|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
16-1372 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2359.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 16 QHFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTL 95
Cdd:PRK00566 5 QDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTR 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 96 SRVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPGLTSLKENQLLSEEEYMIAVDEFGe 175
Cdd:PRK00566 85 SKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYG- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 176 DQFTAMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDLKQKKLMKRLKIVENFMESGNRPEWMIMKVVPVIPPDLRPLV 255
Cdd:PRK00566 164 DEFVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 256 PLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKG 335
Cdd:PRK00566 244 QLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 336 KQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILD 415
Cdd:PRK00566 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 416 EVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHP 495
Cdd:PRK00566 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 496 ANGAPIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALENKIVTLHSKIRGRFKTVdeegkpvsKIFETTPGRM 575
Cdd:PRK00566 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSK--------KLVETTVGRV 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 576 LIGELLPKNFkvPFDTCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVG 655
Cdd:PRK00566 556 IFNEILPEGL--PFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 656 DTENLVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIKAvefdpetgRQKQMNAIYMMSHSGARGSPNQMR 735
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSK--------DQESFNPIYMMADSGARGSASQIR 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 736 QLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDK 815
Cdd:PRK00566 706 QLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDR 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 816 GLTMTAIIDAGQVVASIGVRVLGRTALDDIDHPLTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCSIC 895
Cdd:PRK00566 786 GIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKC 865
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 896 YGRDLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTatvvdqsfleasyegtvqiknrnmlrnsdgnliamgrs 975
Cdd:PRK00566 866 YGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV-------------------------------------- 907
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 976 lavtildergverssqrvaygskvfvddgdkvkrgqrlaewdpytrpmmtevegivhfedvvdglsvleatdestgitkr 1055
Cdd:PRK00566 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1056 qvidwrstprgadlkpaivikdaagnvlkmsrgsdarfflsvdailsvepgtkvsqgdvlarsplesaktkDITGGLPRV 1135
Cdd:PRK00566 908 -----------------------------------------------------------------------DITGGLPRV 916
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1136 AELFEARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPaEDGvEPVEYLIPKGKPFHLQDGDYIEKGDYILDGNPAPHDI 1215
Cdd:PRK00566 917 AELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITP-DDG-EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHDI 994
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1216 LAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDRIEMDDNNDRLIEEGKKPS 1295
Cdd:PRK00566 995 LRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPA 1074
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 494882676 1296 YGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTGGTMTQIRRIATSRDE 1372
Cdd:PRK00566 1075 TGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDE 1151
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
16-1196 |
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: 1834.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 16 QHFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTL 95
Cdd:COG0086 5 EDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 96 SRVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPGLTSLKENQLLSEEEYMIAVDEFGe 175
Cdd:COG0086 85 SKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 176 DQFTAMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDLKQKKLMKRLKIVENFMESGNRPEWMIMKVVPVIPPDLRPLV 255
Cdd:COG0086 164 DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 256 PLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKG 335
Cdd:COG0086 244 PLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 336 KQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILD 415
Cdd:COG0086 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 416 EVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHP 495
Cdd:COG0086 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 496 ANGAPIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALENKIVTLHSKIRGRFKtvdEEGKPVSKIFETTPGRM 575
Cdd:COG0086 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRIT---EDGEQVGKIVETTVGRY 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 576 LIGELLPKNfkVPFdtCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVG 655
Cdd:COG0086 561 LVNEILPQE--VPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFE 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 656 DTENLVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIkavefdpetgrqKQMNAIYMMSHSGARGSPNQMR 735
Cdd:COG0086 637 EANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAF------------SSQNTTYMMADSGARGSADQLR 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 736 QLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDK 815
Cdd:COG0086 705 QLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDR 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 816 GLTMTAIIDAGQVVASIGVRVLGRTALDDIDHPLTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCSIC 895
Cdd:COG0086 785 GITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKC 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 896 YGRDLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSF-LEASYEGTVQIKNRNMLRNSDGNLIAMGR 974
Cdd:COG0086 865 YGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESsIEAKAGGIVRLNNLKVVVNEEGKGVVVSR 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 975 SLAVTILDERGVERSSQRVAYGSKVFVDDGDKVKRGQRLAEWDPYTRPMMTEVEGIVHFEDVVDGLSVLEATDESTGITK 1054
Cdd:COG0086 945 NSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLS 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1055 RQVIDWRSTPRGADLKPAIVIKDAAGNVLKMSRGSDARFFLSVDAILSVEPGTKVsQGDVLARSPLESAKTKDITGGLPR 1134
Cdd:COG0086 1025 IVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGV-AIGVGAAIARIPGLSGGTRDGTGG 1103
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 494882676 1135 VAELFEARRPKDHAIIAEIDGTIRLGRDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQDG 1196
Cdd:COG0086 1104 LARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
20-1357 |
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: 1779.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 20 SIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVR 99
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 100 RERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPGLTSLKENQLLSEEEYMIAVDEFGeDQFT 179
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYG-DGFR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 180 AMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDLKQKKLMKRLKIVENFMESGNRPEWMIMKVVPVIPPDLRPLVPLDG 259
Cdd:TIGR02386 160 AGMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 260 GRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGR 339
Cdd:TIGR02386 240 GRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 340 FRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIR 419
Cdd:TIGR02386 320 FRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 420 EHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGA 499
Cdd:TIGR02386 400 EHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGK 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 500 PIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALENKIVTLHSKIRGRFKtvdeegkpvSKIFETTPGRMLIGE 579
Cdd:TIGR02386 480 PIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTS---------GEILETTVGRVIFNE 550
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 580 LLPKNFkvPFDTCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVGDTEN 659
Cdd:TIGR02386 551 ILPEGF--PYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADK 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 660 LVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIKAvefdpetgRQKQMNAIYMMSHSGARGSPNQMRQLGG 739
Cdd:TIGR02386 629 EVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKK--------DTYKFNPIFMMADSGARGNISQFRQLAG 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 740 MRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDKGLTM 819
Cdd:TIGR02386 701 MRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEV 780
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 820 TAIIDA-GQVVASIGVRVLGRTALDDIDHPLTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCSICYGR 898
Cdd:TIGR02386 781 EAIVEGkDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGR 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 899 DLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATvvdqsfleasyegtvqiknrnmlrnsdgnliamgrslav 978
Cdd:TIGR02386 861 DLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAG--------------------------------------- 901
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 979 tildergverssqrvaygskvfvddgdkvkrgqrlaewdpytrpmmtevegivhfedvvdglsvleatdestgitkrqvi 1058
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1059 dwrstprgadlkpaivikdaagnvlkmsrgsdarfflsvdailsvepgtkvsqgdvlarsplesaKTKDITGGLPRVAEL 1138
Cdd:TIGR02386 902 -----------------------------------------------------------------ASGDITQGLPRVKEL 916
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1139 FEARRPKDHAIIAEIDGTI-RLGRDYKNKRRVIIEPAEDgvEPVEYLIPKGKPFHLQDGDYIEKGDYILDGNPAPHDILA 1217
Cdd:TIGR02386 917 FEARTPKDKAVIAEVDGTVeIIEDIVKNKRVVVIKDEND--EEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLR 994
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1218 IKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDRIEMDDNNDRLIEEGKKPSYG 1297
Cdd:TIGR02386 995 IKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASA 1074
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1298 DPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:TIGR02386 1075 IPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTG 1134
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1367 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1746.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 15 AQHFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVT 94
Cdd:PRK14844 1445 AQSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVT 1524
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 95 LSRVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPGLTSLKENQLLSEEEYMIAVDEFG 174
Cdd:PRK14844 1525 SSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYG 1604
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 175 EDQFTAMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDLKQKKLMKRLKIVENFMESGNRPEWMIMKVVPVIPPDLRPL 254
Cdd:PRK14844 1605 IDSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPL 1684
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 255 VPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPL-KSLSDML 333
Cdd:PRK14844 1685 VSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYkKSISDML 1764
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 334 KGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDI 413
Cdd:PRK14844 1765 KGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDM 1844
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 414 LDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNIL 493
Cdd:PRK14844 1845 LEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVL 1924
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 494 HPANGAPIIVPSQDMVLGLYYLSIMNQNEpGEGMAFSDIGELHHALENKIVTLHSKIRGRFKTVDEEGKPVSKIFETTPG 573
Cdd:PRK14844 1925 SPSNGRPIIVPSKDIVLGIYYLTLQEPKE-DDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSSGETHYKTICTTPG 2003
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 574 RMLIGELLPKNFKVPFDTCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKI 653
Cdd:PRK14844 2004 RLILWQIFPKHENLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATH 2083
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 654 VGDTENLVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIKAVEfdpetgRQKQMNAIYMMSHSGARGSPNQ 733
Cdd:PRK14844 2084 VDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIYD------GNSKYNSVYMMVNSGARGSTSQ 2157
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 734 MRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGT 813
Cdd:PRK14844 2158 MKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKT 2237
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 814 DKGLTMTAIIDAGQVVASIGVRVLGRTALDDIDHPLTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCS 893
Cdd:PRK14844 2238 KNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCS 2317
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 894 ICYGRDLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATV-VDQSFLEASYEGTVQIKNRNMLRNSDGNLIAM 972
Cdd:PRK14844 2318 LCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRgVESSNIIASINAKIKLNNSNIIIDKNGNKIVI 2397
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 973 GRSLAVTILDERGVERSSQRVAYGSKVFVDDGDKVKRGQRLAEWDPYTRPMMTEVEGIVHFEDVVDGLSVLEATDESTGI 1052
Cdd:PRK14844 2398 SRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEVMDESTGI 2477
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1053 TKRQVIDWRSTPRGADLKPAIVIKDAAGNVLKMSRGSDARFFLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGL 1132
Cdd:PRK14844 2478 SSKVVKDWKLYSGGANLRPRIVLLDDNGKVMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGL 2557
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1133 PRVAELFEARRPKDHAIIAEIDGTIRLG-RDYKNKRRVIIEPAEDGVEPVEYLIPKGKPFHLQDGDYIEKGDYILDGNPA 1211
Cdd:PRK14844 2558 PRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLMDGDPD 2637
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1212 PHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDRIEMDDNNDRLIEEG 1291
Cdd:PRK14844 2638 LHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMSNSG 2717
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494882676 1292 KKPSYGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTGGTMTQIRRIA 1367
Cdd:PRK14844 2718 KRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLIMNKVRALS 2793
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
18-1357 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1524.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGI-ICEKCGVEVTLS 96
Cdd:PRK09603 1396 FSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVAITHS 1475
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 97 RVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPGlTSLKENQ---------LLSEEEYM 167
Cdd:PRK09603 1476 KVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPG-EAAYDNEgtklvmkydILNEEQYQ 1554
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 168 IAVDEFGEDQFTAMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDLKQKKLMKRLKIVENFMESGNRPEWMIMKVVPVI 247
Cdd:PRK09603 1555 NISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVL 1634
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 248 PPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLK 327
Cdd:PRK09603 1635 PPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLK 1714
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 328 SLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEK 407
Cdd:PRK09603 1715 SLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKS 1794
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 408 PEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMM 487
Cdd:PRK09603 1795 NEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLML 1874
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 488 STNNILHPANGAPIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALENKIVTLHSKIRgrfkTVDEegkpvSKI 567
Cdd:PRK09603 1875 SSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIR----VLDQ-----GNI 1945
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 568 FETTPGRMLIGELLPkNFkVPFDTCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIP 647
Cdd:PRK09603 1946 IATSAGRMIIKSILP-DF-IPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITP 2023
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 648 ETKAKIVGDTENLVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIKAvefDPETgrqkqMNAIYMMSHSGA 727
Cdd:PRK09603 2024 KDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAK---DKEG-----FNSIYMMADSGA 2095
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 728 RGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVN 807
Cdd:PRK09603 2096 RGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVV 2175
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 808 LVDCGTDKGLTMTAIIDAGQVVASIGVRVLGRTALDDIDHPLTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEV 887
Cdd:PRK09603 2176 SDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKA 2255
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 888 QTGVCSICYGRDLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAT---------------------------- 939
Cdd:PRK09603 2256 PKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASrsqdereivaskegfvrfynlrtytnke 2335
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 940 -------------VVDQSFLEASYEGTVQIKN----------------RNMLRNSD------------------------ 966
Cdd:PRK09603 2336 gkniianrrnasiLVVEPKIKAPFDGELRIETvyeevvvsvkngdqeaKFVLRRSDivkpselagvggkiegkvylpyas 2415
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 967 GNLIAMGRSLAVTILD-----------------------------ERGV------------------------------- 986
Cdd:PRK09603 2416 GHKVHKGGSIADIIQEgwnvpnripyasellvkdndpiaqdvyakEKGIikyyvleanhlerthgikkgdivsekglfav 2495
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 987 -----ERSSQR--VAYGSKVFVDDGDKVKRGQR-----------LAEWDPYTRPMMTEVEGIVHFEDVVDGLSVLEATDE 1048
Cdd:PRK09603 2496 iaddnGREAARhyIARGSEILIDDNSEVSANSViskpttntfktIATWDPYNTPIIADFKGKVSFVDIIAGVTVAEKEDE 2575
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1049 STGITKRQVIDWrsTPRGadLKPAIVIKDAAGNVLkmsrgsdaRFFLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDI 1128
Cdd:PRK09603 2576 NTGITSLVVNDY--IPSG--YKPSLFLEGANGEEI--------RYFLEPKTSIAISDGSSVEQAEVLAKIPKATVKSRDI 2643
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1129 TGGLPRVAELFEAR--RPKDHAIIAEIDGTIRLGRDYKNKRRVIIEpAEDGvEPVEYLIPKGKPFHLQDGDYIEKGDYIL 1206
Cdd:PRK09603 2644 TGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVT-SKDG-RSMDYFVDKGKQILVHADEFVHAGEAMT 2721
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1207 DGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDRIEMDDNNDR 1286
Cdd:PRK09603 2722 DGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENAR 2801
|
1450 1460 1470 1480 1490 1500 1510
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494882676 1287 LIEEGKKPSYGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK09603 2802 VIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
18-810 |
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: 1300.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSR 97
Cdd:cd01609 3 FDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 98 VRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFenyivtepgltslkenqllseeeymiavdefgedq 177
Cdd:cd01609 83 VRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF----------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 178 ftamigaeaiyemlasmnlekiagdlradlaettsdlkqkklmkrlkIVENFMESGNRPEWMIMKVVPVIPPDLRPLVPL 257
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 258 DGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQ 337
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 338 GRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEV 417
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 418 IREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPAN 497
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 498 GAPIIVPSQDMVLGLYYLSIMNQNEPGEGmafsdigelhhalenkivtlhskirgrfktvdeegkpvskIFETTPGRMLI 577
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEG----------------------------------------IIETTVGRVIF 440
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 578 GELLPKNFkvPFdtCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVGDT 657
Cdd:cd01609 441 NEILPEGL--PF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEA 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 658 ENLVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMARIKAVEFDPetgrqkqmnaIYMMSHSGARGSPNQMRQL 737
Cdd:cd01609 517 EEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDPFNP----------IYMMADSGARGSKSQIRQL 586
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494882676 738 GGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVD 810
Cdd:cd01609 587 AGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
18-1357 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1288.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSR 97
Cdd:PRK14906 9 FDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRAK 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 98 VRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVT-------EPGLTSLKE------NQLLSEE 164
Cdd:PRK14906 89 VRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITsvdkearEEDADDLRDelaadlEELDAER 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 165 EYMIAV------------DEFGEDQ------------------------------------------------------- 177
Cdd:PRK14906 169 DRLIEAtrrlsvdyvpedDEFVDDIgdderltaeevraevadiyeeynerkalrreafdafmqiepkqlisdealyremr 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 178 ------FTAMIGAEAIYEMLASMNLEKIAGDLRaDLAETTSDLKQKKLMKRLKIVENFMESGNRPEWMIMKVVPVIPPDL 251
Cdd:PRK14906 249 lnysiyFKGGMGAEAVRDLLDAIDLEKEAEELR-AIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPDL 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 252 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLSD 331
Cdd:PRK14906 328 RPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLAD 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 332 MLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVW 411
Cdd:PRK14906 408 MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYVW 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 412 DILDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNN 491
Cdd:PRK14906 488 DVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNN 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 492 ILHPANGAPIIVPSQDMVLGLYYLSIMNQNEPGEGMAFSDIGELHHALE-NKIVTLHSKI----------RGRFKTVDEE 560
Cdd:PRK14906 568 IKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDaRADLDLQAKIvvrlsrdmtvRGSYGDLEET 647
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 561 gkPVSKIFETTPGRMLIGELLPKNFkvPFdtCNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFG 640
Cdd:PRK14906 648 --KAGERIETTVGRIIFNQVLPEDY--PY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVS 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 641 KDDMVIPETKAKIVGDTENLVKEYEQQYNDGLITQGEKYNKVVDAWGKATEKVAEDMMArikavEFDpetgrqkQMNAIY 720
Cdd:PRK14906 722 VYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLA-----GFD-------EDNPIY 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 721 MMSHSGARGSPNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDV 800
Cdd:PRK14906 790 MMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDV 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 801 AQDCIVNLVDCGTDKGLTMTAIIDAGQVVASIgvrvLGRTALDDIDHPlTGERIVDAGKMILEPDVIE-IEKAGIQSIRI 879
Cdd:PRK14906 870 AQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDP-NGEVLLSAGDYIESMDDLKrLVEAGVTKVQI 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 880 RSALTCEVQTGVCSICYGRDLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAtvvdqsfleasyegtvqiknr 959
Cdd:PRK14906 945 RTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA--------------------- 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 960 nmlrnsdgnliamgrslavtildergverssqrvaygskvfvddGDkvkrgqrlaewdpytrpmmtevegivhfedvvdg 1039
Cdd:PRK14906 1004 --------------------------------------------GD---------------------------------- 1005
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1040 lsvleatdestgitkrqvidwrstprgadlkpaivikdaagnvlkmsrgsdarfflsvdailsvepgtkvsqgdvlarsp 1119
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1120 lesaktkDITGGLPRVAELFEARRPKDHAIIAEIDGTIRLGRDyKNKRRVIIEPAEDGVEpvEYLIPKGKPFH--LQDGD 1197
Cdd:PRK14906 1006 -------DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGD-KTEKTLTIHDQDGNSR--EYVVSARVQFMpgVEDGV 1075
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1198 YIEKGDYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDR 1277
Cdd:PRK14906 1076 EVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNR 1155
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1278 IEMDDNNDRLIEEGKKPSYGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK14906 1156 YEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
16-570 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 847.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 16 QHFDSIRISIASPEKILSWS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIIC 86
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 87 EKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPG-LTSLKENQLLSEEE 165
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGnHKNLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 166 YMIAVDE-FGEDQF-----TAMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDlKQKKLMKRLKIVENFMESGNRPEWM 239
Cdd:PRK02625 167 WLEIEDQiYAEDSElegeeVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGSRPEWM 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 240 IMKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVIT 319
Cdd:PRK02625 246 VLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVV 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 320 GANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQA 399
Cdd:PRK02625 326 GANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAA 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 400 KKLVEKEKPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQ 479
Cdd:PRK02625 406 KKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 480 LEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIMNQN-EPGEGMAFSDIGELHHALENKIVTLHSKIRGRFKTVD 558
Cdd:PRK02625 486 AEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGaQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNGEV 565
|
570
....*....|..
gi 494882676 559 EEGKPVSKIFET 570
Cdd:PRK02625 566 EDDDEDTEPLKT 577
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
17-570 |
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: 827.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 17 HFDSIRISIASPEKILSWS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICE 87
Cdd:TIGR02387 1 RFDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 88 KCGVEVTLSRVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVTEPG-LTSLKENQLLSEEEY 166
Cdd:TIGR02387 81 RCGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGnAKNLKYKQLLTEDQW 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 167 MIAVDE-FGEDQF-----TAMIGAEAIYEMLASMNLEKIAGDLRADLAETTSDlKQKKLMKRLKIVENFMESGNRPEWMI 240
Cdd:TIGR02387 161 LEIEDQiYAEDSEleneeVVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMV 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 241 MKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRGRVITG 320
Cdd:TIGR02387 240 LDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVG 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 321 ANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAK 400
Cdd:TIGR02387 320 ANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 401 KLVEKEKPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQL 480
Cdd:TIGR02387 400 KLIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQT 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 481 EARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIMNQN-EPGEGMAFSDIGELHHALENKIVTLHSKIRGRFKTVDE 559
Cdd:TIGR02387 480 EARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGaEKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVE 559
|
570
....*....|.
gi 494882676 560 EGKPVSKIFET 570
Cdd:TIGR02387 560 TNDPLDEPIKS 570
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
16-555 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 822.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 16 QHFDSIRISIASPEKILSWSY---------GEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRM---KYKG 83
Cdd:CHL00018 5 YKHQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdeKEDP 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 84 IICEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKSLPSRISTLLDMTLKDVERVLYFENYIVT--EPGLTSLKENQLL 161
Cdd:CHL00018 85 KFCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARpiAKKPTFLRLRGLF 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 162 SEE----EYMI----AVDEFGEDQFTAM-IGAEAIYEMLASMNLEKIAGDLRAD---LAETTSD--------LKQKK--L 219
Cdd:CHL00018 165 EYEiqswKYSIplffSTQGFDTFRNREIsTGAGAIREQLADLDLRIIIDNSLVEwkeLGEEGSTgnewedrkIGRRKdfL 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 220 MKRLKIVENFMESGNRPEWMIMKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELR--APGIIIRNE 297
Cdd:CHL00018 245 VRRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQ 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 298 KRMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALE 377
Cdd:CHL00018 325 KKLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIE 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 378 LFKPFIYARLDAKGYSSTVKQAKKLVEKEKPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCT 457
Cdd:CHL00018 405 LFQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCK 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 458 AFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIMNQN-------------EPG 524
Cdd:CHL00018 485 GFNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRgiyanrynpcnrkNST 564
|
570 580 590
....*....|....*....|....*....|.
gi 494882676 525 EGMAFSDIGELHHALENKIVTLHSKIRGRFK 555
Cdd:CHL00018 565 KEPYFSNSYDALGAYRQKRINLDSPLWLRWR 595
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
26-807 |
3.15e-179 |
|
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: 542.41 E-value: 3.15e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 26 ASPEKILSWSYGEIKKPETINYRTFKPERDGlfcarifgpikdyeclcgKYKRMKYKGIICEKCGVEVTLSRVRRERMGH 105
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 106 IELAAPVAHIWFLKSLPSRIstlldmtlkdvervlyfenyivtepgltslkenqllseeeymiavdefgedqftamigae 185
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFL------------------------------------------------------------ 82
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 186 aiyemlasmnlekiagdlradlaettsdlkqkklmkrlkivenfmesgnRPEWMIMKVVPVIPPDLRPLVpldggrfats 265
Cdd:cd00399 83 -------------------------------------------------GPEWMILTCLPVPPPCLRPSV---------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 266 dlndlyrrvinrnnrlkrlielrapgiIIRNEKRMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLL 345
Cdd:cd00399 104 ---------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLM 156
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 346 GKRVDYSGRSVIVTGPELKLHQCGLPKKMALELfkpfiyarldakgysstvkqakklvekekpevwdildeviREHPVLL 425
Cdd:cd00399 157 GKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLF 196
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 426 NRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPS 505
Cdd:cd00399 197 NRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLS 276
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 506 QDMVLGLYYLsimnqnepgegmafsdigelhhalenkivtlhskirgrfktvdeegkpvskifetTPGRMLIGELLPKNf 585
Cdd:cd00399 277 QDTLLGAYLL-------------------------------------------------------TLGKQIVSAALPGG- 300
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 586 kvpfdtcnqemtkkniskMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDD----MVIPETKAKIVGDTENLV 661
Cdd:cd00399 301 ------------------LLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDviddGVIPEEKTELIEEAKKKV 362
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 662 KEYEQQYNDGLITQGEK-------YNKVVDAWGKATEKvaedmMARIKAVEFDPETGRqkqmNAIYMMSHSGARGSPNQM 734
Cdd:cd00399 363 DEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDK-----AGSAASVNLDLVSKF----NSIYVMAMSGAKGSFINI 433
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 735 RQLGGMRGLMAKPSGEI--------------------IETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLT 794
Cdd:cd00399 434 RQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQ 513
|
810
....*....|...
gi 494882676 795 RRLVDVAQDCIVN 807
Cdd:cd00399 514 RRLVKALEDLVVH 526
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
237-513 |
1.20e-156 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 473.93 E-value: 1.20e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 237 EWMIMKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNG--RR 314
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 315 GRVITGankRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARL------- 387
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 388 -------DAK----GYSSTVKQAKKL-VEKEKPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLV 455
Cdd:smart00663 158 lvrngpnGAKyiirGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 494882676 456 CTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLY 513
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
592-1137 |
4.70e-120 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 407.46 E-value: 4.70e-120
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 592 CNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVGDTENLVKEYEQQYNDG 671
Cdd:PRK02597 4 RNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 672 LITQGEKYNKVVDAWGKATEKVAEDMMARIKavEFDPetgrqkqMNAIYMMSHSGARGSPNQMRQLGGMRGLMAKPSGEI 751
Cdd:PRK02597 84 EITEVERFQKVIDTWNETNERLKDEVVKNFR--QNDP-------LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEI 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 752 IETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDKGLTMTAIIDAGQVVAS 831
Cdd:PRK02597 155 IDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIP 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 832 IGVRVLGRTALDDIDHPlTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCSICYGRDLARGTPVNMGEA 911
Cdd:PRK02597 235 LGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEA 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 912 VGVIAAQSIGEPGTQLTMRTFHLGG--TATVVDQsfLEASYEGTVQ----IKNRNM-LRNSDGNLIA-MGRSLAVTILDE 983
Cdd:PRK02597 314 VGIIAAQSIGEPGTQLTMRTFHTGGvfTGEVARQ--VRSPFAGTVEfgkkLRTRPYrTRHGVEALQAeVDFDLVLKPSGK 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 984 RGVERSSqrVAYGSKVFVDDGDKVKRGQRLAE---------WDPYTRPMMTEVEGIVHFEDVVDGlsvlEATDESTGITk 1054
Cdd:PRK02597 392 GKPQKIE--ITQGSLLFVDDGQTVEADQLLAEvaagavkksTEKATKDVICDLAGEVRFADLIPE----EKTDRQGNTT- 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1055 rqvidwRSTPRGAdlkpaiVIKDAAGNVLKMSRGsdarfflsvdAILSVEPGTKVSQGDVLARSPLESAKtkditGGLPR 1134
Cdd:PRK02597 465 ------RKAQRGG------LLWVLSGDVYNLPPG----------AEPVVSNGDRVEEGDVLAETKLVSEH-----GGVVR 517
|
...
gi 494882676 1135 VAE 1137
Cdd:PRK02597 518 LRE 520
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
593-1143 |
1.85e-111 |
|
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: 381.51 E-value: 1.85e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 593 NQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVGDTENLVKEYEQQYNDGL 672
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 673 ITQGEKYNKVVDAWGKATEKVAEDMMARIKavEFDPetgrqkqMNAIYMMSHSGARGSPNQMRQLGGMRGLMAKPSGEII 752
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNFR--QTDP-------LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 753 ETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDKGLTMTAIIDAGQVVaSI 832
Cdd:TIGR02388 155 DLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI-SL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 833 GVRVLGRTALDDIDHPlTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCSICYGRDLARGTPVNMGEAV 912
Cdd:TIGR02388 234 GDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAV 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 913 GVIAAQSIGEPGTQLTMRTFHLGGTATVVDQSFLEASYEGTVQIKNRNMLR-------------NSDGNLIAMGRSlavt 979
Cdd:TIGR02388 313 GIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVEFGKKLRTRgyrtrhgedakqvEVAGLLIIKPTG---- 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 980 ildERGVERSSQRVAYGSKVFVDDGDKVKRGQRLAE---------WDPYTRPMMTEVEGIVHFEDVVDGlsvlEATDEST 1050
Cdd:TIGR02388 389 ---SITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAEialgavrksTEKATKDVASDLAGEVKFDKVVPE----EKTDRQG 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1051 GITkrqvidwRSTPRGAdlkpaiVIKDAAGNVLKMSRGsdarfflsvdAILSVEPGTKVSQGDVLARsplesAKTKDITG 1130
Cdd:TIGR02388 462 NTT-------RIAQRGG------LIWVLSGEVYNLPPG----------AEPVVKNGDRVEQGTVLAE-----TKLSTEHG 513
|
570
....*....|...
gi 494882676 1131 GLPRVAELFEARR 1143
Cdd:TIGR02388 514 GVVRLPESVGDSR 526
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
763-1267 |
5.51e-111 |
|
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: 360.13 E-value: 5.51e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 763 GLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDKGLTMTAIIDAGQVVASIGVRVLGRTAL 842
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 843 DDIDHPLTG----------------------ERIVDAGKMILEPDVIE-----------IEKAGIQSIRIRSALTCEVQT 889
Cdd:pfam04998 81 EFSDLKLEDkfkndllddllllsefslsykkEILVRDSKLGRDRLSKEaqeratllfelLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 890 GVCSICYGRDLARGTPVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATvvdqsflEASYEGTVQIKNRNMlrnsdGNL 969
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVAS-------KNVTLGVPRLKEIIN-----VSK 228
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 970 IAMGRSLAVTILDERGVERSSQRVAYGSKVFVDDGDKVKRGQRLAEWDPYTRPMMTEVEGIVHFEDVVDGLSVLEATDES 1049
Cdd:pfam04998 229 NIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDPE 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1050 TGITKRQVIDwrstprgadlkpaivikdaAGNVLKMSRGSDARFFLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDIT 1129
Cdd:pfam04998 309 TGLLILVIRL-------------------LKILNKSIKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDT 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1130 GGLPRVAELFEARRPKDHAIIAEIDGTIRLgRDYKNKRRVIIEPAEDG-VEPVEYLIPKG--KPFHLQDGDYIEKGDYIL 1206
Cdd:pfam04998 370 GGLRRVDELFMEEDPKLAILVASLLGNITL-RGIPGIKRILVNEDDKGkVEPDWVLETEGvnLLRVLLVPGFVDAGRILS 448
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494882676 1207 DgnpAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDS 1267
Cdd:pfam04998 449 N---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
18-344 |
8.64e-106 |
|
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: 338.50 E-value: 8.64e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYEC-LCGKYKRmkykgiiceKCGVevtls 96
Cdd:pfam04997 4 IKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG----- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 97 rvrreRMGHIELAAPVAHIWFLKslpsristlldMTLKDVERVLYFENYIVTEPGltslkENQLLSEEEYMIAVDEFGed 176
Cdd:pfam04997 70 -----HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENLK-- 126
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 177 qftamIGAEAIYEMLASMNLEKIAG------------------DLRADL--------AETTSDLKQKKLMKRLK----IV 226
Cdd:pfam04997 127 -----MGAKAILELCKKKDLCEHCGgkngvcgsqqpvsrkeglKLKAAIkkskeeeeKEILNPEKVLKIFKRISdedvEI 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 227 ENFMESGNRPEWMIMKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVD 306
Cdd:pfam04997 202 LGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVA 281
|
330 340 350
....*....|....*....|....*....|....*....
gi 494882676 307 ALFDNGRRG-RVITGANKRPLKSLSDMLKGKQGRFRQNL 344
Cdd:pfam04997 282 TLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
592-936 |
1.84e-103 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 360.41 E-value: 1.84e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 592 CNQEMTKKNISKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPETKAKIVGDTENLVKEYEQQYNDG 671
Cdd:CHL00117 10 HNKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYG 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 672 LITQGEKYNKVVDAWGKATEKVAEDMMARIKavEFDPetgrqkqMNAIYMMSHSGARGSPNQMRQLGGMRGLMAKPSGEI 751
Cdd:CHL00117 90 NVHAVEKLRQSIEIWYATSEYLKQEMNPNFR--MTDP-------LNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 752 IETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDKGLTMTAIIDAGQVVAS 831
Cdd:CHL00117 161 IDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGMMIERIL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 832 IGvRVLGRTALDDIDHplTGERIVDAGKMILEPDVIEIEKAGIQSIRIRSALTCEVQTGVCSICYGRDLARGTPVNMGEA 911
Cdd:CHL00117 241 IQ-TLIGRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEA 317
|
330 340
....*....|....*....|....*
gi 494882676 912 VGVIAAQSIGEPGTQLTMRTFHLGG 936
Cdd:CHL00117 318 VGIIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
19-806 |
3.69e-92 |
|
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: 318.42 E-value: 3.69e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 19 DSIRISIASPEKILSWSYGEIKKPETinYrtfkpERDGLfcaRIFGPIKDyeclcgkyKRMkykGII-----CEKCGVev 93
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTCGN-- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 94 tlsrvRRER----MGHIELAAPVAHIWFLKslpsRISTLLDMTLKDVERVLyfenyivtepgLTSLKENQLLSEEEYMIA 169
Cdd:cd02582 62 -----TAGEcpghFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEIEKYLERIRRLKE 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 170 VDEFGEDQFTAMIGAEA----------------------IYEMLASMNLEKIA-GDLRADLAETTSDlkqkklmkRLKIV 226
Cdd:cd02582 122 KWPELVKRVIEKVKKKAkkrkvcphcgapqykiklekptTFYEEKEEGEVKLTpSEIRERLEKIPDE--------DLELL 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 227 eNFMESGNRPEWMIMKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVD 306
Cdd:cd02582 194 -GIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVT 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 307 ALFDNGRRG-RVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYA 385
Cdd:cd02582 273 TYFDNEIPGiPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVT 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 386 RLDakgysstVKQAKKLVEKeKPEVWDILDEVIR---------------------------EH-----PVLLNRAPTLHR 433
Cdd:cd02582 353 EWN-------IEKMRKLVLN-GPDKWPGANYVIRpdgrrirlryvnreelaerlepgwiveRHlidgdIVLFNRQPSLHR 424
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 434 LGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLY 513
Cdd:cd02582 425 MSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAY 504
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 514 YLSIMN----QNEPGEGMAFSDIGELhhalenkivtlhskirgRFKTVDEEGKPvskiFETtpGRMLIGELLPK------ 583
Cdd:cd02582 505 LLTRKTtlftKEEALQLLSAAGYDGL-----------------LPEPAILEPKP----LWT--GKQLFSLFLPKdlnfeg 561
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 584 --NFKVPFDTCNQEMT-------------------KKNI-----SKMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGI 637
Cdd:cd02582 562 kaKVCSGCSECKDEDCpndgyvvikngkllegvidKKAIgaeqpGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGF 641
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 638 SFGKDDMVIPETKAK----IVGDTENLVKEYEQQYNDGLI------TQGEKY-NKVVDAWGKA---TEKVAEDMMarika 703
Cdd:cd02582 642 TIGIDDEDIPEEARKeieeIIKEAEKKVYELIEQYKNGELeplpgrTLEETLeMKIMQVLGKArdeAGKVASKYL----- 716
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 704 vefDPEtgrqkqmNAIYMMSHSGARGSPNQMRQLGGMRGLMAKpSGEIIET-------P--------------IISNFKE 762
Cdd:cd02582 717 ---DPF-------NNAVIMARTGARGSMLNLTQMAACLGQQSV-RGERINRgyrnrtlPhfkpgdlgpeargfVRSSFRD 785
|
890 900 910 920
....*....|....*....|....*....|....*....|....
gi 494882676 763 GLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIV 806
Cdd:cd02582 786 GLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYV 829
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
20-806 |
8.98e-85 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 297.54 E-value: 8.98e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 20 SIRISIASPEKILSWSYGEIKKPETinYrtfkpERDGLfcaRIFGPIKDyeclcgkyKRMkykGII-----CEKCGvevt 94
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTCG---- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 95 lSRVRR--ERMGHIELAAPVAHIWFLKslpsRISTLLDMT--------LKDVERVLYFENYIVTEpGLTSLKENqlLSEE 164
Cdd:PRK08566 66 -GRAGEcpGHFGHIELARPVIHVGFAK----LIYKLLRATcrecgrlkLTEEEIEEYLEKLERLK-EWGSLADD--LIKE 137
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 165 EYMIAVDEF-----GEDQFTAMIGAEAIYEMLASMNLEKI-AGDLRADLAETT-SDLKqkklmkrlkiVENFMESGNRPE 237
Cdd:PRK08566 138 VKKEAAKRMvcphcGEKQYKIKFEKPTTFYEERKEGLVKLtPSDIRERLEKIPdEDLE----------LLGINPEVARPE 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 238 WMIMKVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDN---G-- 312
Cdd:PRK08566 208 WMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNeipGip 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 313 ----RRGRvitgankrPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFI----- 383
Cdd:PRK08566 288 parhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERvtewn 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 384 -------------------YA-RLDAKGYSSTVKQAKKLVEKEKPEvWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTL 443
Cdd:PRK08566 360 ieelreyvlngpekhpganYViRPDGRRIKLTDKNKEELAEKLEPG-WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRV 438
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 444 VEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLS----IMN 519
Cdd:PRK08566 439 LPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTrkstLFT 518
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 520 QNEPGEGMAFSDIGELhhALENKivtlhskirgrfktVDEEGKPvskiFETtpGRMLIGELLPKNFKVPF--------DT 591
Cdd:PRK08566 519 KEEALDLLRAAGIDEL--PEPEP--------------AIENGKP----YWT--GKQIFSLFLPKDLNLEFkakicsgcDE 576
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 592 CNQEMT-------------------KKNIS----KMIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPE 648
Cdd:PRK08566 577 CKKEDCehdayvvikngkllegvidKKAIGaeqgSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDEDIPE 656
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 649 TKAK----IVGDTENLVKEYEQQYNDGLI------TQGEKY-NKVVDAWGKA---TEKVAEDmmarikavEFDPEtgrqk 714
Cdd:PRK08566 657 EAKEeideIIEEAEKRVEELIEAYENGELeplpgrTLEETLeMKIMQVLGKArdeAGEIAEK--------YLGLD----- 723
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 715 qmNAIYMMSHSGARGSPNQMRQLGGMRGLMAKpSGEIIE-------TP--------------IISNFKEGLTVNEYFNST 773
Cdd:PRK08566 724 --NPAVIMARTGARGSMLNLTQMAACVGQQSV-RGERIRrgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFFFHA 800
|
890 900 910
....*....|....*....|....*....|...
gi 494882676 774 HGARKGLADTALKTANSGYLTRRLVDVAQDCIV 806
Cdd:PRK08566 801 MGGREGLVDTAVRTSQSGYMQRRLINALQDLKV 833
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
905-1357 |
7.30e-83 |
|
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: 269.78 E-value: 7.30e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 905 PVNMGEAVGVIAAQSIGEPGTQLTMRTFHLGGTATvvdqsfleasyegtvqiknrnmlrnsdgnliamgrslavtilder 984
Cdd:cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT--------------------------------------------- 36
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 985 gverssqrvaygskvfvddgdkvkrgqrlaewdpytrpmmtevegivhfedvvdglsvleatdestgitkrqvidwrstp 1064
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1065 rgadlkpaivikdaagnvlkmsrgsdarfflsvdailsvepgtkvsqgdvlarsplesaktkDITGGLPRVAELFEARrp 1144
Cdd:cd02655 37 --------------------------------------------------------------DITQGLPRVEELFEAR-- 52
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1145 kdhaiiaeidgtirlgrdyknkrrviiepaedgvepveylipkgkpfhlqdgdyiekgdyildgNPAPHDILAIK--GVE 1222
Cdd:cd02655 53 ----------------------------------------------------------------KINPHDLLRIKflGPE 68
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1223 ALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDRIEMDDNNDRLIEEGKKPSYGDPVLL 1302
Cdd:cd02655 69 AVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLL 148
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 494882676 1303 GITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd02655 149 GITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTG 203
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
999-1357 |
2.86e-77 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 281.50 E-value: 2.86e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 999 VFVDDGDKVKRGQRLAEwdpytrpmmTE--------VEGIVHFEDVVDGLSVLEATDestgitkRQVIDWRSTPR----- 1065
Cdd:PRK02597 845 LLVKDGQQIKPGDVVAR---------TQilckeageVRGIRVGGEAVRRLLVERDED-------TITIPLSGKPTvkvgd 908
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1066 ----GADLKPAIVIkDAAGNVLKMSRGS----DAR-FFLSVDAILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVA 1136
Cdd:PRK02597 909 lvvaGDELAPGVPA-PESGEVEAVSGGSvtlrLGRpYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIE 987
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1137 ELFEARRPKDHAIIAEIDGTIRLgrDYKNKRRV---IIEpaEDGVEpVEYLIPKGKPFHLQDGDYIEKGDYILDGNPAPH 1213
Cdd:PRK02597 988 ELLEARKPKESCILAKKPGTVQI--KYGDDESVdvkVIE--SDGTI-TEYPILPGQNVMVSDGQQVDAGEPLTDGPINPH 1062
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1214 DIL----------------AIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGDSHYIVGDNVDR 1277
Cdd:PRK02597 1063 ELLeiffedlrdrkglyeaALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIEL 1142
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1278 IEMDDNNDRLIEEGKKPSYGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK02597 1143 RQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1222
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
14-936 |
9.44e-74 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 270.74 E-value: 9.44e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 14 PAQHFDSIRISIASPEKILSWSYGEIKKPETINYRTFkPERDGLFCARIfGPIKdyeclcgkykrmkyKGIICEKCGvev 93
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIE--------------PGQKCLTCG--- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 94 TLSRVRRERMGHIELAAPVAHIWFLKslpsRISTLLDMTLKDVERVL-------YFENYIVTEPGLTSLKENQLLSE--E 164
Cdd:PRK14977 66 NLAANCPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKlpqedlnVFKLIEEAHAAARDIPEKRIDDEiiE 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 165 EYMIAVDEFGEDQFTAMIGAEAIYEML---ASMNLEKIAGDLRADLAETTSDLKQKKLMKRLKIVeNFMESGNRPEWMIM 241
Cdd:PRK14977 142 EVRDQVKVYAKKAKECPHCGAPQHELEfeePTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELI-GFDPKKARPEWAVL 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 242 KVVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRG--RVIT 319
Cdd:PRK14977 221 QAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHH 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 320 GANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFI---------------- 383
Cdd:PRK14977 301 KGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenniekmkelving 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 384 ---YARLDAKGYSSTVKQAKKLVEK----------EKPEVWDILDEVIREHP-VLLNRAPTLHRLGIQAFEPTLVEGKAI 449
Cdd:PRK14977 381 pdeFPGANAIRKGDGTKIRLDFLEDkgkdalreaaEQLEIGDIVERHLADGDiVIFNRQPSLHKLSILAHRVKVLPGATF 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 450 QLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIMNqnepgegmAF 529
Cdd:PRK14977 461 RLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDD--------AL 532
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 530 SDIGELhhalenkivtlhSKIRGRFKTVDEEGKPVSKifeTTPGRM-----LIGELLPKNF---------KVPFDTC--- 592
Cdd:PRK14977 533 FDKNEA------------SNIAMLAGITDPLPEPAIK---TKDGPAwtgkqLFSLFLPKDFnfegiakwsAGKAGEAkdp 597
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 593 -----------NQEMTKKNISK------------MIDTVYRHCGQKDTVIFCDRIMQLGFSHACKAGISFGKDDMVIPE- 648
Cdd:PRK14977 598 sclgdgyvlikEGELISGVIDDniigalveepesLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDe 677
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 649 TKAKIVGDTENLVKEYEQqyndgLITQGEKYNKVVDAwgKATEKVAEDMMARiKAVEFD--PETGRQKQM---------- 716
Cdd:PRK14977 678 AKQEIEDDIQGMKDEVSD-----LIDQRKITRKITIY--KGKEELLRGMKEE-EALEADivNELDKARDKagssandcid 749
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 717 --NAIYMMSHSGARGSPNQMRQLGGMRGLMAK--------PSGEIIE---------------TP-----IISNFKEGLTV 766
Cdd:PRK14977 750 adNAGKIMAKTGARGSMANLAQIAGALGQQKRktrigfvlTGGRLHEgykdralshfqegddNPdahgfVKNNYREGLNA 829
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 767 NEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDCIVNLVDCGTDkglTMTAIIDAGQVVASIGVRVLGRTALDDID 846
Cdd:PRK14977 830 AEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETVRD---PHGHIIQFKFGEDGIDPQKLDHGEAFNLE 906
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 847 HPLTGERIVDAGKMILEPDVIEIEKAGIQSI--RIRSALTCEVQ------TGVCSICY-GRDLARGTPVNMGEAVGVIAA 917
Cdd:PRK14977 907 RIIEKQKIEDRGKGASKDEIEELAKEYTKTFnaNLPKLLADAIHgaelkeDELEAICAeGKEGFEKAKVEPGQAIGIISA 986
|
1050
....*....|....*....
gi 494882676 918 QSIGEPGTQLTMRTFHLGG 936
Cdd:PRK14977 987 QSIAEPGTQMTLRTFHAAG 1005
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
979-1357 |
3.39e-71 |
|
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: 262.09 E-value: 3.39e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 979 TILDERGVERSSQRVAYGSKVFVDDGDKVKRGQRLAEWDPYTRPMmTEVEGIVHFEDVVDGLSVLEATDestgitkRQVI 1058
Cdd:TIGR02388 823 SLVLRRDIASDSTQGSTHTSLLVKDGDLIKPGAVIARTQILCKEA-GVVQGIDSGGESIRRLLVERNSD-------RLKV 894
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1059 DWRSTPR---------GADLKPAIV------IKDAAGNVLKMSRGSDARffLSVDAILSVEPGTKVSQGDVLARSPLESA 1123
Cdd:TIGR02388 895 NIKAKPVvktgdlvvaGDELAKGVKaeesgeIEEVASDYVILRIGRPYR--VSPGAVLHIEDGDLVQRGDNLALLVFERA 972
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1124 KTKDITGGLPRVAELFEARRPKDHAIIAEIDGTIRL--GRDYKNKRRVIIEpaEDGVEPvEYLIPKGKPFHLQDGDYIEK 1201
Cdd:TIGR02388 973 KTGDIVQGLPRIEELLEARKPKEACILAKRPGVVQVkyGTDDESVSIKVIE--RDGTIS-EYPLLPGQNIMVSDGQQVTG 1049
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1202 GDYILDGNPAPHDIL----------------AIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAG 1265
Cdd:TIGR02388 1050 GEPLTDGPINPHDILdvffsyykdqdglyeaAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAG 1129
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1266 DSHYIVGDNVDRIEMDDNNDRLIEEGKKPSYGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKEN 1345
Cdd:TIGR02388 1130 DTTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKEN 1209
|
410
....*....|..
gi 494882676 1346 VIVGRLIPAGTG 1357
Cdd:TIGR02388 1210 VIIGRLIPAGTG 1221
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
19-807 |
7.34e-62 |
|
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: 227.03 E-value: 7.34e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 19 DSIRISIASPEKILSWSYGEIKKPETINyRTFKPERDGLFCARIfGPIKdyeclcgkykrmkyKGIICEKCGvevtlsrv 98
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 99 rrERM-------GHIELAAPVAHIWFLkslpsristllDMTLKDVERVLyfenyivtepgltslkenqllseeeymiavd 171
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILRCVC------------------------------- 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 172 efgedqfTAMIGAEAIYEMLasmnlEKIagdlradlaettSDLKQKKLmkrlkiveNFMESGNRPEWMIMKVVPVIPPDL 251
Cdd:cd02733 93 -------KRELSAERVLEIF-----KRI------------SDEDCRIL--------GFDPKFSRPDWMILTVLPVPPPAV 140
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 252 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQESVDALFDNGRRG--RVITGaNKRPLKSL 329
Cdd:cd02733 141 RPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQK-SGRPLKSI 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 330 SDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMAL-----ELFKPFIYARLD------------AKgY 392
Cdd:cd02733 220 RQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLQelvrngpneypgAK-Y 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 393 ---SSTVKQAKKLVEKEKPEVWDILDEVIReH-----PVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFD 464
Cdd:cd02733 299 iirDDGERIDLRYLKKASDLHLQYGYIVER-HlqdgdVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFD 377
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 465 GDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPI--IVpsQDMVLGLYYLS----------IMN-----QNEPGEgM 527
Cdd:cd02733 378 GDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTkrdtflekdqVMNllmwlPDWDGK-I 454
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 528 AFSDIgelhhaLENK-------IVTL---HSKIRGRFKTVDEEGKPVSKIFETtpgRMLI--GELLPKNfkvpfdtcnqe 595
Cdd:cd02733 455 PQPAI------LKPKplwtgkqIFSLiipKINNLIRSSSHHDGDKKWISPGDT---KVIIenGELLSGI----------- 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 596 MTKKNISK----MIDTVYRHCGQKDTVIFCDRI--------MQLGFShackAGISfgkDDMVIPETKAKIvgdtENLVKE 663
Cdd:cd02733 515 LCKKTVGAssggLIHVIWLEYGPEAARDFIGNIqrvvnnwlLHNGFS----IGIG---DTIADKETMKKI----QETIKK 583
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 664 YEQQYNDgLITQGEKyNKVVDAWGKATEKVAEDMMARI--KAVEfdpETGRQKQM-----NAIYMMSHSGARGSPNQMRQ 736
Cdd:cd02733 584 AKRDVIK-LIEKAQN-GELEPQPGKTLRESFENKVNRIlnKARD---KAGKSAQKslsedNNFKAMVTAGSKGSFINISQ 658
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 737 lggMRGLMAKPSGEIIETP-----------------------IISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYL 793
Cdd:cd02733 659 ---IIACVGQQNVEGKRIPfgfrrrtlphfikddygpesrgfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYI 735
|
890
....*....|....
gi 494882676 794 TRRLVDVAQDCIVN 807
Cdd:cd02733 736 QRRLVKAMEDVMVK 749
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
82-798 |
9.70e-60 |
|
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: 221.65 E-value: 9.70e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 82 KGIICEKCGvevtlsrvrrERM-------GHIELAAPVAHIWFLKSlpsrISTLLDMTLKDVERVL-------YFENYIV 147
Cdd:cd02583 42 KDGICETCG----------LNLadcvghfGYIKLELPVFHIGYFKA----IINILQCICKTCSRVLlpeeekrKFLKRLR 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 148 tEPGLTSLKENQLLSEeeymiavdefgedqftamIGAEA--IYEMLASMNLEKIAGDLRAdlaettsdLKQKKLMKRLK- 224
Cdd:cd02583 108 -RPNLDNLQKKALKKK------------------ILEKCkkVRKCPHCGLLKKAQEDLNP--------LKVLNLFKNIPp 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 225 ---IVENFMESGNRPEWMIMKVVPVIPPDLRPLVPLDGGrfATSDLNDL---YRRVINRNNRLKRLIELRAPGIIIRNEK 298
Cdd:cd02583 161 edvELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDW 238
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 299 RMLQESVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALEL 378
Cdd:cd02583 239 DFLQLQCALYINSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKIL 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 379 FKP--------------------------FIYARLDAKGYSstVKQAKKLVEKEKPEVWDI-----LDEVIrehpVLLNR 427
Cdd:cd02583 319 TYPervtrynieklrklvlngpdvhpganFVIKRDGGKKKF--LKYGNRRKIARELKIGDIverhlEDGDI----VLFNR 392
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 428 APTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQD 507
Cdd:cd02583 393 QPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQD 472
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 508 MVLGLYYLS----IMNQNEPGEGMAFSDIGELHHAL-ENKIVtlhskirgrfktvdeegKPVskifETTPGRMLIGELLP 582
Cdd:cd02583 473 FLTASYLLTskdvFFDRAQFCQLCSYMLDGEIKIDLpPPAIL-----------------KPV----ELWTGKQIFSLLLR 531
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 583 KNFKVPFDtCNQEMTKKNISKMIDT--------VYRH----CGQ--KDTV-------IFCDRIMQLGFSHACKA------ 635
Cdd:cd02583 532 PNKKSPVL-VNLEAKEKSYTKKSPDmcpndgyvVIRNsellCGRldKSTLgsgsknsLFYVLLRDYGPEAAAAAmnrlak 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 636 ---------GISFGKDDmVIP-----ETKAKIVGDTENLVKEYEQQYNDG---------------LITQGEkYNKVVDAW 686
Cdd:cd02583 611 lssrwlsnrGFSIGIDD-VTPskellKKKEELVDNGYAKCDEYIKQYKKGklelqpgctaeqtleAKISGE-LSKIREDA 688
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 687 GKATEKvaedmmarikavEFDPEtgrqkqmNAIYMMSHSGARGSPN---QM------------RQLGGM--RGL--MAKP 747
Cdd:cd02583 689 GKACLK------------ELHKS-------NSPLIMALCGSKGSNInisQMiacvgqqiisgkRIPNGFedRTLphFPRN 749
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|....*.
gi 494882676 748 SgeiiETPI----ISN-FKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLV 798
Cdd:cd02583 750 S----KTPAakgfVANsFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLM 801
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1099-1357 |
6.15e-59 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 223.66 E-value: 6.15e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1099 AILSVEPGTKVSQGDVLARSPLESAKTKDITGGLPRVAELFEARrpkdhaiiaeidgtirlgrdyknkrrviiepaedGV 1178
Cdd:CHL00117 1102 ATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEAR----------------------------------SI 1147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1179 EPVEYLIpkgkpfHLQDGDYIEKGDYILdGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQK 1258
Cdd:CHL00117 1148 DSISMNL------EKRLEGWNERITRIL-GIPWGFLIGAELSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSK 1220
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1259 VEITDAGDS-HYIVGDNVD--RIEmddNNDRLIEEgkkPSYGDPVLLGITKASLQTPSFISAASFQETTKVLTEAAIAGK 1335
Cdd:CHL00117 1221 VLVSEDGMSnVFLPGELIGllRAE---RINRALEE---AICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGR 1294
|
250 260
....*....|....*....|..
gi 494882676 1336 TDTLQGLKENVIVGRLIPAGTG 1357
Cdd:CHL00117 1295 IDWLKGLKENVILGGLIPAGTG 1316
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
346-487 |
1.33e-44 |
|
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: 159.00 E-value: 1.33e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 346 GKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFI-----YARL------------------DAKGYSSTVKQAKKL 402
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpynIKRLrqlvengpnvypganyiiRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 403 VEKEKpEVWDILDE-VIREHPVLLNRAPTLHRLGIQAFEPTLVEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLE 481
Cdd:pfam00623 81 LDKEL-EIGDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAE 159
|
....*.
gi 494882676 482 ARVLMM 487
Cdd:pfam00623 160 AEELML 165
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
214-798 |
2.42e-37 |
|
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: 151.95 E-value: 2.42e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 214 LKQKKLMKRLKIVENfMESGNRPEWMIMKVVPVIPPDLRPLVPLDGGRFaTSDLNDLYRRVINRNNRLKRLIELRAPGII 293
Cdd:cd01435 106 VAKLKLLDKGLLVEA-AELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAES 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 294 IRNEKRM---------------LQESVDALFDNGRrgrvITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIV 358
Cdd:cd01435 184 QSKLDLIsgktnseklinawlqLQSAVNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVIS 259
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 359 TGPELKLHQCGLPKKMALEL-F----KPFIYARL------------------DAKG-----YSSTVKQAKKLVEKEKPEV 410
Cdd:cd01435 260 PDPFIETNEIGIPLVFAKKLtFpepvTPFNVEELrqavingpdvypganaieDEDGrlillSALSEERRKALAKLLLLLS 339
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 411 WDIL-----DEVIReH-----PVLLNRAPTLHRLGIQAF-------EptlvegKAIQLHPLVCTAFNADFDGDQMAVHVP 473
Cdd:cd01435 340 SAKLllngpKKVYR-HlldgdVVLLNRQPTLHKPSIMAHkvrvlpgE------KTLRLHYANCKSYNADFDGDEMNLHFP 412
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 474 LSLEAQLEARVLMMSTNNILHPANGAPI---IvpsQDMVLGLYYLSI----MNQNEPGEGMAFSDIGELHHALENKIVTL 546
Cdd:cd01435 413 QSELARAEAYYIASTDNQYLVPTDGKPLrglI---QDHVVSGVLLTSrdtfFTREEYQQLVYAALRPLFTSDKDGRIKLL 489
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 547 HSKIRgrfktvdeegKPVSK-----IFETtpgrmLIGELLPKNFKVPFDTCNQEMTKKNISKMIDtvyrhcGQKD--TVI 619
Cdd:cd01435 490 PPAIL----------KPKPLwtgkqVIST-----ILKNLIPGNAPLLNLSGKKKTKKKVGGGKWG------GGSEesQVI 548
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 620 FCDRIM--------QLGFS-----HAC-------------------------KAGISFGKDDMVipetkakivgdtenLV 661
Cdd:cd01435 549 IRNGELltgvldksQFGASayglvHAVyelyggetagkllsalgrlftaylqMRGFTCGIEDLL--------------LT 614
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 662 KEYEQQYNDGLitqgEKYNKVVDawgKATEKVAEDMMARI--KAVE-FDPEtGRQKQM--NAIYMMSHSGARGSPNQMRQ 736
Cdd:cd01435 615 PKADEKRRKIL----RKAKKLGL---EAAAEFLGLKLNKVtsSIIKaCLPK-GLLKPFpeNNLQLMVQSGAKGSMVNASQ 686
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 737 LGGMRG----------LMAK----PSGEIIET-P-----IISNFKEGLTVNEYFnsTH---GaRKGLADTALKTANSGYL 793
Cdd:cd01435 687 ISCLLGqqelegrrvpLMVSgktlPSFPPYDTsPraggfITDRFLTGIRPQEYF--FHcmaG-REGLIDTAVKTSRSGYL 763
|
....*
gi 494882676 794 TRRLV 798
Cdd:cd01435 764 QRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
491-644 |
5.93e-34 |
|
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: 128.13 E-value: 5.93e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 491 NILHPANGAPIIVPSQDMVLGLYYLSIMNqnepgegmAFSDIGELHHALENKIVTLHSKIRGRFKTvdeegkpvSKIFET 570
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAILKPIKP--------LWTGKQ 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 571 TPGRMLIGELLPKNF-KVPFDTCNQEMTK-------------------KNISKMIDTVYRHCGQKDTVIFCDRIMQLGFS 630
Cdd:pfam04983 65 TFSRLLPNEINPKGKpKTNEEDLCENDSYvlinngelisgvidkktvgKSLGSLIHIIYKEYGPEETAKFLDRLQKLGFR 144
|
170
....*....|....
gi 494882676 631 HACKAGISFGKDDM 644
Cdd:pfam04983 145 YLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1212-1357 |
8.54e-25 |
|
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: 102.11 E-value: 8.54e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1212 PHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEitdagdshyivgdnvdriemddnndrlieeg 1291
Cdd:cd00630 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGG------------------------------- 98
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 494882676 1292 kkpsygdpvLLGITKASL--QTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd00630 99 ---------LRGVTRSGFraSKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
673-761 |
5.71e-22 |
|
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: 92.04 E-value: 5.71e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 673 ITQGEKYNKVVDAWGKATEKVAEDMMARIKAVEFDPeTGR-----QKQMNAIYMMSHSGARGSPNQMRQLGGMRGLMAKP 747
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKARDP-AGNiasksLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
90 100
....*....|....*....|....*....
gi 494882676 748 SGEI---------------IETPIISNFK 761
Cdd:pfam05000 80 GKRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
86-516 |
1.45e-19 |
|
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: 95.16 E-value: 1.45e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 86 CEKCGvevtlSRVRRE---RMGHIELAAPVAHIWFLKslpsristlldmtlkDVERVLyfeNYIVtePGLTSLKENQLLS 162
Cdd:cd10506 34 CTTCG-----AKDNKKcegHFGVIKLPVTIYHPYFIS---------------EVAQIL---NKIC--PGCKSIKQKKKKP 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 163 EEEYMiavdefGEDQFTAMIGAEAIYEMLASMNLEKIA-GDLRADLAETTsdlkqKKLMKRLKIvenfmesgnRPEWMIM 241
Cdd:cd10506 89 PRETL------PPDYWDFIPKDGQQEESCVTKNLPILSlAQVKKILKEID-----PKLIAKGLP---------RQEGLFL 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 242 KVVPVIPPDLRplVPLDGGRFATsdlndlyrrvinrnnrlkrlielrAPGIIIRNEKRMLQESVDAlfdngrRGRvitgA 321
Cdd:cd10506 149 KCLPVPPNCHR--VTEFTHGFST------------------------GSRLIFDERTRAYKKLVDF------IGT----A 192
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 322 NKrplKSLSDMLKGKQgrFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFkpfIYARLDAKGYSSTVKQA-K 400
Cdd:cd10506 193 NE---SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLT---VSERVSSWNRERLQEYCdL 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 401 KLVEKEK--PEVWDILDEVIREHP----------------VLLNRAPTLHRLGIQAFEPTLVE-GKAIQLHPLVCTAFNA 461
Cdd:cd10506 265 TLLLKGVigVRRNGRLVGVRSHNTlqigdvihrplvdgdvVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRG 344
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 494882676 462 DFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLS 516
Cdd:cd10506 345 DFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMT 399
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1227-1357 |
6.29e-16 |
|
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: 83.67 E-value: 6.29e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1227 YLVNEI--QEV--YRlqgVVINDKHIEVIVRQM---------------LQKVEI---TDAGDSHYIVGDNVDRIE---MD 1281
Cdd:COG0086 560 YLVNEIlpQEVpfYN---QVINKKHIEVIIRQMyrrcglketvifldrLKKLGFkyaTRAGISIGLDDMVVPKEKqeiFE 636
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1282 DNNDRLIE------EGK--KPSYGDPVLLGITKASLQTPSFISAA-SFQETTKVLTEAAIAGKTDTLQGL---------- 1342
Cdd:COG0086 637 EANKEVKEiekqyaEGLitEPERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmakp 716
|
170
....*....|....*...
gi 494882676 1343 KENVI---VGRLIPAGTG 1357
Cdd:COG0086 717 SGNIIetpIGSNFREGLG 734
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
909-1357 |
4.87e-14 |
|
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: 75.47 E-value: 4.87e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVvdqsfleasyegtvqiknrNMlrnsdgnliAMGRSLAVTILDERGVER 988
Cdd:TIGR02389 44 GEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEL-------------------NV---------TLGLPRLIEIVDARKTPS 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 989 SSQRVAYGSKVFVDDGDKVKRGQRLAEWdpytrpmmTEVEGIVH--FEDVVDGLSVLEATDEST---GITKRQVIDwrst 1063
Cdd:TIGR02389 96 TPSMTIYLEDEYEKDREKAEEVAKKIEA--------TKLEDVAKdiSIDLADMTVIIELDEEQLkerGITVDDVEK---- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1064 prgadlkpaivIKDAAGNVLKMSRGSDarfflsvDAILSVEPGTkvsqgdvlarsplesaktkditgglPRVAELFEaRR 1143
Cdd:TIGR02389 164 -----------AIKKAKLGKVIEIDMD-------NNTITIKPGN-------------------------PSLKELRK-LK 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1144 PKDHAIiaEIDGTirlgrdyKNKRRVIIEPAEDgvepvEYLIpKGKPFHLQDGDYIEKGDYILDGNPAPHDILAIKGVEA 1223
Cdd:TIGR02389 200 EKIKNL--HIKGI-------KGIKRVVIRKEGD-----EYVI-YTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGIEA 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1224 LASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGdSHYIVGdnvdriemddnndrlieegkkpsygdpvllg 1303
Cdd:TIGR02389 265 ARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG-RHGISG------------------------------- 312
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 494882676 1304 itkaslQTPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:TIGR02389 313 ------EKASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTG 360
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
909-1357 |
7.18e-13 |
|
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: 71.90 E-value: 7.18e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTAtvvdqsfleasyegtvqiknrnmlrnsdgnliamgrSLAVTildeRGVER 988
Cdd:cd06528 40 GEAVGIVAAQSIGEPGTQMTLRTFHYAGVA------------------------------------EINVT----LGLPR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 989 SSQRVAYGSKvfvddgdkvkrgqrlaewdPYTrPMMT---EVEgivHFEDVVDGLSV---LEATDESTgITKRQVIDWRS 1062
Cdd:cd06528 80 LIEIVDARKE-------------------PST-PTMTiylEEE---YKYDREKAEEVarkIEETTLEN-LAEDISIDLFN 135
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1063 TprgadlkpAIVIK-DAagNVLKmSRGsdarffLSVDAILSVEPGTKVSqgdvlARSPLESAKTKDITGGLPRVAELFEA 1141
Cdd:cd06528 136 M--------RITIElDE--EMLE-DRG------ITVDDVLKAIEKLKKG-----KVGEEGDVTLIVLKAEEPSIKELRKL 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1142 RRPKDHAIIAEIDGTirlgrdyknkRRVIIEPAEDgvepvEYLI-----PKGKPFHLQDGDY--IEKGDyildgnpaPHD 1214
Cdd:cd06528 194 AEKILNTKIKGIKGI----------KRVIVRKEED-----EYVIytegsNLKAVLKVEGVDPtrTTTNN--------IHE 250
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1215 ILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGdSHYIVGDnvdriemddnndrlieegkKP 1294
Cdd:cd06528 251 IEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIG-RHGIAGE-------------------KP 310
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 494882676 1295 SygdpVLlgitkaslqtpsfiSAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd06528 311 S----VL--------------ARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
909-1357 |
3.32e-12 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 69.87 E-value: 3.32e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTATVvdqsfleasyegtvqiknrNMlrnsdgnliAMGRSLAVTILDERGVer 988
Cdd:PRK04309 59 GEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEI-------------------NV---------TLGLPRLIEIVDARKE-- 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 989 ssqrvaygskvfvddgdkvkrgqrlaewdPYTrPMMT-------------------EVEGiVHFEDVvdglsvleATDES 1049
Cdd:PRK04309 109 -----------------------------PST-PMMTiylkdeyaydrekaeevarKIEA-TTLENL--------AKDIS 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1050 TGITKRQVIdwrstprgADLKPAIVIKdaagnvlkmsRGsdarffLSVDAILSVEPGTKVSQGDVlarspleSAKTKDIT 1129
Cdd:PRK04309 150 VDLANMTII--------IELDEEMLED----------RG------LTVDDVKEAIEKKKGGEVEI-------EGNTLIIS 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1130 GGLPRVAELFEARRPKDHAIIAEIDGTirlgrdyknkRRVIIEPAEDgvepvEY-LIPKGKPFhlqdGDYIEkgdyiLDG 1208
Cdd:PRK04309 199 PKEPSYRELRKLAEKIRNIKIKGIKGI----------KRVIIRKEGD-----EYvIYTEGSNL----KEVLK-----VEG 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1209 NPA-------PHDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGdSHYIVGDnvdriemd 1281
Cdd:PRK04309 255 VDAtrtttnnIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIG-RHGVSGE-------- 325
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 494882676 1282 dnndrlieegkKPSygdpVLlgitkaslqtpsfiSAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK04309 326 -----------KAS----VL--------------ARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
906-1357 |
1.34e-11 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 68.68 E-value: 1.34e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 906 VNMGEAVGVIAAQSIGEPGTQLTMRTFHlggtatvvdqsfleasYEGTVQIKnrnmlrnsdgnlIAMGRSLAVTILDERG 985
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFH----------------YAGVAEMN------------VTLGLPRLIEIVDARK 230
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 986 VERSSQRVAYGSKVFVDDGDKVKRGQRLAEWDPytrpmMTEVEGIVhfEDVVDgLSVLEATDEStgitkrqvidwrstpr 1065
Cdd:PRK14897 231 KPSTPTMTIYLKKDYREDEEKVREVAKKIENTT-----LIDVADII--TDIAE-MSVVVELDEE---------------- 286
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1066 gadlkpaiVIKDaagnvlkmsrgsdarfflsvdailsvepgTKVSQGDVLARSPLESAKTKDITGGL-------PRVAEL 1138
Cdd:PRK14897 287 --------KMKE-----------------------------RLIEYDDILAAISKLTFKTVEIDDGIirlkpqqPSFKKL 329
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1139 FEARRPKDHAIIAEIDGTirlgrdyknkRRVIIEPAEDGVEPVEYliPKGKpfHLQDGDYIEKGDYILDGNPAPHDILAI 1218
Cdd:PRK14897 330 YLLAEKVKSLTIKGIKGI----------KRAIARKENDERRWVIY--TQGS--NLKDVLEIDEVDPTRTYTNDIIEIATV 395
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1219 KGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGdSHYIVGDnvdriemddnndrlieegkkpsygd 1298
Cdd:PRK14897 396 LGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIG-RHGISGE------------------------- 449
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*....
gi 494882676 1299 pvllgitKASLqtpsfISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK14897 450 -------KSSV-----LARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
909-938 |
6.90e-11 |
|
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: 62.05 E-value: 6.90e-11
10 20 30
....*....|....*....|....*....|
gi 494882676 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTA 938
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVA 30
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
909-938 |
7.59e-10 |
|
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: 61.85 E-value: 7.59e-10
10 20 30
....*....|....*....|....*....|
gi 494882676 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTA 938
Cdd:cd02736 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVA 39
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
906-936 |
9.09e-10 |
|
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: 61.82 E-value: 9.09e-10
10 20 30
....*....|....*....|....*....|.
gi 494882676 906 VNMGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
906-936 |
1.39e-08 |
|
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: 58.76 E-value: 1.39e-08
10 20 30
....*....|....*....|....*....|.
gi 494882676 906 VNMGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
Cdd:cd02584 24 VHPGEMVGTIAAQSIGEPATQMTLNTFHFAG 54
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
1318-1357 |
1.19e-07 |
|
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: 55.67 E-value: 1.19e-07
10 20 30 40
....*....|....*....|....*....|....*....|
gi 494882676 1318 ASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd02584 364 CSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1220-1357 |
1.35e-07 |
|
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: 54.92 E-value: 1.35e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1220 GVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEItdagdshyivgdnvdriemddnndrlieegkkpsygdp 1299
Cdd:cd02736 199 GIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV-------------------------------------- 240
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1300 vlLGITKASLQ--TPSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd02736 241 --LGITRFGIAkmKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1213-1357 |
3.87e-07 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 54.90 E-value: 3.87e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494882676 1213 HDILAIKGVEALASYLVNEIQEVYRLQGVVINDKHIEVIVRQMLQKVEITDAGdSHYIVGdnvdriemddnndrliEEGk 1292
Cdd:PRK14898 736 IEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIG-RHGVAG----------------EKG- 797
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 494882676 1293 kpsygdpvllgitkaslqtpSFISAASFQETTKVLTEAAIAGKTDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK14898 798 --------------------SVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
910-929 |
5.20e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 41.42 E-value: 5.20e-03
|
| |
