14906 798 GNIKQIRQLAGMRGlMADMKGEII-------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRT 856
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 788 AETGYIQRRLVKAMEDCKI-NYDCSVRDGsgrvfqflygddgfdatylehnviesfysfrgsrtmfgkrrVTLPLnfkrl 866
Cdd:PRK14906 857 ADSGYLTRRLVDVAQDVIVrEEDCGTDEG-----------------------------------------VTYPL----- 890
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 867 ilseeMKNSGFVSEGRISECRVEllDFVGnlkfltnkifsksstlADAIIYFMQPKFLSSlnLEGLRNLVEE-IKREILR 945
Cdd:PRK14906 891 -----VKPKGDVDTNLIGRCLLE--DVCD----------------PNGEVLLSAGDYIES--MDDLKRLVEAgVTKVQIR 945
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|..
gi 2313927249 946 GIV-CANE----------------------MVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK14906 946 TLMtCHAEygvcqkcygwdlatrrpvnigtAVGIIAAQSIGEPGTQLTMRTF 997
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
4-974 |
2.30e-43 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 172.50 E-value: 2.30e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 4 GHMELARPVFHIGFL----SKIKKIL-------ETVCFYCSKI-------KLLKKECKSSKIKN-ARDSRNrLNRVWSLC 64
Cdd:PRK14844 1534 GHIELASPVAHIWFLkslpSRIGALLdmslrdiENILYSDNYIvidplvsPFEKGEIISEKAYNeAKDSYG-IDSFVAMQ 1612
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 65 KTKTLcgdktegsgcgnRQPLIKkegLNLVAFMKDDEGKL--ILSGEKVYSILKRIPDSDleelGFNPSTSRPEWMVLTV 142
Cdd:PRK14844 1613 GVEAI------------RELLTR---LDLHEIRKDLRLELesVASEIRRKKIIKRLRIVE----NFIKSGNRPEWMILTT 1673
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 143 LLVPPPPVRPSVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNeiSGQPQAVQKS 222
Cdd:PRK14844 1674 IPILPPDLRPLVSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDN--SRRNALVNKA 1751
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 223 GRP--LKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISELGVPKRVAMIHTFPEKVNSFNLEKMEELVKKgp 300
Cdd:PRK14844 1752 GAVgyKKSISDMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKF-- 1829
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 301 feypgANYIIREDGQRI-DLRynrSSIIKEgytverhmldgDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPY 379
Cdd:PRK14844 1830 -----ASKLIRAEKPEVwDML---EEVIKE-----------HPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAF 1890
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 380 NADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLVQDTLIGVRRLT-------SLDSF--FSEREmmsl 450
Cdd:PRK14844 1891 NADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPSNGRPIIVPSKDIVLGIYYLTlqepkedDLPSFgaFCEVE---- 1966
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 451 iYKSRNTIKSIRPSIKRPIRlytgkqlYSINLPTLNYKRYSNIDGSFvssfvssnsfvssntntntntntntntntnnln 530
Cdd:PRK14844 1967 -HSLSDGTLHIHSSIKYRME-------YINSSGETHYKTICTTPGRL--------------------------------- 2005
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 531 tnnlntnlntnkMVVQFFEYIDRILND--SNILIVKgnlllgtldkksvgnTQGGIIHVIKNDYGCDSTVKFFDgsQRMV 608
Cdd:PRK14844 2006 ------------ILWQIFPKHENLGFDliNQVLTVK---------------EITSIVDLVYRNCGQSATVAFSD--KLMV 2056
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 609 NAYltYYSSFScGIGDTIADKYTMRKIVESIDLAKREVDTIIKSAREG---RMERMaglskfrtfeSKIILALNKARDVS 685
Cdd:PRK14844 2057 LGF--EYATFS-GVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGlitRSERY----------NKVIDEWSKCTDMI 2123
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 686 GKSAQECL------ASSNNVKQMVLAGSKGSfinISQVTACVGQQNVEGQriPFGFRERTlPHFSkfdygpgsrgfvenS 759
Cdd:PRK14844 2124 ANDMLKAIsiydgnSKYNSVYMMVNSGARGS---TSQMKQLAGMRGLMTK--PSGEIIET-PIIS--------------N 2183
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 760 FLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKI-NYDCSVRDGSgrvfqflygddGFDATYLEHNV 838
Cdd:PRK14844 2184 FREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVtKHDCKTKNGL-----------VVRATVEGSTI 2252
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 839 IESFYSFRGSRTmfGKRRVTLPLNFKRLILSEEMknsgfVSEGRISECRVELLDFVGNLKFLTNKIFSKSSTLAdaiiyf 918
Cdd:PRK14844 2253 VASLESVVLGRT--AANDIYNPVTKELLVKAGEL-----IDEDKVKQINIAGLDVVKIRSPLTCEISPGVCSLC------ 2319
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*..
gi 2313927249 919 mqpkflsslnleglrnlveeIKREILRG-IVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK14844 2320 --------------------YGRDLATGkIVSIGEAVGVIAAQSVGEPGTQLTMRTF 2356
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
649-756 |
8.57e-41 |
|
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 145.58 E-value: 8.57e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 649 IIKSAREGRMERMAGLSKFRTFESKIILALNKARDVSGKSAQECLASSNNVKQMVLAGSKGSFINISQVTACVGQQNVEG 728
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 2313927249 729 QRIPFGFRERTLPHFSKFDYGPGSRGFV 756
Cdd:pfam05000 81 KRIPFGFSGRTLPHFKKDDEGPESRGFV 108
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
177-974 |
2.20e-38 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 155.61 E-value: 2.20e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 177 NNNLRRYEREGAPAHVVRDYEQLLQFHVATLMDNEISGQPqAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARSV 256
Cdd:PRK00566 266 NNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRP-VTGPNNRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSV 344
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 257 ITPDSNISISELGVPKRVAMihtfpekvnsfnlekmeELVKkgPFeypganyIIREdgqridlrynrssIIKEGYT---- 332
Cdd:PRK00566 345 IVVGPELKLHQCGLPKKMAL-----------------ELFK--PF-------IMKK-------------LVERGLAttik 385
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 333 -----VERHM------LDgDV-----VLFNRQPSLHKMSMMAhtvkvmkkltF----------RLNLSATTPYNADFDGD 386
Cdd:PRK00566 386 sakkmVEREDpevwdvLE-EVikehpVLLNRAPTLHRLGIQA----------FepvliegkaiQLHPLVCTAFNADFDGD 454
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 387 EMNLHMPQSYQTMAELKELAyLPTQ-IVSPQSNRPVMGLVQDTLIGVRRLTSLD-------SFFSEREMMSLIYKSR--- 455
Cdd:PRK00566 455 QMAVHVPLSLEAQAEARVLM-LSSNnILSPANGKPIIVPSQDMVLGLYYLTRERegakgegMVFSSPEEALRAYENGevd 533
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 456 -NTIKSIRpsIKRPIRLYT--GKQLYSINLPTlNYkRYSNIDgsfvssfvssnsfvssntntntntntntntntnnlntn 532
Cdd:PRK00566 534 lHARIKVR--ITSKKLVETtvGRVIFNEILPE-GL-PFINVN-------------------------------------- 571
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 533 nlntnlntnkmvvqffeyidrilndsnilivkgnlllGTLDKKSVGNtqggIIHVIKNDYGCDSTVKFFDgsqRMvnAYL 612
Cdd:PRK00566 572 -------------------------------------KPLKKKEISK----IINEVYRRYGLKETVIFLD---KI--KDL 605
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 613 TYYSSF----SCGIGDTI--ADKYTMrkivesIDLAKREVDTIIKSAREGRM---ERmaglskfrtfESKIILALNKARD 683
Cdd:PRK00566 606 GFKYATrsgiSIGIDDIVipPEKKEI------IEEAEKEVAEIEKQYRRGLItdgER----------YNKVIDIWSKATD 669
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 684 VSGKSAQECL----ASSNNVKQMVLAGSKGSFINISQVTacvgqqnvegqripfgfrertlphfskfdygpGSRG----- 754
Cdd:PRK00566 670 EVAKAMMKNLskdqESFNPIYMMADSGARGSASQIRQLA--------------------------------GMRGlmakp 717
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 755 ---FVEN----SFLSGLTPEEFYFHTMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKIN-YDCsvrdGSgrvfqflygD 826
Cdd:PRK00566 718 sgeIIETpiksNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVReDDC----GT---------D 784
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 827 DGFDATYL--EHNVIESFYSFRGSRTMFgkRRVTLPLNFKRLILSEEMknsgfvsegrISEcrvelldfvgnlkfltnki 904
Cdd:PRK00566 785 RGIEVTAIieGGEVIEPLEERILGRVLA--EDVVDPETGEVIVPAGTL----------IDE------------------- 833
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 905 fskssTLADAIIyfmqpkflsslnleglRNLVEEIK-REIL-----RGiVCAN---------------EMVGTLASQSIG 963
Cdd:PRK00566 834 -----EIADKIE----------------EAGIEEVKiRSVLtcetrHG-VCAKcygrdlatgklvnigEAVGVIAAQSIG 891
|
890
....*....|.
gi 2313927249 964 EPATQMTLNTF 974
Cdd:PRK00566 892 EPGTQLTMRTF 902
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
411-625 |
1.23e-37 |
|
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: 138.14 E-value: 1.23e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 411 QIVSPQSNRPVMGLVQDTLIGVRRLTSLDSFFSEREMMSLIYksrNTIKSIRPSIKRPIR-LYTGKQLYSINLP-TLNYK 488
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDTFFDREEVMQLLM---YGIVLPHPAILKPIKpLWTGKQTFSRLLPnEINPK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 489 RYSNIDGSFVSsfvssnsfvssntntntntntntntntnnlntnnlntnlntnkmvvqffeyidriLNDSNILIVKGNLL 568
Cdd:pfam04983 78 GKPKTNEEDLC-------------------------------------------------------ENDSYVLINNGELI 102
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*..
gi 2313927249 569 LGTLDKKSVGNTQGGIIHVIKNDYGCDSTVKFFDGSQRMVNAYLTYYsSFSCGIGDT 625
Cdd:pfam04983 103 SGVIDKKTVGKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFRYLTKS-GFSIGIDDI 158
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
177-469 |
3.12e-35 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 143.51 E-value: 3.12e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 177 NNNLRRYE--REGAPAHVVRDYEQLLQFHVATLMDNEISGQPqAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSAR 254
Cdd:CHL00018 303 NNTLTDLLttSRSTPGELVMCQKKLLQEAVDALLDNGIRGQP-MRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGR 381
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 255 SVITPDSNISISELGVPKRVAM--IHTFpekvnsfnleKMEELVKKGPFEYPG-ANYIIRedgqridlryNRSSIIKEgy 331
Cdd:CHL00018 382 SVIVVGPSLSLHQCGLPREIAIelFQPF----------VIRGLIRQHLASNIRaAKSKIR----------EKEPIVWE-- 439
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 332 tVERHMLDGDVVLFNRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQ 411
Cdd:CHL00018 440 -ILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMN 518
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 2313927249 412 IVSPQSNRPVMGLVQDTLIGVRRLTSLDSffseremmSLIYKSRNTIKSIRPSIKRPI 469
Cdd:CHL00018 519 LLSPAIGDPISVPSQDMLLGLYVLTIGNR--------RGIYANRYNPCNRKNSTKEPY 568
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
108-437 |
2.86e-34 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 140.27 E-value: 2.86e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 108 GEKVYSILKRIPDSDleelGFNPSTSRPEWMVLTVLLVPPPPVRPSVIMDGILRGEDDLTHKLSDIVKANNNLRRYEREG 187
Cdd:PRK02625 219 GQKRAKLIKRLRVID----NFIATGSRPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEIL 294
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 188 APAHVVRDYEQLLQFHVATLMDNEISGQpQAVQKSGRPLKSISARLKGKEGRVRGNLMGKRVDFSARSVITPDSNISISE 267
Cdd:PRK02625 295 APEIIVRNEKRMLQEAVDALIDNGRRGR-TVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQ 373
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 268 LGVPKRVAmIHTFPEKVnsfnlekMEELVKKGPFEYPGA--NYIIREDGQRIDlrynrssiikegytVERHMLDGDVVLF 345
Cdd:PRK02625 374 CGLPKEMA-IELFQPFV-------IHRLIRQGIVNNIKAakKLIQRADPEVWQ--------------VLEEVIEGHPVLL 431
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 346 NRQPSLHKMSMMAHTVKVMKKLTFRLNLSATTPYNADFDGDEMNLHMPQSYQTMAELKELAYLPTQIVSPQSNRPVMGLV 425
Cdd:PRK02625 432 NRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAEARLLMLASNNILSPATGEPIVTPS 511
|
330
....*....|..
gi 2313927249 426 QDTLIGVRRLTS 437
Cdd:PRK02625 512 QDMVLGCYYLTA 523
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
927-974 |
3.05e-16 |
|
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: 82.25 E-value: 3.05e-16
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 2313927249 927 LNLEGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:cd02584 3 LNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIGEPATQMTLNTF 50
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
930-974 |
6.84e-10 |
|
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: 61.99 E-value: 6.84e-10
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 2313927249 930 EGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:TIGR02389 23 EELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTF 67
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
927-974 |
7.23e-10 |
|
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: 61.88 E-value: 7.23e-10
10 20 30 40
....*....|....*....|....*....|....*....|....*...
gi 2313927249 927 LNLEGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:cd06528 16 LTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIGEPGTQMTLRTF 63
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
697-974 |
9.63e-10 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 62.71 E-value: 9.63e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 697 NNVKQMVLAGSKGsfiNISQVTACVGQQ----NVEGQRIpfgfrerTLPhfskfdygpgsrgfVENSFLSGLTPEEFYFH 772
Cdd:PRK02597 120 NSVYMMAFSGARG---NMSQVRQLVGMRglmaNPQGEII-------DLP--------------IKTNFREGLTVTEYVIS 175
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 773 TMGGREGLIDTAIKTAETGYIQRRLVKAMEDCKI-NYDCsvrdGSGRvfqflygddgfdatyleHNVIESfysfrgsrtM 851
Cdd:PRK02597 176 SYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVrEEDC----GTTR-----------------GIVVEA---------M 225
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 852 FGKRRVTLPLN---FKRLILSEEMKNSGFVSEGRISECRVELldfvgnlkfltnkifskSSTLADAIIyfMQPKFLSSLN 928
Cdd:PRK02597 226 DDGDRVLIPLGdrlLGRVLAEDVVDPEGEVIAERNTAIDPDL-----------------AKKIEKAGV--EEVMVRSPLT 286
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2313927249 929 LEGLRNlveeikreilrgiVCAN---------------EMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK02597 287 CEAARS-------------VCRKcygwslahnhlvdlgEAVGIIAAQSIGEPGTQLTMRTF 334
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
930-974 |
5.00e-09 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 59.47 E-value: 5.00e-09
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 2313927249 930 EGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK04309 38 EEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIGEPGTQMTMRTF 82
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
944-974 |
4.83e-08 |
|
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: 55.66 E-value: 4.83e-08
10 20 30
....*....|....*....|....*....|.
gi 2313927249 944 LRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:cd02735 3 MRSLVEPGEAVGLLAAQSIGEPSTQMTLNTF 33
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
926-974 |
6.50e-08 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 56.36 E-value: 6.50e-08
10 20 30 40
....*....|....*....|....*....|....*....|....*....
gi 2313927249 926 SLNLEGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:PRK14897 157 ELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIGEPGTQMTMRTF 205
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
952-974 |
3.65e-07 |
|
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: 50.88 E-value: 3.65e-07
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
954-974 |
6.09e-06 |
|
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: 49.14 E-value: 6.09e-06
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
952-974 |
1.72e-05 |
|
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: 46.75 E-value: 1.72e-05
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
775-974 |
9.19e-05 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 46.47 E-value: 9.19e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 775 GGREGLIDTAIKTAETGYIQRRLVKAME-------DCKINYDCSVrdgSGRVfqflygddgfdatylehnviesfysfrg 847
Cdd:CHL00117 184 GARKGVVDTAVRTADAGYLTRRLVEVVQhivvretDCGTTRGISV---SPRN---------------------------- 232
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 848 srtmfgkRRVTLPLNFKRLIlseemknsgfvseGRIsecrveLLDFVgnlkFLTNKIFSK-----SSTLADAIIYFMQPK 922
Cdd:CHL00117 233 -------GMMIERILIQTLI-------------GRV------LADDI----YIGSRCIATrnqdiGIGLANRFITFRAQP 282
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2313927249 923 FL--SSLNLEGLR--------------NLVEeikreilrgivcANEMVGTLASQSIGEPATQMTLNTF 974
Cdd:CHL00117 283 ISirSPLTCRSTSwicqlcygwslahgDLVE------------LGEAVGIIAGQSIGEPGTQLTLRTF 338
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
887-971 |
1.77e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 42.19 E-value: 1.77e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2313927249 887 RVELLDFVGNLKfltNKIFSKSSTLADaiiyfmqpkflssLNLEGLRNLVEEIKREILRGIVCANEMVGTLASQSIGEPA 966
Cdd:PRK14898 9 KIEDLDLPRSLK---DELFEKLSKRDG-------------VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPG 72
|
....*
gi 2313927249 967 TQMTL 971
Cdd:PRK14898 73 TQMSL 77
|
|
| |
