|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
3-1200 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2378.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 3 DVN--NFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGV 80
Cdd:PRK00566 1 DVNkqDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 81 EVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLEKKTLLSEAEFRDYYD 160
Cdd:PRK00566 81 EVTRSKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 161 KYPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDEL-ESATGQRLTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIR 239
Cdd:PRK00566 161 EYGDEFVAKMGAEAIKELLKNIDLEAEAEELREELkETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 240 PMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHM 319
Cdd:PRK00566 241 PLVQLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDM 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 320 LKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWD 399
Cdd:PRK00566 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 400 VLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNI 479
Cdd:PRK00566 401 VLEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 480 LNPKDGKPVVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVHASSFnnptfteeqnkKILA 559
Cdd:PRK00566 481 LSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSK-----------KLVE 549
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 560 TSVGKIIFNEIIPDSFAYINEPtqenlerktpnryfidpttlgegglkeyfeneeliEPFNKKFLGNIIAEVFNRFSITD 639
Cdd:PRK00566 550 TTVGRVIFNEILPEGLPFINVN-----------------------------------KPLKKKEISKIINEVYRRYGLKE 594
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 640 TSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGE 719
Cdd:PRK00566 595 TVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKA 674
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 720 LMQSLDKT----NPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTA 795
Cdd:PRK00566 675 MMKNLSKDqesfNPIYMMADSGARGSASQIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTA 754
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 796 LKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETIRHPETDEIIIRPDELITPE 875
Cdd:PRK00566 755 LKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEE 834
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 876 IAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVagsDITQ 955
Cdd:PRK00566 835 IADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITG 911
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 956 GLPRIQEIFEARNPKGQAVITEIEGVVEDIKLAKDRQQEIVVKGANETRSYLASGTSRIIVEIGQPVQRGEVLTEGSIEP 1035
Cdd:PRK00566 912 GLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDP 991
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1036 KNYLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKHRK 1115
Cdd:PRK00566 992 HDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGK 1071
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1116 RPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRRYSDVKYEKTAKP 1195
Cdd:PRK00566 1072 EPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDE 1151
|
....*
gi 577414957 1196 VAEVE 1200
Cdd:PRK00566 1152 EEAEA 1156
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
9-1186 |
0e+00 |
|
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: 1981.82 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 9 YMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGVEVTKSKVR 88
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 89 RERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLEKKTLLSEAEFRDYYDKYPGQFVA 168
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 169 KMGAEGIKDLLEEIDLDEELKLLRDELESATGQR-LTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGG 247
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQkRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 248 RFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRF 327
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 328 RQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEEVIRE 407
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 408 HPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKP 487
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 488 VVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVHASSfnnptfteeqnkKILATSVGKIIF 567
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSG------------EILETTVGRVIF 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 568 NEIIPDSFAYINEPtqenlerktpnryfidpttlgegglkeyfeneeliEPFNKKFLGNIIAEVFNRFSITDTSMMLDRM 647
Cdd:TIGR02386 549 NEILPEGFPYINDN-----------------------------------EPLSKKEISSLIDLLYEVHGIEETAEMLDKI 593
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 648 KDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGELMQSLDKT 727
Cdd:TIGR02386 594 KALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKD 673
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 728 ----NPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTALKTADSGY 803
Cdd:TIGR02386 674 tykfNPIFMMADSGARGNISQFRQLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGY 753
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 804 LTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEG-TEMIEPFIERIEGRYSKETIRHPETDEIIIRPDELITPEIAKKITD 882
Cdd:TIGR02386 754 LTRRLVDVAQDVVVREEDCGTEEGIEVEAIVEGkDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIEN 833
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 883 AGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGS--DITQGLPRI 960
Cdd:TIGR02386 834 SGIEKVKVRSVLTCESEHGVCQKCYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGAsgDITQGLPRV 913
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 961 QEIFEARNPKGQAVITEIEGVVEDIKLAKDRQQEIVVKGAN-ETRSYLASGTSRIIVEIGQPVQRGEVLTEGSIEPKNYL 1039
Cdd:TIGR02386 914 KELFEARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDENdEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLL 993
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1040 SVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKHRKRPAT 1119
Cdd:TIGR02386 994 RIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPAS 1073
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 577414957 1120 AKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRRYSD 1186
Cdd:TIGR02386 1074 AIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYKE 1140
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1-1183 |
0e+00 |
|
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: 1662.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1 MIDVNNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGV 80
Cdd:COG0086 1 MAFVEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 81 EVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLEKKTLLSEAEFRDYYD 160
Cdd:COG0086 81 EVTLSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 161 KYPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATG-QRLTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIR 239
Cdd:COG0086 161 EYGDEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSeQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLR 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 240 PMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHM 319
Cdd:COG0086 241 PLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDM 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 320 LKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWD 399
Cdd:COG0086 321 LKGKQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWD 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 400 VLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNI 479
Cdd:COG0086 401 ILEEVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNI 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 480 LNPKDGKPVVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVHASSfnnptfTEEQNKKILA 559
Cdd:COG0086 481 LSPANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITE------DGEQVGKIVE 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 560 TSVGKIIFNEIIPDSFAYINeptqenlerktpnryfidpttlgegglkeyfeneeliEPFNKKFLGNIIAEVFNRFSITD 639
Cdd:COG0086 555 TTVGRYLVNEILPQEVPFYN-------------------------------------QVINKKHIEVIIRQMYRRCGLKE 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 640 TSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGE 719
Cdd:COG0086 598 TVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESF 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 720 LMQSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTALKTA 799
Cdd:COG0086 678 LMAAFSSQNTTYMMADSGARGSADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTA 757
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 800 DSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETIRHPETDEIIIRPDELITPEIAKK 879
Cdd:COG0086 758 DSGYLTRRLVDVAQDVIVTEEDCGTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEI 837
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 880 ITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSditqglpR 959
Cdd:COG0086 838 IEEAGIDSVKVRSVLTCETRGGVCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASR-------A 910
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 960 IQEIFEARNPKGQAVITEIEGVVEDIKL---AKDRQQEIVVKGANETRSYLASGTSRIIVEIGQPVQRGEVLTEGSIEPK 1036
Cdd:COG0086 911 AEESSIEAKAGGIVRLNNLKVVVNEEGKgvvVSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHT 990
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1037 NYLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKhrKR 1116
Cdd:COG0086 991 PPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGV--II 1068
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 577414957 1117 PATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRR 1183
Cdd:COG0086 1069 GGLDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKT 1135
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
3-1203 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1482.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 3 DVNNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGVEV 82
Cdd:PRK14906 5 DVTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEV 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 83 TKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVV-------------------------- 136
Cdd:PRK14906 85 TRAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleel 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 137 ---------------------------------------VDPGPTGL-----EKKTLLSEA------------------- 153
Cdd:PRK14906 165 daerdrlieatrrlsvdyvpeddefvddigdderltaeeVRAEVADIyeeynERKALRREAfdafmqiepkqlisdealy 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 154 -EFRDYYDKYpgqFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQRLTRAIKRLEVVESFRNSGNKPSWMILDVLP 232
Cdd:PRK14906 245 rEMRLNYSIY---FKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIP 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 233 IIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRP 312
Cdd:PRK14906 322 VIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRP 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 313 LKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIER 392
Cdd:PRK14906 402 LKSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDR 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 393 MDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARML 472
Cdd:PRK14906 482 GASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVL 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 473 MLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAY-ANGFVHLHTRIGVH-------ASSF 544
Cdd:PRK14906 562 MLSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYdARADLDLQAKIVVRlsrdmtvRGSY 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 545 NNptFTEEQNKKILATSVGKIIFNEIIPDSFAYINeptqenlerktpnryfidpttlgegglkeyFEneeliepFNKKFL 624
Cdd:PRK14906 642 GD--LEETKAGERIETTVGRIIFNQVLPEDYPYLN------------------------------YK-------MVKKDI 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 625 GNIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNA 704
Cdd:PRK14906 683 GRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQ 762
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 705 VVEIWTDAKDQIQGELMQSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFIST 784
Cdd:PRK14906 763 VVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFIST 842
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 785 HGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIerieGRYSKETIRHPETDEI 864
Cdd:PRK14906 843 HGARKGLVDTALRTADSGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNLI----GRCLLEDVCDPNGEVL 918
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 865 IIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFH 944
Cdd:PRK14906 919 LSAGDYIESMDDLKRLVEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFH 998
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 945 TGGVAGSDITQGLPRIQEIFEARNPKGQAVITEIEGVvedIKLAKDRQQEI--VVKGANETRSYLASGTSRII--VEIGQ 1020
Cdd:PRK14906 999 SGGVAGDDITQGLPRVAELFEARKPKGEAVLAEISGT---LQITGDKTEKTltIHDQDGNSREYVVSARVQFMpgVEDGV 1075
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1021 PVQRGEVLTEGSIEPKNYLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLPGSLVDI 1100
Cdd:PRK14906 1076 EVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNR 1155
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1101 HNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTG 1180
Cdd:PRK14906 1156 YEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
|
1290 1300
....*....|....*....|...
gi 577414957 1181 MRRYSDVKYEKTAKPVAEVESQT 1203
Cdd:PRK14906 1236 LSRYRDVGLTYHGQKVDGPTSKS 1258
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
5-821 |
0e+00 |
|
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: 1325.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 5 NNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGVEVTK 84
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 85 SKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFasyvvvdpgptglekktllseaefrdyydkypg 164
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 165 qfvakmgaegikdlleeidldeelkllrdelesatgqrltraikrleVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQL 244
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 245 DGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQ 324
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 325 GRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEEV 404
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 405 IREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKD 484
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 485 GKPVVTPSQDMVLGNYYLTLERKDAVNTGaifnntnevlkayangfvhlhtrigvhassfnnptfteeqnkkILATSVGK 564
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEG-------------------------------------------IIETTVGR 437
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 565 IIFNEIIPDSFAYINeptqenlerktpnryfidpttlgegglkeyfeneeliEPFNKKFLGNIIAEVFNRFSITDTSMML 644
Cdd:cd01609 438 VIFNEILPEGLPFIN-------------------------------------KTLKKKVLKKLINECYDRYGLEETAELL 480
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 645 DRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGELMQSL 724
Cdd:cd01609 481 DDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNL 560
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 725 DK--TNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTALKTADSG 802
Cdd:cd01609 561 DKdpFNPIYMMADSGARGSKSQIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSG 640
|
810
....*....|....*....
gi 577414957 803 YLTRRLVDVAQDVIVREED 821
Cdd:cd01609 641 YLTRRLVDVAQDVIVTEED 659
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
3-975 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1133.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 3 DVNNFHYMkigLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGM-VCDRCGVE 81
Cdd:PRK09603 1395 DFSSFQLT---LASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVA 1471
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 82 VTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLE--------KKTLLSEA 153
Cdd:PRK09603 1472 ITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDnegtklvmKYDILNEE 1551
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 154 EFRDYYDKYPGQ-FVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQ-RLTRAIKRLEVVESFRNSGNKPSWMILDVL 231
Cdd:PRK09603 1552 QYQNISRRYEDRgFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDaKKKKLIKRLKVVESFLNSGNRPEWMMLTVL 1631
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 232 PIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNR 311
Cdd:PRK09603 1632 PVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKR 1711
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 312 PLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIE 391
Cdd:PRK09603 1712 PLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIE 1791
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 392 RMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARM 471
Cdd:PRK09603 1792 QKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKV 1871
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 472 LMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERKDAVNTGAIFNNTNEVLKAYANGFVHLHTRIGVhassfnnptfte 551
Cdd:PRK09603 1872 LMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRV------------ 1939
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 552 EQNKKILATSVGKIIFNEIIPDsfayineptqenlerktpnryFIdPTTLGEGGLKeyfeneeliepfnKKFLGNIIAEV 631
Cdd:PRK09603 1940 LDQGNIIATSAGRMIIKSILPD---------------------FI-PTDLWNRPMK-------------KKDIGVLVDYV 1984
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 632 FNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTD 711
Cdd:PRK09603 1985 HKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTE 2064
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 712 AKDQIQGELMQSL--DKT--NPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGA 787
Cdd:PRK09603 2065 VNDKMSKEMMTAIakDKEgfNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGA 2144
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 788 RKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETIRHPETDEIIIR 867
Cdd:PRK09603 2145 RKGLADTALKTANAGYLTRKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLY 2224
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 868 PDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGG 947
Cdd:PRK09603 2225 ADTLIDEEGAKKVVEAGIKSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGG 2304
|
970 980 990
....*....|....*....|....*....|....*.
gi 577414957 948 VAGSDI--------TQGLPRIQEIFEARNPKGQAVI 975
Cdd:PRK09603 2305 TASRSQdereivasKEGFVRFYNLRTYTNKEGKNII 2340
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-1181 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1128.95 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 7 FHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDRCGVEVTKSK 86
Cdd:PRK14844 1448 FNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSK 1527
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 87 VRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPGPTGLEKKTLLSEAEFRDYYDKYP-GQ 165
Cdd:PRK14844 1528 VRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGiDS 1607
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 166 FVAKMGAEGIKDLLEEIDLDEELKLLRDELES-ATGQRLTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQL 244
Cdd:PRK14844 1608 FVAMQGVEAIRELLTRLDLHEIRKDLRLELESvASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSL 1687
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 245 DGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLK-SLSHMLKGK 323
Cdd:PRK14844 1688 ESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLKGK 1767
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 324 QGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEE 403
Cdd:PRK14844 1768 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEE 1847
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 404 VIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPK 483
Cdd:PRK14844 1848 VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPS 1927
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 484 DGKPVVTPSQDMVLGNYYLTLERKDAVNTgAIFNNTNEVLKAYANGFVHLHTRIGVHASSFNNptfTEEQNKKILATSVG 563
Cdd:PRK14844 1928 NGRPIIVPSKDIVLGIYYLTLQEPKEDDL-PSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINS---SGETHYKTICTTPG 2003
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 564 KIIFNEIIpdsfayinePTQENLERKTPNRYFIdpttlgeggLKEyfeneeliepfnkkfLGNIIAEVFNRFSITDTSMM 643
Cdd:PRK14844 2004 RLILWQIF---------PKHENLGFDLINQVLT---------VKE---------------ITSIVDLVYRNCGQSATVAF 2050
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 644 LDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEEERYNAVVEIWTDAKDQIQGELMQS 723
Cdd:PRK14844 2051 SDKLMVLGFEYATFSGVSFSRCDMVIPETKATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKA 2130
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 724 L------DKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLTVLEYFISTHGARKGLADTALK 797
Cdd:PRK14844 2131 IsiydgnSKYNSVYMMVNSGARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALK 2210
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 798 TADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETIRHPETDEIIIRPDELITPEIA 877
Cdd:PRK14844 2211 TANSGYLTRRLVDVSQNCIVTKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKV 2290
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 878 KKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGV--------- 948
Cdd:PRK14844 2291 KQINIAGLDVVKIRSPLTCEISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVmtrgvessn 2370
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 --------------------------------------------------------------------------------
Cdd:PRK14844 2371 iiasinakiklnnsniiidkngnkivisrscevvlidslgseklkhsvpygaklyvdeggsvkigdkvaewdpytlpiit 2450
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 --------------------------------------------------------------------------------
Cdd:PRK14844 2451 ektgtvsyqdlkdgisitevmdestgisskvvkdwklysgganlrprivllddngkvmtlasgveacyfipigavlnvqd 2530
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 949 -----AGS-------------DITQGLPRIQEIFEARNPKGQAVITEIEGVVedIKLAKDR--QQEIVVKGANETRS--- 1005
Cdd:PRK14844 2531 gqkvhAGDvitrtpresvktrDITGGLPRVIELFEARRPKEHAIVSEIDGYV--AFSEKDRrgKRSILIKPVDEQISpve 2608
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1006 YLASGTSRIIVEIGQPVQRGEVLTEGSIEPKNYLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRII 1085
Cdd:PRK14844 2609 YLVSRSKHVIVNEGDFVRKGDLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEIT 2688
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1086 EAGDTKLLPGSLVDIHNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGL 1165
Cdd:PRK14844 2689 DPGDTMYLVGESIDKLEVDRENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGL 2768
|
1370
....*....|....*.
gi 577414957 1166 KENVIIGKLIPAGTGM 1181
Cdd:PRK14844 2769 KENVIVGRLIPAGTGL 2784
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
5-576 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 860.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 5 NNFHYMKIGLASPEKIRSWS---------FGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVC 75
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 76 DRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPG-PTGLEKKTLLSEAE 154
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGnHKNLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 155 FRDYYDK-------YPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQRLTRAIKRLEVVESFRNSGNKPSWMI 227
Cdd:PRK02625 167 WLEIEDQiyaedseLEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLIKRLRVIDNFIATGSRPEWMV 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 228 LDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTG 307
Cdd:PRK02625 247 LDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVG 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 308 PGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAK 387
Cdd:PRK02625 327 ANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAK 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 388 SKIERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQA 467
Cdd:PRK02625 407 KLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQA 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 468 EARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERKDAVN-TGAIFNNTNEVLKAYANGFVHLHTRIGVHassFNN 546
Cdd:PRK02625 487 EARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQKgAGRYFASLEDVIMAFEQGRIDLHAWVWVR---FNG 563
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 577414957 547 PTFTEEQNKKILA--------------------------------TSVGKIIFNEIIPDSFA 576
Cdd:PRK02625 564 EVEDDDEDTEPLKtetledgtrieqyryrrdrfdedgnlisqyilTTVGRVIMNKTIQDALA 625
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
7-577 |
0e+00 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 829.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 7 FHYMKIGLASPEKIRSWS---------FGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVRYKGMVCDR 77
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 78 CGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVVVDPG-PTGLEKKTLLSEAEFR 156
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGnAKNLKYKQLLTEDQWL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 157 DYYDK-------YPGQFVAKMGAEGIKDLLEEIDLDEELKLLRDELESATGQRLTRAIKRLEVVESFRNSGNKPSWMILD 229
Cdd:TIGR02387 162 EIEDQiyaedseLENEEVVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLIKRLRVIDNFIATSSRPEWMVLD 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 230 VLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPG 309
Cdd:TIGR02387 242 VIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGAN 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 310 NRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKELVQREIATNIKNAKSK 389
Cdd:TIGR02387 322 NRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKKL 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 390 IERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEA 469
Cdd:TIGR02387 402 IQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTEA 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 470 RMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLERKDAV-NTGAIFNNTNEVLKAYANGFVHLHTRIGVHassFNNPT 548
Cdd:TIGR02387 482 RLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEkGRGRYFSSLEDAIHAYEDGRIDLHDWIWVR---FNGEV 558
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 577414957 549 FTEEQNKKILA--------------------------------TSVGKIIFNEIIPDSFAY 577
Cdd:TIGR02387 559 ETNDPLDEPIKsedlsdgtrieqwtyrrdrfdedgalisqyilTTTGRIIMNHTIIEALVA 619
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
1-571 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 813.37 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1 MIDVNNFHYMKIGLASPEKIRSWS---------FGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECSCGKYKRVR-- 69
Cdd:CHL00018 1 MIDRYKHQQLRIGLASPQQIRAWAerilpngeiVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIGde 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 70 -YKGMVCDRCGVEVTKSKVRRERMGHIELAAPVSHIWYFKGIPSRMGLLLDMSPRALEEVIYFASYVV--VDPGPTGLEK 146
Cdd:CHL00018 81 kEDPKFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRL 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 147 KTLLS-EAEFRDY----------YDKYPGQFVAKmGAEGIKDLLEEIDLD-------EELKLLRDELESAT-------GQ 201
Cdd:CHL00018 161 RGLFEyEIQSWKYsiplffstqgFDTFRNREIST-GAGAIREQLADLDLRiiidnslVEWKELGEEGSTGNewedrkiGR 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 202 RLTRAIKRLEVVESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLG--APGI 279
Cdd:CHL00018 240 RKDFLVRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGE 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 280 IVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPK 359
Cdd:CHL00018 320 LVMCQKKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPR 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 360 EMALELFKPFVMKELVQREIATNIKNAKSKIERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLH 439
Cdd:CHL00018 400 EIAIELFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLH 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 440 PLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLER------------- 506
Cdd:CHL00018 480 PLVCKGFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNrrgiyanrynpcn 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 507 KDAVNTGAIFNNTNEVLKAYANGFVHLHT------------------RIGVHASS-------FNNPTFTEEQNKKILA-- 559
Cdd:CHL00018 560 RKNSTKEPYFSNSYDALGAYRQKRINLDSplwlrwrldqriiasrevPIEVQYESlgtyheiYEHYLIVKSRKKEILSiy 639
|
650
....*....|....
gi 577414957 560 --TSVGKIIFNEII 571
Cdd:CHL00018 640 irTTVGRILFNREI 653
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
15-820 |
2.41e-169 |
|
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: 511.59 E-value: 2.41e-169
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 15 ASPEKIRSWSFGEVKKPETINYRTLKPEKDGlfcerifgptkdwecscgKYKRVRYKGMVCDRCGVEVTKSKVRRERMGH 94
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 95 IELAAPVSHIWYFKGIPSRMGllldmspraleeviyfasyvvvdpgptglekktllseaefrdyydkypgqfvakmgaeg 174
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 175 ikdlleeidldeelkllrdelesatgqrltraikrlevvesfrnsgnkPSWMILDVLPIIPPEIRPMVqldggrfatsdl 254
Cdd:cd00399 84 ------------------------------------------------PEWMILTCLPVPPPCLRPSV------------ 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 255 ndlyrrvinrnnrlkrlldlgapgiIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLKSLSHMLKGKQGRFRQNLLGK 334
Cdd:cd00399 104 -------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMGK 158
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 335 RVDYSGRSVIAVGPSLKMYQCGLPKEMALELfkpfvmkelvqreiatniknakskiermddevwdvleeviREHPVLLNR 414
Cdd:cd00399 159 RVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFNR 198
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 415 APTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQD 494
Cdd:cd00399 199 QPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQD 278
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 495 MVLGNYYLTLerkdavntgaifnntnevlkayangfvhlhtrigvhassfnnptfteeqnkkilatsvGKIIFNEIIPds 574
Cdd:cd00399 279 TLLGAYLLTL----------------------------------------------------------GKQIVSAALP-- 298
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 575 fayineptqenlerktpnryfidpttlgegglkeyfeneeliepfnkkflGNIIAEVFNRFSITDTSMMLDRMKDLGFKF 654
Cdd:cd00399 299 --------------------------------------------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVF 328
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 655 SSKAGITVGVADIVVLPD----KQQILDEHEKLVDRITKQFNRGLIT-------EEERYNAVVEIWTDAKDQIQGELMQS 723
Cdd:cd00399 329 LTTSGFSVGIGDVIDDGVipeeKTELIEEAKKKVDEVEEAFQAGLLTaqegmtlEESLEDNILDFLNEARDKAGSAASVN 408
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 724 LD---KTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKI--------------------IELPITSSFREGLTVLEY 780
Cdd:cd00399 409 LDlvsKFNSIYVMAMSGAKGSFINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEY 488
|
810 820 830 840
....*....|....*....|....*....|....*....|
gi 577414957 781 FISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREE 820
Cdd:cd00399 489 FFHAMGGREGLVDTAVKTAESGYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
224-500 |
9.99e-162 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 482.40 E-value: 9.99e-162
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 224 SWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNG--RR 301
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 302 GRPVTGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFVMKEL------- 374
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 375 -----------VQREIATNIKNAK-SKIERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLV 442
Cdd:smart00663 158 lvrngpngakyIIRGKKTNLKLAKkSKIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 577414957 443 TTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNY 500
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
620-1030 |
3.50e-134 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 442.51 E-value: 3.50e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 620 NKKFLGNIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEE 699
Cdd:PRK02597 9 DKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEV 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 700 ERYNAVVEIWTDAKDQIQGELMQSLDKTNP---IFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLT 776
Cdd:PRK02597 89 ERFQKVIDTWNETNERLKDEVVKNFRQNDPlnsVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLT 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 777 VLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSKETI 856
Cdd:PRK02597 169 VTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLGDRLLGRVLAEDV 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 857 RHPEtDEIIIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGT 936
Cdd:PRK02597 249 VDPE-GEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGIIAAQSIGEPGT 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 937 QLTMRTFHTGGVAGSDItqglpriqeifearnpkGQAVITEIEGVVEDIKLAK----------DRQQ-------EIVVKG 999
Cdd:PRK02597 328 QLTMRTFHTGGVFTGEV-----------------ARQVRSPFAGTVEFGKKLRtrpyrtrhgvEALQaevdfdlVLKPSG 390
|
410 420 430
....*....|....*....|....*....|.
gi 577414957 1000 ANETRSYLASGTSRIIVEIGQPVQRGEVLTE 1030
Cdd:PRK02597 391 KGKPQKIEITQGSLLFVDDGQTVEADQLLAE 421
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
620-1030 |
4.47e-123 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 410.01 E-value: 4.47e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 620 NKKFLGNIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITEE 699
Cdd:TIGR02388 8 DKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGEITEV 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 700 ERYNAVVEIWTDAKDQIQGELMQSLDKTNP---IFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGLT 776
Cdd:TIGR02388 88 ERFQKVIDTWNGTNEELKDEVVNNFRQTDPlnsVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDLPIKTNFREGLT 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 777 VLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEpFIERIEGRYSKETI 856
Cdd:TIGR02388 168 VTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKIS-LGDRLLGRLVAEDV 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 857 RHPEtDEIIIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGT 936
Cdd:TIGR02388 247 LHPE-GEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAVGIIAAQSIGEPGT 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 937 QLTMRTFHTGGV----------AGSDITQGLPRIQEIFEARNPKGQ-AVITEIEGVVedikLAKDRQQeivvkGANETRS 1005
Cdd:TIGR02388 326 QLTMRTFHTGGVftgevarqvrSKIDGTVEFGKKLRTRGYRTRHGEdAKQVEVAGLL----IIKPTGS-----ITNKAQE 396
|
410 420
....*....|....*....|....*
gi 577414957 1006 YLASGTSRIIVEIGQPVQRGEVLTE 1030
Cdd:TIGR02388 397 IEVTQGSLLFVEDGQTVDAGQLLAE 421
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
619-955 |
1.00e-117 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 397.77 E-value: 1.00e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 619 FNKKFLGNIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPDKQQILDEHEKLVDRITKQFNRGLITE 698
Cdd:CHL00117 14 IDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYGNVHA 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 699 EERYNAVVEIWTDAKDQIQGELMQSL---DKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELPITSSFREGL 775
Cdd:CHL00117 94 VEKLRQSIEIWYATSEYLKQEMNPNFrmtDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQIIDLPIQSNFREGL 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 776 TVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGteMIE-PFIERIEGRYSKE 854
Cdd:CHL00117 174 SLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGM--MIErILIQTLIGRVLAD 251
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 855 TIRHpeTDEIIIRPDELITPEIAKKITDAGIEQMYIRSAFTCNARHGVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEP 934
Cdd:CHL00117 252 DIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEAVGIIAGQSIGEP 329
|
330 340
....*....|....*....|.
gi 577414957 935 GTQLTMRTFHTGGVAGSDITQ 955
Cdd:CHL00117 330 GTQLTLRTFHTGGVFTGGTAE 350
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
916-1181 |
2.15e-108 |
|
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: 338.35 E-value: 2.15e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 916 KVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAgSDITQGLPRIQEIFEARNpkgqaviteiegvvediklakdrqqei 995
Cdd:cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVA-TDITQGLPRVEELFEARK--------------------------- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 996 vvkganetrsylasgtsriiveigqpvqrgevltegsIEPKNYLSVA--GLNATESYLLKEVQKVYRMQGVEIDDKHVEV 1073
Cdd:cd02655 54 -------------------------------------INPHDLLRIKflGPEAVQKYLVEEIQKVYRSQGVNINDKHIEI 96
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1074 MVRQMLRKVRIIEAGDTKLLPGSLVDIHNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDA 1153
Cdd:cd02655 97 IVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKASLNTESFISAASFQETTKVLTEA 176
|
250 260
....*....|....*....|....*...
gi 577414957 1154 AIKGKRDDLLGLKENVIIGKLIPAGTGM 1181
Cdd:cd02655 177 AIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
5-331 |
1.50e-104 |
|
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: 332.72 E-value: 1.50e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 5 NNFHYMKIGLASPEKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFGPTKDWECS-CGKYKRvrykgmvcdRCGVevt 83
Cdd:pfam04997 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECEtCGKKKK---------DCPG--- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 84 kskvrreRMGHIELAAPVSHIWYFKgipsrmgllldMSPRALEEVIYFASYVVVDPGptgleKKTLLSEAEFRDYYDKYp 163
Cdd:pfam04997 70 -------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENL- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 164 gqfvaKMGAEGIKDLLEEIDL-------------------DEELKLL--------RDELESATGQRLTRAIKRLE----V 212
Cdd:pfam04997 126 -----KMGAKAILELCKKKDLcehcggkngvcgsqqpvsrKEGLKLKaaikkskeEEEKEILNPEKVLKIFKRISdedvE 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 213 VESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAV 292
Cdd:pfam04997 201 ILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHV 280
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 577414957 293 DALIDNGRRG-RPVTGPGNRPLKSLSHMLKGKQGRFRQNL 331
Cdd:pfam04997 281 ATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
9-826 |
2.77e-104 |
|
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: 349.62 E-value: 2.77e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 9 YMKIGLASPEKIRSWSFGEVKKPETinYrtlkpEKDGLfceRIFGPTKDwecscgkyKR--VRYKGMVCDRCGVevtksk 86
Cdd:cd02582 6 GIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRlgVIEPGLRCKTCGN------ 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 87 vRRER----MGHIELAAPVSHIWYFKGI--------PSRMGLLL--------------------DMSPRALEEVIYFASY 134
Cdd:cd02582 62 -TAGEcpghFGHIELARPVIHVGFAKHIydllratcRSCGRILLpeeeiekylerirrlkekwpELVKRVIEKVKKKAKK 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 135 VVVDPGpTGLEKKTLLSEAEFRDYYDKYPGQfvAKMGAEGIKDLLEEIdLDEELKLLrdelesatgqrltraikrlevve 214
Cdd:cd02582 141 RKVCPH-CGAPQYKIKLEKPTTFYEEKEEGE--VKLTPSEIRERLEKI-PDEDLELL----------------------- 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 215 SFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDA 294
Cdd:cd02582 194 GIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTT 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 295 LIDNGRRGRPV----TGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFV 370
Cdd:cd02582 274 YFDNEIPGIPParhrSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPER 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 371 --------MKELVQ-----------------REIATNIKNAKSKIERMddEVWDVLEEVIRE-HPVLLNRAPTLHRLGIQ 424
Cdd:cd02582 351 vtewniekMRKLVLngpdkwpganyvirpdgRRIRLRYVNREELAERL--EPGWIVERHLIDgDIVLFNRQPSLHRMSIM 428
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 425 AFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTl 504
Cdd:cd02582 429 AHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLT- 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 505 eRKDAVNTgaifnnTNEVLK-AYANGFVHLhtrIGVHASSFNNPTFTeeqnkkilatsvGKIIFNEIIPDSFAY-----I 578
Cdd:cd02582 508 -RKTTLFT------KEEALQlLSAAGYDGL---LPEPAILEPKPLWT------------GKQLFSLFLPKDLNFegkakV 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 579 NEPTQENLERKTPNRYFIdpttlgegglkeYFENEELIE-PFNKKFLG-----NIIAEVFNRFSITDTSMMLDRMKDLGF 652
Cdd:cd02582 566 CSGCSECKDEDCPNDGYV------------VIKNGKLLEgVIDKKAIGaeqpgSLLHRIAKEYGNEVARRFLDSVTRLAI 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 653 KFSSKAGITVGVADIvVLPDK-----QQILDEHEKLVDRITKQFNRGLI------TEEERYNA-VVEIWTDAKDQIQGEL 720
Cdd:cd02582 634 RFIELRGFTIGIDDE-DIPEEarkeiEEIIKEAEKKVYELIEQYKNGELeplpgrTLEETLEMkIMQVLGKARDEAGKVA 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 721 MQSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAApSGKIIE-------LP--------------ITSSFREGLTVLE 779
Cdd:cd02582 713 SKYLDPFNNAVIMARTGARGSMLNLTQMAACLGQQSV-RGERINrgyrnrtLPhfkpgdlgpeargfVRSSFRDGLSPTE 791
|
890 900 910 920
....*....|....*....|....*....|....*....|....*..
gi 577414957 780 YFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVrEEDcGTDR 826
Cdd:cd02582 792 FFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYV-EYD-GTVR 836
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
11-826 |
9.79e-99 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 334.90 E-value: 9.79e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 11 KIGLASPEKIRSWSFGEVKKPETinYrtlkpEKDGLfceRIFGPTKDwecscgkyKR--VRYKGMVCDRCGvevTKSKVR 88
Cdd:PRK08566 13 KFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRlgVIDPGLRCKTCG---GRAGEC 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 89 RERMGHIELAAPVSHIWY---------------------------FKGIPSRMGLLLDMSPRALEEVIYFASYVVVDP-- 139
Cdd:PRK08566 72 PGHFGHIELARPVIHVGFakliykllratcrecgrlklteeeieeYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPhc 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 140 G----PTGLEKKTLLSEAEFRDYYdkypgqfvaKMGAEGIKDLLEEIDlDEELKLLRDELESAtgqrltraikrlevves 215
Cdd:PRK08566 152 GekqyKIKFEKPTTFYEERKEGLV---------KLTPSDIRERLEKIP-DEDLELLGINPEVA----------------- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 216 frnsgnKPSWMILDVLPIIPPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDAL 295
Cdd:PRK08566 205 ------RPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTY 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 296 IDNGRRGRPV----TGpgnRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPF-- 369
Cdd:PRK08566 279 FDNEIPGIPParhrSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPErv 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 370 ------VMKELVQ-----------------REIATNIKNAKSKIERMDDEvWDVLEEVIREHPVLLNRAPTLHRLGIQAF 426
Cdd:PRK08566 356 tewnieELREYVLngpekhpganyvirpdgRRIKLTDKNKEELAEKLEPG-WIVERHLIDGDIVLFNRQPSLHRMSIMAH 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 427 EPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTler 506
Cdd:PRK08566 435 RVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLT--- 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 507 kdavNTGAIFNNTnEVLkayangfvHLHTRIGVHASSFNNPTFteeQNKKILATsvGKIIFNEIIPDSF-----AYINEP 581
Cdd:PRK08566 512 ----RKSTLFTKE-EAL--------DLLRAAGIDELPEPEPAI---ENGKPYWT--GKQIFSLFLPKDLnlefkAKICSG 573
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 582 TQENLERKTPNRYFIdpttlgegglkeYFENEELIE-PFNKK----FLGNIIAEVFNRFSITDTSMMLDRMKDLGFKFSS 656
Cdd:PRK08566 574 CDECKKEDCEHDAYV------------VIKNGKLLEgVIDKKaigaEQGSILDRIVKEYGPERARRFLDSVTRLAIRFIM 641
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 657 KAGITVGVADiVVLPDK-----QQILDEHEKLVDRITKQFNRGLIT-------EEERYNAVVEIWTDAKDQIQGELMQSL 724
Cdd:PRK08566 642 LRGFTTGIDD-EDIPEEakeeiDEIIEEAEKRVEELIEAYENGELEplpgrtlEETLEMKIMQVLGKARDEAGEIAEKYL 720
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 725 DKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIE------LP--------------ITSSFREGLTVLEYFIST 784
Cdd:PRK08566 721 GLDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHA 800
|
890 900 910 920
....*....|....*....|....*....|....*....|..
gi 577414957 785 HGARKGLADTALKTADSGYLTRRLVDVAQDVIVrEEDcGTDR 826
Cdd:PRK08566 801 MGGREGLVDTAVRTSQSGYMQRRLINALQDLKV-EYD-GTVR 840
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
10-1180 |
2.95e-98 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 342.01 E-value: 2.95e-98
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 10 MKIGLASPEKIRSWSFGEVKKPETINYRTLkPEKDGLFCERIFGPTKDWEC-SCGKYKRvrykgmvcdRCgvevtkskvr 88
Cdd:PRK14977 12 IIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRLGTIEPGQKClTCGNLAA---------NC---------- 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 89 RERMGHIELAAPVSHIWYFKGIPSRMG--------LLLDMSPRALEEVIYFA-SYVVVDPG---PTGLEKKTLLSEAEFR 156
Cdd:PRK14977 72 PGHFGHIELAEPVIHIAFIDNIKDLLNstchkcakLKLPQEDLNVFKLIEEAhAAARDIPEkriDDEIIEEVRDQVKVYA 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 157 DYYDKYP--GQFVAKMGAEGIKDLLEEIDLdEELKLLRDELEsatgQRLTRAIKRLEVVESFRNSGNKPSWMILDVLPII 234
Cdd:PRK14977 152 KKAKECPhcGAPQHELEFEEPTIFIEKTEI-EEHRLLPIEIR----DIFEKIIDDDLELIGFDPKKARPEWAVLQAFLVP 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 235 PPEIRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVT--GPGNRP 312
Cdd:PRK14977 227 PLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGIPQAhhKGSGRP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 313 LKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFV--------MKELVQR------- 377
Cdd:PRK14977 307 LKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenniekMKELVINgpdefpg 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 378 ----------EIATNIKNAKSKIERMDD----EVWDVLEEVIREHP-VLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLV 442
Cdd:PRK14977 387 anairkgdgtKIRLDFLEDKGKDALREAaeqlEIGDIVERHLADGDiVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAV 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 443 TTAYNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTleRKDAVNTgaifnntnev 522
Cdd:PRK14977 467 CPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT--KDDALFD---------- 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 523 lkayANGFVHLHTRIGVhASSFNNPTfTEEQNKKILatsVGKIIFNEIIPDSFAYINEPTQENLERKTPNryfiDPTTLG 602
Cdd:PRK14977 535 ----KNEASNIAMLAGI-TDPLPEPA-IKTKDGPAW---TGKQLFSLFLPKDFNFEGIAKWSAGKAGEAK----DPSCLG 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 603 EGGLkeYFENEELIEP-FNKKFLGNIIAEvfnRFSITDTsMMLDRMKDLGFKFSSKA-----------GITVGVADIVVl 670
Cdd:PRK14977 602 DGYV--LIKEGELISGvIDDNIIGALVEE---PESLIDR-IAKDYGEAVAIEFLNKIliiakkeilhyGFSNGPGDLII- 674
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 671 PD--KQQILDEHEKLVDRITK------------------QFNRGLITEEERYNAVVEIWTDAKDQIQGELMQSLDKTNPI 730
Cdd:PRK14977 675 PDeaKQEIEDDIQGMKDEVSDlidqrkitrkitiykgkeELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAG 754
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 731 FMMSDSGARGNASNFTQLAGMRGLMAAPSGKIIELP----------------------------ITSSFREGLTVLEYFI 782
Cdd:PRK14977 755 KIMAKTGARGSMANLAQIAGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFF 834
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 783 STHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMI--------EPF-IERIEGRY-- 851
Cdd:PRK14977 835 HAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRDPHGHIIQFKFGEDGIdpqkldhgEAFnLERIIEKQki 914
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 852 --SKETIRHPETDEIIIRPDELITPEIAKKITDAgieqmYIRSAFTCNARHGVCEKcyGKNLATGEKVEVGEAVGTIAAQ 929
Cdd:PRK14977 915 edRGKGASKDEIEELAKEYTKTFNANLPKLLADA-----IHGAELKEDELEAICAE--GKEGFEKAKVEPGQAIGIISAQ 987
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 930 SIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEAR------------NPKGQAVITEIEGVVEDIK----------- 986
Cdd:PRK14977 988 SIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARakpstptmdiylDDECKEDIEKAIEIARNLKelkvraliads 1067
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 987 ----------------------------------LAKDRQQEIVVKG---------ANETRSYLAS-------------- 1009
Cdd:PRK14977 1068 aidnaneiklikpdkralengcipmerfaeieaaLAKGKKFEMELEDdliildlveAADRDKPLATliairnkildkpvk 1147
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1010 ---GTSRIIVEIGQPVQRGE------------VLTEGSIEPKNYLS--------VAGLNATESYLLKEVQKVYRMQGVEI 1066
Cdd:PRK14977 1148 gvpDIERAWVELVEKDGRDEwiiqtsgsnlaaVLEMKCIDIANTITndcfeiagTLGIEAARNAIFNELASILEDQGLEV 1227
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1067 DDKHVEVMVRQMLRKvriieagdtkllpGSLVDIHNFTDANREAFkhrkrpatakpvllgitkaSLETESFLSAASFQET 1146
Cdd:PRK14977 1228 DNRYIMLVADIMCSR-------------GTIEAIGLQAAGVRHGF-------------------AGEKDSPLAKAAFEIT 1275
|
1370 1380 1390
....*....|....*....|....*....|....
gi 577414957 1147 TRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTG 1180
Cdd:PRK14977 1276 THTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
13-818 |
6.80e-83 |
|
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: 287.13 E-value: 6.80e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 13 GLASPEKIRSWSFGEVKKPETINyRTLKPEKDGLFCERIFGPTKDWEC-SCGKykrvryKGMVCDrcGvevtkskvrreR 91
Cdd:cd02733 6 GILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRMGTIDRNSRCqTCGG------DMKECP--G-----------H 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 92 MGHIELAAPVSHIWYFKGIpsrmgllldmspraleeviyfasyvvvdpgptgleKKTLLSeaefrdyydkypgqfVAK-- 169
Cdd:cd02733 66 FGHIELAKPVFHIGFLTKI-----------------------------------LKILRC---------------VCKre 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 170 MGAEGIKDLLEEIDlDEELKLLrdelesatGQRLTRAikrlevvesfrnsgnKPSWMILDVLPIIPPEIRPMVQLDGGRF 249
Cdd:cd02733 96 LSAERVLEIFKRIS-DEDCRIL--------GFDPKFS---------------RPDWMILTVLPVPPPAVRPSVVMDGSAR 151
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 250 ATSDLNDLYRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRP-VTGPGNRPLKSLSHMLKGKQGRFR 328
Cdd:cd02733 152 SEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGLPqATQKSGRPLKSIRQRLKGKEGRIR 231
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 329 QNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALEL-FKPFV-------MKELVQR-----------------EIATNI 383
Cdd:cd02733 232 GNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMNLtFPEIVtpfnidrLQELVRNgpneypgakyiirddgeRIDLRY 311
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 384 KNAKS--------KIER--MDDEVwdvleevirehpVLLNRAPTLHRLGIQafeptlveGRAIRLHPL--------VTTA 445
Cdd:cd02733 312 LKKASdlhlqygyIVERhlQDGDV------------VLFNRQPSLHKMSMM--------GHRVKVLPYstfrlnlsVTTP 371
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 446 YNADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTleRKDavntgaIFNNTNEVLka 525
Cdd:cd02733 372 YNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVMGIVQDTLLGVRKLT--KRD------TFLEKDQVM-- 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 526 yaNGFVHLHTRIG-VHASSFNNPtfteeqnkKILATsvGKIIFNEIIPDSfayineptqeNLERKTPNRYFIDPTTLGEG 604
Cdd:cd02733 442 --NLLMWLPDWDGkIPQPAILKP--------KPLWT--GKQIFSLIIPKI----------NNLIRSSSHHDGDKKWISPG 499
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 605 GLKEYFENEELIE-PFNKKFLG----NIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIV----VLPDKQQ 675
Cdd:cd02733 500 DTKVIIENGELLSgILCKKTVGassgGLIHVIWLEYGPEAARDFIGNIQRVVNNWLLHNGFSIGIGDTIadkeTMKKIQE 579
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 676 ILDEHEKLVDRITKQFNRGLITEEERY-------NAVVEIWTDAKDQIQGELMQSLDKTNPIFMMSDSGARGNASNFTQl 748
Cdd:cd02733 580 TIKKAKRDVIKLIEKAQNGELEPQPGKtlresfeNKVNRILNKARDKAGKSAQKSLSEDNNFKAMVTAGSKGSFINISQ- 658
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 749 agmrglMAAPSGK-IIE------------LP--------------ITSSFREGLTVLEYFISTHGARKGLADTALKTADS 801
Cdd:cd02733 659 ------IIACVGQqNVEgkripfgfrrrtLPhfikddygpesrgfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAET 732
|
890
....*....|....*..
gi 577414957 802 GYLTRRLVDVAQDVIVR 818
Cdd:cd02733 733 GYIQRRLVKAMEDVMVK 749
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
952-1186 |
1.08e-70 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 259.54 E-value: 1.08e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 952 DITQGLPRIQEIFEARNPKGQAVITEIEGVVEdIKLAKDRQQEIVVKGANETRS-YLASGTSRIIVEIGQPVQRGEVLTE 1030
Cdd:PRK02597 978 DIIQGLPRIEELLEARKPKESCILAKKPGTVQ-IKYGDDESVDVKVIESDGTITeYPILPGQNVMVSDGQQVDAGEPLTD 1056
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1031 GSIEPKNYLSV----------------AGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLP 1094
Cdd:PRK02597 1057 GPINPHELLEIffedlrdrkglyeaalEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLP 1136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1095 GSLVDIHNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKL 1174
Cdd:PRK02597 1137 GELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRL 1216
|
250
....*....|..
gi 577414957 1175 IPAGTGMRRYSD 1186
Cdd:PRK02597 1217 IPAGTGFSGFEE 1228
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
93-818 |
4.11e-70 |
|
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: 252.08 E-value: 4.11e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 93 GHIELAAPVSHIWYFKGI----------PSRmgLLLDmspraLEEVIYFASYVVvDPGPTGLEKKTLlseaefrdyyDKY 162
Cdd:cd02583 61 GYIKLELPVFHIGYFKAIinilqcicktCSR--VLLP-----EEEKRKFLKRLR-RPNLDNLQKKAL----------KKK 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 163 PGQFVAKMGA----EGIKDLLEEIDldeELKLLRdelesatgqrLTRAIKRLEVVESFRNS-GNKPSWMILDVLPIIPPE 237
Cdd:cd02583 123 ILEKCKKVRKcphcGLLKKAQEDLN---PLKVLN----------LFKNIPPEDVELLLMNPlAGRPENLILTRIPVPPLC 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 238 IRPMVQLDGGrfATSDLNDL---YRRVINRNNRLKRLLDLGAPGIIVQNEKRMLQEAVDALIDNGRRGRPVTGPGNRPLK 314
Cdd:cd02583 190 IRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPKKPIR 267
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 315 SLSHMLKGKQGRFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKP-------------------------- 368
Cdd:cd02583 268 GFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPervtrynieklrklvlngpdvhpgan 347
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 369 FVMKELVQREIatNIKNAKSKIERMDDEVWDVLEEVIREHP-VLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYN 447
Cdd:cd02583 348 FVIKRDGGKKK--FLKYGNRRKIARELKIGDIVERHLEDGDiVLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYN 425
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 448 ADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTleRKDavntgaIFNNTNEvlkaya 527
Cdd:cd02583 426 ADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLT--SKD------VFFDRAQ------ 491
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 528 ngFVHLHTRIGVHASSFNNPTFTeeqnkkILA-----TsvGKIIFNEIIpdsFAYINEPTQENLERKTPNRYFIDPT-TL 601
Cdd:cd02583 492 --FCQLCSYMLDGEIKIDLPPPA------ILKpvelwT--GKQIFSLLL---RPNKKSPVLVNLEAKEKSYTKKSPDmCP 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 602 GEGGLkeYFENEELIE-PFNKKFLG----NIIAEVFNR-FSITDTSMMLDRMKDLGFKFSSKAGITVGVADivVLPD--- 672
Cdd:cd02583 559 NDGYV--VIRNSELLCgRLDKSTLGsgskNSLFYVLLRdYGPEAAAAAMNRLAKLSSRWLSNRGFSIGIDD--VTPSkel 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 673 ---KQQILDEHEKLVDRITKQFNRGLI------TEEErynaVVEIwtdakdQIQGEL-----------MQSLDKTNPIFM 732
Cdd:cd02583 635 lkkKEELVDNGYAKCDEYIKQYKKGKLelqpgcTAEQ----TLEA------KISGELskiredagkacLKELHKSNSPLI 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 733 MSDSGARGNASNFTQLAGMRGlMAAPSGKIIE-------LP--------------ITSSFREGLTVLEYFISTHGARKGL 791
Cdd:cd02583 705 MALCGSKGSNINISQMIACVG-QQIISGKRIPngfedrtLPhfprnsktpaakgfVANSFYSGLTPTEFFFHTMSGREGL 783
|
810 820
....*....|....*....|....*..
gi 577414957 792 ADTALKTADSGYLTRRLVDVAQDVIVR 818
Cdd:cd02583 784 VDTAVKTAETGYMQRRLMKALEDLSVQ 810
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
774-1090 |
3.38e-65 |
|
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: 230.32 E-value: 3.38e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 774 GLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREEDCGTDRGLLVSDIKEGTEMIEPFIERIEGRYSK 853
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 854 ETIRHPETDEIIIRP---------------------------DELITPEI------AKKITDAGIEQMYIRSAFTCNARH 900
Cdd:pfam04998 81 EFSDLKLEDKFKNDLlddllllsefslsykkeilvrdsklgrDRLSKEAQeratllFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 901 GVCEKCYGKNLATGEKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFE--------------- 965
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINvsknikspsltvylf 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 966 ---------ARNPKGQAVITEIEGVVEDIKLAKDR---------QQEIVVK----------------------------- 998
Cdd:pfam04998 241 devgrelekAKKVYGAIEKVTLGSVVESGEILYDPdpfntpiisDVKGVVKffdiidevtneeeidpetgllilvirllk 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 999 -------------------------------------------------GANETRSYLA--------------------- 1008
Cdd:pfam04998 321 ilnksikkvvkseviprsirnkvdegrdiaigeitafiikiskkirqdtGGLRRVDELFmeedpklailvasllgnitlr 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1009 --SGTSRIIV---EIGQPVQRGEVLTEGSIEPKNY-------------------LSVAGLNATESYLLKEVQKVYRMQGV 1064
Cdd:pfam04998 401 giPGIKRILVnedDKGKVEPDWVLETEGVNLLRVLlvpgfvdagrilsndiheiLEILGIEAARNALLNEIRNVYRFQGI 480
|
490 500
....*....|....*....|....*.
gi 577414957 1065 EIDDKHVEVMVRQMLRKVRIIEAGDT 1090
Cdd:pfam04998 481 YINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
952-1184 |
5.92e-64 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 238.21 E-value: 5.92e-64
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 952 DITQGLPRIQEIFEARNPKGQAVITEIEGVVEDIKLAKDRQQEIVVKGANETRS-YLASGTSRIIVEIGQPVQRGEVLTE 1030
Cdd:TIGR02388 976 DIVQGLPRIEELLEARKPKEACILAKRPGVVQVKYGTDDESVSIKVIERDGTISeYPLLPGQNIMVSDGQQVTGGEPLTD 1055
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1031 GSIEPKNYLSV----------------AGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDTKLLP 1094
Cdd:TIGR02388 1056 GPINPHDILDVffsyykdqdglyeaaqESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLP 1135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1095 GSLVDIHNFTDANREAFKHRKRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKL 1174
Cdd:TIGR02388 1136 GELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRL 1215
|
250
....*....|
gi 577414957 1175 IPAGTGMRRY 1184
Cdd:TIGR02388 1216 IPAGTGFSSY 1225
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
951-1184 |
5.33e-59 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 222.89 E-value: 5.33e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 951 SDITQGLPRIQEIFEARnpkgqavitEIEGVVEDIklakdrqqEIVVKGANEtrsylasGTSRIIveigqpvqrgevlte 1030
Cdd:CHL00117 1129 GDITQGLPKVEQLLEAR---------SIDSISMNL--------EKRLEGWNE-------RITRIL--------------- 1169
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1031 gsIEPKNYLSVAGLNATES--YLLKEVQKVYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDT-KLLPGSLVDIHNFTDAN 1107
Cdd:CHL00117 1170 --GIPWGFLIGAELSIAQSqiSLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLVSEDGMSnVFLPGELIGLLRAERIN 1247
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 577414957 1108 ReAFKhrkRPATAKPVLLGITKASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGMRRY 1184
Cdd:CHL00117 1248 R-ALE---EAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGL 1320
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
333-475 |
1.52e-50 |
|
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: 175.95 E-value: 1.52e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 333 GKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELFKPFV--------MKELV-----QREIATNIKN---AKSKIE----R 392
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpynikrLRQLVengpnVYPGANYIIRingARRDLRyqkrR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 393 MDDEVW--DVLEE-VIREHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVTTAYNADFDGDQMAVHVPLSKEAQAEA 469
Cdd:pfam00623 81 LDKELEigDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*.
gi 577414957 470 RMLMLA 475
Cdd:pfam00623 161 EELMLV 166
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
188-809 |
6.23e-49 |
|
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: 187.78 E-value: 6.23e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 188 LKLLRDELEsatgqRLTRAIKRLEV--VESFRNSGNKPSWMILDVLPIIPPEIRPMVQLDGGRFaTSDLNDLYRRVINRN 265
Cdd:cd01435 95 FRISKWEVK-----LFVAKLKLLDKglLVEAAELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDN 168
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 266 NRLKRLLDLGAPGIIVQNEKRM---------------LQEAVDALIDNGRrgrpVTGPGNRPLKSLSHMLKGKQGRFRQN 330
Cdd:cd01435 169 QQIRDLLASMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMN 244
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 331 LLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALEL--------FKPFVMKELV--------------------------- 375
Cdd:cd01435 245 MMGKRVNYAARSVISPDPFIETNEIGIPLVFAKKLtfpepvtpFNVEELRQAVingpdvypganaiededgrlillsals 324
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 376 --QREIATNIKNAKSKIERMDDEVWDVLEEVIREHPVLLNRAPTLHRLGIQAF-------EptlvegRAIRLHPLVTTAY 446
Cdd:cd01435 325 eeRRKALAKLLLLLSSAKLLLNGPKKVYRHLLDGDVVLLNRQPTLHKPSIMAHkvrvlpgE------KTLRLHYANCKSY 398
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 447 NADFDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGNYYLTLerKDavntgaIFNNTNEvlkay 526
Cdd:cd01435 399 NADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLRGLIQDHVVSGVLLTS--RD------TFFTREE----- 465
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 527 angFVHL--HTRIGVHASSFNNPTFTEE---QNKKILATsvGK----IIFNEIIPDSFAYINEPTQENLERKTPNRYFID 597
Cdd:cd01435 466 ---YQQLvyAALRPLFTSDKDGRIKLLPpaiLKPKPLWT--GKqvisTILKNLIPGNAPLLNLSGKKKTKKKVGGGKWGG 540
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 598 PttLGEGglKEYFENEELIE-----------------PFNKKFLGNIIAEVFNRFSitdtsmmldRMkdlgF-KFSSKAG 659
Cdd:cd01435 541 G--SEES--QVIIRNGELLTgvldksqfgasayglvhAVYELYGGETAGKLLSALG---------RL----FtAYLQMRG 603
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 660 ITVGVADIVVLPD----KQQILDEHEKLVDRITKQFNrGLITeeeryNAVVEiwtdakDQIQGELMQSLDKTNPI--F-M 732
Cdd:cd01435 604 FTCGIEDLLLTPKadekRRKILRKAKKLGLEAAAEFL-GLKL-----NKVTS------SIIKACLPKGLLKPFPEnnLqL 671
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 733 MSDSGARGNASNFTQLAGMRG----------LMaaPSGKiiELP--------------ITSSFREGLTVLEYFISTHGAR 788
Cdd:cd01435 672 MVQSGAKGSMVNASQISCLLGqqelegrrvpLM--VSGK--TLPsfppydtspraggfITDRFLTGIRPQEYFFHCMAGR 747
|
730 740
....*....|....*....|.
gi 577414957 789 KGLADTALKTADSGYLTRRLV 809
Cdd:cd01435 748 EGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
920-1181 |
5.67e-43 |
|
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: 153.73 E-value: 5.67e-43
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 920 GEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEARNPkgqaviteiegvvediklakdrqQEIvvkg 999
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAASI-----------------------HEM---- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1000 anetrsylasgtsriiveigqpvqrgevltegsiepknyLSVAGLNATESYLLKEVQKVYRMQGVEIDDKHVEVMVRQML 1079
Cdd:cd00630 54 ---------------------------------------LEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMT 94
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1080 RKVriieagdtkllpgslvdihnftdanreafkhrkrpatakpVLLGITKASL--ETESFLSAASFQETTRVLTDAAIKG 1157
Cdd:cd00630 95 YSG----------------------------------------GLRGVTRSGFraSKTSPLMRASFEKTTKHLLDAAAAG 134
|
250 260
....*....|....*....|....
gi 577414957 1158 KRDDLLGLKENVIIGKLIPAGTGM 1181
Cdd:cd00630 135 EKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
478-667 |
1.14e-42 |
|
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: 153.17 E-value: 1.14e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 478 NILNPKDGKPVVTPSQDMVLGNYYLTLERkdavntgaIFNNTNEVLKAYANGFVHLHTRIGVHASSfnnptfteeqnKKI 557
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAILKPIKP-----------LWT 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 558 LATSVGKIIFNEIIPDSFAYINEPtqenLERKTPNRYFIDPTTLGEGGLKEYFENeeliepfnkKFLGNIIAEVFNRFSI 637
Cdd:pfam04983 62 GKQTFSRLLPNEINPKGKPKTNEE----DLCENDSYVLINNGELISGVIDKKTVG---------KSLGSLIHIIYKEYGP 128
|
170 180 190
....*....|....*....|....*....|
gi 577414957 638 TDTSMMLDRMKDLGFKFSSKAGITVGVADI 667
Cdd:pfam04983 129 EETAKFLDRLQKLGFRYLTKSGFSIGIDDI 158
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
916-1181 |
1.44e-32 |
|
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: 128.87 E-value: 1.44e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 916 KVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEI----------------------FEARNPKGQ- 972
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIinasknistpiitaklendrdeKSARIVKGRi 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 973 ------AVITEIEGVVE------DIKLAKDRQQE---------------------IVVKGanetrsylASGTSRIIVEIG 1019
Cdd:cd02736 86 ektylgEVASYIEEVYSpddcyiLIKLDKKIIEKlqlsksnlyfllqslkrklpdVVVSG--------IPEVKRAVINKD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1020 QPVQRGEVLTEGS----------IEPKNYLS--------VAGLNATESYLLKEVQKVYRMQGVEIDDKHVevmvrqMLrk 1081
Cdd:cd02736 158 KKKGKYKLLVEGYglravmntpgVIGTRTTSnhimevekVLGIEAARSTIINEIQYTMKSHGMSIDPRHI------ML-- 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1082 vriieagdtkllpgsLVDIhnftdanreafkhrkrpATAKPVLLGITKASLE--TESFLSAASFQETTRVLTDAAIKGKR 1159
Cdd:cd02736 230 ---------------LADL-----------------MTFKGEVLGITRFGIAkmKESVLMLASFEKTTDHLFNAALHGRK 277
|
330 340
....*....|....*....|..
gi 577414957 1160 DDLLGLKENVIIGKLIPAGTGM 1181
Cdd:cd02736 278 DSIEGVSECIIMGKPMPIGTGL 299
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
916-1181 |
8.43e-29 |
|
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: 119.66 E-value: 8.43e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 916 KVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEAR---------------------------- 967
Cdd:cd06528 36 LIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARkepstptmtiyleeeykydrekaeevar 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 968 ----------------NPKGQAVITEI-EGVVEDIKLAKDRQQEIVVKGANETRSYLASGTSrIIVEIGQP--------- 1021
Cdd:cd06528 116 kieettlenlaedisiDLFNMRITIELdEEMLEDRGITVDDVLKAIEKLKKGKVGEEGDVTL-IVLKAEEPsikelrkla 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1022 ------------------VQRGE----VLTEGSIEPKnYLSVAGLNATESY-------------------LLKEVQKVYR 1060
Cdd:cd06528 195 ekilntkikgikgikrviVRKEEdeyvIYTEGSNLKA-VLKVEGVDPTRTTtnniheieevlgieaarnaIINEIKRTLE 273
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1061 MQGVEIDDKHVevmvrqMLrkvriieagdtkllpgsLVDIHNFTdanreafkhrkrpATAKPVllGITKASLETESFLSA 1140
Cdd:cd06528 274 EQGLDVDIRHI------ML-----------------VADIMTYD-------------GEVRQI--GRHGIAGEKPSVLAR 315
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 577414957 1141 ASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGM 1181
Cdd:cd06528 316 AAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGD 356
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
917-1181 |
7.38e-28 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 117.25 E-value: 7.38e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 917 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEAR-NP-------------------------- 969
Cdd:PRK04309 56 VEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARkEPstpmmtiylkdeyaydrekaeevark 135
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 970 ------------------KGQAVIT--------------EIEGVVEDIKLAKDRQQEIVVKGANETRSYLA--------- 1008
Cdd:PRK04309 136 ieattlenlakdisvdlaNMTIIIEldeemledrgltvdDVKEAIEKKKGGEVEIEGNTLIISPKEPSYRElrklaekir 215
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1009 -------SGTSRIIV--EIGQPVqrgeVLTEGSiEPKNYLSVAGLNATESY-------------------LLKEVQKVYR 1060
Cdd:PRK04309 216 nikikgiKGIKRVIIrkEGDEYV----IYTEGS-NLKEVLKVEGVDATRTTtnniheieevlgieaarnaIIEEIKNTLE 290
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1061 MQGVEIDDKHVevmvrqMLrkvriieagdtkllpgsLVDIHNFTDANREAFKHrkrpatakpvllGItkaSLETESFLSA 1140
Cdd:PRK04309 291 EQGLDVDIRHI------ML-----------------VADMMTWDGEVRQIGRH------------GV---SGEKASVLAR 332
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 577414957 1141 ASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGM 1181
Cdd:PRK04309 333 AAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGD 373
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
917-1181 |
1.66e-26 |
|
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: 112.84 E-value: 1.66e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 917 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEAR-------------------NPKGQAVI-- 975
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDARktpstpsmtiyledeyekdREKAEEVAkk 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 976 ---TEIEGVVEDIK---------------------LAKDRQQEIVVKGANETRSYLASGTSRIIVEIGQP---------- 1021
Cdd:TIGR02389 121 ieaTKLEDVAKDISidladmtviieldeeqlkergITVDDVEKAIKKAKLGKVIEIDMDNNTITIKPGNPslkelrklke 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1022 -----------------VQRGE----VLTEGSiEPKNYLSVAGLNATESY-------------------LLKEVQKVYRM 1061
Cdd:TIGR02389 201 kiknlhikgikgikrvvIRKEGdeyvIYTEGS-NLKEVLKLEGVDKTRTTtndiheiaevlgieaarnaIIEEIKRTLEE 279
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1062 QGVEIDDKHVevmvrqMLrkvriieagdtkllpgsLVDIHNFTDANREAFKHrkrpatakpvllGITKaslETESFLSAA 1141
Cdd:TIGR02389 280 QGLDVDIRHL------ML-----------------VADLMTWDGEVRQIGRH------------GISG---EKASVLARA 321
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 577414957 1142 SFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTGM 1181
Cdd:TIGR02389 322 AFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGD 361
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
915-1188 |
1.99e-23 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 105.66 E-value: 1.99e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 915 EKVEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFEARN-------------------------- 968
Cdd:PRK14897 177 ARVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKkpstptmtiylkkdyredeekvreva 256
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 969 ----------------------------------------------PKGQAVITEIEGVVEDIKLAKDRQQEIVVKgANE 1002
Cdd:PRK14897 257 kkienttlidvadiitdiaemsvvveldeekmkerlieyddilaaiSKLTFKTVEIDDGIIRLKPQQPSFKKLYLL-AEK 335
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1003 TRSYLASGTS---RIIVEIGQPVQRGEVLTEGS----------IEP-KNYL-------SVAGLNATESYLLKEVQKVYRM 1061
Cdd:PRK14897 336 VKSLTIKGIKgikRAIARKENDERRWVIYTQGSnlkdvleideVDPtRTYTndiieiaTVLGIEAARNAIIHEAKRTLQE 415
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1062 QGVEIDDKHVevmvrqMLrkvriieagdtkllpgsLVDIHNFTDANREAFKHrkrpatakpvllGItkaSLETESFLSAA 1141
Cdd:PRK14897 416 QGLNVDIRHI------ML-----------------VADMMTFDGSVKAIGRH------------GI---SGEKSSVLARA 457
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|..
gi 577414957 1142 SFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTG-----MRRYSDVK 1188
Cdd:PRK14897 458 AFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGavslvYKGRKKVK 509
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
314-817 |
2.38e-21 |
|
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: 100.56 E-value: 2.38e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 314 KSLSHMLKGKQgrFRQNLLGKRVDYSGRSVIAVGPSLKMYQCGLPKEMALELfkpfVMKELVQReiaTNIKNAKSKIERM 393
Cdd:cd10506 195 SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERL----TVSERVSS---WNRERLQEYCDLT 265
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 394 ----------------------DDEVWDVLEEVIRE-HPVLLNRAPTLHRLGIQAFEPTLVE-GRAIRLHPLVTTAYNAD 449
Cdd:cd10506 266 lllkgvigvrrngrlvgvrshnTLQIGDVIHRPLVDgDVVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRGD 345
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 450 FDGDQMAVHVPLSKEAQAEARMLMLAAQNILNPKDGKPVVTPSQDMVLGnYYLTLERKDAVNtgaifnntnevlKAYANG 529
Cdd:cd10506 346 FDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLA-AHLMTERGVFLD------------KAQMQQ 412
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 530 FVHLHTRIG-----VHASSFNNPTFTeeqnkkilatsvGKIIFNEIIPDSFAYineptqenlerKTP-NRYFIdpttlge 603
Cdd:cd10506 413 LQMLCPSQLpppaiIKSPPSNGPLWT------------GKQLFQMLLPTDLDY-----------SFPsNLVFI------- 462
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 604 gglkeyfENEELIEPFNKKFLG----NIIAEVFNRFSITDTSMMLDRMKDLGFKFSSKAGITVGVADIVVLPD---KQQI 676
Cdd:cd10506 463 -------SDGELISSSGGSSWLrdseGNLFSILVKHGPGKALDFLDSAQGLLCEWLSMRGFSVSLSDLYLSSDsysRQKM 535
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 677 LDEHEKLVDRITKQFNRGLI---------------------TEEERY---------NAVVEIWTDAKDQIQGELMQSLDK 726
Cdd:cd10506 536 IEEISLGLREAEIACNIKQLlvdsrkdflsgsgeendvssdVERVIYerqksaalsQASVSAFKQVFRDIQNLVYKYASK 615
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 727 TNPIFMMSDSGARGNASNFTQLAGMRGL----------------MAA----PSGKIIELP-------------ITSSFRE 773
Cdd:cd10506 616 DNSLLAMIKAGSKGSLLKLVQQSGCLGLqlslvklsyriprqlsCAAwnsqKSPRVIEKDgsectesyipygvVESSFLD 695
|
570 580 590 600
....*....|....*....|....*....|....*....|....*
gi 577414957 774 GLTVLEYFISTHGARKGLADtalKTAD-SGYLTRRLVDVAQDVIV 817
Cdd:cd10506 696 GLNPLECFVHSITSRDSSFS---SNADlPGTLFRKLMFFMRDIYV 737
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
696-772 |
6.73e-20 |
|
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: 85.88 E-value: 6.73e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 696 ITEEERYNAVVEIWTDAKDQIQGELM----------------QSLDKTNPIFMMSDSGARGNASNFTQLAGMRGLMAAPS 759
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALInnilnkardpagniasKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 577414957 760 G---------------KIIELPITSSFR 772
Cdd:pfam05000 81 KripfgfsgrtlphfkKDDEGPESRGFV 108
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1066-1184 |
1.18e-18 |
|
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: 92.53 E-value: 1.18e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1066 IDDKHVEVMVRQM---------------LRKVRI---IEAGDTKLLPGSLVD---IHNFTDANREAFKHRK--------R 1116
Cdd:COG0086 577 INKKHIEVIIRQMyrrcglketvifldrLKKLGFkyaTRAGISIGLDDMVVPkekQEIFEEANKEVKEIEKqyaeglitE 656
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1117 PATAKPVLLGITKASLETESFLSAA-SFQETTRVLTDAAIKGKRDDLLGL----------KENVI---IGKLIPAGTGMR 1182
Cdd:COG0086 657 PERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmakpSGNIIetpIGSNFREGLGVL 736
|
..
gi 577414957 1183 RY 1184
Cdd:COG0086 737 EY 738
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
920-1180 |
3.62e-17 |
|
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: 85.33 E-value: 3.62e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 920 GEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEIFE-ARNPKGQAVITEIE-GVVEDIKLAKDRQQEI-- 995
Cdd:cd02584 27 GEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINvAKNIKTPSLTVYLEpGFAKDEEKAKKIQSRLeh 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 996 ---------------------VVK-------------GANETRSYLASGTSRIIVEIGQPVQRGevLTEGSI------EP 1035
Cdd:cd02584 107 ttlkdvtaateiyydpdpqntVIEedkefvesyfefpDEDVEQDRLSPWLLRIELDRKKMTDKK--LSMEQIakkikeEF 184
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1036 KNYLSV----------------------AGLNATESYLLKEVQkvYRM------QGVEIDDKHVevmVRQMLRKVRIIEA 1087
Cdd:cd02584 185 KDDLNVifsddnaeklviririinddeeKEEDSEDDVFLKKIE--SNMlsdmtlKGIEGIRKVF---IREENKKKVDIET 259
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1088 GDTKLLPGSLVDihnfTD--ANREAFKHR----KRPATAKPV----LLGI--TKASLETE-----SF------------- 1137
Cdd:cd02584 260 GEFKKREEWVLE----TDgvNLREVLSHPgvdpTRTTSNDIVeifeVLGIeaARKALLKElrnviSFdgsyvnyrhlall 335
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 577414957 1138 -------------------------LSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTG 1180
Cdd:cd02584 336 cdvmtqrghlmaitrhginrqdtgpLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
917-963 |
6.91e-14 |
|
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: 74.15 E-value: 6.91e-14
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 577414957 917 VEVGEAVGTIAAQSIGEPGTQLTMRTFHTGGVAGSDITQGLPRIQEI 963
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREI 53
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
936-1180 |
4.45e-13 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 73.77 E-value: 4.45e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 936 TQLTMRTFHTGGVAGSDITQGLPRIQEIFEARNPKGQAVITEieGVVEDIKLAKDRQQEIVVKGANETRSYLASG----- 1010
Cdd:PRK14898 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTV--HLKGEYATDREKAEEVAKKIESLTLGDVATSiaidl 618
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1011 -TSRIIVEIGQPVQRGEVLT----EGSIEPKN-----------YLSVAglnaTESY--LLKEVQK--------------- 1057
Cdd:PRK14898 619 wTQSIKVELDEETLADRGLTiesvEEAIEKKLgvkidrkgtvlYLKPK----TPSYkaLRKRIPKiknivlkgipgierv 694
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 577414957 1058 VYRMQGVEIDDKHVEVMVRQMLRKVRIIEAGDT-KLLPGSLVDIHNF--TDANREAFKHRKRPA---------------- 1118
Cdd:PRK14898 695 LVKKEEHENDEEYVLYTQGSNLREVFKIEGVDTsRTTTNNIIEIQEVlgIEAARNAIINEMMNTleqqglevdirhlmlv 774
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 577414957 1119 ----TAKPVLLGITK--ASLETESFLSAASFQETTRVLTDAAIKGKRDDLLGLKENVIIGKLIPAGTG 1180
Cdd:PRK14898 775 adimTADGEVKPIGRhgVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
917-940 |
1.36e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 42.96 E-value: 1.36e-03
10 20
....*....|....*....|....
gi 577414957 917 VEVGEAVGTIAAQSIGEPGTQLTM 940
Cdd:PRK14898 54 VEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
