|
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: 2378.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 16 QTFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTL 95
Cdd:PRK00566 5 QDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTR 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 96 SRVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPGLTSLKEHQLLSEEEYMIAVDEFGe 175
Cdd:PRK00566 85 SKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYG- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 176 DQFTALIGAEAIYELLASMELEKIAADLRVDLAETTSDLKQKKLMKRLKIVENFLESGNRPEWMIMKIVPVIPPDLRPLV 255
Cdd:PRK00566 164 DEFVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 256 PLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKG 335
Cdd:PRK00566 244 QLDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 336 KQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERPEVWDILD 415
Cdd:PRK00566 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 416 EVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHP 495
Cdd:PRK00566 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 496 ANGAPIIVPSQDMVLGLYYLSIVADKEPGEGMMFADMGELQHALENKVVTLHTKIKGRFKTVdaegkpvsKIYDTTPGRM 575
Cdd:PRK00566 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSK--------KLVETTVGRV 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 576 ITGELLPKnvNVPFDICNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVA 655
Cdd:PRK00566 556 IFNEILPE--GLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 656 DTEALTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMMARLKAvefdpvtgRQKQMNSVYMMSHSGARGSVNQMR 735
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSK--------DQESFNPIYMMADSGARGSASQIR 705
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 736 QLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEI 815
Cdd:PRK00566 706 QLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDR 785
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 816 GLTMQPIVDAGQIVASIGQRVLGRTALDPILHPTTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCAKC 895
Cdd:PRK00566 786 GIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKC 865
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 896 YGRDLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTaqvvdssyleasyegtvklrnrnvvrnsdgnlvvmgrn 975
Cdd:PRK00566 866 YGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV-------------------------------------- 907
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 976 mavlildntgkeravhrvtygsrlfvdeadtvkrgqriaewdpytrpimtevegyvefedlvdglsvsesadestgitkr 1055
Cdd:PRK00566 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1056 vvidwrstprgsdlkpamvikdkagkilklskggdarfmlsvesilsvepgahvkagdviarlpmesaktkDITGGLPRV 1135
Cdd:PRK00566 908 -----------------------------------------------------------------------DITGGLPRV 916
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1136 AELFEARRPKDHAVIAEIDGTVRFGRDYKNKRRIIIEPNDDtiEPVEYLIPKGKPFHLQDGDVIEKGEYILDGNPAPHDI 1215
Cdd:PRK00566 917 AELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDG--EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHDI 994
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1216 LAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIELEEINERLIEEGKKPG 1295
Cdd:PRK00566 995 LRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPA 1074
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 501039963 1296 SGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTGGMTNQIRRIATARDE 1372
Cdd:PRK00566 1075 TGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDE 1151
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
16-1195 |
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: 1843.65 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 16 QTFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTL 95
Cdd:COG0086 5 EDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 96 SRVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPGLTSLKEHQLLSEEEYMIAVDEFGe 175
Cdd:COG0086 85 SKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 176 DQFTALIGAEAIYELLASMELEKIAADLRVDLAETTSDLKQKKLMKRLKIVENFLESGNRPEWMIMKIVPVIPPDLRPLV 255
Cdd:COG0086 164 DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 256 PLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKG 335
Cdd:COG0086 244 PLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 336 KQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERPEVWDILD 415
Cdd:COG0086 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 416 EVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHP 495
Cdd:COG0086 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 496 ANGAPIIVPSQDMVLGLYYLSIVADKEPGEGMMFADMGELQHALENKVVTLHTKIKGRFKTvdaEGKPVSKIYDTTPGRM 575
Cdd:COG0086 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITE---DGEQVGKIVETTVGRY 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 576 ITGELLPKnvNVPFdiCNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVA 655
Cdd:COG0086 561 LVNEILPQ--EVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFE 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 656 DTEALTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMMARLkavefdpvtgrqKQMNSVYMMSHSGARGSVNQMR 735
Cdd:COG0086 637 EANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAF------------SSQNTTYMMADSGARGSADQLR 704
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 736 QLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEI 815
Cdd:COG0086 705 QLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDR 784
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 816 GLTMQPIVDAGQIVASIGQRVLGRTALDPILHPTTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCAKC 895
Cdd:COG0086 785 GITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKC 864
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 896 YGRDLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQ-VVDSSYLEASYEGTVKLRNRNVVRNSDGNLVVMGR 974
Cdd:COG0086 865 YGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASrAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSR 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 975 NMAVLILDNTGKERAVHRVTYGSRLFVDEADTVKRGQRIAEWDPYTRPIMTEVEGYVEFEDLVDGLSVSESADESTGITK 1054
Cdd:COG0086 945 NSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLS 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1055 RVVIDWRSTPRGSDLKPAMVIKDKAGKILKLSKGGDARFMLSVESILSVEPGAHVKAGDVIARLPMESAKTKDITGGLPR 1134
Cdd:COG0086 1025 IVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGL 1104
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 501039963 1135 VAELFEARRPKDHAVIAEIDGTVRFGRDYKNKRRIIIEPNDDTIEPVEYLIPKGKPFHLQD 1195
Cdd:COG0086 1105 ARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 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 501039963 20 SIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSRVR 99
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 100 RERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPGLTSLKEHQLLSEEEYMIAVDEFGeDQFT 179
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYG-DGFR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 180 ALIGAEAIYELLASMELEKIAADLRVDLAETTSDLKQKKLMKRLKIVENFLESGNRPEWMIMKIVPVIPPDLRPLVPLDG 259
Cdd:TIGR02386 160 AGMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDG 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 260 GRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGR 339
Cdd:TIGR02386 240 GRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGR 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 340 FRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERPEVWDILDEVIR 419
Cdd:TIGR02386 320 FRQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIK 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 420 EHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGA 499
Cdd:TIGR02386 400 EHPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGK 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 500 PIIVPSQDMVLGLYYLSIVADKEPGEGMMFADMGELQHALENKVVTLHTKIKGRFKtvdaegkpvSKIYDTTPGRMITGE 579
Cdd:TIGR02386 480 PIVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTS---------GEILETTVGRVIFNE 550
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 580 LLPKnvNVPFDICNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVADTEA 659
Cdd:TIGR02386 551 ILPE--GFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADK 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 660 LTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMMARLKAvefdpvtgRQKQMNSVYMMSHSGARGSVNQMRQLGG 739
Cdd:TIGR02386 629 EVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKK--------DTYKFNPIFMMADSGARGNISQFRQLAG 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 740 MRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEIGLTM 819
Cdd:TIGR02386 701 MRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEV 780
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 820 QPIVDA-GQIVASIGQRVLGRTALDPILHPTTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCAKCYGR 898
Cdd:TIGR02386 781 EAIVEGkDEIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGR 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 899 DLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQvvdssyleasyegtvklrnrnvvrnsdgnlvvmgrnmav 978
Cdd:TIGR02386 861 DLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAG--------------------------------------- 901
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 979 lildntgkeravhrvtygsrlfvdeadtvkrgqriaewdpytrpimtevegyvefedlvdglsvsesadestgitkrvvi 1058
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1059 dwrstprgsdlkpamvikdkagkilklskggdarfmlsvesilsvepgahvkagdviarlpmesaKTKDITGGLPRVAEL 1138
Cdd:TIGR02386 902 -----------------------------------------------------------------ASGDITQGLPRVKEL 916
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1139 FEARRPKDHAVIAEIDGTVRF-GRDYKNKRRIIIEPNDDtiEPVEYLIPKGKPFHLQDGDVIEKGEYILDGNPAPHDILA 1217
Cdd:TIGR02386 917 FEARTPKDKAVIAEVDGTVEIiEDIVKNKRVVVIKDEND--EEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLR 994
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1218 IKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIELEEINERLIEEGKKPGSG 1297
Cdd:TIGR02386 995 IKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASA 1074
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1298 NPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 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: 1734.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 15 AQTFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVT 94
Cdd:PRK14844 1445 AQSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVT 1524
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 95 LSRVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPGLTSLKEHQLLSEEEYMIAVDEFG 174
Cdd:PRK14844 1525 SSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYG 1604
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 175 EDQFTALIGAEAIYELLASMELEKIAADLRVDLAETTSDLKQKKLMKRLKIVENFLESGNRPEWMIMKIVPVIPPDLRPL 254
Cdd:PRK14844 1605 IDSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPL 1684
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 255 VPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPL-KSLSDML 333
Cdd:PRK14844 1685 VSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYkKSISDML 1764
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 334 KGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERPEVWDI 413
Cdd:PRK14844 1765 KGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDM 1844
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 414 LDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNIL 493
Cdd:PRK14844 1845 LEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVL 1924
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 494 HPANGAPIIVPSQDMVLGLYYLSIVADKEpGEGMMFADMGELQHALENKVVTLHTKIKGRFKTVDAEGKPVSKIYDTTPG 573
Cdd:PRK14844 1925 SPSNGRPIIVPSKDIVLGIYYLTLQEPKE-DDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSSGETHYKTICTTPG 2003
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 574 RMITGELLPKNVNVPFDICNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKI 653
Cdd:PRK14844 2004 RLILWQIFPKHENLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKATH 2083
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 654 VADTEALTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMmarLKAVEfdpVTGRQKQMNSVYMMSHSGARGSVNQ 733
Cdd:PRK14844 2084 VDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDM---LKAIS---IYDGNSKYNSVYMMVNSGARGSTSQ 2157
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 734 MRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGA 813
Cdd:PRK14844 2158 MKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKHDCKT 2237
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 814 EIGLTMQPIVDAGQIVASIGQRVLGRTALDPILHPTTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCA 893
Cdd:PRK14844 2238 KNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISPGVCS 2317
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 894 KCYGRDLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGT-AQVVDSSYLEASYEGTVKLRNRNVVRNSDGNLVVM 972
Cdd:PRK14844 2318 LCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVmTRGVESSNIIASINAKIKLNNSNIIIDKNGNKIVI 2397
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 973 GRNMAVLILDNTGKERAVHRVTYGSRLFVDEADTVKRGQRIAEWDPYTRPIMTEVEGYVEFEDLVDGLSVSESADESTGI 1052
Cdd:PRK14844 2398 SRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEVMDESTGI 2477
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1053 TKRVVIDWRSTPRGSDLKPAMVIKDKAGKILKLSKGGDARFMLSVESILSVEPGAHVKAGDVIARLPMESAKTKDITGGL 1132
Cdd:PRK14844 2478 SSKVVKDWKLYSGGANLRPRIVLLDDNGKVMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRDITGGL 2557
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1133 PRVAELFEARRPKDHAVIAEIDGTVRFG-RDYKNKRRIIIEPNDDTIEPVEYLIPKGKPFHLQDGDVIEKGEYILDGNPA 1211
Cdd:PRK14844 2558 PRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLMDGDPD 2637
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1212 PHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIELEEINERLIEEG 1291
Cdd:PRK14844 2638 LHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDAMSNSG 2717
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501039963 1292 KKPGSGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTGGMTNQIRRIA 1367
Cdd:PRK14844 2718 KRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLIMNKVRALS 2793
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
18-1372 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1531.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGI-ICEKCGVEVTLS 96
Cdd:PRK09603 1396 FSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKCGVAITHS 1475
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 97 RVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPG--------LTSLKEHQLLSEEEYMI 168
Cdd:PRK09603 1476 KVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGeaaydnegTKLVMKYDILNEEQYQN 1555
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 169 AVDEFGEDQFTALIGAEAIYELLASMELEKIAADLRVDLAETTSDLKQKKLMKRLKIVENFLESGNRPEWMIMKIVPVIP 248
Cdd:PRK09603 1556 ISRRYEDRGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMMLTVLPVLP 1635
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 249 PDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKS 328
Cdd:PRK09603 1636 PDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGANKRPLKS 1715
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 329 LSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERP 408
Cdd:PRK09603 1716 LSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKRMIEQKSN 1795
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 409 EVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMS 488
Cdd:PRK09603 1796 EVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAECKVLMLS 1875
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 489 TNNILHPANGAPIIVPSQDMVLGLYYLSIVADKEPGEGMMFADMGELQHALENKVVTLHTKIkgrfKTVDAegkpvSKIY 568
Cdd:PRK09603 1876 SMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKI----RVLDQ-----GNII 1946
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 569 DTTPGRMITGELLPKnvNVPFDICNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPD 648
Cdd:PRK09603 1947 ATSAGRMIIKSILPD--FIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMEDIITPK 2024
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 649 TKAKIVADTEALTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMMARLKAvefdpvtgRQKQMNSVYMMSHSGAR 728
Cdd:PRK09603 2025 DKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAK--------DKEGFNSIYMMADSGAR 2096
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 729 GSVNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISE 808
Cdd:PRK09603 2097 GSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDVSQNVKVVS 2176
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 809 VDCGAEIGLTMQPIVDAGQIVASIGQRVLGRTALDPILHPTTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETR 888
Cdd:PRK09603 2177 DDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIRTPVTCKAP 2256
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 889 NGVCAKCYGRDLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTA-QVVDSSYLEASYEGTVKLRNRNVVRNSDG 967
Cdd:PRK09603 2257 KGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTAsRSQDEREIVASKEGFVRFYNLRTYTNKEG 2336
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 968 -NLVVMGRNMAVL------------------------------------------------------------------- 979
Cdd:PRK09603 2337 kNIIANRRNASILvvepkikapfdgelrietvyeevvvsvkngdqeakfvlrrsdivkpselagvggkiegkvylpyasg 2416
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 980 -------------------------------------------------------------------------------I 980
Cdd:PRK09603 2417 hkvhkggsiadiiqegwnvpnripyasellvkdndpiaqdvyakekgiikyyvleanhlerthgikkgdivsekglfavI 2496
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 981 LDNTGKERAVHRVTYGSRLFVDEADTVK-----------RGQRIAEWDPYTRPIMTEVEGYVEFEDLVDGLSVSESADES 1049
Cdd:PRK09603 2497 ADDNGREAARHYIARGSEILIDDNSEVSansviskpttnTFKTIATWDPYNTPIIADFKGKVSFVDIIAGVTVAEKEDEN 2576
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1050 TGITKRVVIDWrsTPRGsdLKPAMVIKDKAGKILklskggdaRFMLSVESILSVEPGAHVKAGDVIARLPMESAKTKDIT 1129
Cdd:PRK09603 2577 TGITSLVVNDY--IPSG--YKPSLFLEGANGEEI--------RYFLEPKTSIAISDGSSVEQAEVLAKIPKATVKSRDIT 2644
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1130 GGLPRVAELFEAR--RPKDHAVIAEIDGTVRFGRDYKNKRRIIIEPNDDTIepVEYLIPKGKPFHLQDGDVIEKGEYILD 1207
Cdd:PRK09603 2645 GGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRS--MDYFVDKGKQILVHADEFVHAGEAMTD 2722
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1208 GNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIELEEINERL 1287
Cdd:PRK09603 2723 GVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLFKEENARV 2802
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1288 IEEGKKPGSGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTGGMTNQIRRIA 1367
Cdd:PRK09603 2803 IALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMYKNKKIVLR 2882
|
....*
gi 501039963 1368 TARDE 1372
Cdd:PRK09603 2883 TLEDD 2887
|
|
| 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: 1298.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSR 97
Cdd:cd01609 3 FDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 98 VRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFenyivtepgltslkehqllseeeymiavdefgedq 177
Cdd:cd01609 83 VRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF----------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 178 ftaligaeaiyellasmelekiaadlrvdlaettsdlkqkklmkrlkIVENFLESGNRPEWMIMKIVPVIPPDLRPLVPL 257
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 258 DGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQ 337
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 338 GRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERPEVWDILDEV 417
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 418 IREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPAN 497
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 498 GAPIIVPSQDMVLGLYYLSIVADKEPGEGMMfadmgelqhalenkvvtlhtkikgrfktvdaegkpvskiyDTTPGRMIT 577
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEGII----------------------------------------ETTVGRVIF 440
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 578 GELLPKNVnvpFDIcNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVADT 657
Cdd:cd01609 441 NEILPEGL---PFI-NKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEA 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 658 EALTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMMARLKAVEFdpvtgrqkqmNSVYMMSHSGARGSVNQMRQL 737
Cdd:cd01609 517 EEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDPF----------NPIYMMADSGARGSKSQIRQL 586
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 501039963 738 GGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVD 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: 1287.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 18 FDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEKCGVEVTLSR 97
Cdd:PRK14906 9 FDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRAK 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 98 VRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVT-------EPGLTSLKEH------QLLSEE 164
Cdd:PRK14906 89 VRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITsvdkearEEDADDLRDElaadleELDAER 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 165 EYMIAV------------DEFGEDQ------------------------------------------------------- 177
Cdd:PRK14906 169 DRLIEAtrrlsvdyvpedDEFVDDIgdderltaeevraevadiyeeynerkalrreafdafmqiepkqlisdealyremr 248
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 178 ------FTALIGAEAIYELLASMELEKIAADLRvDLAETTSDLKQKKLMKRLKIVENFLESGNRPEWMIMKIVPVIPPDL 251
Cdd:PRK14906 249 lnysiyFKGGMGAEAVRDLLDAIDLEKEAEELR-AIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPDL 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 252 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSD 331
Cdd:PRK14906 328 RPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLAD 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 332 MLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKKLVEKERPEVW 411
Cdd:PRK14906 408 MLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYVW 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 412 DILDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNN 491
Cdd:PRK14906 488 DVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSNN 567
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 492 ILHPANGAPIIVPSQDMVLGLYYLSIVADKEPGEGMMFADMGELQHALE-NKVVTLHTKI--------KGRFKTVDAEGK 562
Cdd:PRK14906 568 IKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDaRADLDLQAKIvvrlsrdmTVRGSYGDLEET 647
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 563 PVSKIYDTTPGRMITGELLPKnvNVPFdiCNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKD 642
Cdd:PRK14906 648 KAGERIETTVGRIIFNQVLPE--DYPY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVY 723
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 643 DMVIPDTKAKIVADTEALTTEYEQQYNDGLITQGEKYNKVVDAWGKATDKITEEMMArlkavEFDpvtgrqkQMNSVYMM 722
Cdd:PRK14906 724 DATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLA-----GFD-------EDNPIYMM 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 723 SHSGARGSVNQMRQLGGMRGLMAKPSGEIIETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQ 802
Cdd:PRK14906 792 ADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDVAQ 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 803 DAIISEVDCGAEIGLTMqPIVDAGqivASIGQRVLGRTALDPILHPtTGEVIVEAGRMIEEK-DVEIIEKAAIQSIRIRS 881
Cdd:PRK14906 872 DVIVREEDCGTDEGVTY-PLVKPK---GDVDTNLIGRCLLEDVCDP-NGEVLLSAGDYIESMdDLKRLVEAGVTKVQIRT 946
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 882 ALTCETRNGVCAKCYGRDLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAqvvdssyleasyegtvklrnrnv 961
Cdd:PRK14906 947 LMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA----------------------- 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 962 vrnsdgnlvvmgrnmavlildntgkeravhrvtygsrlfvdeadtvkrgqriaewdpytrpimtevegyvefedlvdgls 1041
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1042 vsesadestgitkrvvidwrstprgsdlkpamvikdkagkilklskgGDarfmlsvesilsvepgahvkagdviarlpme 1121
Cdd:PRK14906 1004 -----------------------------------------------GD------------------------------- 1005
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1122 saktkDITGGLPRVAELFEARRPKDHAVIAEIDGTVRFGRDyKNKRRIIIEPNDDTIEpvEYLIPKGKPFH--LQDGDVI 1199
Cdd:PRK14906 1006 -----DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGD-KTEKTLTIHDQDGNSR--EYVVSARVQFMpgVEDGVEV 1077
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1200 EKGEYILDGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIE 1279
Cdd:PRK14906 1078 RVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYE 1157
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 1280 LEEINERLIEEGKKPGSGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK14906 1158 FEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTG 1235
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
16-576 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 833.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 16 QTFDSIRISIASPEKILSWS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIIC 86
Cdd:PRK02625 7 NRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVC 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 87 EKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPG-LTSLKEHQLLSEEE 165
Cdd:PRK02625 87 ERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGnHKNLKYKQLLTEDQ 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 166 YMIAVDE-FGEDQF-----TALIGAEAIYELLASMELEKIAADLRVDLAETTSDlKQKKLMKRLKIVENFLESGNRPEWM 239
Cdd:PRK02625 167 WLEIEDQiYAEDSElegeeVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGSRPEWM 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 240 IMKIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVIT 319
Cdd:PRK02625 246 VLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVV 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 320 GANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQA 399
Cdd:PRK02625 326 GANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAA 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 400 KKLVEKERPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQ 479
Cdd:PRK02625 406 KKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQ 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 480 LEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYL-SIVADKEPGEGMMFADMGELQHALENKVVTLHTKIKGRF---- 554
Cdd:PRK02625 486 AEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLtAENPGAQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFngev 565
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 501039963 555 ----------KTV------------------DAEGKPVSKIYDTTPGRMI 576
Cdd:PRK02625 566 edddedteplKTEtledgtrieqyryrrdrfDEDGNLISQYILTTVGRVI 615
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
18-517 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 817.99 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 18 FDSIRISIASPEKILSWSY---------GEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRM---KYKGII 85
Cdd:CHL00018 7 HQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdeKEDPKF 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 86 CEKCGVEVTLSRVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVT--EPGLTSLKEHQLLSE 163
Cdd:CHL00018 87 CEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFARpiAKKPTFLRLRGLFEY 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 164 E----EYMI----AVDEFGEDQFTAL-IGAEAIYELLASMELEKIAADLRVD---LAETTSD--------LKQKK--LMK 221
Cdd:CHL00018 167 EiqswKYSIplffSTQGFDTFRNREIsTGAGAIREQLADLDLRIIIDNSLVEwkeLGEEGSTgnewedrkIGRRKdfLVR 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 222 RLKIVENFLESGNRPEWMIMKIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELR--APGIIIRNEKR 299
Cdd:CHL00018 247 RIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQKK 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 300 MLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELF 379
Cdd:CHL00018 327 LLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELF 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 380 KPFIYARLDAKGYSSTVKQAKKLVEKERPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAF 459
Cdd:CHL00018 407 QPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGF 486
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 460 NADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSI 517
Cdd:CHL00018 487 NADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTI 544
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
18-570 |
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: 811.89 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 18 FDSIRISIASPEKILSWS---------YGEIKKPETINYRTFKPERDGLFCARIFGPIKDYECLCGKYKRMKYKGIICEK 88
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 89 CGVEVTLSRVRRERMGHIELAAPVAHIWFLKSLPSRIGTLLDMTLKDIERVLYFENYIVTEPG-LTSLKEHQLLSEEEYM 167
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGnAKNLKYKQLLTEDQWL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 168 IAVDE-FGEDQFTAL-----IGAEAIYELLASMELEKIAADLRVDLAETTSDlKQKKLMKRLKIVENFLESGNRPEWMIM 241
Cdd:TIGR02387 162 EIEDQiYAEDSELENeevvgIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 242 KIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRGRVITGA 321
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 322 NKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARLDAKGYSSTVKQAKK 401
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 402 LVEKERPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLE 481
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 482 ARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIV-ADKEPGEGMMFADMGELQHALENKVVTLHTKIKGRFKTVDAE 560
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALnPGAEKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVET 560
|
570
....*....|
gi 501039963 561 GKPVSKIYDT 570
Cdd:TIGR02387 561 NDPLDEPIKS 570
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
26-803 |
4.28e-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: 542.02 E-value: 4.28e-179
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 26 ASPEKILSWSYGEIKKPETINYRTFKPERDGlfcarifgpikdyeclcgKYKRMKYKGIICEKCGVEVTLSRVRRERMGH 105
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 106 IELAAPVAHIWFLKSLPSRIGtlldmtlkdiervlyfenyivtepgltslkehqllseeeymiavdefgedqftaligae 185
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 186 aiyellasmelekiaadlrvdlaettsdlkqkklmkrlkivenflesgnrPEWMIMKIVPVIPPDLRPLVpldggrfats 265
Cdd:cd00399 84 --------------------------------------------------PEWMILTCLPVPPPCLRPSV---------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 266 dlndlyrrvinrnnrlkrlielrapgiIIRNEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLL 345
Cdd:cd00399 104 ---------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLM 156
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 346 GKRVDYSGRSVIVTGPELKLHQCGLPKKMALELfkpfiyarldakgysstvkqakklvekerpevwdildeviREHPVLL 425
Cdd:cd00399 157 GKRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLF 196
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 426 NRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPS 505
Cdd:cd00399 197 NRQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLS 276
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 506 QDMVLGLYYLsivadkepgegmmfadmgelqhalenkvvtlhtkikgrfktvdaegkpvskiydtTPGRMITGELLPKNv 585
Cdd:cd00399 277 QDTLLGAYLL-------------------------------------------------------TLGKQIVSAALPGG- 300
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 586 nvpfdicnqemtkkniskMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDD----MVIPDTKAKIVADTEALT 661
Cdd:cd00399 301 ------------------LLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDviddGVIPEEKTELIEEAKKKV 362
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 662 TEYEQQYNDGLITQGEK-------YNKVVDAWGKATDKiteemMARLKAVEFDPVTGRqkqmNSVYMMSHSGARGSVNQM 734
Cdd:cd00399 363 DEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDK-----AGSAASVNLDLVSKF----NSIYVMAMSGAKGSFINI 433
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 735 RQLGGMRGLMAKPSGEI--------------------IETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLT 794
Cdd:cd00399 434 RQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQ 513
|
....*....
gi 501039963 795 RRLVDVAQD 803
Cdd:cd00399 514 RRLVKALED 522
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
237-513 |
4.39e-156 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 472.39 E-value: 4.39e-156
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 237 EWMIMKIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNG--RR 314
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 315 GRVITGankRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFIYARL------- 387
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 388 -------DAK----GYSSTVKQAKKL-VEKERPEVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLV 455
Cdd:smart00663 158 lvrngpnGAKyiirGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 456 CTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLY 513
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
592-1137 |
7.62e-123 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 415.16 E-value: 7.62e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 592 CNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVADTEALTTEYEQQYNDG 671
Cdd:PRK02597 4 RNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRG 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 672 LITQGEKYNKVVDAWGKATDKITEEMMARLKavEFDPvtgrqkqMNSVYMMSHSGARGSVNQMRQLGGMRGLMAKPSGEI 751
Cdd:PRK02597 84 EITEVERFQKVIDTWNETNERLKDEVVKNFR--QNDP-------LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEI 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 752 IETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEIGLTMQPIVDAGQIVAS 831
Cdd:PRK02597 155 IDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIP 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 832 IGQRVLGRTALDPILHPtTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCAKCYGRDLARGTPVNQGEA 911
Cdd:PRK02597 235 LGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEA 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 912 VGVIAAQSIGEPGTQLTMRTFHLGG-----TAQVVdssylEASYEGTV----KLRNRNvVRNSDGNLVVMGRNMAVLILD 982
Cdd:PRK02597 314 VGIIAAQSIGEPGTQLTMRTFHTGGvftgeVARQV-----RSPFAGTVefgkKLRTRP-YRTRHGVEALQAEVDFDLVLK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 983 NTGKERAV-HRVTYGSRLFVDEADTVKRGQRIAE---------WDPYTRPIMTEVEGYVEFEDLVdglsVSESADESTGI 1052
Cdd:PRK02597 388 PSGKGKPQkIEITQGSLLFVDDGQTVEADQLLAEvaagavkksTEKATKDVICDLAGEVRFADLI----PEEKTDRQGNT 463
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1053 TkrvvidwRSTPRGsdlkpamvikdkaGKILKLSkgGDArFMLSVESILSVEPGAHVKAGDVIARlpmesAKTKDITGGL 1132
Cdd:PRK02597 464 T-------RKAQRG-------------GLLWVLS--GDV-YNLPPGAEPVVSNGDRVEEGDVLAE-----TKLVSEHGGV 515
|
....*
gi 501039963 1133 PRVAE 1137
Cdd:PRK02597 516 VRLRE 520
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
763-1269 |
1.49e-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: 361.67 E-value: 1.49e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 763 GLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEIGLTMQPIVDAGQIVASIGQRVLGR--- 839
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRfti 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 840 -------------TALDPILhpTTGEVIVEAGRMIEEKDV-------------------EIIEKAAIQSIRIRSALTCET 887
Cdd:pfam04998 81 efsdlkledkfknDLLDDLL--LLSEFSLSYKKEILVRDSklgrdrlskeaqeratllfELLLKSGLESKRVRSELTCNS 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 888 RNGVCAKCYGRDLARGTPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQvvdssylEASYEGTVKLRNRnvvrnSDG 967
Cdd:pfam04998 159 KAFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVAS-------KNVTLGVPRLKEI-----INV 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 968 NLVVMGRNMAVLILDNTGKERAVHRVTYGSRLFVDEADTVKRGQRIAEWDPYTRPIMTEVEGYVEFEDLVDGLSVSESAD 1047
Cdd:pfam04998 227 SKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEID 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1048 ESTGITKRVVIDwrstprgsdlkpaMVIKDKAGKILKLSkggdarFMLSVESILSVEPGAHVKAGDVIARLPMESAKTKD 1127
Cdd:pfam04998 307 PETGLLILVIRL-------------LKILNKSIKKVVKS------EVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQ 367
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1128 ITGGLPRVAELFEARRPKDHAVIAEIDGTVRFGRDYKNKRRIIIEPNDDTIEPVEYLIPKG--KPFHLQDGDVIEKGEYI 1205
Cdd:pfam04998 368 DTGGLRRVDELFMEEDPKLAILVASLLGNITLRGIPGIKRILVNEDDKGKVEPDWVLETEGvnLLRVLLVPGFVDAGRIL 447
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501039963 1206 LDgnpAPHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGY 1269
Cdd:pfam04998 448 SN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHGI 508
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
593-1143 |
3.02e-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: 380.74 E-value: 3.02e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 593 NQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVADTEALTTEYEQQYNDGL 672
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 673 ITQGEKYNKVVDAWGKATDKITEEMMARLKavEFDPvtgrqkqMNSVYMMSHSGARGSVNQMRQLGGMRGLMAKPSGEII 752
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNFR--QTDP-------LNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEII 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 753 ETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEIGLTMQPIVDAGQIVaSI 832
Cdd:TIGR02388 155 DLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI-SL 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 833 GQRVLGRTALDPILHPtTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCAKCYGRDLARGTPVNQGEAV 912
Cdd:TIGR02388 234 GDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLGEAV 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 913 GVIAAQSIGEPGTQLTMRTFHLGGTAQVVDSSYLEASYEGTV----KLRNRNvVRNSDGNLVVMGRNMAVLILDNTGKER 988
Cdd:TIGR02388 313 GIIAAQSIGEPGTQLTMRTFHTGGVFTGEVARQVRSKIDGTVefgkKLRTRG-YRTRHGEDAKQVEVAGLLIIKPTGSIT 391
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 989 AVHR---VTYGSRLFVDEADTVKRGQRIAEwdpytrpimtevegyvefedlvdgLSVSESADESTGITKRVVIDWRSTPR 1065
Cdd:TIGR02388 392 NKAQeieVTQGSLLFVEDGQTVDAGQLLAE------------------------IALGAVRKSTEKATKDVASDLAGEVK 447
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1066 GSDLKPAMViKDKAGKILKLSKGGDARFMLSVEsILSVEPGAH--VKAGD-VIARLPMESAKTKDITGGLPRVAELFEAR 1142
Cdd:TIGR02388 448 FDKVVPEEK-TDRQGNTTRIAQRGGLIWVLSGE-VYNLPPGAEpvVKNGDrVEQGTVLAETKLSTEHGGVVRLPESVGDS 525
|
.
gi 501039963 1143 R 1143
Cdd:TIGR02388 526 R 526
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
592-1015 |
6.33e-108 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 373.51 E-value: 6.33e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 592 CNQEMTKKNISKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTKAKIVADTEALTTEYEQQYNDG 671
Cdd:CHL00117 10 HNKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYG 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 672 LITQGEKYNKVVDAWGKATDKITEEMMARLKavEFDPVtgrqkqmNSVYMMSHSGARGSVNQMRQLGGMRGLMAKPSGEI 751
Cdd:CHL00117 90 NVHAVEKLRQSIEIWYATSEYLKQEMNPNFR--MTDPL-------NPVYMMSFSGARGNASQVHQLVGMRGLMSDPQGQI 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 752 IETPIISNFKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDAIISEVDCGAEIGLTMQPIVDaGQIVAS 831
Cdd:CHL00117 161 IDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNG-MMIERI 239
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 832 IGQRVLGRTALDPILHptTGEVIVEAGRMIEEKDVEIIEKAAIQSIRIRSALTCETRNGVCAKCYGRDLARGTPVNQGEA 911
Cdd:CHL00117 240 LIQTLIGRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELGEA 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 912 VGVIAAQSIGEPGTQLTMRTFHLGG--TAQVVDssYLEASYEGTVKLRNRNV--VRNSDGNLVVMGRNMAVLILDNTGKe 987
Cdd:CHL00117 318 VGIIAGQSIGEPGTQLTLRTFHTGGvfTGGTAE--QVRAPFNGKIKFNEDLVhpTRTRHGHPAFLCKIDLYVTIESEDI- 394
|
410 420 430
....*....|....*....|....*....|
gi 501039963 988 raVHRVT--YGSRLFVDEADTVKRGQRIAE 1015
Cdd:CHL00117 395 --IHNVNipPKSLLLVQNDQYVESEQVIAE 422
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
15-344 |
2.69e-105 |
|
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: 337.34 E-value: 2.69e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 15 AQTFDSIRISIASPEKILSWSYGEIKKPETINYRTFKPERDGLFCARIFGPIKDYEC-LCGKYKRmkykgiiceKCGVev 93
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 94 tlsrvrreRMGHIELAAPVAHIWFLKslpsrigtlldMTLKDIERVLYFENYIVTEPGltslkEHQLLSEEEYMIAVDEF 173
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 174 GedqftalIGAEAIYELLASM----------------------ELEKIAADLRVD----LAETTSDLKQKKLMKRLK--- 224
Cdd:pfam04997 126 K-------MGAKAILELCKKKdlcehcggkngvcgsqqpvsrkEGLKLKAAIKKSkeeeEKEILNPEKVLKIFKRISded 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 225 -IVENFLESGNRPEWMIMKIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQE 303
Cdd:pfam04997 199 vEILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQE 278
|
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 501039963 304 AVDALFDNGRRG-RVITGANKRPLKSLSDMLKGKQGRFRQNL 344
Cdd:pfam04997 279 HVATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
19-803 |
7.07e-87 |
|
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: 303.01 E-value: 7.07e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 19 DSIRISIASPEKILSWSYGEIKKPETinYrtfkpERDGLfcaRIFGPIKDyeclcgkyKRMkykGII-----CEKCGVev 93
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTCGN-- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 94 tlsrvRRER----MGHIELAAPVAHIWFLKslpsRIGTLLDMTLKDIERVLyfenyivtepgLTSLKEHQLLSEEEYMIA 169
Cdd:cd02582 62 -----TAGEcpghFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEIEKYLERIRRLKE 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 170 VDEFGEDQFTALIgaeaIYELLASM-------ELEKIAADlRVDLAETTSDLKQKKLM-----KRL-KIVENFLESGN-- 234
Cdd:cd02582 122 KWPELVKRVIEKV----KKKAKKRKvcphcgaPQYKIKLE-KPTTFYEEKEEGEVKLTpseirERLeKIPDEDLELLGid 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 235 ----RPEWMIMKIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFD 310
Cdd:cd02582 197 pktaRPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFD 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 311 NGRRG-RVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKP-------- 381
Cdd:cd02582 277 NEIPGiPPARHRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPervtewni 356
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 382 ------------------FIYaRLDAKGYSSTVKQAKKLVEKERPEvWDILDEVIREHPVLLNRAPTLHRLGIQAFEPTL 443
Cdd:cd02582 357 ekmrklvlngpdkwpganYVI-RPDGRRIRLRYVNREELAERLEPG-WIVERHLIDGDIVLFNRQPSLHRMSIMAHRVRV 434
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 444 IEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSIVADKEP 523
Cdd:cd02582 435 LPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRKTTLFT 514
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 524 GEgmmfadmgELQHALEnkvvtlHTKIKG-RFKTVDAEGKPvskiYDTtpGRMITGELLPK--------NVNVPFDICNQ 594
Cdd:cd02582 515 KE--------EALQLLS------AAGYDGlLPEPAILEPKP----LWT--GKQLFSLFLPKdlnfegkaKVCSGCSECKD 574
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 595 EMT-------------------KKNI-----SKMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIPDTK 650
Cdd:cd02582 575 EDCpndgyvvikngkllegvidKKAIgaeqpGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEEA 654
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 651 AK----IVADTEALTTEYEQQYNDGL--ITQGEKYNKVVDawgkatDKITEEM-MARLKAVE-----FDPvtgrqkqMNS 718
Cdd:cd02582 655 RKeieeIIKEAEKKVYELIEQYKNGElePLPGRTLEETLE------MKIMQVLgKARDEAGKvaskyLDP-------FNN 721
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 719 VYMMSHSGARGSVNQMRQLGGMRGLMAKpSGEIIET-------P--------------IISNFKEGLTVNEYFNSTHGAR 777
Cdd:cd02582 722 AVIMARTGARGSMLNLTQMAACLGQQSV-RGERINRgyrnrtlPhfkpgdlgpeargfVRSSFRDGLSPTEFFFHAMGGR 800
|
890 900
....*....|....*....|....*.
gi 501039963 778 KGLADTALKTANSGYLTRRLVDVAQD 803
Cdd:cd02582 801 EGLVDTAVRTSQSGYMQRRLINALQD 826
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
905-1357 |
4.04e-84 |
|
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: 273.63 E-value: 4.04e-84
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 905 PVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQvvdssyleasyegtvklrnrnvvrnsdgnlvvmgrnmavlildnt 984
Cdd:cd02655 2 LVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT--------------------------------------------- 36
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 985 gkeravhrvtygsrlfvdeadtvkrgqriaewdpytrpimtevegyvefedlvdglsvsesadestgitkrvvidwrstp 1064
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1065 rgsdlkpamvikdkagkilklskggdarfmlsvesilsvepgahvkagdviarlpmesaktkDITGGLPRVAELFEARrp 1144
Cdd:cd02655 37 --------------------------------------------------------------DITQGLPRVEELFEAR-- 52
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1145 kdhaviaeidgtvrfgrdyknkrriiiepnddtiepveylipkgkpfhlqdgdviekgeyildgNPAPHDILAIK--GVE 1222
Cdd:cd02655 53 ----------------------------------------------------------------KINPHDLLRIKflGPE 68
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1223 ALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIELEEINERLIEEGKKPGSGNPVLL 1302
Cdd:cd02655 69 AVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLL 148
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 501039963 1303 GITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd02655 149 GITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTG 203
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
994-1357 |
2.39e-81 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 294.21 E-value: 2.39e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 994 TYGS---RLFVDEADTVKRGQRIA------EWDPYTRPIMTEVEG----YVEFEDlvDGLSVSESADESTGITKRVVidw 1060
Cdd:PRK02597 837 SHGSthtELLVKDGQQIKPGDVVArtqilcKEAGEVRGIRVGGEAvrrlLVERDE--DTITIPLSGKPTVKVGDLVV--- 911
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1061 rstpRGSDLKPAMVIkDKAGKILKLSKGG----DAR-FMLSVESILSVEPGAHVKAGDVIARLPMESAKTKDITGGLPRV 1135
Cdd:PRK02597 912 ----AGDELAPGVPA-PESGEVEAVSGGSvtlrLGRpYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRI 986
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1136 AELFEARRPKDHAVIAEIDGTVRFgrDYKNKRRI---IIEpNDDTIEpvEYLIPKGKPFHLQDGDVIEKGEYILDGNPAP 1212
Cdd:PRK02597 987 EELLEARKPKESCILAKKPGTVQI--KYGDDESVdvkVIE-SDGTIT--EYPILPGQNVMVSDGQQVDAGEPLTDGPINP 1061
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1213 HDIL----------------AIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVD 1276
Cdd:PRK02597 1062 HELLeiffedlrdrkglyeaALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIE 1141
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1277 RIELEEINERLIEEGKKPGSGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGT 1356
Cdd:PRK02597 1142 LRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGT 1221
|
.
gi 501039963 1357 G 1357
Cdd:PRK02597 1222 G 1222
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
20-803 |
5.89e-80 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 283.29 E-value: 5.89e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 20 SIRISIASPEKILSWSYGEIKKPETinYrtfkpERDGLfcaRIFGPIKDyeclcgkyKRMkykGII-----CEKCGvevt 94
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTCG---- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 95 lSRVRR--ERMGHIELAAPVAHIWFLKslpsRIGTLLDMT--------LKDIERVLYFENyivtepgLTSLKEHQLLSEE 164
Cdd:PRK08566 66 -GRAGEcpGHFGHIELARPVIHVGFAK----LIYKLLRATcrecgrlkLTEEEIEEYLEK-------LERLKEWGSLADD 133
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 165 EYMIAVDEF---------GEDQFTalIGAE---AIYELLASmELEKIaadlrvdlaeTTSDLKQkklmkRL-KIVENFLE 231
Cdd:PRK08566 134 LIKEVKKEAakrmvcphcGEKQYK--IKFEkptTFYEERKE-GLVKL----------TPSDIRE-----RLeKIPDEDLE 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 232 ------SGNRPEWMIMKIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAV 305
Cdd:PRK08566 196 llginpEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHV 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 306 DALFDN---G------RRGRvitgankrPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMAL 376
Cdd:PRK08566 276 TTYFDNeipGipparhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAK 347
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 377 ELFKPFI------------------------YA-RLDAKGYSSTVKQAKKLVEKERPEvWDILDEVIREHPVLLNRAPTL 431
Cdd:PRK08566 348 ELTVPERvtewnieelreyvlngpekhpganYViRPDGRRIKLTDKNKEELAEKLEPG-WIVERHLIDGDIVLFNRQPSL 426
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 432 HRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLG 511
Cdd:PRK08566 427 HRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISG 506
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 512 LYYLS----IVADKEPGEGMMFADMGELQhaLENKvvtlhtkikgrfktVDAEGKPvskiYDTtpGRMITGELLPKNVNV 587
Cdd:PRK08566 507 AYLLTrkstLFTKEEALDLLRAAGIDELP--EPEP--------------AIENGKP----YWT--GKQIFSLFLPKDLNL 564
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 588 PF--------DICNQEMT-------------------KKNIS----KMIDHVYRHCGQKETVIFCDRIMQLGFAHACRAG 636
Cdd:PRK08566 565 EFkakicsgcDECKKEDCehdayvvikngkllegvidKKAIGaeqgSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRG 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 637 ISFGKDDMVIPDTKAK----IVADTEALTTEYEQQYNDGLI------TQGEKY-NKVVDAWGKATDKiTEEMMARlkavE 705
Cdd:PRK08566 645 FTTGIDDEDIPEEAKEeideIIEEAEKRVEELIEAYENGELeplpgrTLEETLeMKIMQVLGKARDE-AGEIAEK----Y 719
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 706 FDPVtgrqkqmNSVYMMSHSGARGS-VN--QMRQLGG---------MRGLMAK-----PSGEIieTP-----IISNFKEG 763
Cdd:PRK08566 720 LGLD-------NPAVIMARTGARGSmLNltQMAACVGqqsvrgeriRRGYRDRtlphfKPGDL--GAeargfVRSSYKSG 790
|
890 900 910 920
....*....|....*....|....*....|....*....|
gi 501039963 764 LTVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQD 803
Cdd:PRK08566 791 LTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQD 830
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
997-1357 |
7.82e-75 |
|
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: 273.26 E-value: 7.82e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 997 SRLFVDEADTVKRGQRIAEWDPYTRPiMTEVEGYVEFEDLVDGLSVSESADestgitkRVVIDWRSTPR---------GS 1067
Cdd:TIGR02388 841 TSLLVKDGDLIKPGAVIARTQILCKE-AGVVQGIDSGGESIRRLLVERNSD-------RLKVNIKAKPVvktgdlvvaGD 912
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1068 DLKPAmVIKDKAGKILKLSkgGD------AR-FMLSVESILSVEPGAHVKAGDVIARLPMESAKTKDITGGLPRVAELFE 1140
Cdd:TIGR02388 913 ELAKG-VKAEESGEIEEVA--SDyvilriGRpYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLE 989
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1141 ARRPKDHAVIAEIDGTVR--FGRDYKNKRRIIIEpNDDTIEpvEYLIPKGKPFHLQDGDVIEKGEYILDGNPAPHDIL-- 1216
Cdd:TIGR02388 990 ARKPKEACILAKRPGVVQvkYGTDDESVSIKVIE-RDGTIS--EYPLLPGQNIMVSDGQQVTGGEPLTDGPINPHDILdv 1066
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1217 --------------AIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGYIPGDHVDRIELEE 1282
Cdd:TIGR02388 1067 ffsyykdqdglyeaAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQ 1146
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501039963 1283 INERLIEEGKKPGSGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:TIGR02388 1147 VNEAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTG 1221
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
14-1357 |
1.53e-73 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 269.97 E-value: 1.53e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 14 PAQTFDSIRISIASPEKILSWSYGEIKKPETINYRTFkPERDGLFCARIfGPIKdyeclcgkykrmkyKGIICEKCGvev 93
Cdd:PRK14977 5 AVKAIDGIIFGLISPADARKIGFAEITAPEAYDEDGL-PVQGGLLDGRL-GTIE--------------PGQKCLTCG--- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 94 TLSRVRRERMGHIELAAPVAHIWFLKslpsRIGTLLDMTLKDIERVL-------YFENYIVTEPGLTSLKEHQLLSE--E 164
Cdd:PRK14977 66 NLAANCPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKlpqedlnVFKLIEEAHAAARDIPEKRIDDEiiE 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 165 EYMIAVDEFGEDQFTALIGAEAIYELL---ASMELEKIAADLRVDLAETTSDLKQKKLMKRLKIVeNFLESGNRPEWMIM 241
Cdd:PRK14977 142 EVRDQVKVYAKKAKECPHCGAPQHELEfeePTIFIEKTEIEEHRLLPIEIRDIFEKIIDDDLELI-GFDPKKARPEWAVL 220
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 242 KIVPVIPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRG--RVIT 319
Cdd:PRK14977 221 QAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHH 300
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 320 GANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFI---------------- 383
Cdd:PRK14977 301 KGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenniekmkelving 380
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 384 ---YARLDAKGYSSTVKQAKKLVEK----------ERPEVWDILDEVIREHP-VLLNRAPTLHRLGIQAFEPTLIEGKAI 449
Cdd:PRK14977 381 pdeFPGANAIRKGDGTKIRLDFLEDkgkdalreaaEQLEIGDIVERHLADGDiVIFNRQPSLHKLSILAHRVKVLPGATF 460
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 450 QLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSivadkepgegmmf 529
Cdd:PRK14977 461 RLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLIT------------- 527
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 530 admgelqhaLENKVVTLH--TKIKGRFKTVDAEGKPVSKiydTTPGRMITGE-----LLPKNVNV--------------- 587
Cdd:PRK14977 528 ---------KDDALFDKNeaSNIAMLAGITDPLPEPAIK---TKDGPAWTGKqlfslFLPKDFNFegiakwsagkageak 595
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 588 -PFDICNQEMTKKN---ISKMIDH----------------VYRHCGQKETVIFCDRIMQLGFAHACRAGISFGKDDMVIP 647
Cdd:PRK14977 596 dPSCLGDGYVLIKEgelISGVIDDniigalveepeslidrIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIP 675
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 648 D-TKAKIVADTEALTTEYEQqyndgLITQGEKYNKVVDAwgKATDKITEEMMARlKAVEFDPVTGRQK------------ 714
Cdd:PRK14977 676 DeAKQEIEDDIQGMKDEVSD-----LIDQRKITRKITIY--KGKEELLRGMKEE-EALEADIVNELDKardkagssandc 747
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 715 --QMNSVYMMSHSGARGSVNQMRQLGGMRGLMAK--------PSGEIIE---------------TP-----IISNFKEGL 764
Cdd:PRK14977 748 idADNAGKIMAKTGARGSMANLAQIAGALGQQKRktrigfvlTGGRLHEgykdralshfqegddNPdahgfVKNNYREGL 827
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 765 TVNEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDaIISEVDcgaeiGLTMQPIvdaGQIVasigQRVLGRTALDP 844
Cdd:PRK14977 828 NAAEFFFHAMGGREGLIDKARRTEDSGYFQRRLANALED-IRLEYD-----ETVRDPH---GHII----QFKFGEDGIDP 894
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 845 I-------LHPT---TGEVIVEAGRMIEEKDVEIIEKAAIQSIRIR-----------SALTCETRNGVCAKcyGRDLARG 903
Cdd:PRK14977 895 QkldhgeaFNLEriiEKQKIEDRGKGASKDEIEELAKEYTKTFNANlpklladaihgAELKEDELEAICAE--GKEGFEK 972
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 904 TPVNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQVVDSSYLEASYE----------GTVKLRNRNVVRNSDGNLVVMG 973
Cdd:PRK14977 973 AKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIElvdarakpstPTMDIYLDDECKEDIEKAIEIA 1052
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 974 RNMAVLILDNTGKERAVHRVTYgSRLFVDEADTVKRG----QRIAEwdpYTRPIMTEVEGYVEFEDLVDGLSVSESADes 1049
Cdd:PRK14977 1053 RNLKELKVRALIADSAIDNANE-IKLIKPDKRALENGcipmERFAE---IEAALAKGKKFEMELEDDLIILDLVEAAD-- 1126
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1050 TGITKRVVIDWRStprgsdlkpamvikdkagKILKLSkggdarfmlsvesilsvepgahVKAGDVIARLPMESAKTKDIT 1129
Cdd:PRK14977 1127 RDKPLATLIAIRN------------------KILDKP----------------------VKGVPDIERAWVELVEKDGRD 1166
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1130 GGLPRVAElfearrpKDHAVIAEIDGTvrfgrdykNKRRIIIEpnddtiepveylipkgkpfhlqdgDVIEkgeyildgn 1209
Cdd:PRK14977 1167 EWIIQTSG-------SNLAAVLEMKCI--------DIANTITN------------------------DCFE--------- 1198
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1210 paphdILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKveitesgdtGYIpgdhvdrielEEIneRLIE 1289
Cdd:PRK14977 1199 -----IAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVADIMCSR---------GTI----------EAI--GLQA 1252
|
1450 1460 1470 1480 1490 1500
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 1290 EGKKPGsgnpvllgiTKASLQTPsfISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK14977 1253 AGVRHG---------FAGEKDSP--LAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1099-1357 |
6.74e-63 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 236.37 E-value: 6.74e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1099 SILSVEPGAHVKAGDVIARLPMESAKTKDITGGLPRVAELFEARrpkdhaviaeidgtvrfgrdYKNKRRIIIEPNDDTI 1178
Cdd:CHL00117 1102 ATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEAR--------------------SIDSISMNLEKRLEGW 1161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1179 EPVeylIPKgkpfhlqdgdviekgeyILdGNPAPHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQK 1258
Cdd:CHL00117 1162 NER---ITR-----------------IL-GIPWGFLIGAELSIAQSQISLVNKIQKVYRSQGVQISDKHIEIIVRQMTSK 1220
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1259 VEITESGDT-GYIPGDHVDRIELEEINERLieegKKPGSGNPVLLGITKASLQTPSFISAASFQETTRVLTEAAVAGKMD 1337
Cdd:CHL00117 1221 VLVSEDGMSnVFLPGELIGLLRAERINRAL----EEAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRID 1296
|
250 260
....*....|....*....|
gi 501039963 1338 TLQGLKENVIVGRLIPAGTG 1357
Cdd:CHL00117 1297 WLKGLKENVILGGLIPAGTG 1316
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
82-798 |
4.02e-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: 222.81 E-value: 4.02e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 82 KGIICEKCGvevtlsrvrrERM-------GHIELAAPVAHIWFLKSlpsrIGTLLDMTLKDIERVLyfenyivtepglts 154
Cdd:cd02583 42 KDGICETCG----------LNLadcvghfGYIKLELPVFHIGYFKA----IINILQCICKTCSRVL-------------- 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 155 lkehqlLSEEEYmiavdefgeDQFTALIgAEAIYELLASMELEKIAADL--------RVDLAETTSD----LKQKKLMKR 222
Cdd:cd02583 94 ------LPEEEK---------RKFLKRL-RRPNLDNLQKKALKKKILEKckkvrkcpHCGLLKKAQEdlnpLKVLNLFKN 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 223 LK----IVENFLESGNRPEWMIMKIVPVIPPDLRPLVPLDGGrfATSDLNDL---YRRVINRNNRLKRLIELRAPGIIIR 295
Cdd:cd02583 158 IPpedvELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIM 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 296 NEKRMLQEAVDALFDNGRRGRVITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMA 375
Cdd:cd02583 236 EDWDFLQLQCALYINSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVA 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 376 LELFKP--------------------------FIYARLDAKGYSstVKQAKKLVEKERPEVWDI-----LDEVIrehpVL 424
Cdd:cd02583 316 KILTYPervtrynieklrklvlngpdvhpganFVIKRDGGKKKF--LKYGNRRKIARELKIGDIverhlEDGDI----VL 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 425 LNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVP 504
Cdd:cd02583 390 FNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAA 469
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 505 SQDMVLGLYYLS---IVADKEpgE-GMMFADMGELQHALEN------KVVTLHTkikgrfktvdaeGKPvskiydttpgr 574
Cdd:cd02583 470 TQDFLTASYLLTskdVFFDRA--QfCQLCSYMLDGEIKIDLpppailKPVELWT------------GKQ----------- 524
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 575 mITGELLPKNVNVPFDIcNQEMTKKNISKMIDH--------VYRH----CGQ--KETV-------IFCDRIMQLGFAHAC 633
Cdd:cd02583 525 -IFSLLLRPNKKSPVLV-NLEAKEKSYTKKSPDmcpndgyvVIRNsellCGRldKSTLgsgsknsLFYVLLRDYGPEAAA 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 634 RA---------------GISFGKDDmVIP-----DTKAKIVADTEALTTEYEQQYNDG---------------LITQGEk 678
Cdd:cd02583 603 AAmnrlaklssrwlsnrGFSIGIDD-VTPskellKKKEELVDNGYAKCDEYIKQYKKGklelqpgctaeqtleAKISGE- 680
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 679 YNKVVDAWGKATdkiteemMARLkavefdpvtgrqKQMNSVYMMSHSGARGS---------------VNQMRQLGGM--R 741
Cdd:cd02583 681 LSKIREDAGKAC-------LKEL------------HKSNSPLIMALCGSKGSninisqmiacvgqqiISGKRIPNGFedR 741
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 501039963 742 GL--MAKPSgeiiETPI----ISN-FKEGLTVNEYFNSTHGARKGLADTALKTANSGYLTRRLV 798
Cdd:cd02583 742 TLphFPRNS----KTPAakgfVANsFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLM 801
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
19-806 |
3.27e-58 |
|
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: 215.86 E-value: 3.27e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 19 DSIRISIASPEKILSWSYGEIKKPETINyRTFKPERDGLFCARIfGPIKdyeclcgkykrmkyKGIICEKCGvevtlsrv 98
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 99 rrERM-------GHIELAAPVAHIWFLkslpsrigtllDMTLKDIERVLyfenyivtepgltslkehqllseeeymiavd 171
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILRCVC------------------------------- 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 172 efgedqfTALIGAEAIYELLasmelEKIaadlrvdlaettSDLKQKKLmkrlkiveNFLESGNRPEWMIMKIVPVIPPDL 251
Cdd:cd02733 93 -------KRELSAERVLEIF-----KRI------------SDEDCRIL--------GFDPKFSRPDWMILTVLPVPPPAV 140
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 252 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLIELRAPGIIIRNEKRMLQEAVDALFDNGRRG--RVITGaNKRPLKSL 329
Cdd:cd02733 141 RPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQK-SGRPLKSI 219
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 330 SDMLKGKQGRFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMAL-----ELFKPFIYARLdakgysstvkqaKKLVE 404
Cdd:cd02733 220 RQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRL------------QELVR 287
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 405 KeRPEVWDILDEVIRE---------HP----------------------VLLNRAPTLHRLGIQAFEPTLIEGKAIQLHP 453
Cdd:cd02733 288 N-GPNEYPGAKYIIRDdgeridlryLKkasdlhlqygyiverhlqdgdvVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNL 366
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 454 LVCTAFNADFDGDQMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPI--IVpsQDMVLGLYYLS---IVADKEpgegmm 528
Cdd:cd02733 367 SVTTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTkrdTFLEKD------ 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 529 faDMGELQHALENKvvtlhtkikgrfktvdaEGK-PVSKIYdtTPGRMITGE-----LLPKNVNVPFDICNQEMTKKNIS 602
Cdd:cd02733 439 --QVMNLLMWLPDW-----------------DGKiPQPAIL--KPKPLWTGKqifslIIPKINNLIRSSSHHDGDKKWIS 497
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 603 KMIDHVYRHCGQKETVIFCDRIM---QLGFAH---------ACRA----------------GISFGKDDMvIPDtkAKIV 654
Cdd:cd02733 498 PGDTKVIIENGELLSGILCKKTVgasSGGLIHviwleygpeAARDfigniqrvvnnwllhnGFSIGIGDT-IAD--KETM 574
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 655 ADTEALTTEYEQQYNDgLITQGEKY---------------NKVVDAWGKATDKITEEMMARLkavefdpvtgrqKQMNSV 719
Cdd:cd02733 575 KKIQETIKKAKRDVIK-LIEKAQNGelepqpgktlresfeNKVNRILNKARDKAGKSAQKSL------------SEDNNF 641
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 720 YMMSHSGARGSVNQMRQlggMRGLMAKPSGEIIETP-----------------------IISNFKEGLTVNEYFNSTHGA 776
Cdd:cd02733 642 KAMVTAGSKGSFINISQ---IIACVGQQNVEGKRIPfgfrrrtlphfikddygpesrgfVENSYLRGLTPQEFFFHAMGG 718
|
890 900 910
....*....|....*....|....*....|
gi 501039963 777 RKGLADTALKTANSGYLTRRLVDVAQDAII 806
Cdd:cd02733 719 REGLIDTAVKTAETGYIQRRLVKAMEDVMV 748
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
346-487 |
3.84e-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: 157.85 E-value: 3.84e-44
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 346 GKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFKPFI-----YARL------------------DAKGYSSTVKQAKKL 402
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpynIKRLrqlvengpnvypganyiiRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 403 VEKERpEVWDILDE-VIREHPVLLNRAPTLHRLGIQAFEPTLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLE 481
Cdd:pfam00623 81 LDKEL-EIGDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAE 159
|
....*.
gi 501039963 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 |
3.88e-39 |
|
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: 157.73 E-value: 3.88e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 214 LKQKKLMKRLKIVENfLESGNRPEWMIMKIVPVIPPDLRPLVPLDGGRFaTSDLNDLYRRVINRNNRLKRLIELRAPGII 293
Cdd:cd01435 106 VAKLKLLDKGLLVEA-AELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAES 183
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 294 IRNEKRM---------------LQEAVDALFDNGRrgrvITGANKRPLKSLSDMLKGKQGRFRQNLLGKRVDYSGRSVIV 358
Cdd:cd01435 184 QSKLDLIsgktnseklinawlqLQSAVNELFDSTK----APKSGKKSPPGIKQLLEKKEGLFRMNMMGKRVNYAARSVIS 259
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 359 TGPELKLHQCGLPKKMALEL-F----KPFIYARL------------------DAKG-----YSSTVKQAKKLVEKERPEV 410
Cdd:cd01435 260 PDPFIETNEIGIPLVFAKKLtFpepvTPFNVEELrqavingpdvypganaieDEDGrlillSALSEERRKALAKLLLLLS 339
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 411 WDIL-----DEVIReH-----PVLLNRAPTLHRLGIQAFEPTLIEG-KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQ 479
Cdd:cd01435 340 SAKLllngpKKVYR-HlldgdVVLLNRQPTLHKPSIMAHKVRVLPGeKTLRLHYANCKSYNADFDGDEMNLHFPQSELAR 418
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 480 LEARVLMMSTNNILHPANGAPI---IvpsQDMVLGLYYLSIvADKepgegmmFADMGELQHALENKVVTLHTKIK-GRFK 555
Cdd:cd01435 419 AEAYYIASTDNQYLVPTDGKPLrglI---QDHVVSGVLLTS-RDT-------FFTREEYQQLVYAALRPLFTSDKdGRIK 487
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 556 TVdaegkPVSKIYdttPGRMITGE---------LLPKNVNVPFDICNQEMTKKNISKMIDhvyrhcGQKE--TVIFCDRI 624
Cdd:cd01435 488 LL-----PPAILK---PKPLWTGKqvistilknLIPGNAPLLNLSGKKKTKKKVGGGKWG------GGSEesQVIIRNGE 553
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 625 M--------QLG-----FAHAC-------------------------RAGISFGKDDMVipdtkakivadteaLTTEYEQ 666
Cdd:cd01435 554 LltgvldksQFGasaygLVHAVyelyggetagkllsalgrlftaylqMRGFTCGIEDLL--------------LTPKADE 619
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 667 QYNDgLITQGEK--YNKVVDAWGKATDKITEE-----MMARLKavefdpvtgRQKQMNSVYMMSHSGARGS-VNQMrQLG 738
Cdd:cd01435 620 KRRK-ILRKAKKlgLEAAAEFLGLKLNKVTSSiikacLPKGLL---------KPFPENNLQLMVQSGAKGSmVNAS-QIS 688
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 739 GMRG----------LMAK----PSGEIIET-P-----IISNFKEGLTVNEYFnsTH---GaRKGLADTALKTANSGYLTR 795
Cdd:cd01435 689 CLLGqqelegrrvpLMVSgktlPSFPPYDTsPraggfITDRFLTGIRPQEYF--FHcmaG-REGLIDTAVKTSRSGYLQR 765
|
...
gi 501039963 796 RLV 798
Cdd:cd01435 766 CLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
491-644 |
7.68e-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: 127.74 E-value: 7.68e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 491 NILHPANGAPIIVPSQDMVLGLYYLSIVADkepgegmmFADMGELQHALENKVVTLHTKIKGRFKTvdaegkpvSKIYDT 570
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDT--------FFDREEVMQLLMYGIVLPHPAILKPIKP--------LWTGKQ 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 571 TPGRMITGELLPKNVNVPFD-----------ICNQE-----MTKK----NISKMIDHVYRHCGQKETVIFCDRIMQLGFA 630
Cdd:pfam04983 65 TFSRLLPNEINPKGKPKTNEedlcendsyvlINNGElisgvIDKKtvgkSLGSLIHIIYKEYGPEETAKFLDRLQKLGFR 144
|
170
....*....|....
gi 501039963 631 HACRAGISFGKDDM 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 |
4.13e-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: 102.88 E-value: 4.13e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1212 PHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMlqkveiTESGDtgyipgdhvdrieleeinerlieeg 1291
Cdd:cd00630 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVM------TYSGG------------------------- 98
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 1292 kkpgsgnpvLLGITKASL--QTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 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 |
9.17e-21 |
|
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: 88.58 E-value: 9.17e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 673 ITQGEKYNKVVDAWGKATDKITEEMMARLKAVEFDPvTGR-----QKQMNSVYMMSHSGARGSVNQMRQLGGMRGLMAKP 747
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKARDP-AGNiasksLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
90 100
....*....|....*....|....*....
gi 501039963 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 ... |
327-536 |
4.47e-20 |
|
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: 96.70 E-value: 4.47e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 327 KSLSDMLKGKQgrFRQNLLGKRVDYSGRSVIVTGPELKLHQCGLPKKMALELFkpfIYARLDAKGYSSTVKQA-KKLVEK 405
Cdd:cd10506 195 SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLT---VSERVSSWNRERLQEYCdLTLLLK 269
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 406 ER--PEVWDILDEVIREHP----------------VLLNRAPTLHRLGIQAFEPTLIE-GKAIQLHPLVCTAFNADFDGD 466
Cdd:cd10506 270 GVigVRRNGRLVGVRSHNTlqigdvihrplvdgdvVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRGDFDGD 349
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 467 QMAVHVPLSLEAQLEARVLMMSTNNILHPANGAPIIVPSQDMVLGLYYLSivadkEPGEGMMFADMGELQ 536
Cdd:cd10506 350 CLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMT-----ERGVFLDKAQMQQLQ 414
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
879-1357 |
4.68e-20 |
|
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: 97.15 E-value: 4.68e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 879 IRSALTCETRNGVC--AKCYGRDLARgtPVNQG---EAVGV------IAAQSIGEpgTQLTMRTFHLGGTAQVvdSSYLe 947
Cdd:COG0086 42 ERDGLFCERIFGPCkdYECYCGKYKR--MVYKGvvcEKCGVevtlskVRRERMGH--IELAMPVFHIWGLKSL--PSRI- 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 948 asyegtvklrnrnvvrnsdGNLVVMgrnmavlildntgKERAVHRVTY-GSRLFVDEADT-VKRGQRIAEwDPYtRPIMT 1025
Cdd:COG0086 115 -------------------GLLLDM-------------SLRDLERVLYfESYVVIDPGDTpLEKGQLLTE-DEY-REILE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1026 EVE-------GYVEFEDLVDGLSVSESADE-------STGITKRVVIDWR----STPRGSDLKPAMVIKDKAGKIlklsk 1087
Cdd:COG0086 161 EYGdefvakmGAEAIKDLLGRIDLEKESEElreelkeTTSEQKRKKLIKRlkvvEAFRESGNRPEWMILDVLPVI----- 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1088 GGDARFMLSVEsilsvepgahvkaGDVIArlpmesakTKDITGGLPRVAELF-------EARRPKD----------HAVI 1150
Cdd:COG0086 236 PPDLRPLVPLD-------------GGRFA--------TSDLNDLYRRVINRNnrlkrllELKAPDIivrnekrmlqEAVD 294
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1151 AEIDGTVRF----------------------GR----------DYKnKRRIIIEPNDDTIE----PVEYLIPKGKPF--- 1191
Cdd:COG0086 295 ALFDNGRRGravtgankrplkslsdmlkgkqGRfrqnllgkrvDYS-GRSVIVVGPELKLHqcglPKKMALELFKPFiyr 373
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1192 ----------------------------------------------H----------LQDGDVI-------------EKG 1202
Cdd:COG0086 374 kleerglattiksakkmvereepevwdileevikehpvllnraptlHrlgiqafepvLIEGKAIqlhplvctafnadFDG 453
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1203 E------------------------YIL---DGNPA------------------------------PHDILAI---KGVE 1222
Cdd:COG0086 454 DqmavhvplsleaqlearllmlstnNILspaNGKPIivpsqdmvlglyyltreregakgegmifadPEEVLRAyenGAVD 533
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1223 ALAS----------------------YLVNEI--QEV--YRlqgVLINDKHIEVIVRQM---------------LQKVEI 1261
Cdd:COG0086 534 LHARikvritedgeqvgkivettvgrYLVNEIlpQEVpfYN---QVINKKHIEVIIRQMyrrcglketvifldrLKKLGF 610
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1262 ---TESGDTGYIPGDHVDRIE---LEEINERLIE------EGK--KPGSGNPVLLGITKASLQTPSFISAA-SFQETTRV 1326
Cdd:COG0086 611 kyaTRAGISIGLDDMVVPKEKqeiFEEANKEVKEiekqyaEGLitEPERYNKVIDGWTKASLETESFLMAAfSSQNTTYM 690
|
730 740 750 760
....*....|....*....|....*....|....*....|....
gi 501039963 1327 LTEAAVAGKMDTLQGL----------KENVI---VGRLIPAGTG 1357
Cdd:COG0086 691 MADSGARGSADQLRQLagmrglmakpSGNIIetpIGSNFREGLG 734
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
909-1357 |
7.27e-14 |
|
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: 74.98 E-value: 7.27e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGtaqvvdssyleasyegtvkLRNRNVVrnsdgnlvvmgrnmavlildnTGKER 988
Cdd:cd06528 40 GEAVGIVAAQSIGEPGTQMTLRTFHYAG-------------------VAEINVT---------------------LGLPR 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 989 AVHrvtygsrlFVDeadtvkrgqriAEWDPYTrPIMTEvegYVEFE---DLVDGLSVSESADEST--GITKRVVIDWRST 1063
Cdd:cd06528 80 LIE--------IVD-----------ARKEPST-PTMTI---YLEEEykyDREKAEEVARKIEETTleNLAEDISIDLFNM 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1064 PRGSDLKPAMvIKDKagkilklskggdarfMLSVESILSVEPGAhvKAGDVIARlpmESAKTKDITGGLPRVAELFEARR 1143
Cdd:cd06528 137 RITIELDEEM-LEDR---------------GITVDDVLKAIEKL--KKGKVGEE---GDVTLIVLKAEEPSIKELRKLAE 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1144 PKDHAVIAEIDGTvrfgrdyknkRRIIIEPNDDtiepvEYLI-PKGKPFhlqdGDVIEkgeyiLDG-NPA------PHDI 1215
Cdd:cd06528 196 KILNTKIKGIKGI----------KRVIVRKEED-----EYVIyTEGSNL----KAVLK-----VEGvDPTrtttnnIHEI 251
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1216 LAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMlqkveiTESGdtgyipgdhvdriELEEInerlieeGKKPG 1295
Cdd:cd06528 252 EEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIM------TYDG-------------EVRQI-------GRHGI 305
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501039963 1296 SGNpvllgitkaslqTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd06528 306 AGE------------KPSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
909-1357 |
4.68e-13 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 72.57 E-value: 4.68e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQVvdssyleasyegtvklrnrNVVRnsdgNL-----VVMGRN------MA 977
Cdd:PRK04309 59 GEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEI-------------------NVTL----GLprlieIVDARKepstpmMT 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 978 VLILDNTGKERavhrvtygsrlfvDEADTVKRgqRIaewdpytrpimteveGYVEFEDLVDGLSVsesadesTGITKRVV 1057
Cdd:PRK04309 116 IYLKDEYAYDR-------------EKAEEVAR--KI---------------EATTLENLAKDISV-------DLANMTII 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1058 IdwrstprgsDLKPAMvIKDKagkilklskggdarfMLSVESIlsVEPGAHVKAGDViarlpMESAKTKDITGGLPRVAE 1137
Cdd:PRK04309 159 I---------ELDEEM-LEDR---------------GLTVDDV--KEAIEKKKGGEV-----EIEGNTLIISPKEPSYRE 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1138 LFEARRPKDHAVIAEIDGTvrfgrdyknkRRIIIEPNDDtiepvEY-LIPKGKPFhlqdGDVIEkgeyiLDGNPA----- 1211
Cdd:PRK04309 207 LRKLAEKIRNIKIKGIKGI----------KRVIIRKEGD-----EYvIYTEGSNL----KEVLK-----VEGVDAtrttt 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1212 --PHDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMlqkveiTESGdtgyipgdhvdriELEEINERLIE 1289
Cdd:PRK04309 263 nnIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMM------TWDG-------------EVRQIGRHGVS 323
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 1290 EGKkpgsgnpvllgitkaslqtPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK04309 324 GEK-------------------ASVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
906-1357 |
3.60e-12 |
|
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: 69.70 E-value: 3.60e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 906 VNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAqvvdssyleasyEGTVKLRNRNVVRNSDGNLVVMGRNMAVLILDNTG 985
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVA------------ELNVTLGLPRLIEIVDARKTPSTPSMTIYLEDEYE 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 986 KERavhrvtygsrlfvDEADTVKRgqRIaewdpytrpimteveGYVEFEDLVDGLSVSESAdestgitKRVVIDwrstPR 1065
Cdd:TIGR02389 109 KDR-------------EKAEEVAK--KI---------------EATKLEDVAKDISIDLAD-------MTVIIE----LD 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1066 GSDLKPAMVIKDKAGKILKLSKGGDARFMLSVESILSVEPGAhvkagdviarlpmesaktkditgglPRVAELFEaRRPK 1145
Cdd:TIGR02389 148 EEQLKERGITVDDVEKAIKKAKLGKVIEIDMDNNTITIKPGN-------------------------PSLKELRK-LKEK 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1146 DHAViaEIDGTvrfgrdyKNKRRIIIEPNDDtiepvEYLIpkgkpfhLQDGDVIEKGEYILDGNPAP------HDILAIK 1219
Cdd:TIGR02389 202 IKNL--HIKGI-------KGIKRVVIRKEGD-----EYVI-------YTEGSNLKEVLKLEGVDKTRtttndiHEIAEVL 260
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1220 GVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMlqkveiTESGdtgyipgdhvdriELEEINERLIEEGKkpgsgnp 1299
Cdd:TIGR02389 261 GIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLM------TWDG-------------EVRQIGRHGISGEK------- 314
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 501039963 1300 vllgitkaslqtPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:TIGR02389 315 ------------ASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTG 360
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
906-1367 |
6.32e-11 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 66.76 E-value: 6.32e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 906 VNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGTAQVVdssyleasyegtvklrnrnvvrnsdgnlVVMGRNMAVLILDntg 985
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMN----------------------------VTLGLPRLIEIVD--- 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 986 keravhrvtygsrlfvdeadtvkrgqriAEWDPYTrPIMTEV--EGYVEFEDLV-------DGLSVSESADESTGITKRV 1056
Cdd:PRK14897 228 ----------------------------ARKKPST-PTMTIYlkKDYREDEEKVrevakkiENTTLIDVADIITDIAEMS 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1057 VIdWRSTPRgsdlkpamVIKDKagkilklskggdarfmlsvesilsvepgaHVKAGDVIARLPMESAKTKDITGGL---- 1132
Cdd:PRK14897 279 VV-VELDEE--------KMKER-----------------------------LIEYDDILAAISKLTFKTVEIDDGIirlk 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1133 ---PRVAELFEARRPKDHAVIAEIDGTvrfgrdyknKRRIIIEPNDDTiepvEYLIpkgkpfHLQD---GDVIEKGEyiL 1206
Cdd:PRK14897 321 pqqPSFKKLYLLAEKVKSLTIKGIKGI---------KRAIARKENDER----RWVI------YTQGsnlKDVLEIDE--V 379
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1207 DGNPAP----HDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEITESGDTGyIPGDhvdrielee 1282
Cdd:PRK14897 380 DPTRTYtndiIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHG-ISGE--------- 449
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1283 inerlieegkkpgsgnpvllgitKASLqtpsfISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTGGMTNQ 1362
Cdd:PRK14897 450 -----------------------KSSV-----LARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAVSLV 501
|
....*
gi 501039963 1363 IRRIA 1367
Cdd:PRK14897 502 YKGRK 506
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
909-938 |
8.93e-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: 61.66 E-value: 8.93e-11
10 20 30
....*....|....*....|....*....|
gi 501039963 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTA 938
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVA 30
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
906-936 |
7.57e-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: 7.57e-10
10 20 30
....*....|....*....|....*....|.
gi 501039963 906 VNQGEAVGVIAAQSIGEPGTQLTMRTFHLGG 936
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
909-938 |
8.67e-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: 61.47 E-value: 8.67e-10
10 20 30
....*....|....*....|....*....|
gi 501039963 909 GEAVGVIAAQSIGEPGTQLTMRTFHLGGTA 938
Cdd:cd02736 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVA 39
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
906-1357 |
3.33e-09 |
|
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: 60.68 E-value: 3.33e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 906 VNQGEAVGVIAAQSIGEPGTQLTMRTFHLGGtaqvVDSSyleasyegTVKL---RNR---NVVRNsdgnlvVMGRNMAVL 979
Cdd:cd02584 24 VHPGEMVGTIAAQSIGEPATQMTLNTFHFAG----VSAK--------NVTLgvpRLKeiiNVAKN------IKTPSLTVY 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 980 ILDNTGK-ERAVHRVtyGSRLfvdEADTVKRGQRIAE--WDP-YTRPIMTE----VEGYVEFEDLVDGLSvsesaDESTG 1051
Cdd:cd02584 86 LEPGFAKdEEKAKKI--QSRL---EHTTLKDVTAATEiyYDPdPQNTVIEEdkefVESYFEFPDEDVEQD-----RLSPW 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1052 ITkRVVID-WRSTPRGSDLkpamvikDKAGKILKLSKGGDARFMLSVESILSVEpgahvkagdVIARLpMESAKTKDITG 1130
Cdd:cd02584 156 LL-RIELDrKKMTDKKLSM-------EQIAKKIKEEFKDDLNVIFSDDNAEKLV---------IRIRI-INDDEEKEEDS 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1131 GLPRVAELFEARRPKDHAVIAEIDGTVRFGRdYKNKRRIIIEpnddtiepveylipkgkpfhlqDGDVIEKGEYILDGN- 1209
Cdd:cd02584 218 EDDVFLKKIESNMLSDMTLKGIEGIRKVFIR-EENKKKVDIE----------------------TGEFKKREEWVLETDg 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1210 PAPHDILAIKGVEALASYlVNEIQEVYRLQGvlindkhIEVIVRQMLQKVEITESGDTGYIPGDH----VD----RIELE 1281
Cdd:cd02584 275 VNLREVLSHPGVDPTRTT-SNDIVEIFEVLG-------IEAARKALLKELRNVISFDGSYVNYRHlallCDvmtqRGHLM 346
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 501039963 1282 EINERlieegkkpgsgnpvllGITKASLQTpsfISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:cd02584 347 AITRH----------------GINRQDTGP---LMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1220-1359 |
4.18e-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: 53.38 E-value: 4.18e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1220 GVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMLQKVEItesgdtgyipgdhvdrieleeinerlieegkkpgsgnp 1299
Cdd:cd02736 199 GIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMTFKGEV-------------------------------------- 240
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 501039963 1300 vlLGITKASLQ--TPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTGGM 1359
Cdd:cd02736 241 --LGITRFGIAkmKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGLF 300
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1213-1357 |
5.93e-06 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 51.05 E-value: 5.93e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 501039963 1213 HDILAIKGVEALASYLVNEIQEVYRLQGVLINDKHIEVIVRQMlqkveiTESGdtgyipgdhvdriELEEInerlieeGK 1292
Cdd:PRK14898 736 IEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIM------TADG-------------EVKPI-------GR 789
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 501039963 1293 KPGSGNpvllgitkaslqTPSFISAASFQETTRVLTEAAVAGKMDTLQGLKENVIVGRLIPAGTG 1357
Cdd:PRK14898 790 HGVAGE------------KGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
902-929 |
5.19e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 41.42 E-value: 5.19e-03
10 20
....*....|....*....|....*...
gi 501039963 902 RGTPVNQGEAVGVIAAQSIGEPGTQLTM 929
Cdd:PRK14898 50 LNALVEPYEAVGIVAAQSIGEPGTQMSL 77
|
|
| |
