|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
16-1374 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2399.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 16 EFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALA 95
Cdd:PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 96 KVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKYQLLNDEQYFEALEEFGDD 175
Cdd:PRK00566 86 KVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGDE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 176 FDARMGAEAVFQLLGAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVMTVLPVLPPDLRPLVPL 255
Cdd:PRK00566 166 FVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 256 DGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ 335
Cdd:PRK00566 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQ 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 336 GRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKKMVERELPEVWDVLAEV 415
Cdd:PRK00566 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEV 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 416 IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN 495
Cdd:PRK00566 406 IKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 496 GEPIIVPSQDVVLGLYYMTREAINAKGEGRVFADLQEVDRVFRAGEAALHAKVKVRInetirhkdgsltKNTRIVDTTVG 575
Cdd:PRK00566 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRI------------TSKKLVETTVG 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 576 RALLFQVVPAGLPYDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARIID 655
Cdd:PRK00566 554 RVIFNEILPEGLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 656 AATAEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLSKekvidregkevDQESFNSMYMMADSGARGSAA 735
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSK-----------DQESFNPIYMMADSGARGSAS 702
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 736 QIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDCG 815
Cdd:PRK00566 703 QIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCG 782
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 816 TERGLIMTPHIEGGDVVEPLGERVLGRVIARDVPKPGTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCETRHGIC 895
Cdd:PRK00566 783 TDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVC 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 896 AKCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAasrtsaadsvqvknggairlhnlkhveradgalva 975
Cdd:PRK00566 863 AKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV----------------------------------- 907
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 976 vsrsgelaiaddfgrereryklpygavisvkegdkvdagaivakwdphthpivtemdgtvafvgmeegitikrqtdeltg 1055
Cdd:PRK00566 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1056 ltnievldakdrptsgkDIrpavklidangkdlllpgtdvpaqyflppnalvnlsdgakvhvgdviaripqetsktrdiT 1135
Cdd:PRK00566 908 -----------------DI------------------------------------------------------------T 910
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1136 GGLPRVADLFEARRPKEPAILAEISGTISFGKETKGKRRLVITPTDGtDPYEELIPKWRHLNVFEGEQVSRGEVISDGPS 1215
Cdd:PRK00566 911 GGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDG-EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSI 989
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1216 NPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKGDQVELTHVLEENEQLVGN 1295
Cdd:PRK00566 990 DPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAE 1069
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516237908 1296 DRFVAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSERKRQRE 1374
Cdd:PRK00566 1070 GKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPA 1148
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
15-1199 |
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: 1937.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 15 EEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVAL 94
Cdd:COG0086 5 EDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTL 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 95 AKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKYQLLNDEQYFEALEEFGD 174
Cdd:COG0086 85 SKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYGD 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 175 DFDARMGAEAVFQLLGAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVMTVLPVLPPDLRPLVP 254
Cdd:COG0086 165 EFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVP 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 255 LDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGK 334
Cdd:COG0086 245 LDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGK 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 335 QGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKKMVERELPEVWDVLAE 414
Cdd:COG0086 325 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEE 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 415 VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Cdd:COG0086 405 VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPA 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 495 NGEPIIVPSQDVVLGLYYMTREAINAKGEGRVFADLQEVDRVFRAGEAALHAKVKVRINETirhkdgsLTKNTRIVDTTV 574
Cdd:COG0086 485 NGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITED-------GEQVGKIVETTV 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 575 GRALLFQVVPAGLPYdvVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARII 654
Cdd:COG0086 558 GRYLVNEILPQEVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIF 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 655 DAATAEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLSkekvidregkevdqeSFNSMYMMADSGARGSA 734
Cdd:COG0086 636 EEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS---------------SQNTTYMMADSGARGSA 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 735 AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDC 814
Cdd:COG0086 701 DQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDC 780
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 815 GTERGLIMTPHIEGGDVVEPLGERVLGRVIARDVPKPGTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCETRHGI 894
Cdd:COG0086 781 GTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGV 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 895 CAKCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADSVQVKNGGAIRLHNLKHVERADGALV 974
Cdd:COG0086 861 CAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGV 940
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 975 AVSRSGELAIADDFGRERERYKLPYGAVISVKEGDKVDAGAIVAKWDPHTHPIVTEMDGTVAFVGMEEGITIKRQTDELT 1054
Cdd:COG0086 941 VVSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEET 1020
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1055 GLTNIEVLDAKDRPTSGKDIRPAVKLIDANGKDLLLPGTDVPAQYFLPPNALVNLSDGAKVHVGDVIARIPQETSKTRDI 1134
Cdd:COG0086 1021 GGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDG 1100
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516237908 1135 TGGLPRVADLFEARRPKEPAILAEISGTISFGKETKGKRRLVITPTDGTDPYEELIPKWRHLNVF 1199
Cdd:COG0086 1101 TGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
19-1368 |
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: 1821.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 19 AIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALAKVR 98
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 99 RERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKYQLLNDEQYFEALEEFGDDFDA 178
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 179 RMGAEAVFQLLGAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVMTVLPVLPPDLRPLVPLDGG 258
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 259 RFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRF 338
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 339 RQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKKMVERELPEVWDVLAEVIRE 418
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 419 HPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEP 498
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 499 IIVPSQDVVLGLYYMTREAINAKGEGRVFADLQEVDRVFRAGEAALHAKVKVRInetirhkdgsltkNTRIVDTTVGRAL 578
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRT-------------SGEILETTVGRVI 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 579 LFQVVPAGLPYDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARIIDAAT 658
Cdd:TIGR02386 548 FNEILPEGFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEAD 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 659 AEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLSKekvidregkevDQESFNSMYMMADSGARGSAAQIR 738
Cdd:TIGR02386 628 KEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKK-----------DTYKFNPIFMMADSGARGNISQFR 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 739 QLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDCGTER 818
Cdd:TIGR02386 697 QLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEE 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 819 GLIMTPHIEGGD-VVEPLGERVLGRVIARDVPKPGTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCETRHGICAK 897
Cdd:TIGR02386 777 GIEVEAIVEGKDeIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQK 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 898 CYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSaadsvqvknggairlhnlkhveradgalvavs 977
Cdd:TIGR02386 857 CYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASG-------------------------------- 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 978 rsgelaiaddfgrereryklpygavisvkegdkvdagaivakwdphthpivtemdgtvafvgmeegitikrqtdeltglt 1057
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1058 nievldakdrptsgkdirpavklidangkdlllpgtdvpaqyflppnalvnlsdgakvhvgdviaripqetsktrDITGG 1137
Cdd:TIGR02386 905 ---------------------------------------------------------------------------DITQG 909
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1138 LPRVADLFEARRPKEPAILAEISGTISFGKET-KGKRRLVITPtDGTDPYEELIPKWRHLNVFEGEQVSRGEVISDGPSN 1216
Cdd:TIGR02386 910 LPRVKELFEARTPKDKAVIAEVDGTVEIIEDIvKNKRVVVIKD-ENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSID 988
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1217 PHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKGDQVELTHVLEENEQLVGND 1296
Cdd:TIGR02386 989 PHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQG 1068
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516237908 1297 RFVAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSE 1368
Cdd:TIGR02386 1069 KKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYKE 1140
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
8-1375 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1602.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 8 LKNQGQLEEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGV-ICE 86
Cdd:PRK09603 1387 IKEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCE 1466
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 87 KCGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPG--------MTTLEKYQ 158
Cdd:PRK09603 1467 KCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGeaaydnegTKLVMKYD 1546
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 159 LLNDEQYFEALEEFGD-DFDARMGAEAVFQLLGAIDLEHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWM 237
Cdd:PRK09603 1547 ILNEEQYQNISRRYEDrGFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWM 1626
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 238 VMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAIT 317
Cdd:PRK09603 1627 MLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVK 1706
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 318 GSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAA 397
Cdd:PRK09603 1707 GANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQA 1786
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 398 KKMVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQ 477
Cdd:PRK09603 1787 KRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAI 1866
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 478 LEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREAINAKGEGRVFADLQEVDRVFRAGEAALHAKVKVrinetir 557
Cdd:PRK09603 1867 AECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRV------- 1939
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 558 hkdgslTKNTRIVDTTVGRALLFQVVPAGLPYDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGV 637
Cdd:PRK09603 1940 ------LDQGNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGI 2013
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 638 SIGVNDFVIPDEKARIIDAATAEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLskekvidregkEVDQE 717
Cdd:PRK09603 2014 SISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAI-----------AKDKE 2082
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 718 SFNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLT 797
Cdd:PRK09603 2083 GFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLT 2162
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 798 RRLVDVAQDLVVTEVDCGTERGLIMTPHIEGGDVVEPLGERVLGRVIARDVPKPGTEEIIVPAGTLVDERWVEFLELNSV 877
Cdd:PRK09603 2163 RKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGI 2242
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 878 DEVVVRSPITCETRHGICAKCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADSVQVKNGGA 957
Cdd:PRK09603 2243 KSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGF 2322
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 958 IRLHNLK---------------------------------------HVE------------------------------- 967
Cdd:PRK09603 2323 VRFYNLRtytnkegkniianrrnasilvvepkikapfdgelrietvYEEvvvsvkngdqeakfvlrrsdivkpselagvg 2402
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 968 -----------------RADGALV-------------------------------------------------------- 974
Cdd:PRK09603 2403 gkiegkvylpyasghkvHKGGSIAdiiqegwnvpnripyasellvkdndpiaqdvyakekgiikyyvleanhlerthgik 2482
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 975 ---AVSRSGELA-IADDFGRERERYKLPYGAVISVKEGDKVDAGA-----------IVAKWDPHTHPIVTEMDGTVAFVG 1039
Cdd:PRK09603 2483 kgdIVSEKGLFAvIADDNGREAARHYIARGSEILIDDNSEVSANSviskpttntfkTIATWDPYNTPIIADFKGKVSFVD 2562
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1040 MEEGITIKRQTDELTGLTNIEVLDAkdRPTSGKdirPAVKLIDANGKDLllpgtdvpaQYFLPPNALVNLSDGAKVHVGD 1119
Cdd:PRK09603 2563 IIAGVTVAEKEDENTGITSLVVNDY--IPSGYK---PSLFLEGANGEEI---------RYFLEPKTSIAISDGSSVEQAE 2628
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1120 VIARIPQETSKTRDITGGLPRVADLFEAR--RPKEPAILAEISGTISFGKETKGKRRLVITPTDGtDPYEELIPKWRHLN 1197
Cdd:PRK09603 2629 VLAKIPKATVKSRDITGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDG-RSMDYFVDKGKQIL 2707
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1198 VFEGEQVSRGEVISDGPSNPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKG 1277
Cdd:PRK09603 2708 VHADEFVHAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEG 2787
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1278 DQVELTHVLEENEQLV--GNDRFVAkyERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGR 1355
Cdd:PRK09603 2788 DLVSKKLFKEENARVIalKGEPAIA--EPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGR 2865
|
1530 1540
....*....|....*....|
gi 516237908 1356 LIPAGTGLaYHSERKRQREL 1375
Cdd:PRK09603 2866 MIPVGTGM-YKNKKIVLRTL 2884
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1363 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1590.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 15 EEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVAL 94
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 95 AKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKYQLLNDEQYFEALEEFG- 173
Cdd:PRK14844 1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGi 1605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 174 DDFDARMGAEAVFQLLGAIDLeHEIGR-LREEIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVMTVLPVLPPDLRPL 252
Cdd:PRK14844 1606 DSFVAMQGVEAIRELLTRLDL-HEIRKdLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPL 1684
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 253 VPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLK-SLADMI 331
Cdd:PRK14844 1685 VSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDML 1764
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 332 KGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKKMVERELPEVWDV 411
Cdd:PRK14844 1765 KGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDM 1844
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 412 LAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNIL 491
Cdd:PRK14844 1845 LEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVL 1924
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 492 SPANGEPIIVPSQDVVLGLYYMTREAINaKGEGRVFADLQEVDRVFRAGEAALHAKVKVRINETirHKDGSLTKNTriVD 571
Cdd:PRK14844 1925 SPSNGRPIIVPSKDIVLGIYYLTLQEPK-EDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYI--NSSGETHYKT--IC 1999
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 572 TTVGRALLFQVVPA--GLPYDVVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDE 649
Cdd:PRK14844 2000 TTPGRLILWQIFPKheNLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPET 2079
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 650 KARIIDAATAEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLSkekVIDREGKevdqesFNSMYMMADSG 729
Cdd:PRK14844 2080 KATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAIS---IYDGNSK------YNSVYMMVNSG 2150
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 730 ARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVV 809
Cdd:PRK14844 2151 ARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIV 2230
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 810 TEVDCGTERGLIMTPHIEGGDVVEPLGERVLGRVIARDVPKPGTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCE 889
Cdd:PRK14844 2231 TKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCE 2310
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 890 TRHGICAKCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAADSVQVKNGGAIRLHNLKHVERA 969
Cdd:PRK14844 2311 ISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDK 2390
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 970 DGALVAVSRSGELAIADDFGRERERYKLPYGAVISVKEGDKVDAGAIVAKWDPHTHPIVTEMDGTVAFVGMEEGITIKRQ 1049
Cdd:PRK14844 2391 NGNKIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEV 2470
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1050 TDELTGLTNIEVLDAKDRpTSGKDIRPAVKLIDANGKDLLLpGTDVPAQYFLPPNALVNLSDGAKVHVGDVIARIPQETS 1129
Cdd:PRK14844 2471 MDESTGISSKVVKDWKLY-SGGANLRPRIVLLDDNGKVMTL-ASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESV 2548
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1130 KTRDITGGLPRVADLFEARRPKEPAILAEISGTISFG-KETKGKRRLVITPTD-GTDPYEELIPKWRHLNVFEGEQVSRG 1207
Cdd:PRK14844 2549 KTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDeQISPVEYLVSRSKHVIVNEGDFVRKG 2628
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1208 EVISDGPSNPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKGDQVELTHVLE 1287
Cdd:PRK14844 2629 DLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDR 2708
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516237908 1288 ENEQLVGNDRFVAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGL 1363
Cdd:PRK14844 2709 ENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
15-813 |
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: 1322.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 15 EEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVAL 94
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 95 AKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFesyvvidpgmttlekyqllndeqyfealeefgd 174
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 175 dfdarmgaeavfqllgaidleheigrlreeipqtnsetkikklskrlkLMEAFQGSGNKPEWMVMTVLPVLPPDLRPLVP 254
Cdd:cd01609 128 ------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQ 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 255 LDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGK 334
Cdd:cd01609 160 LDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGK 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 335 QGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKKMVERELPEVWDVLAE 414
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 415 VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 495 NGEPIIVPSQDVVLGLYYMTREAINAKGEGrvfadlqevdrvfrageaalhakvkvrinetirhkdgsltkntrIVDTTV 574
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTKERKGDKGEG--------------------------------------------IIETTV 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 575 GRALLFQVVPAGLPYdvVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARII 654
Cdd:cd01609 436 GRVIFNEILPEGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEII 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 655 DAATAEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLskekvidregkevDQESFNSMYMMADSGARGSA 734
Cdd:cd01609 514 KEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNL-------------DKDPFNPIYMMADSGARGSK 580
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516237908 735 AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVD 813
Cdd:cd01609 581 SQIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
16-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1300.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 16 EFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVALA 95
Cdd:PRK14906 8 NFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRA 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 96 KVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVV----------------------------- 146
Cdd:PRK14906 88 KVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleeldae 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 147 ------------------------------------IDPGMT---------------------TLEKYQLLNDEQYFEAL 169
Cdd:PRK14906 168 rdrlieatrrlsvdyvpeddefvddigdderltaeeVRAEVAdiyeeynerkalrreafdafmQIEPKQLISDEALYREM 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 170 E-EFGDDFDARMGAEAVFQLLGAIDLEHEIGRLREeIPQTNSETKIKKLSKRLKLMEAFQGSGNKPEWMVMTVLPVLPPD 248
Cdd:PRK14906 248 RlNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRA-IIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPD 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 249 LRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLA 328
Cdd:PRK14906 327 LRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLA 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 329 DMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKKMVERELPEV 408
Cdd:PRK14906 407 DMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYV 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 409 WDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTN 488
Cdd:PRK14906 487 WDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSN 566
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 489 NILSPANGEPIIVPSQDVVLGLYYMTREAINAKGEGRVFADLQEVDRVFRA-GEAALHAKVKVRINETIR----HKDGSL 563
Cdd:PRK14906 567 NIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDArADLDLQAKIVVRLSRDMTvrgsYGDLEE 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 564 TKNTRIVDTTVGRALLFQVVPAGLPYdvVNQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVND 643
Cdd:PRK14906 647 TKAGERIETTVGRIIFNQVLPEDYPY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYD 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 644 FVIPDEKARIIDAATAEVKEIESQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLSKekvidregkevdqesFNSMY 723
Cdd:PRK14906 725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFDE---------------DNPIY 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 724 MMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV 803
Cdd:PRK14906 790 MMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDV 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 804 AQDLVVTEVDCGTERGLIMTPHIEGGDVVEPLgervLGRVIARDVPKPgTEEIIVPAGTLVD-----ERWVEflelNSVD 878
Cdd:PRK14906 870 AQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDP-NGEVLLSAGDYIEsmddlKRLVE----AGVT 940
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 879 EVVVRSPITCETRHGICAKCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAAsrtsaadsvqvknggai 958
Cdd:PRK14906 941 KVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA----------------- 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 959 rlhnlkhveradgalvavsrsgelaiaddfgrereryklpygavisvkeGDkvdagaivakwdphthpivtemdgtvafv 1038
Cdd:PRK14906 1004 -------------------------------------------------GD----------------------------- 1005
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1039 gmeegitikrqtdeltgltnievldakdrptsgkdirpavklidangkdlllpgtdvpaqyflppnalvnlsdgakvhvg 1118
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1119 dviaripqetsktrDITGGLPRVADLFEARRPKEPAILAEISGTISFGKETKGKrrlVITPTDGTDPYEELIPKWR---H 1195
Cdd:PRK14906 1006 --------------DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEK---TLTIHDQDGNSREYVVSARvqfM 1068
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1196 LNVFEGEQVSRGEVISDGPSNPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFI 1275
Cdd:PRK14906 1069 PGVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYL 1148
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1276 KGDQVELTHVLEENEQLVGNDRFVAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGR 1355
Cdd:PRK14906 1149 PGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGK 1228
|
1450
....*....|...
gi 516237908 1356 LIPAGTGLAYHSE 1368
Cdd:PRK14906 1229 PIPAGTGLSRYRD 1241
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
10-583 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 841.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 10 NQGQLEEFDAIRIGLASPEMIRSWS---------FGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKH 80
Cdd:PRK02625 2 NLRTENRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRH 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 81 RGVICEKCGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPG-MTTLEKYQL 159
Cdd:PRK02625 82 RGIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGnHKNLKYKQL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 160 LNDEQYFEALEE-FGDDFD------ARMGAEAVFQLLGAIDLEHEIGRLREEIPQTNSEtKIKKLSKRLKLMEAFQGSGN 232
Cdd:PRK02625 162 LTEDQWLEIEDQiYAEDSElegeevVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGS 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 233 KPEWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRR 312
Cdd:PRK02625 241 RPEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRR 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 313 GRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMAT 392
Cdd:PRK02625 321 GRTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVN 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 393 TIKAAKKMVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPL 472
Cdd:PRK02625 401 NIKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPL 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 473 TLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREAINA-KGEGRVFADLQEVDRVFRAGEAALHAKVKVR 551
Cdd:PRK02625 481 SLEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAqKGAGRYFASLEDVIMAFEQGRIDLHAWVWVR 560
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 552 IN-------------ETIRHKDGSLTKN---------------TRIVDTTVGRALLFQVV 583
Cdd:PRK02625 561 FNgevedddedteplKTETLEDGTRIEQyryrrdrfdedgnliSQYILTTVGRVIMNKTI 620
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
17-587 |
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: 816.13 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 17 FDAIRIGLASPEMIRSWS---------FGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVICEK 87
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 88 CGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKY-QLLNDEQYF 166
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYkQLLTEDQWL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 167 EALEE-FGDDFD------ARMGAEAVFQLLGAIDLEHEIGRLREEIPQTNSEtKIKKLSKRLKLMEAFQGSGNKPEWMVM 239
Cdd:TIGR02387 162 EIEDQiYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 240 TVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGS 319
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 320 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLEARGMATTIKAAKK 399
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 400 MVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE 479
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 480 ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREAINA-KGEGRVFADLQEVDRVFRAGEAALHAKVKVRINETI-- 556
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAeKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVet 560
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|....*....
gi 516237908 557 ----------------------------RHKDGSLTknTRIVDTTVGRALLFQVVPAGL 587
Cdd:TIGR02387 561 ndpldepiksedlsdgtrieqwtyrrdrFDEDGALI--SQYILTTTGRIIMNHTIIEAL 617
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
16-519 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 798.34 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 16 EFDAIRIGLASPEMIRSWS---------FGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKR---LKHRGV 83
Cdd:CHL00018 6 KHQQLRIGLASPQQIRAWAerilpngeiVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVigdEKEDPK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 84 ICEKCGVEVALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFE-SYVVIDPGMTTLEKY-QLLN 161
Cdd:CHL00018 86 FCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDfSFARPIAKKPTFLRLrGLFE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 162 DE----QYFEALEEFGDDFDARM------GAEAVFQLLGAIDLEHEIGRLREEI-------PQTN--SETKIKK----LS 218
Cdd:CHL00018 166 YEiqswKYSIPLFFSTQGFDTFRnreistGAGAIREQLADLDLRIIIDNSLVEWkelgeegSTGNewEDRKIGRrkdfLV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 219 KRLKLMEAFQGSGNKPEWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLA--APDIIVRNEK 296
Cdd:CHL00018 246 RRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQK 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 297 RMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALEL 376
Cdd:CHL00018 326 KLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 377 FKPFIFGKLEARGMATTIKAAKKMVERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAA 456
Cdd:CHL00018 406 FQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 485
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516237908 457 YNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREAIN 519
Cdd:CHL00018 486 FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRR 548
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
25-811 |
0e+00 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 612.52 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 25 ASPEMIRSWSFGEVKKPETINYRTFKPERDGlfcakifgpvkdyeclcgKYKRLKHRGVICEKCGVEVALAKVRRERMGH 104
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 105 IELASPVAHIWFLKSLPSRIGllldmtlrdiervlyfesyvvidpgmttlekyqllndeqyfealeefgddfdarmgaea 184
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 185 vfqllgaidleheigrlreeipqtnsetkikklskrlklmeafqgsgnkPEWMVMTVLPVLPPDLRPLVpldggrfatsd 264
Cdd:cd00399 84 -------------------------------------------------PEWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 265 lndlyrrvinrnnrlkrlldlaapdiIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLG 344
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 345 KRVDYSGRSVITVGPTLRLHQCGLPKKMALELfkpfifgkleargmattikaakkmverelpevwdvlaeviREHPVLLN 424
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 425 RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ 504
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 505 DVVLGLYYMTREAinakgegrvfadlqevdrvfrageaalhakvkvrinetirhkdgsltkntrivdttvgrallfQVVP 584
Cdd:cd00399 278 DTLLGAYLLTLGK---------------------------------------------------------------QIVS 294
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 585 AGLPYDVVNQsmkkkaisklinhCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVND----FVIPDEKARIIDAATAE 660
Cdd:cd00399 295 AALPGGLLHT-------------VTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDviddGVIPEEKTELIEEAKKK 361
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 661 VKEIESQYASGLVTQGEK-------YNKVIDLWSKANDEVSKAMMTNLSKekvidregkevdQESFNSMYMMADSGARGS 733
Cdd:cd00399 362 VDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNLDL------------VSKFNSIYVMAMSGAKGS 429
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 734 AAQIRQLAGMRGLMAKPDGSI--------------------IETPITANFREGLNVLQYFISTHGARKGLADTALKTANS 793
Cdd:cd00399 430 FINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAES 509
|
810
....*....|....*...
gi 516237908 794 GYLTRRLVDVAQDLVVTE 811
Cdd:cd00399 510 GYLQRRLVKALEDLVVHY 527
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
235-511 |
2.42e-161 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 486.26 E-value: 2.42e-161
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 235 EWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNG--RR 312
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 313 GRAITGsnkRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFGKLE------ 386
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 387 ------------ARGMATTIKAAKKM-VERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV 453
Cdd:smart00663 158 lvrngpngakyiIRGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 516237908 454 CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLY 511
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
766-1272 |
5.12e-136 |
|
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: 427.93 E-value: 5.12e-136
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 766 GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDCGTERGLIMTPHIEGGDVVEPLGERVLGRVIA 845
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 846 RDVPKPGTEEIIVPAGTLVDERW---------------------------------VEFLELNSVDEVVVRSPITCETRH 892
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSefslsykkeilvrdsklgrdrlskeaqeratllFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 893 GICAKCYGRDLARGHQVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAAdsvqvkngGAIRLHNLKhveraDGA 972
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTL--------GVPRLKEII-----NVS 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 973 LVAVSRSGELAIADDFGRERERYKLPYGAVISVKEGDKVDAGAIVAKWDPHTHPIVTEMDGTVAFVGMEEGITIKRQTDE 1052
Cdd:pfam04998 228 KNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1053 LTGLTNIEVLDAKDRPTSGKDIrpavklidangkdlllpgtdvpAQYFLPPNALVNLSDGAKVHVGDVIARIPQETSKTR 1132
Cdd:pfam04998 308 ETGLLILVIRLLKILNKSIKKV----------------------VKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKI 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1133 DITGGLPRVADLFEARRPKEPAILAEISGTISFGKETKGKRRLVITPTDGTDPYE------ELIPKWRHLNVFegEQVSR 1206
Cdd:pfam04998 366 RQDTGGLRRVDELFMEEDPKLAILVASLLGNITLRGIPGIKRILVNEDDKGKVEPdwvletEGVNLLRVLLVP--GFVDA 443
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 516237908 1207 GEVISDgpsNPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDS 1272
Cdd:pfam04998 444 GRILSN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
593-1134 |
2.85e-131 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 438.66 E-value: 2.85e-131
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 593 NQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARIIDAATAEVKEIESQYASGL 672
Cdd:PRK02597 5 NRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 673 VTQGEKYNKVIDLWSKANDEVSKAMMTNLSKEKVIdregkevdqesfNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDG 752
Cdd:PRK02597 85 ITEVERFQKVIDTWNETNERLKDEVVKNFRQNDPL------------NSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 753 SIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDCGTERGLIMTPHIEGGDVV 832
Cdd:PRK02597 153 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 833 EPLGERVLGRVIARDVPKPgTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCETRHGICAKCYGRDLARGHQVNIG 912
Cdd:PRK02597 233 IPLGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLG 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 913 EAVGVIAAQSIGEPGTQLTMRTFHIGGAAS-------RTSAADSVQVKNGGAIRLHNLKHVERADGALVAvsrsGELAIA 985
Cdd:PRK02597 312 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTgevarqvRSPFAGTVEFGKKLRTRPYRTRHGVEALQAEVD----FDLVLK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 986 DDFGRERERYKLPYGAVISVKEGDKVDAGAIVAKwdphthpivtemdgtVAFVGMEEGiTIKRQTDELTGLTNiEVLDAK 1065
Cdd:PRK02597 388 PSGKGKPQKIEITQGSLLFVDDGQTVEADQLLAE---------------VAAGAVKKS-TEKATKDVICDLAG-EVRFAD 450
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1066 DRPTSGKDIRPAVKLIDANGKDLLLPGTDVpaqYFLPPNALVNLSDGAKVHVGDVIA------------RIPQETSKTRD 1133
Cdd:PRK02597 451 LIPEEKTDRQGNTTRKAQRGGLLWVLSGDV---YNLPPGAEPVVSNGDRVEEGDVLAetklvsehggvvRLRESSGDSRE 527
|
.
gi 516237908 1134 I 1134
Cdd:PRK02597 528 V 528
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
593-1212 |
8.19e-125 |
|
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: 418.87 E-value: 8.19e-125
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 593 NQSMKKKAISKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARIIDAATAEVKEIESQYASGL 672
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 673 VTQGEKYNKVIDLWSKANDEVSKAMMTNLSKEKVIdregkevdqesfNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDG 752
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNFRQTDPL------------NSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 753 SIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDCGTERGLIMTPHIEGGDVV 832
Cdd:TIGR02388 152 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 833 EpLGERVLGRVIARDVPKPgTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCETRHGICAKCYGRDLARGHQVNIG 912
Cdd:TIGR02388 232 S-LGDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLG 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 913 EAVGVIAAQSIGEPGTQLTMRTFHIGGAAS-------RTSAADSVQVKNGGAIRLHNLKHVERA-----DGALVAVSRSG 980
Cdd:TIGR02388 310 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTgevarqvRSKIDGTVEFGKKLRTRGYRTRHGEDAkqvevAGLLIIKPTGS 389
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 981 ELAIAddfgrerERYKLPYGAVISVKEGDKVDAGAIVAKWDPHTHPIVTEMdgtvafvgmeegiTIKRQTDELTGltniE 1060
Cdd:TIGR02388 390 ITNKA-------QEIEVTQGSLLFVEDGQTVDAGQLLAEIALGAVRKSTEK-------------ATKDVASDLAG----E 445
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1061 VLDAKDRPTSGKDIRPAVKLIDANGKDLLLPGTDVpaqYFLPPNALVNLSDGAKVHVGDVIARIPQETsktrdITGGLPR 1140
Cdd:TIGR02388 446 VKFDKVVPEEKTDRQGNTTRIAQRGGLIWVLSGEV---YNLPPGAEPVVKNGDRVEQGTVLAETKLST-----EHGGVVR 517
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516237908 1141 VADLFEARRPKEPAILAEISGTISFGKETKGKRRL-VITPTDGTdpyeelipKWRhLNVFEGEQVSRGEVISD 1212
Cdd:TIGR02388 518 LPESVGDSREVEIITASVLLDQAKVIEESSQGRELyHIETADGQ--------RFR-LKAAPGTKVQNGQVVAE 581
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
593-939 |
1.06e-111 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 384.29 E-value: 1.06e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 593 NQSMKKKA----ISKLINHcyrvVGLKDTVIFADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARIIDAATAEVKEIESQY 668
Cdd:CHL00117 11 NKVIDKTAlkrlISWLIDH----FGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHY 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 669 ASGLVTQGEKYNKVIDLWSKANDEVSKAMMTNLskekvidregKEVDqeSFNSMYMMADSGARGSAAQIRQLAGMRGLMA 748
Cdd:CHL00117 87 HYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNF----------RMTD--PLNPVYMMSFSGARGNASQVHQLVGMRGLMS 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 749 KPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEVDCGTERGLIMTPHiEG 828
Cdd:CHL00117 155 DPQGQIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPR-NG 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 829 GDVVEPLGERVLGRVIARDVPKpgTEEIIVPAGTLVDERWVEFLELNSVDEVVVRSPITCETRHGICAKCYGRDLARGHQ 908
Cdd:CHL00117 234 MMIERILIQTLIGRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDL 311
|
330 340 350
....*....|....*....|....*....|.
gi 516237908 909 VNIGEAVGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:CHL00117 312 VELGEAVGIIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-342 |
6.10e-108 |
|
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: 344.27 E-value: 6.10e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 14 LEEFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYEC-LCGKYKRlkhrgviceKCGVev 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 93 alakvrreRMGHIELASPVAHIWFLKslpsrigllldMTLRDIERVLYFESYVVIDPGmttleKYQLLNDEQYFEALEEF 172
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 173 gddfdaRMGAEAVFQLLGAIDL------------------EHEIGRLREEIPQTNSE--------TKIKKLSKRLK---- 222
Cdd:pfam04997 126 ------KMGAKAILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKKSKEEeekeilnpEKVLKIFKRISdedv 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 223 LMEAFQGSGNKPEWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEA 302
Cdd:pfam04997 200 EILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEH 279
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 516237908 303 VDALLDNGRRG-RAITGSNKRPLKSLADMIKGKQGRFRQNL 342
Cdd:pfam04997 280 VATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
18-809 |
4.63e-103 |
|
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA polymerase (RNAP). Archaeal RNAP is closely related to RNA polymerases in eukaryotes based on the subunit compositions. Archaeal RNAP is a large multi-protein complex, made up of 11 to 13 subunits, depending on the species, that are responsible for the synthesis of RNA. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shaped structure. The largest eukaryotic RNAP subunit is encoded by two separate archaeal subunits (A' and A'') which correspond to the N- and C-terminal domains of eukaryotic RNAP II Rpb1, respectively. The N-terminal domain of Rpb1 forms part of the active site and includes the head and the core of one clamp as well as the pore and funnel structures of RNAP II. Based on a structural comparison among the archaeal, bacterial and eukaryotic RNAPs the DNA binding channel and the active site are part of A' subunit which is conserved. The strong similarity between subunit A' and the N-terminal domain of Rpb1 suggests a similar functional and structural role for these two proteins.
Pssm-ID: 259846 [Multi-domain] Cd Length: 861 Bit Score: 349.24 E-value: 4.63e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 18 DAIRIGLASPEMIRSWSFGEVKKPETinYrtfkpERDGLfcaKIFGPVKDyeclcgkyKRLkhrGVI-----CEKCGvev 92
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTCG--- 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 93 ALAKVRRERMGHIELASPVAHIWFLKslpsRIGLLLDMTLRDIERVLyfesyvvidpgMTTLEKyqllndEQYFEALEEF 172
Cdd:cd02582 61 NTAGECPGHFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEI------EKYLERIRRL 119
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 173 G--DDFDARMGAEAVFQLL---------GAIDLEheigrLREEIPQTNSETKIKKLSK--------RLK-------LMEA 226
Cdd:cd02582 120 KekWPELVKRVIEKVKKKAkkrkvcphcGAPQYK-----IKLEKPTTFYEEKEEGEVKltpseireRLEkipdedlELLG 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 227 FQGSGNKPEWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDAL 306
Cdd:cd02582 195 IDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTY 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 307 LDNGRRG--RAITGSnKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPfifgk 384
Cdd:cd02582 275 FDNEIPGipPARHRS-GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVP----- 348
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 385 leargMATT---IKAAKKMVERElPEVW---------------------DVLAE------VIREH-----PVLLNRAPTL 429
Cdd:cd02582 349 -----ERVTewnIEKMRKLVLNG-PDKWpganyvirpdgrrirlryvnrEELAErlepgwIVERHlidgdIVLFNRQPSL 422
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 430 HRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLG 509
Cdd:cd02582 423 HRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISG 502
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 510 LYYMTR--------EAINAKGEGRVFADLQE-----------------------VDRVFRAGEAALHAKVKVRINET--- 555
Cdd:cd02582 503 AYLLTRkttlftkeEALQLLSAAGYDGLLPEpailepkplwtgkqlfslflpkdLNFEGKAKVCSGCSECKDEDCPNdgy 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 556 IRHKDGSLTKNTrIVDTTVGRallFQVVpaglpydvvnqsmkkkaisKLINHCYRVVGLKDTVIFADQLMYTGFAYSTLS 635
Cdd:cd02582 583 VVIKNGKLLEGV-IDKKAIGA---EQPG-------------------SLLHRIAKEYGNEVARRFLDSVTRLAIRFIELR 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 636 GVSIGVNDFVIPDEKAR----IIDAATAEVKEIESQYASGLV------TQGEKY-NKVIDLWSKANDEVSKAMMTNLSKe 704
Cdd:cd02582 640 GFTIGIDDEDIPEEARKeieeIIKEAEKKVYELIEQYKNGELeplpgrTLEETLeMKIMQVLGKARDEAGKVASKYLDP- 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 705 kvidregkevdqesFNSMYMMADSGARGSAAQIRQLAGM------------RGLMAKP--------DGSIIETPITANFR 764
Cdd:cd02582 719 --------------FNNAVIMARTGARGSMLNLTQMAAClgqqsvrgerinRGYRNRTlphfkpgdLGPEARGFVRSSFR 784
|
890 900 910 920
....*....|....*....|....*....|....*....|....*
gi 516237908 765 EGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVV 809
Cdd:cd02582 785 DGLSPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYV 829
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
19-818 |
6.90e-92 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 317.95 E-value: 6.90e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 19 AIRIGLASPEMIRSWSFGEVKKPETinYrtfkpERDGLfcaKIFGPVKDyeclcgkyKRLkhrGVI-----CEKCGveva 93
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTCG---- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 94 laKVRRE---RMGHIELASPVAHIWFLKslpsRIGLLLDMTLRDIERVLYFESyvvidpgmtTLEKYQllndeQYFEALE 170
Cdd:PRK08566 66 --GRAGEcpgHFGHIELARPVIHVGFAK----LIYKLLRATCRECGRLKLTEE---------EIEEYL-----EKLERLK 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 171 EFGDDFDarmgaeavfQLLGAIdleHEIGRLREEIPQTNSETKIKKLSKRLKLMEAFQGSGNK----------------- 233
Cdd:PRK08566 126 EWGSLAD---------DLIKEV---KKEAAKRMVCPHCGEKQYKIKFEKPTTFYEERKEGLVKltpsdirerlekipded 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 234 ------------PEWMVMTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQE 301
Cdd:PRK08566 194 lellginpevarPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQY 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 302 AVDALLDN---G------RRGRaitgsnkrPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKM 372
Cdd:PRK08566 274 HVTTYFDNeipGipparhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAI 345
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 373 ALELFKPfifgkleargMATT---IKAAKKMVERElPEVW---------------------DVLAE------VIREH--- 419
Cdd:PRK08566 346 AKELTVP----------ERVTewnIEELREYVLNG-PEKHpganyvirpdgrrikltdknkEELAEklepgwIVERHlid 414
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 420 --PVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGE 497
Cdd:PRK08566 415 gdIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGG 494
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 498 PIIVPSQDVVLGLYYMTR--------EAINAKGEGRVfADLQEVDRVFRAGEAALHAKvkvRINETIRHKDGSLTKNTRI 569
Cdd:PRK08566 495 PIIGGIQDHISGAYLLTRkstlftkeEALDLLRAAGI-DELPEPEPAIENGKPYWTGK---QIFSLFLPKDLNLEFKAKI 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 570 VDTTVGRallfqvVPAGLPYD----VVNQSMK-----KKAIS----KLINHCYRVVGLKDTVIFADQLMYTGFAYSTLSG 636
Cdd:PRK08566 571 CSGCDEC------KKEDCEHDayvvIKNGKLLegvidKKAIGaeqgSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRG 644
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 637 VSIGVNDFVIPDE-KARI---IDAATAEVKEIESQYASGLV------TQGEKY-NKVIDLWSKANDEVSKAMMTNLSKek 705
Cdd:PRK08566 645 FTTGIDDEDIPEEaKEEIdeiIEEAEKRVEELIEAYENGELeplpgrTLEETLeMKIMQVLGKARDEAGEIAEKYLGL-- 722
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 706 vidregkevdqesFNSMYMMADSGARGSAAQIRQLAGM------------RGLMAK-----PDGSIieTP-----ITANF 763
Cdd:PRK08566 723 -------------DNPAVIMARTGARGSMLNLTQMAACvgqqsvrgerirRGYRDRtlphfKPGDL--GAeargfVRSSY 787
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|....*
gi 516237908 764 REGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVtEVDcGTER 818
Cdd:PRK08566 788 KSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKV-EYD-GTVR 840
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
18-1362 |
6.79e-86 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 308.11 E-value: 6.79e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 18 DAIRIGLASPEMIRSWSFGEVKKPETInyrtfkpERDGLfcaKIFGPVKDyeclcGKYKRLKHRgvicEKCGVEVALAKV 97
Cdd:PRK14977 10 DGIIFGLISPADARKIGFAEITAPEAY-------DEDGL---PVQGGLLD-----GRLGTIEPG----QKCLTCGNLAAN 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 98 RRERMGHIELASPVAHIWFLKslpsRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKYQLLNDEQYF--EALEEFGDD 175
Cdd:PRK14977 71 CPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIddEIIEEVRDQ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 176 FDARM---------GA---EAVFQLLGAIDLEHEIGRlREEIPQTNSEtKIKKLSKRLKLMEAFQGSGNKPEWMVMTVLP 243
Cdd:PRK14977 147 VKVYAkkakecphcGApqhELEFEEPTIFIEKTEIEE-HRLLPIEIRD-IFEKIIDDDLELIGFDPKKARPEWAVLQAFL 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 244 VLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSNK 321
Cdd:PRK14977 225 VPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHHKGSG 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 322 RPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFG--------KLEARG---- 389
Cdd:PRK14977 305 RPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNenniekmkELVINGpdef 384
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 390 -------MATTIKAAKKMVERELPEVWDVLAE------VIREH-----PVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP 451
Cdd:PRK14977 385 pganairKGDGTKIRLDFLEDKGKDALREAAEqleigdIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPGATFRLHP 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 452 LVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREainakgegRVFADLQ 531
Cdd:PRK14977 465 AVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKD--------DALFDKN 536
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 532 EVDRVF-RAGEAALHAKvkvrinETIRHKDGSLtkntrivdtTVGRALLFQVVPAGLPYDVVNQSMKKKA---------- 600
Cdd:PRK14977 537 EASNIAmLAGITDPLPE------PAIKTKDGPA---------WTGKQLFSLFLPKDFNFEGIAKWSAGKAgeakdpsclg 601
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 601 -----------ISKLI--NHCYRVVGLKDTVI--------------FADQLMYTGFAYSTLSGVSIGVNDFVIPDEKARI 653
Cdd:PRK14977 602 dgyvlikegelISGVIddNIIGALVEEPESLIdriakdygeavaieFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKQE 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 654 IDAATAEVKEIESQyasglVTQGEKYNKVIDLWsKANDEVSKAMMTNLSKEKVIDRE-GKEVDQESF---------NSMY 723
Cdd:PRK14977 682 IEDDIQGMKDEVSD-----LIDQRKITRKITIY-KGKEELLRGMKEEEALEADIVNElDKARDKAGSsandcidadNAGK 755
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 724 MMADSGARGSAAQIRQLAGMRGLMA-KPDGSIIETP---------------------------ITANFREGLNVLQYFIS 775
Cdd:PRK14977 756 IMAKTGARGSMANLAQIAGALGQQKrKTRIGFVLTGgrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFH 835
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 776 THGARKGLADTALKTANSGYLTRRLVDVAQDLVVtEVDcgterGLIMTPH------IEGGDVVEPLG---------ERVL 840
Cdd:PRK14977 836 AMGGREGLIDKARRTEDSGYFQRRLANALEDIRL-EYD-----ETVRDPHghiiqfKFGEDGIDPQKldhgeafnlERII 909
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 841 GRVIARDVPKPGTEEIIvpaGTLVDERWVEF---LELNSVDEVVVRSPITCETRhGICAKcyGRDLARGHQVNIGEAVGV 917
Cdd:PRK14977 910 EKQKIEDRGKGASKDEI---EELAKEYTKTFnanLPKLLADAIHGAELKEDELE-AICAE--GKEGFEKAKVEPGQAIGI 983
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 918 IAAQSIGEPGTQLTMRTFHIGGAASRtsaadsvqvknggairlhNLKHveradgalvAVSRSGELAIAddfgrererYKL 997
Cdd:PRK14977 984 ISAQSIAEPGTQMTLRTFHAAGIKAM------------------DVTH---------GLERFIELVDA---------RAK 1027
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 998 PYGAVISVKEGDKVDAgaivakwdphthpivtemdgtvafvGMEEGITIKRQTDELTGLTNIEVlDAKDRPTSGKDIRPA 1077
Cdd:PRK14977 1028 PSTPTMDIYLDDECKE-------------------------DIEKAIEIARNLKELKVRALIAD-SAIDNANEIKLIKPD 1081
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1078 VKLIDANGkdlllpgtdVPAQYFLppNALVNLSDGAKVHVgdviaripqETSKTRDITgglprvaDLFE-ARRPKEPAIL 1156
Cdd:PRK14977 1082 KRALENGC---------IPMERFA--EIEAALAKGKKFEM---------ELEDDLIIL-------DLVEaADRDKPLATL 1134
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1157 AEISGTIsFGKETKG----KRRLVIT-PTDGTDPYEELIPKWRHLNVFEGEQVSRGEVISDgpsNPHDILRLLGVSALAK 1231
Cdd:PRK14977 1135 IAIRNKI-LDKPVKGvpdiERAWVELvEKDGRDEWIIQTSGSNLAAVLEMKCIDIANTITN---DCFEIAGTLGIEAARN 1210
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1232 YIVNEIQDVYRLQGVKINDKHIETILRQM-----LRKVEVSDTGDSSFIKGDQvelthvleeneqlvgndrfvakyervl 1306
Cdd:PRK14977 1211 AIFNELASILEDQGLEVDNRYIMLVADIMcsrgtIEAIGLQAAGVRHGFAGEK--------------------------- 1263
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*.
gi 516237908 1307 lgitkaslstESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTG 1362
Cdd:PRK14977 1264 ----------DSPLAKAAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
909-1363 |
2.70e-80 |
|
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: 262.46 E-value: 2.70e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 909 VNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASrtsaadsvqvknggairlhnlkhveradgalvavsrsgelaiaddf 988
Cdd:cd02655 3 VELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT---------------------------------------------- 36
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 989 grereryklpygavisvkegdkvdagaivakwdphthpivtemdgtvafvgmeegitikrqtdeltgltnievldakdrp 1068
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1069 tsgkDIrpavklidangkdlllpgtdvpaqyflppnalvnlsdgakvhvgdviaripqetsktrdiTGGLPRVADLFEAR 1148
Cdd:cd02655 37 ----DI------------------------------------------------------------TQGLPRVEELFEAR 52
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1149 RPkepailaeisgtisfgketkgkrrlvitptdgtdpyeelipkwrhlnvfegeqvsrgevisdgpsNPHDILRL--LGV 1226
Cdd:cd02655 53 KI-----------------------------------------------------------------NPHDLLRIkfLGP 67
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1227 SALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKGDQVELTHVLEENEQLVGNDRFVAKYERVL 1306
Cdd:cd02655 68 EAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVL 147
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*..
gi 516237908 1307 LGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGL 1363
Cdd:cd02655 148 LGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1005-1368 |
1.57e-79 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 288.43 E-value: 1.57e-79
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1005 VKEGDKVDAGAIVAkwdphTHPIVTEMDGTVAfvGMEEG------ITIKRQTDELT-GLTNIEVLDAKDRPTSGKDIRPA 1077
Cdd:PRK02597 847 VKDGQQIKPGDVVA-----RTQILCKEAGEVR--GIRVGgeavrrLLVERDEDTITiPLSGKPTVKVGDLVVAGDELAPG 919
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1078 VKlIDANGKDLLLPGTDVPAQ----YFLPPNALVNLSDGAKVHVGDVIARIPQETSKTRDITGGLPRVADLFEARRPKEP 1153
Cdd:PRK02597 920 VP-APESGEVEAVSGGSVTLRlgrpYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKES 998
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1154 AILAEISGTISFGKETKGKRRLVITPTDGTDPYEELIPKwRHLNVFEGEQVSRGEVISDGPSNPHDILR----------- 1222
Cdd:PRK02597 999 CILAKKPGTVQIKYGDDESVDVKVIESDGTITEYPILPG-QNVMVSDGQQVDAGEPLTDGPINPHELLEiffedlrdrkg 1077
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1223 -----LLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKGDQVELTHVLEENEQLVGNDR 1297
Cdd:PRK02597 1078 lyeaaLEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGG 1157
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 516237908 1298 FVAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSE 1368
Cdd:PRK02597 1158 APAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEE 1228
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1005-1368 |
4.77e-76 |
|
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: 277.12 E-value: 4.77e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1005 VKEGDKVDAGAIVAKWDphthpIVTEMDGTVAfvGMEEG------ITIKRQTDELT-GLTNIEVLDAKDRPTSGKDIRPA 1077
Cdd:TIGR02388 845 VKDGDLIKPGAVIARTQ-----ILCKEAGVVQ--GIDSGgesirrLLVERNSDRLKvNIKAKPVVKTGDLVVAGDELAKG 917
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1078 VKLiDANGKDLLLPGTDVPAQ----YFLPPNALVNLSDGAKVHVGDVIARIPQETSKTRDITGGLPRVADLFEARRPKEP 1153
Cdd:TIGR02388 918 VKA-EESGEIEEVASDYVILRigrpYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARKPKEA 996
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1154 AILAEISGT--ISFGKETKGKRRLVITpTDGTDPYEELIPKwRHLNVFEGEQVSRGEVISDGPSNPHDILRLL------- 1224
Cdd:TIGR02388 997 CILAKRPGVvqVKYGTDDESVSIKVIE-RDGTISEYPLLPG-QNIMVSDGQQVTGGEPLTDGPINPHDILDVFfsyykdq 1074
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1225 ---------GVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKGDQVELTHVLEENEQLVGN 1295
Cdd:TIGR02388 1075 dglyeaaqeSLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAIT 1154
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516237908 1296 DRFVAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSE 1368
Cdd:TIGR02388 1155 GGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYEE 1227
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
18-809 |
2.88e-69 |
|
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: 248.99 E-value: 2.88e-69
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 18 DAIRIGLASPEMIRSWSFGEVKKPETINyRTFKPERDGLFCAKIfGPVKdyeclcgkykrlkhRGVICEKCGvevalakv 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 98 rrERM-------GHIELASPVAHIWFLkslpsriglllDMTLRDIERVlyfesyvvidpgmttlekyqllnDEQYFeale 170
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILRCV-----------------------CKREL---- 96
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 171 efgddfdarmGAEAVFQLLGAIDLEheigrlreeipqtnsETKIKKLSKRLKlmeafqgsgnKPEWMVMTVLPVLPPDLR 250
Cdd:cd02733 97 ----------SAERVLEIFKRISDE---------------DCRILGFDPKFS----------RPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 251 PLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSnKRPLKSLA 328
Cdd:cd02733 142 PSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQKS-GRPLKSIR 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 329 DMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMAL-----ELFKPFIFGKLE---ARGMATTIKAakKM 400
Cdd:cd02733 221 QRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLQelvRNGPNEYPGA--KY 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 401 VERE---------LPEVWDVLAE---VIREH-----PVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDG 463
Cdd:cd02733 299 IIRDdgeridlryLKKASDLHLQygyIVERHlqdgdVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDG 378
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 464 DQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPI--IVpsQDVVLGLYYMTREainakgegRVFADLQEV-------- 533
Cdd:cd02733 379 DEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTKR--------DTFLEKDQVmnllmwlp 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 534 -----------------------------DRVFRAGEAALHAKVKVRIN---ETIRHKDGSLTknTRIVD-TTVGRAllf 580
Cdd:cd02733 449 dwdgkipqpailkpkplwtgkqifsliipKINNLIRSSSHHDGDKKWISpgdTKVIIENGELL--SGILCkKTVGAS--- 523
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 581 qvvPAGLPYDVVNqSMKKKAISKLINHCYRVVGlkdtvifaDQLMYTGFaystlsgvSIGVNDfVIPDEK-----ARIID 655
Cdd:cd02733 524 ---SGGLIHVIWL-EYGPEAARDFIGNIQRVVN--------NWLLHNGF--------SIGIGD-TIADKEtmkkiQETIK 582
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 656 AATAEVKEIESQYASGLVTQGEKY-------NKVIDLWSKANDEVSKAMMTNLSKekvidregkevdqesFNSMYMMADS 728
Cdd:cd02733 583 KAKRDVIKLIEKAQNGELEPQPGKtlresfeNKVNRILNKARDKAGKSAQKSLSE---------------DNNFKAMVTA 647
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 729 GARGSAAQIRQLAG-----------------MRGL--MAKPDGSIIETP-ITANFREGLNVLQYFISTHGARKGLADTAL 788
Cdd:cd02733 648 GSKGSFINISQIIAcvgqqnvegkripfgfrRRTLphFIKDDYGPESRGfVENSYLRGLTPQEFFFHAMGGREGLIDTAV 727
|
890 900
....*....|....*....|.
gi 516237908 789 KTANSGYLTRRLVDVAQDLVV 809
Cdd:cd02733 728 KTAETGYIQRRLVKAMEDVMV 748
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
103-809 |
6.80e-63 |
|
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: 231.28 E-value: 6.80e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 103 GHIELASPVAHIWFLKSL----------PSRIglLLDmtlrDIERVLYFESyvVIDPGMTTLEKYQL---LNDEQ----- 164
Cdd:cd02583 61 GYIKLELPVFHIGYFKAIinilqcicktCSRV--LLP----EEEKRKFLKR--LRRPNLDNLQKKALkkkILEKCkkvrk 132
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 165 --YFEALEEFGDDFDARMgaeaVFQLLGAIDleheigrlREEIPqtnsetkikklskrLKLMEAFQGSgnkPEWMVMTVL 242
Cdd:cd02583 133 cpHCGLLKKAQEDLNPLK----VLNLFKNIP--------PEDVE--------------LLLMNPLAGR---PENLILTRI 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 243 PVLPPDLRPLVPLDGGrfATSDLNDL---YRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGS 319
Cdd:cd02583 184 PVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQ 261
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 320 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKP-------------------- 379
Cdd:cd02583 262 PKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPervtrynieklrklvlngpd 341
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 380 ------FIFGKLEarGMATTIKAAKKM-----------VERELpEVWDVlaevirehpVLLNRAPTLHRLGIQAFEPVLI 442
Cdd:cd02583 342 vhpganFVIKRDG--GKKKFLKYGNRRkiarelkigdiVERHL-EDGDI---------VLFNRQPSLHRLSIMAHRAKVM 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 443 EGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTREainakg 522
Cdd:cd02583 410 PWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTSK------ 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 523 egRVFADLQEVDRV---FRAGEAAL--------------------------HAKVKVRIN------------ETIRHKDG 561
Cdd:cd02583 484 --DVFFDRAQFCQLcsyMLDGEIKIdlpppailkpvelwtgkqifslllrpNKKSPVLVNleakeksytkksPDMCPNDG 561
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 562 SLT-KNTRIVDTTVGRALLfqvvpaGlpydvvnqSMKKKAISKLINHCY-----RVVGLKDTVIFADQLMYTGFaystls 635
Cdd:cd02583 562 YVViRNSELLCGRLDKSTL------G--------SGSKNSLFYVLLRDYgpeaaAAAMNRLAKLSSRWLSNRGF------ 621
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 636 gvSIGVNDfVIP-----DEKARIIDAATAEVKEIESQYASG-LVTQG---------EKYNKVIdlwSKANDEVSKAMMTN 700
Cdd:cd02583 622 --SIGIDD-VTPskellKKKEELVDNGYAKCDEYIKQYKKGkLELQPgctaeqtleAKISGEL---SKIREDAGKACLKE 695
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 701 LSKekvidregkevdqesFNSMYMMADSGARGSAAQIRQ---------LAGMRglmaKPDGSI----------IETPIT- 760
Cdd:cd02583 696 LHK---------------SNSPLIMALCGSKGSNINISQmiacvgqqiISGKR----IPNGFEdrtlphfprnSKTPAAk 756
|
810 820 830 840 850
....*....|....*....|....*....|....*....|....*....|...
gi 516237908 761 ---AN-FREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVV 809
Cdd:cd02583 757 gfvANsFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSV 809
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1110-1373 |
5.20e-61 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 230.21 E-value: 5.20e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1110 SDGAKVHV--------GDVIARIPQETSKTRDITGGLPRVADLFEARrPKEPailaeISGTIsfgketkgkrrlvitptd 1181
Cdd:CHL00117 1099 TPGATVHGhygeilyeGDTLVTLIYEKSRSGDITQGLPKVEQLLEAR-SIDS-----ISMNL------------------ 1154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1182 gtdpyEELIPKWrhlnvfegeqvsrgevisdgpsnPHDILRLLGV------SA---LAK---YIVNEIQDVYRLQGVKIN 1249
Cdd:CHL00117 1155 -----EKRLEGW-----------------------NERITRILGIpwgfliGAelsIAQsqiSLVNKIQKVYRSQGVQIS 1206
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1250 DKHIETILRQMLRKVEVSDTGDSS-FIKGDQVELTH------VLEEneqlvgndrfVAKYERVLLGITKASLSTESFISA 1322
Cdd:CHL00117 1207 DKHIEIIVRQMTSKVLVSEDGMSNvFLPGELIGLLRaerinrALEE----------AICYRPILLGITKASLNTQSFISE 1276
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|.
gi 516237908 1323 ASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGLAYHSERKRQR 1373
Cdd:CHL00117 1277 ASFQETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSKQH 1327
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
344-485 |
6.26e-47 |
|
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: 165.55 E-value: 6.26e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 344 GKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIF--------------GKLEA---------RGMATTIKAAKKM 400
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVtpynikrlrqlvenGPNVYpganyiiriNGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 401 VERELPEVWDVLAEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA 480
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 516237908 481 RALMM 485
Cdd:pfam00623 161 EELML 165
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
210-801 |
1.69e-40 |
|
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: 161.97 E-value: 1.69e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 210 SETKIKKLSKRLKL-----MEAFQGSGNKPEWMVMTVLPVLPPDLRPLVPLDGGRFaTSDLNDLYRRVINRNNRLKRLLD 284
Cdd:cd01435 98 SKWEVKLFVAKLKLldkglLVEAAELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLA 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 285 LAAPDIIVRNEKRM---------------LQEAVDALLDNGrrgraitgSNKRPLKSLADMIKG----KQGRFRQNLLGK 345
Cdd:cd01435 177 SMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDST--------KAPKSGKKSPPGIKQllekKEGLFRMNMMGK 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 346 RVDYSGRSVITVGPTLRLHQCGLPKKMAL--------------ELFKPFIFGK---------LEARGMaTTIKAAKKMVE 402
Cdd:cd01435 249 RVNYAARSVISPDPFIETNEIGIPLVFAKkltfpepvtpfnveELRQAVINGPdvypganaiEDEDGR-LILLSALSEER 327
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 403 RELPEVWDVLAEVIREHP---------------VLLNRAPTLHRLGIQA-FEPVLIEGKAIQLHPLVCAAYNADFDGDQM 466
Cdd:cd01435 328 RKALAKLLLLLSSAKLLLngpkkvyrhlldgdvVLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNADFDGDEM 407
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 467 AVHVPLTLEAQLEARALMMSTNNILSPANGEPI---IvpsQDVVLGLYYMTReainakgEGRVF--ADLQEVdrVFRAGE 541
Cdd:cd01435 408 NLHFPQSELARAEAYYIASTDNQYLVPTDGKPLrglI---QDHVVSGVLLTS-------RDTFFtrEEYQQL--VYAALR 475
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 542 AALHAKVKVRIN-------------------ETIRHkdgSLTKNTRIVDTTVGRALLFQVVPAGLPYDVVNQSM------ 596
Cdd:cd01435 476 PLFTSDKDGRIKllppailkpkplwtgkqviSTILK---NLIPGNAPLLNLSGKKKTKKKVGGGKWGGGSEESQviirng 552
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 597 -------KKKAISK----LINHCYRVVGLKDtvifADQLMyTGFA-----YSTLSGVSIGVNDFVIPD--EKAR--IIDA 656
Cdd:cd01435 553 elltgvlDKSQFGAsaygLVHAVYELYGGET----AGKLL-SALGrlftaYLQMRGFTCGIEDLLLTPkaDEKRrkILRK 627
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 657 ATAEVKEIESQYAsglvtqGEKYNKVidlwskANDEVSKAMMTNLSKekvidregkevdqeSF--NSMYMMADSGARGS- 733
Cdd:cd01435 628 AKKLGLEAAAEFL------GLKLNKV------TSSIIKACLPKGLLK--------------PFpeNNLQLMVQSGAKGSm 681
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 734 --AAQI------RQLAGMR-GLMA--------KP-DGSiietP-----ITANFREGLNVLQYFISTHGARKGLADTALKT 790
Cdd:cd01435 682 vnASQIscllgqQELEGRRvPLMVsgktlpsfPPyDTS----PraggfITDRFLTGIRPQEYFFHCMAGREGLIDTAVKT 757
|
730
....*....|.
gi 516237908 791 ANSGYLTRRLV 801
Cdd:cd01435 758 SRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
489-643 |
6.12e-37 |
|
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 136.60 E-value: 6.12e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 489 NILSPANGEPIIVPSQDVVLGLYYMTREainakgegRVFADLQEVDRVFRAGEAALHAKVKVRINEtirhkdgsltknTR 568
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRE--------DTFFDREEVMQLLMYGIVLPHPAILKPIKP------------LW 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 569 IVDTTVGRALLFQVVPAGLPYD------------VVNQSMKK----------KAISKLINHCYRVVGLKDTVIFADQLMY 626
Cdd:pfam04983 61 TGKQTFSRLLPNEINPKGKPKTneedlcendsyvLINNGELIsgvidkktvgKSLGSLIHIIYKEYGPEETAKFLDRLQK 140
|
170
....*....|....*..
gi 516237908 627 TGFAYSTLSGVSIGVND 643
Cdd:pfam04983 141 LGFRYLTKSGFSIGIDD 157
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
673-764 |
1.61e-25 |
|
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: 102.44 E-value: 1.61e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 673 VTQGEKYNKVIDLWSKANDEVSKAMMTNLsKEKVIDREGK--EVDQESFNSMYMMADSGARGSAAQIRQLAGMRGLMAKP 750
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNI-LNKARDPAGNiaSKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
90 100
....*....|....*....|....*....
gi 516237908 751 DGSI---------------IETPITANFR 764
Cdd:pfam05000 80 GKRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1215-1363 |
1.48e-24 |
|
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: 101.34 E-value: 1.48e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1215 SNPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGDSSFIKgdqvelthvleeneqlvg 1294
Cdd:cd00630 48 ASIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGGLRGVTRSGFRA------------------ 109
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 516237908 1295 ndrfvakyervllgitkaslSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGL 1363
Cdd:cd00630 110 --------------------SKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
338-516 |
2.37e-18 |
|
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: 91.31 E-value: 2.37e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 338 FRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKP--------------FIFGKLEARGM----ATTIKAAKK 399
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVServsswnrerlqeyCDLTLLLKGVIgvrrNGRLVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 400 MVERElpeVWDVLAEVIRE-HPVLLNRAPTLHRLGIQAFE-PVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQ 477
Cdd:cd10506 286 HNTLQ---IGDVIHRPLVDgDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQAR 362
|
170 180 190
....*....|....*....|....*....|....*....
gi 516237908 478 LEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRE 516
Cdd:cd10506 363 AELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTER 401
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1231-1370 |
2.99e-17 |
|
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: 87.91 E-value: 2.99e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1231 KYIVNEI--QDVYRLQGVkINDKHIETILRQMLRKVEVSDT------------------GDSSFIKGDQV---ELTHVLE 1287
Cdd:COG0086 559 RYLVNEIlpQEVPFYNQV-INKKHIEVIIRQMYRRCGLKETvifldrlkklgfkyatraGISIGLDDMVVpkeKQEIFEE 637
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1288 ENEQLVG-----NDRFV---AKYERVLLGITKASLSTESFISAA-SFQETTRVLTEAAVTGKRDFL------RGLKEN-- 1350
Cdd:COG0086 638 ANKEVKEiekqyAEGLItepERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLrqlagmRGLMAKps 717
|
170 180 190
....*....|....*....|....*....|
gi 516237908 1351 -----VVVGRLIPAGTGLAY-----HSERK 1370
Cdd:COG0086 718 gniieTPIGSNFREGLGVLEyfistHGARK 747
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
912-1362 |
5.16e-16 |
|
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: 81.64 E-value: 5.16e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 912 GEAVGVIAAQSIGEPGTQLTMRTFHIGGAAsrtsaadSVQVKNgGAIRLhnlkhVERADGALVAVSRSGELAIADDFGRE 991
Cdd:TIGR02389 44 GEAVGIVAAQSIGEPGTQMTMRTFHYAGVA-------ELNVTL-GLPRL-----IEIVDARKTPSTPSMTIYLEDEYEKD 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 992 RERYKlpygAVISVKEGDKVDAgaiVAKwdphthpivtemDGTVAFVGMEEGITIKRQTDELTGLTNIEVLDAKDRPTSG 1071
Cdd:TIGR02389 111 REKAE----EVAKKIEATKLED---VAK------------DISIDLADMTVIIELDEEQLKERGITVDDVEKAIKKAKLG 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1072 KDIRPAVKlidaNGKDLLLPGTDVPAQYFLppnaLVNlsdgakvhvgdviaripqetsKTRDITgglprvadlfearrpk 1151
Cdd:TIGR02389 172 KVIEIDMD----NNTITIKPGNPSLKELRK----LKE---------------------KIKNLH---------------- 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1152 epailaeISGtisfgkeTKGKRRLVITPTDgtdpyEELIPKWRHLN---VFEGEQVSRGEVISDgpsNPHDILRLLGVSA 1228
Cdd:TIGR02389 207 -------IKG-------IKGIKRVVIRKEG-----DEYVIYTEGSNlkeVLKLEGVDKTRTTTN---DIHEIAEVLGIEA 264
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1229 LAKYIVNEIQDVYRLQGVKINDKHIetilrqMLrkveVSDtgdssfikgdqvelthvleeneqlvgndrfVAKYERVLLG 1308
Cdd:TIGR02389 265 ARNAIIEEIKRTLEEQGLDVDIRHL------ML----VAD------------------------------LMTWDGEVRQ 304
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 516237908 1309 ITKASLSTE--SFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTG 1362
Cdd:TIGR02389 305 IGRHGISGEkaSVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTG 360
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
908-1362 |
1.92e-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: 76.52 E-value: 1.92e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 908 QVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRtsaadSVQVkngGAIRLhnlkhVERADGALVAVSRSGELAIADD 987
Cdd:cd06528 36 LIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEI-----NVTL---GLPRL-----IEIVDARKEPSTPTMTIYLEEE 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 988 FGRERERyklpygAVISVKEGDKVDAGAIVAK--WDPHTHPIVTEMDGTVafvgMEE-GITIKrqtdeltgltniEVLDA 1064
Cdd:cd06528 103 YKYDREK------AEEVARKIEETTLENLAEDisIDLFNMRITIELDEEM----LEDrGITVD------------DVLKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1065 KDRPTSGkdirpavKLIDANGKDLLLPGTDVPaqyflPPNALVNLSDgakvhvgdviaripqetsKTRDITgglprvadl 1144
Cdd:cd06528 161 IEKLKKG-------KVGEEGDVTLIVLKAEEP-----SIKELRKLAE------------------KILNTK--------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1145 fearrpkepailaeISGtisfgkeTKGKRRLVITPTDGtdpyeELIPKWRHLN---VFEGEQVSRGEVISDgpsNPHDIL 1221
Cdd:cd06528 202 --------------IKG-------IKGIKRVIVRKEED-----EYVIYTEGSNlkaVLKVEGVDPTRTTTN---NIHEIE 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1222 RLLGVSALAKYIVNEIQDVYRLQGVKINDKHIetilrqMLrkveVSDtgdssfikgdqvelthvleeneqlvgndrfVAK 1301
Cdd:cd06528 253 EVLGIEAARNAIINEIKRTLEEQGLDVDIRHI------ML----VAD------------------------------IMT 292
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 516237908 1302 YERVLLGITKASLSTE--SFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTG 1362
Cdd:cd06528 293 YDGEVRQIGRHGIAGEkpSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
912-941 |
2.49e-11 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 67.18 E-value: 2.49e-11
10 20 30
....*....|....*....|....*....|
gi 516237908 912 GEAVGVIAAQSIGEPGTQLTMRTFHIGGAA 941
Cdd:PRK04309 59 GEAVGVVAAQSIGEPGTQMTMRTFHYAGVA 88
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
912-943 |
2.98e-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: 63.21 E-value: 2.98e-11
10 20 30
....*....|....*....|....*....|..
gi 516237908 912 GEAVGVIAAQSIGEPGTQLTMRTFHIGGAASR 943
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASM 32
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
909-1373 |
6.95e-11 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 66.37 E-value: 6.95e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 909 VNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRTSAAdsvqvkngGAIRLhnlkhVERADGALVAVSRSGELAIADDF 988
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTL--------GLPRL-----IEIVDARKKPSTPTMTIYLKKDY 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 989 GRERERyklpygavisVKEgdkvdagaiVAKwdphthpivtemdgtvafvgmeegitikrqtdeltGLTNIEVLDAKDRP 1068
Cdd:PRK14897 246 REDEEK----------VRE---------VAK-----------------------------------KIENTTLIDVADII 271
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1069 TSGKDIRPAVKLIDANGKDlllpgtdvpaqyflppnalvnlsdgAKVHVGDVIARIPQETSKTRDITGGLPRVadlfear 1148
Cdd:PRK14897 272 TDIAEMSVVVELDEEKMKE-------------------------RLIEYDDILAAISKLTFKTVEIDDGIIRL------- 319
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1149 RPKEPAI-----LAE------ISGTISFGK---ETKGKRRLVITPTDGTDPYEelipkwrhlnVFEGEQVSRGEVISDgp 1214
Cdd:PRK14897 320 KPQQPSFkklylLAEkvksltIKGIKGIKRaiaRKENDERRWVIYTQGSNLKD----------VLEIDEVDPTRTYTN-- 387
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1215 sNPHDILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIetilrqMLrkveVSDTGDSSfikgdqvelthvleeneqlvG 1294
Cdd:PRK14897 388 -DIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHI------ML----VADMMTFD--------------------G 436
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1295 NDRFVAKYervllGItkaSLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTG---LAYhSERKR 1371
Cdd:PRK14897 437 SVKAIGRH-----GI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGavsLVY-KGRKK 507
|
..
gi 516237908 1372 QR 1373
Cdd:PRK14897 508 VK 509
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
912-942 |
2.47e-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: 63.39 E-value: 2.47e-10
10 20 30
....*....|....*....|....*....|.
gi 516237908 912 GEAVGVIAAQSIGEPGTQLTMRTFHIGGAAS 942
Cdd:cd02736 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVAS 40
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
909-939 |
3.77e-09 |
|
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: 59.90 E-value: 3.77e-09
10 20 30
....*....|....*....|....*....|.
gi 516237908 909 VNIGEAVGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
908-944 |
5.07e-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: 60.30 E-value: 5.07e-09
10 20 30
....*....|....*....|....*....|....*..
gi 516237908 908 QVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRT 944
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKN 59
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1219-1363 |
1.05e-08 |
|
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: 58.38 E-value: 1.05e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1219 DILRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIetilrqMLrkvevsdTGDSSFIKGDqvelthvleeneqLVGNDRF 1298
Cdd:cd02736 193 EVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHI------ML-------LADLMTFKGE-------------VLGITRF 246
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 516237908 1299 vakyervllGITKASlstESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTGL 1363
Cdd:cd02736 247 ---------GIAKMK---ESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTGL 299
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1149-1362 |
4.44e-06 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 51.43 E-value: 4.44e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1149 RPKEPAI-----LAEISGTISFgKETKGKRRLVITpTDGTDPYEELIPKWRHLN---VFEGEQVSRGEVISDgpsNPHDI 1220
Cdd:PRK14898 664 KPKTPSYkalrkRIPKIKNIVL-KGIPGIERVLVK-KEEHENDEEYVLYTQGSNlreVFKIEGVDTSRTTTN---NIIEI 738
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 1221 LRLLGVSALAKYIVNEIQDVYRLQGVKINDKHIETILRQMLRKVEVSDTGdssfikgdqvelTHvleeneqlvgndrfva 1300
Cdd:PRK14898 739 QEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIMTADGEVKPIG------------RH---------------- 790
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 516237908 1301 kyervllGItkaSLSTESFISAASFQETTRVLTEAAVTGKRDFLRGLKENVVVGRLIPAGTG 1362
Cdd:PRK14898 791 -------GV---AGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
913-1100 |
8.45e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.73 E-value: 8.45e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 913 EAVGVIAAQSIGEPGTQLTMrtfhiggaasrtSAADSVQVKNGGAIRLHNLkhveradGALVAvsrsgelAIADDFGRER 992
Cdd:PRK14898 58 EAVGIVAAQSIGEPGTQMSL------------PYDEKIIVKEGGETRVTEI-------GKLVD-------ELIDKFGFEK 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 516237908 993 ----ERYKLPYGA-VISVKEGDKVDagaivakWDPHTHPIVTEMDGTVAFVGMEEGITIkRQTDELTGLTNievLDAKDR 1067
Cdd:PRK14898 112 igghEVCDLPIEIyALSLDQDEKVH-------WKRIISVIRHKANGKLIKIKTESGRTI-RATPYHSFVTR---KDNEVI 180
|
170 180 190
....*....|....*....|....*....|....*...
gi 516237908 1068 PTSGKDIR-----PAVKLIDANGKDLLLPGTDVPAQYF 1100
Cdd:PRK14898 181 PVEGSELKigdwlPVVRSLPANCQEAIDLREYLPASDY 218
|
|
| |
