|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
21-1376 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2427.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 21 EFDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEKCGVEVTTA 100
Cdd:PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 101 KVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKYQLLTDEEYYNALEEHGDE 180
Cdd:PRK00566 86 KVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGDE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 181 FTAKMGAEAVQDLLKDIDLEAEIARLREEIPQTTSETKLKKASKRLKLMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPL 260
Cdd:PRK00566 166 FVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 261 EGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ 340
Cdd:PRK00566 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQ 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 341 GRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKKMVERETPEVWDVLASV 420
Cdd:PRK00566 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEV 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 421 IRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN 500
Cdd:PRK00566 406 IKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 501 GEPIIVPSQDVVLGLYYITRDAVNAKGEGMVFADTHEVNRALATGKVAIHARVKVRVHqtvidengereqQTIIVDTTPG 580
Cdd:PRK00566 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRIT------------SKKLVETTVG 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 581 RCLLWEVVPQGLSFDMINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIID 660
Cdd:PRK00566 554 RVIFNEILPEGLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 661 KAETEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMDNLsytlvknkqgeDEKQKSFNSIYMMSDSGARGSAA 740
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNL-----------SKDQESFNPIYMMADSGARGSAS 702
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 741 QIRQLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCG 820
Cdd:PRK00566 703 QIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCG 782
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 821 TAGGLVMTPFIQGGDVIEPLRDRVLGRVTAEDVRRASDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTFGVC 900
Cdd:PRK00566 783 TDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVC 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 901 ARCYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAasrtsaansvqvrnkgtvrfhnvktvqhakghlvs 980
Cdd:PRK00566 863 AKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV----------------------------------- 907
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 981 vsrsgeigiaddlgrereryklpygasilikdgesveaggivatwdphthplvtevagkarfsqiadgvtatsktddatg 1060
Cdd:PRK00566 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1061 mttveilpvtarpasgkdlrpaivldttdggeqfyflpqntivtvrdgetigvgdvigrvpqetsrtrDITGGLPRVADL 1140
Cdd:PRK00566 908 --------------------------------------------------------------------DITGGLPRVAEL 919
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1141 FEARKPKEHAILAEVSGVVSFGKETKGKNRLVITPDDGsEIYEELIPKWRQINVFEGEHVNRGETISDGPQNPHDILRLK 1220
Cdd:PRK00566 920 FEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDG-EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHDILRVL 998
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1221 GEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQENQAVLAQNKFPAKFER 1300
Cdd:PRK00566 999 GVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGRP 1078
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 480084187 1301 QLMGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGLAYHLERRRQEAEAAEFE 1376
Cdd:PRK00566 1079 VLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDEEEA 1154
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
21-1195 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 1912.21 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 21 EFDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEKCGVEVTTA 100
Cdd:COG0086 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVTLS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 101 KVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKYQLLTDEEYYNALEEHGDE 180
Cdd:COG0086 86 KVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYGDE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 181 FTAKMGAEAVQDLLKDIDLEAEIARLREEIPQTTSETKLKKASKRLKLMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPL 260
Cdd:COG0086 166 FVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLVPL 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 261 EGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ 340
Cdd:COG0086 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKGKQ 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 341 GRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKKMVERETPEVWDVLASV 420
Cdd:COG0086 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILEEV 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 421 IRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN 500
Cdd:COG0086 406 IKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSPAN 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 501 GEPIIVPSQDVVLGLYYITRDAVNAKGEGMVFADTHEVNRALATGKVAIHARVKVRvhqtvIDENGEREQQtiIVDTTPG 580
Cdd:COG0086 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVR-----ITEDGEQVGK--IVETTVG 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 581 RCLLWEVVPQGLSFdmINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIID 660
Cdd:COG0086 559 RYLVNEILPQEVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFE 636
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 661 KAETEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMDNLSytlvknkqgedekqkSFNSIYMMSDSGARGSAA 740
Cdd:COG0086 637 EANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS---------------SQNTTYMMADSGARGSAD 701
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 741 QIRQLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCG 820
Cdd:COG0086 702 QLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCG 781
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 821 TAGGLVMTPFIQGGDVIEPLRDRVLGRVTAEDVRRASDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTFGVC 900
Cdd:COG0086 782 TDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVC 861
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 901 ARCYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASRTSAANSVQVRNKGTVRFHNVKTVQHAKGHLVS 980
Cdd:COG0086 862 AKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVV 941
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 981 VSRSGEIGIADDLGRERERYKLPYGASILIKDGESVEAGGIVATWDPHTHPLVTEVAGKARFSQIADGVTATSKTDDATG 1060
Cdd:COG0086 942 VSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETG 1021
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1061 MTTVEILPVTARPASGKDLRPAIVLDTTDGGEQ---------FYFLPQNTIVTVRDGETIGVGDVIGRVPQETSRTRDIT 1131
Cdd:COG0086 1022 GLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLllggtdaaaAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDGT 1101
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 480084187 1132 GGLPRVADLFEARKPKEHAILAEVSGVVSFGKETKGKNRLVITPDDGSEIYEELIPKWRQINVF 1195
Cdd:COG0086 1102 GGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
24-1362 |
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: 1836.99 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 24 RIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEKCGVEVTTAKVR 103
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 104 RERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKYQLLTDEEYYNALEEHGDEFTA 183
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 184 KMGAEAVQDLLKDIDLEAEIARLREEIPQTTSETKLKKASKRLKLMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPLEGG 263
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 264 RFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRF 343
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 344 RQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKKMVERETPEVWDVLASVIRQ 423
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 424 HPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEP 503
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 504 IIVPSQDVVLGLYYITRDAVNAKGEGMVFADTHEVNRALATGKVAIHARVKVRVHqtvidenGEreqqtiIVDTTPGRCL 583
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTS-------GE------ILETTVGRVI 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 584 LWEVVPQGLSFDMINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIIDKAE 663
Cdd:TIGR02386 548 FNEILPEGFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEAD 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 664 TEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMDNLSytlvknkqgedEKQKSFNSIYMMSDSGARGSAAQIR 743
Cdd:TIGR02386 628 KEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLK-----------KDTYKFNPIFMMADSGARGNISQFR 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 744 QLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCGTAG 823
Cdd:TIGR02386 697 QLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEE 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 824 GLVMTPFIQGGD-VIEPLRDRVLGRVTAEDVRRASDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTFGVCAR 902
Cdd:TIGR02386 777 GIEVEAIVEGKDeIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQK 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 903 CYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASRTSaansvqvrnkgtvrfhnvktvqhakghlvsvs 982
Cdd:TIGR02386 857 CYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASG-------------------------------- 904
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 983 rsgeigiaddlgrereryklpygasilikdgesveaggivatwdphthplvtevagkarfsqiadgvtatsktddatgmt 1062
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1063 tveilpvtarpasgkdlrpaivldttdggeqfyflpqntivtvrdgetigvgdvigrvpqetsrtrDITGGLPRVADLFE 1142
Cdd:TIGR02386 905 ------------------------------------------------------------------DITQGLPRVKELFE 918
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1143 ARKPKEHAILAEVSGVVSFGKETKGKNRLVITPDDGSEIYEELIPKWRQINVFEGEHVNRGETISDGPQNPHDILRLKGE 1222
Cdd:TIGR02386 919 ARTPKDKAVIAEVDGTVEIIEDIVKNKRVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIKGI 998
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1223 VALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQENQAVLAQNKFPAKFERQL 1302
Cdd:TIGR02386 999 QAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIPQL 1078
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1303 MGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGLAYH 1362
Cdd:TIGR02386 1079 LGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTY 1138
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1371 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1589.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 15 EGHAPVEFDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGV-ICEKC 93
Cdd:PRK09603 1389 EDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCEKC 1468
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 94 GVEVTTAKVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPG--------MTPFEKYQLL 165
Cdd:PRK09603 1469 GVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGeaaydnegTKLVMKYDIL 1548
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 166 TDEEYYNALEEHGDE-FTAKMGAEAVQDLLKDIDLEAEIARLREEIPQTTSETKLKKASKRLKLMEAFKDSNNKPEWMVM 244
Cdd:PRK09603 1549 NEEQYQNISRRYEDRgFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWMML 1628
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 245 NVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGS 324
Cdd:PRK09603 1629 TVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVKGA 1708
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 325 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKK 404
Cdd:PRK09603 1709 NKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQAKR 1788
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 405 MVERETPEVWDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLE 484
Cdd:PRK09603 1789 MIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAIAE 1868
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 485 ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYITRDAVNAKGEGMVFADTHEVNRALATGKVAIHARVKvrvhqTVIDE 564
Cdd:PRK09603 1869 CKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIR-----VLDQG 1943
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 565 NgereqqtiIVDTTPGRCLLWEVVPQGLSFDMINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSV 644
Cdd:PRK09603 1944 N--------IIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISI 2015
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 645 GMEDMLIPPTKQVIIDKAETEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMdnlsyTLVKNKQGedekqkSF 724
Cdd:PRK09603 2016 SMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMM-----TAIAKDKE------GF 2084
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 725 NSIYMMSDSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRR 804
Cdd:PRK09603 2085 NSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRK 2164
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 805 LVDVAQDLVITEPDCGTAGGLVMTPFIQGGDVIEPLRDRVLGRVTAEDVRRASDDEVVLPRGTLIDEKIAAQLEEAGVDE 884
Cdd:PRK09603 2165 LIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKS 2244
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 885 VKVRSVIACESTFGVCARCYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASRTSAANSVQVRNKGTVR 964
Cdd:PRK09603 2245 ITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGFVR 2324
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 965 FHNVKTVQHAKGHLVSVSR----------------SGEIG---------------------------------------- 988
Cdd:PRK09603 2325 FYNLRTYTNKEGKNIIANRrnasilvvepkikapfDGELRietvyeevvvsvkngdqeakfvlrrsdivkpselagvggk 2404
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 --------------------------------------------------------------------------------
Cdd:PRK09603 2405 iegkvylpyasghkvhkggsiadiiqegwnvpnripyasellvkdndpiaqdvyakekgiikyyvleanhlerthgikkg 2484
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 989 -----------IADDLGRERERYKLPYGASILIKDGESVEAGG-----------IVATWDPHTHPLVTEVAGKARFSQIA 1046
Cdd:PRK09603 2485 divsekglfavIADDNGREAARHYIARGSEILIDDNSEVSANSviskpttntfkTIATWDPYNTPIIADFKGKVSFVDII 2564
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1047 DGVTATSKTDDATGMTTV---EILPVTarpasgkdLRPAIVLDTTDGGEQFYFLPQNTIVTVRDGETIGVGDVIGRVPQE 1123
Cdd:PRK09603 2565 AGVTVAEKEDENTGITSLvvnDYIPSG--------YKPSLFLEGANGEEIRYFLEPKTSIAISDGSSVEQAEVLAKIPKA 2636
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1124 TSRTRDITGGLPRVADLFEAR--KPKEHAILAEVSGVVSFGKETKGKNRLVITPDDGSEIyEELIPKWRQINVFEGEHVN 1201
Cdd:PRK09603 2637 TVKSRDITGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSM-DYFVDKGKQILVHADEFVH 2715
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1202 RGETISDGPQNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRV 1281
Cdd:PRK09603 2716 AGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKLF 2795
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1282 VQENQAVLAQNKFPAKFERQLMGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGL-- 1359
Cdd:PRK09603 2796 KEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTGMyk 2875
|
1530
....*....|....
gi 480084187 1360 --AYHLERRRQEAE 1371
Cdd:PRK09603 2876 nkKIVLRTLEDDPK 2889
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
22-1359 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1547.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 22 FDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEKCGVEVTTAK 101
Cdd:PRK14844 1448 FNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTSSK 1527
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 102 VRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKYQLLTDEEYYNALEEHG-DE 180
Cdd:PRK14844 1528 VRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGiDS 1607
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 181 FTAKMGAEAVQDLLKDIDLEAEIARLREEIPQTTSETKLKKASKRLKLMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPL 260
Cdd:PRK14844 1608 FVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLVSL 1687
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 261 EGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLK-SLADMIKGK 339
Cdd:PRK14844 1688 ESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLKGK 1767
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 340 QGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKKMVERETPEVWDVLAS 419
Cdd:PRK14844 1768 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDMLEE 1847
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 420 VIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 499
Cdd:PRK14844 1848 VIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLSPS 1927
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 500 NGEPIIVPSQDVVLGLYYITRDAVNaKGEGMVFADTHEVNRALATGKVAIHARVKVRVHQtvIDENGEREQQTIIvdTTP 579
Cdd:PRK14844 1928 NGRPIIVPSKDIVLGIYYLTLQEPK-EDDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEY--INSSGETHYKTIC--TTP 2002
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 580 GRCLLWEVVP--QGLSFDMINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQV 657
Cdd:PRK14844 2003 GRLILWQIFPkhENLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKAT 2082
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 658 IIDKAETEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMDNLSYTlvknkqgeDEKQKsFNSIYMMSDSGARG 737
Cdd:PRK14844 2083 HVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIY--------DGNSK-YNSVYMMVNSGARG 2153
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 738 SAAQIRQLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEP 817
Cdd:PRK14844 2154 STSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTKH 2233
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 818 DCGTAGGLVMTPFIQGGDVIEPLRDRVLGRVTAEDVRRASDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTF 897
Cdd:PRK14844 2234 DCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEISP 2313
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 898 GVCARCYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASRTSAANSVQVRNKGTVRFHNVKTVQHAKGH 977
Cdd:PRK14844 2314 GVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNGN 2393
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 978 LVSVSRSGEIGIADDLGRERERYKLPYGASILIKDGESVEAGGIVATWDPHTHPLVTEVAGKARFSQIADGVTATSKTDD 1057
Cdd:PRK14844 2394 KIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEVMDE 2473
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1058 ATGMTTvEILPVTARPASGKDLRPAIVL--------DTTDGGEQFYFLPQNTIVTVRDGETIGVGDVIGRVPQETSRTRD 1129
Cdd:PRK14844 2474 STGISS-KVVKDWKLYSGGANLRPRIVLlddngkvmTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESVKTRD 2552
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1130 ITGGLPRVADLFEARKPKEHAILAEVSGVVSFG-KETKGKNRLVITP-DDGSEIYEELIPKWRQINVFEGEHVNRGETIS 1207
Cdd:PRK14844 2553 ITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPvDEQISPVEYLVSRSKHVIVNEGDFVRKGDLLM 2632
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1208 DGPQNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQENQA 1287
Cdd:PRK14844 2633 DGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRENDA 2712
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 480084187 1288 VLAQNKFPAKFERQLMGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGL 1359
Cdd:PRK14844 2713 MSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGL 2784
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
21-818 |
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: 1323.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 21 EFDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEKCGVEVTTA 100
Cdd:cd01609 2 DFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRS 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 101 KVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFesyvvtdpgmtpfekyqlltdeeyynaleehgde 180
Cdd:cd01609 82 KVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF---------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 181 ftakmgaeavqdllkdidleaeiarlreeipqttsetklkkaskrlkLMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPL 260
Cdd:cd01609 128 -----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQL 160
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 261 EGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ 340
Cdd:cd01609 161 DGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQ 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 341 GRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKKMVERETPEVWDVLASV 420
Cdd:cd01609 241 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEV 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 421 IRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN 500
Cdd:cd01609 321 IKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAS 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 501 GEPIIVPSQDVVLGLYYITRDAVNAKGEGmvfadthevnralatgkvaiharvkvrvhqtvidengereqqtiIVDTTPG 580
Cdd:cd01609 401 GKPIVTPSQDMVLGLYYLTKERKGDKGEG--------------------------------------------IIETTVG 436
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 581 RCLLWEVVPQGLSFdmINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIID 660
Cdd:cd01609 437 RVIFNEILPEGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIK 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 661 KAETEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMDNLsytlvknkqgedeKQKSFNSIYMMSDSGARGSAA 740
Cdd:cd01609 515 EAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNL-------------DKDPFNPIYMMADSGARGSKS 581
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 480084187 741 QIRQLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPD 818
Cdd:cd01609 582 QIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
21-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1306.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 21 EFDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEKCGVEVTTA 100
Cdd:PRK14906 8 NFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVTRA 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 101 KVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVT---------------------------- 152
Cdd:PRK14906 88 KVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIITsvdkeareedaddlrdelaadleeldae 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 153 ----------------------------DPGMTP------------------------FEKY------QLLTDEEYYNAL 174
Cdd:PRK14906 168 rdrlieatrrlsvdyvpeddefvddigdDERLTAeevraevadiyeeynerkalrreaFDAFmqiepkQLISDEALYREM 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 175 E-EHGDEFTAKMGAEAVQDLLKDIDLEAEIARLREeIPQTTSETKLKKASKRLKLMEAFKDSNNKPEWMVMNVLPVLPPD 253
Cdd:PRK14906 248 RlNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRA-IIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIPPD 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 254 LRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLA 333
Cdd:PRK14906 327 LRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKSLA 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 334 DMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKKMVERETPEV 413
Cdd:PRK14906 407 DMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGASYV 486
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 414 WDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTN 493
Cdd:PRK14906 487 WDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLSSN 566
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 494 NILSPANGEPIIVPSQDVVLGLYYITRDAVNAKGEGMVFADTHEVNRAL-ATGKVAIHARVKVRVHQ--TVIDENGERE- 569
Cdd:PRK14906 567 NIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYdARADLDLQAKIVVRLSRdmTVRGSYGDLEe 646
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 570 -QQTIIVDTTPGRCLLWEVVPQGLSFdmINLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMED 648
Cdd:PRK14906 647 tKAGERIETTVGRIIFNQVLPEDYPY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSVYD 724
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 649 MLIPPTKQVIIDKAETEVREIEQQFEQGFVTAGERYNKVVDIWARTNDQVAKAMMDNLSytlvknkqgedekqkSFNSIY 728
Cdd:PRK14906 725 ATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFD---------------EDNPIY 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 729 MMSDSGARGSAAQIRQLAGMRGLMAKPDGSIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV 808
Cdd:PRK14906 790 MMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLVDV 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 809 AQDLVITEPDCGTAGGLVMTPFIQGGDVIEPLrdrvLGRVTAEDVRRAsDDEVVLPRGTLIDEKIA-AQLEEAGVDEVKV 887
Cdd:PRK14906 870 AQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDP-NGEVLLSAGDYIESMDDlKRLVEAGVTKVQI 944
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 888 RSVIACESTFGVCARCYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAAsrtsaansvqvrnkgtvrfhn 967
Cdd:PRK14906 945 RTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA--------------------- 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 968 vktvqhakghlvsvsrsgeigiaddlgrereryklpygasilikdgesveaggivatwdphthplvtevagkarfsqiad 1047
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1048 gvtatsktddatgmttveilpvtarpasgkdlrpaivldttdggeqfyflpqntivtvrdgetigvGDvigrvpqetsrt 1127
Cdd:PRK14906 1004 ------------------------------------------------------------------GD------------ 1005
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1128 rDITGGLPRVADLFEARKPKEHAILAEVSGVVSFGKETKGKNRLVITPDDGSEIYEELIPKWRQINVFEGEHVNRGETIS 1207
Cdd:PRK14906 1006 -DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEKTLTIHDQDGNSREYVVSARVQFMPGVEDGVEVRVGQQIT 1084
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1208 DGPQNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQENQA 1287
Cdd:PRK14906 1085 RGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQVNRYEFEDTANN 1164
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 480084187 1288 VLAQNKFPAKFERQLMGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGL-AYH 1362
Cdd:PRK14906 1165 LILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPAGTGLsRYR 1240
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
22-573 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 824.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 22 FDRIRIGLASPEMIKSWSH---------GEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEK 92
Cdd:PRK02625 9 FDYVKIGLASPERIRQWGQrtlpngqvvGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 93 CGVEVTTAKVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKY-QLLTDEEY- 170
Cdd:PRK02625 89 CGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGNHKNLKYkQLLTEDQWl 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 171 ------YNALEEHGDEFTAKMGAEAVQDLLKDIDLEAEIARLREEIPQTTSEtKLKKASKRLKLMEAFKDSNNKPEWMVM 244
Cdd:PRK02625 169 eiedqiYAEDSELEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGSRPEWMVL 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 245 NVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGS 324
Cdd:PRK02625 248 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 327
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 325 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKK 404
Cdd:PRK02625 328 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 407
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 405 MVERETPEVWDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLE 484
Cdd:PRK02625 408 LIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQAE 487
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 485 ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYITRDAVNA-KGEGMVFADTHEVNRALATGKVAIHARVKVRVHQTVID 563
Cdd:PRK02625 488 ARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAqKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFNGEVED 567
|
570
....*....|
gi 480084187 564 ENGEREQQTI 573
Cdd:PRK02625 568 DDEDTEPLKT 577
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
21-519 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 806.05 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 21 EFDRIRIGLASPEMIKSWSH---------GEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRM---KYKGV 88
Cdd:CHL00018 6 KHQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVIgdeKEDPK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 89 ICEKCGVEVTTAKVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFE-SYVVTDPGMTPFEKYQLLTD 167
Cdd:CHL00018 86 FCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDfSFARPIAKKPTFLRLRGLFE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 168 EEYYNALEEHGDEFTAKM-----------GAEAVQDLLKDIDLEAEIARLREEI-------------PQTTSETKLKKAS 223
Cdd:CHL00018 166 YEIQSWKYSIPLFFSTQGfdtfrnreistGAGAIREQLADLDLRIIIDNSLVEWkelgeegstgnewEDRKIGRRKDFLV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 224 KRLKLMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLA--APDIIVRNEK 301
Cdd:CHL00018 246 RRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQK 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 302 RMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALEL 381
Cdd:CHL00018 326 KLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 382 FKPFIFAKLQASGQATTIKAAKKMVERETPEVWDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAA 461
Cdd:CHL00018 406 FQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 485
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 480084187 462 FNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYIT 519
Cdd:CHL00018 486 FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLT 543
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
22-569 |
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: 798.03 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 22 FDRIRIGLASPEMIKSWSH---------GEVKKPETINYRTFKPERDGLFCAKIFGPVKDYECLCGKYKRMKYKGVICEK 92
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGQrtlpngqvvGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 93 CGVEVTTAKVRRERMGHIDLASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKY-QLLTDEEY- 170
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGNAKNLKYkQLLTEDQWl 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 171 ------YNALEEHGDEFTAKMGAEAVQDLLKDIDLEAEIARLREEIPQTTSEtKLKKASKRLKLMEAFKDSNNKPEWMVM 244
Cdd:TIGR02387 162 eiedqiYAEDSELENEEVVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 245 NVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRGRAITGS 324
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 325 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQASGQATTIKAAKK 404
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 405 MVERETPEVWDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLE 484
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 485 ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYITRDAVNA-KGEGMVFADTHEVNRALATGKVAIHARVKVRVHQTVID 563
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAeKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVET 560
|
....*.
gi 480084187 564 ENGERE 569
Cdd:TIGR02387 561 NDPLDE 566
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
30-816 |
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: 590.94 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 30 ASPEMIKSWSHGEVKKPETINYRTFKPERDGlfcakifgpvkdyeclcgKYKRMKYKGVICEKCGVEVTTAKVRRERMGH 109
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 110 IDLASPVAHIWFLKSLPSRIGllldmtlrdiervlyfesyvvtdpgmtpfekyqlltdeeyynaleehgdeftakmgaea 189
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 190 vqdllkdidleaeiarlreeipqttsetklkkaskrlklmeafkdsnnkPEWMVMNVLPVLPPDLRPLVpleggrfatsd 269
Cdd:cd00399 84 -------------------------------------------------PEWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 270 lndlyrrvinrnnrlkrlldlaapdiIVRNEKRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLG 349
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 350 KRVDYSGRSVITVGPTLRLHQCGLPKKMALELfkpfifaklqasgqattikaakkmveretpevwdvlasviRQHPVMLN 429
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 430 RAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ 509
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 510 DVVLGLYYITRdavnakgegmvfadthevnralatgkvaiharvkvrvhqtvidengereqqtiivdttpgrclLWEVVP 589
Cdd:cd00399 278 DTLLGAYLLTL---------------------------------------------------------------GKQIVS 294
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 590 QGLSfdminlemtkkniSKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDML----IPPTKQVIIDKAETE 665
Cdd:cd00399 295 AALP-------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGIGDVIddgvIPEEKTELIEEAKKK 361
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 666 VREIEQQFEQGFVTAGER-------YNKVVDIWARTNDQVAKAMMDNLsytlvknkqgedEKQKSFNSIYMMSDSGARGS 738
Cdd:cd00399 362 VDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNL------------DLVSKFNSIYVMAMSGAKGS 429
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 739 AAQIRQLAGMRGLMAKPDGSI--------------------IETPIKANFREGLTVLQYFISTHGARKGLADTALKTANS 798
Cdd:cd00399 430 FINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAES 509
|
810
....*....|....*...
gi 480084187 799 GYLTRRLVDVAQDLVITE 816
Cdd:cd00399 510 GYLQRRLVKALEDLVVHY 527
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
240-516 |
6.06e-157 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 474.31 E-value: 6.06e-157
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 240 EWMVMNVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNG--RR 317
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 318 GRAITGsnkRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIF---------- 387
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVtplnidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 388 --------AKLQASGQATTIKAAKKM-VERETPEVWDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLV 458
Cdd:smart00663 158 lvrngpngAKYIIRGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 480084187 459 CAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLY 516
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
771-1268 |
1.67e-135 |
|
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: 426.38 E-value: 1.67e-135
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 771 GLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCGTAGGLVMTPFIQGGDVIEPLRDRVLGRVTA 850
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 851 EDVRRASDDEVVLPRGTLIDE---------------------------------KIAAQLEEAGVDEVKVRSVIACESTF 897
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLlsefslsykkeilvrdsklgrdrlskeaqeratLLFELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 898 GVCARCYGRDLARGHLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASRtsaaNSVQvrnkGTVRFHNVKTVQhakgh 977
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASK----NVTL----GVPRLKEIINVS----- 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 978 LVSVSRSGEIGIADDLGRERERYKLPYGASILIKDGESVEAGGIVATWDPHTHPLVTEVAGKARFSQIADGVTATSKTDD 1057
Cdd:pfam04998 228 KNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1058 ATGMTTVEILPVTARPASGKDLRpaivldttdggeQFYFLPQNTIVTVRDGETIGVGDVIGRVPQETSRTRDITGGLPRV 1137
Cdd:pfam04998 308 ETGLLILVIRLLKILNKSIKKVV------------KSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKIRQDTGGLRRV 375
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1138 ADLFEARKPKEHAILAEVSGVVSFgKETKGKNRLVITPDDGSEIYE------ELIPKWRQINVFegEHVNRGETISDgpq 1211
Cdd:pfam04998 376 DELFMEEDPKLAILVASLLGNITL-RGIPGIKRILVNEDDKGKVEPdwvletEGVNLLRVLLVP--GFVDAGRILSN--- 449
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*..
gi 480084187 1212 NPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDT 1268
Cdd:pfam04998 450 DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
603-1056 |
1.90e-134 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 447.52 E-value: 1.90e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 603 KKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIIDKAETEVREIEQQFEQGFVTAGE 682
Cdd:PRK02597 10 KKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGEITEVE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 683 RYNKVVDIWARTNDQVAKAMmdnlsytlVKNKQGEDekqkSFNSIYMMSDSGARGSAAQIRQLAGMRGLMAKPDGSIIET 762
Cdd:PRK02597 90 RFQKVIDTWNETNERLKDEV--------VKNFRQND----PLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQGEIIDL 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 763 PIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCGTAGGLVMTPFIQGGDVIEPLRD 842
Cdd:PRK02597 158 PIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVLIPLGD 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 843 RVLGRVTAEDVRRAsDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTFGVCARCYGRDLARGHLVNPGESVGV 922
Cdd:PRK02597 238 RLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLGEAVGI 316
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 923 MAAQSIGEPGTQLTMRTFHVGGAASRTSAAnsvQVRNK--GTVRF-HNVKTVQHAKGHLVS---VSRSGEIGIADDLGRE 996
Cdd:PRK02597 317 IAAQSIGEPGTQLTMRTFHTGGVFTGEVAR---QVRSPfaGTVEFgKKLRTRPYRTRHGVEalqAEVDFDLVLKPSGKGK 393
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 480084187 997 RERYKLPYGASILIKDGESVEAGGIVA---------TWDPHTHPLVTEVAGKARFSQiadgVTATSKTD 1056
Cdd:PRK02597 394 PQKIEITQGSLLFVDDGQTVEADQLLAevaagavkkSTEKATKDVICDLAGEVRFAD----LIPEEKTD 458
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
598-1130 |
6.76e-123 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 413.48 E-value: 6.76e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 598 NLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIIDKAETEVREIEQQFEQGF 677
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 678 VTAGERYNKVVDIWARTNDQVAKAMMDNLSYTlvknkqgedekqKSFNSIYMMSDSGARGSAAQIRQLAGMRGLMAKPDG 757
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNFRQT------------DPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 758 SIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCGTAGGLVMTPFIQGGDVI 837
Cdd:TIGR02388 152 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 838 EpLRDRVLGRVTAEDVRRaSDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTFGVCARCYGRDLARGHLVNPG 917
Cdd:TIGR02388 232 S-LGDRLLGRLVAEDVLH-PEGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLG 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 918 ESVGVMAAQSIGEPGTQLTMRTFHVGGAASRTSAAnsvQVRNK--GTVRF-HNVKTVQHAKGHLVSVSRSGEIGIADDLG 994
Cdd:TIGR02388 310 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVAR---QVRSKidGTVEFgKKLRTRGYRTRHGEDAKQVEVAGLLIIKP 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 995 RER-----ERYKLPYGASILIKDGESVEAGGIVA---------TWDPHTHPLVTEVAGKARFsqiaDGVTATSKTDDATG 1060
Cdd:TIGR02388 387 TGSitnkaQEIEVTQGSLLFVEDGQTVDAGQLLAeialgavrkSTEKATKDVASDLAGEVKF----DKVVPEEKTDRQGN 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1061 MTT--------------VEILPVTARPasgkdlrpaiVLDTTDGGEQFYFLPQNTIVTVRDGETigvgdvigRVPQETSR 1126
Cdd:TIGR02388 463 TTRiaqrggliwvlsgeVYNLPPGAEP----------VVKNGDRVEQGTVLAETKLSTEHGGVV--------RLPESVGD 524
|
....
gi 480084187 1127 TRDI 1130
Cdd:TIGR02388 525 SREV 528
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
598-1023 |
3.58e-118 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 402.78 E-value: 3.58e-118
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 598 NLEMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPPTKQVIIDKAETEVREIEQQFEQGF 677
Cdd:CHL00117 11 NKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYGN 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 678 VTAGERYNKVVDIWARTNDQVAKAMMDNLSYTlvknkqgeDekqkSFNSIYMMSDSGARGSAAQIRQLAGMRGLMAKPDG 757
Cdd:CHL00117 91 VHAVEKLRQSIEIWYATSEYLKQEMNPNFRMT--------D----PLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQG 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 758 SIIETPIKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEPDCGTAGGLVMTPFiQGGDVI 837
Cdd:CHL00117 159 QIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPR-NGMMIE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 838 EPLRDRVLGRVTAEDVRraSDDEVVLPRGTLIDEKIAAQLEEAGVDEVKVRSVIACESTFGVCARCYGRDLARGHLVNPG 917
Cdd:CHL00117 238 RILIQTLIGRVLADDIY--IGSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELG 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 918 ESVGVMAAQSIGEPGTQLTMRTFHVGG-----AASrtsaansvQVRNK--GTVRF-----HNVKTvQHakGHLVSVSRSG 985
Cdd:CHL00117 316 EAVGIIAGQSIGEPGTQLTLRTFHTGGvftggTAE--------QVRAPfnGKIKFnedlvHPTRT-RH--GHPAFLCKID 384
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 480084187 986 ---EIGIADDLgrerERYKLPYGASILIKDGESVEAGGIVA 1023
Cdd:CHL00117 385 lyvTIESEDII----HNVNIPPKSLLLVQNDQYVESEQVIA 421
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
21-347 |
2.16e-105 |
|
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 337.34 E-value: 2.16e-105
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 21 EFDRIRIGLASPEMIKSWSHGEVKKPETINYRTFKPERDGLFCAKIFGPVKDYEC-LCGKYKRmkykgviceKCGVevtt 99
Cdd:pfam04997 3 KIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG---- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 100 akvrreRMGHIDLASPVAHIWFLKslpsrigllldMTLRDIERVLYFESYVVTDPGmtpfeKYQLLTDEEYYNALEEhgd 179
Cdd:pfam04997 70 ------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLEN--- 124
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 180 eftAKMGAEAVQDLLKDIDL------------------EAEIARLREEIP--QTTSETKLKKASKRLKL----------M 229
Cdd:pfam04997 125 ---LKMGAKAILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKksKEEEEKEILNPEKVLKIfkrisdedveI 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 230 EAFKDSNNKPEWMVMNVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVD 309
Cdd:pfam04997 202 LGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHVA 281
|
330 340 350
....*....|....*....|....*....|....*....
gi 480084187 310 ALLDNGRRG-RAITGSNKRPLKSLADMIKGKQGRFRQNL 347
Cdd:pfam04997 282 TLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
19-841 |
1.06e-99 |
|
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: 339.61 E-value: 1.06e-99
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 19 PVEFDRIRIGLASPEMIKSWSHGEVKKPETinYrtfkpERDGLfcaKIFGPVKDyeclcgkyKRMkykGVI-----CEKC 93
Cdd:cd02582 1 PKRIKGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTC 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 94 GvevTTAKVRRERMGHIDLASPVAHIWFLKslpsRIGLLLDMTLRDIERVLyfesyvvtdpgMTPFEKYQLLtdeEYYNA 173
Cdd:cd02582 60 G---NTAGECPGHFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEIEKYL---ERIRR 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 174 LEEHGDEfTAKMGAEAVQDLLKDIDL----EAEIARLREEIPQTTSETKlKKASKRLKLME----------------AFK 233
Cdd:cd02582 119 LKEKWPE-LVKRVIEKVKKKAKKRKVcphcGAPQYKIKLEKPTTFYEEK-EEGEVKLTPSEirerlekipdedlellGID 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 234 DSNNKPEWMVMNVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLD 313
Cdd:cd02582 197 PKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFD 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 314 NGRRG--RAITGSnKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKLQ 391
Cdd:cd02582 277 NEIPGipPARHRS-GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEWN 355
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 392 asgqattIKAAKKMVEReTPEVW---------------------DVLAS------VIRQH-----PVMLNRAPTLHRLGL 439
Cdd:cd02582 356 -------IEKMRKLVLN-GPDKWpganyvirpdgrrirlryvnrEELAErlepgwIVERHlidgdIVLFNRQPSLHRMSI 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 440 QAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYIT 519
Cdd:cd02582 428 MAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLT 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 520 RD------------AVNAKGEGMVFADTHEVNRALATGKVAI----------HARVKVRVH-QTVIDENGEREQQTIIVD 576
Cdd:cd02582 508 RKttlftkeealqlLSAAGYDGLLPEPAILEPKPLWTGKQLFslflpkdlnfEGKAKVCSGcSECKDEDCPNDGYVVIKN 587
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 577 ttpGRCLlwevvpQGLsFDminlemtKKNI-----SKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLI 651
Cdd:cd02582 588 ---GKLL------EGV-ID-------KKAIgaeqpGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDI 650
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 652 PPT--KQV--IIDKAETEVREIEQQFEQGFVTA--GERY-----NKVVDIWARTNDQVAKAMMDNLSytlvknkqgedek 720
Cdd:cd02582 651 PEEarKEIeeIIKEAEKKVYELIEQYKNGELEPlpGRTLeetleMKIMQVLGKARDEAGKVASKYLD------------- 717
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 721 qkSFNSIYMMSDSGARGSAAQIRQLAGM------------RGLMAKP--------DGSIIETPIKANFREGLTVLQYFIS 780
Cdd:cd02582 718 --PFNNAVIMARTGARGSMLNLTQMAAClgqqsvrgerinRGYRNRTlphfkpgdLGPEARGFVRSSFRDGLSPTEFFFH 795
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 480084187 781 THGARKGLADTALKTANSGYLTRRLVDVAQDLVItEPDcGT----AGGLVMtpFIQGGDVIEPLR 841
Cdd:cd02582 796 AMGGREGLVDTAVRTSQSGYMQRRLINALQDLYV-EYD-GTvrdsRGNIIQ--FKYGEDGVDPAK 856
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
19-853 |
2.70e-89 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 310.63 E-value: 2.70e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 19 PVEFDRIRIGLASPEMIKSWSHGEVKKPETinYrtfkpERDGLfcaKIFGPVKDyeclcgkyKRMkykGVI-----CEKC 93
Cdd:PRK08566 6 PKRIGSIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTC 64
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 94 GvevTTAKVRRERMGHIDLASPVAHIWFLKslpsRIGLLLDMTLRDIERVLyfesyvvtdpgmtpfekyqlLTDEEY--- 170
Cdd:PRK08566 65 G---GRAGECPGHFGHIELARPVIHVGFAK----LIYKLLRATCRECGRLK--------------------LTEEEIeey 117
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 171 ---YNALEEHGDEftakmgaeaVQDLLKDIDLEAEIAR-----------LREEIP------QTTSETKLKKASKR----- 225
Cdd:PRK08566 118 lekLERLKEWGSL---------ADDLIKEVKKEAAKRMvcphcgekqykIKFEKPttfyeeRKEGLVKLTPSDIRerlek 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 226 -----LKLMeAFKDSNNKPEWMVMNVLPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNE 300
Cdd:PRK08566 189 ipdedLELL-GINPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDL 267
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 301 KRMLQESVDALLDN---G------RRGRaitgsnkrPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQC 371
Cdd:PRK08566 268 WELLQYHVTTYFDNeipGipparhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEV 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 372 GLPKKMALELFKPFIFAKLQasgqattIKAAKKMVEReTPEVWDVLASVIR---------------------------QH 424
Cdd:PRK08566 340 GVPEAIAKELTVPERVTEWN-------IEELREYVLN-GPEKHPGANYVIRpdgrrikltdknkeelaeklepgwiveRH 411
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 425 -----PVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 499
Cdd:PRK08566 412 lidgdIVLFNRQPSLHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPR 491
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 500 NGEPIIVPSQDVVLGLYYITRD--------------AVNAKGEGMVfADTHEVNRALATGKVAI----------HARVKV 555
Cdd:PRK08566 492 YGGPIIGGIQDHISGAYLLTRKstlftkeealdllrAAGIDELPEP-EPAIENGKPYWTGKQIFslflpkdlnlEFKAKI 570
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 556 -RVHQTVIDENGEREQQTIIVDttpGRCLlwevvpQGlSFDminlemtKKNIS----KLINSCYRKLGLKDTVIFADQLM 630
Cdd:PRK08566 571 cSGCDECKKEDCEHDAYVVIKN---GKLL------EG-VID-------KKAIGaeqgSILDRIVKEYGPERARRFLDSVT 633
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 631 YLGFRQATRSGVSVGMEDMLIPP--TKQV--IIDKAETEVREIEQQFEQGFV------TAGE-RYNKVVDIWARTNDQVA 699
Cdd:PRK08566 634 RLAIRFIMLRGFTTGIDDEDIPEeaKEEIdeIIEEAEKRVEELIEAYENGELeplpgrTLEEtLEMKIMQVLGKARDEAG 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 700 KAMMDNLSytlvknkqgedekqkSFNSIYMMSDSGARGSAAQIRQLAGM------------RGLMAK-----PDGSIieT 762
Cdd:PRK08566 714 EIAEKYLG---------------LDNPAVIMARTGARGSMLNLTQMAACvgqqsvrgerirRGYRDRtlphfKPGDL--G 776
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 763 P-----IKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLvITEPDcGT----AGGLVMtpFIQG 833
Cdd:PRK08566 777 AeargfVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDL-KVEYD-GTvrdtRGNIVQ--FKYG 852
|
970 980
....*....|....*....|....*....
gi 480084187 834 GDVIEPLR---------DRVLGRVTAEDV 853
Cdd:PRK08566 853 EDGVDPMKsdhgkpvdvDRIIERVLGKEV 881
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
23-1358 |
4.83e-83 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 299.25 E-value: 4.83e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 23 DRIRIGLASPEMIKSWSHGEVKKPETInyrtfkpERDGLfcaKIFGPVKDyeclcGKYKRMKyKGVICEKCGvevTTAKV 102
Cdd:PRK14977 10 DGIIFGLISPADARKIGFAEITAPEAY-------DEDGL---PVQGGLLD-----GRLGTIE-PGQKCLTCG---NLAAN 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 103 RRERMGHIDLASPVAHIWFLKslpsRIGLLLDMTLRDIERVLYFESYVVTDPGMTPFEKY-----QLLTDEEYYNALEEH 177
Cdd:PRK14977 71 CPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAardipEKRIDDEIIEEVRDQ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 178 GDEFTAKM------GAEAVQDLLKDI-----DLEAEIARLreeIPQTTSEtKLKKASKRLKLMEAFKDSNNKPEWMVMNV 246
Cdd:PRK14977 147 VKVYAKKAkecphcGAPQHELEFEEPtifieKTEIEEHRL---LPIEIRD-IFEKIIDDDLELIGFDPKKARPEWAVLQA 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 247 LPVLPPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRG--RAITGS 324
Cdd:PRK14977 223 FLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHHKG 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 325 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFI------------------ 386
Cdd:PRK14977 303 SGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenniekmkelvingpd 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 387 -FAKLQASGQATTIKAAKKMVERETPEVWDVLAS------VIRQH-----PVMLNRAPTLHRLGLQAFEPILIEGKAIRL 454
Cdd:PRK14977 383 eFPGANAIRKGDGTKIRLDFLEDKGKDALREAAEqleigdIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPGATFRL 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 455 HPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYITR-DAVNAKGEGMVFA 533
Cdd:PRK14977 463 HPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKdDALFDKNEASNIA 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 534 D------------THEVNRALATGKVAIHARVKVRVHQTVIDE--NGEREQQTIIVDTTPGRCLLWEVVPQGLSFDMINL 599
Cdd:PRK14977 543 MlagitdplpepaIKTKDGPAWTGKQLFSLFLPKDFNFEGIAKwsAGKAGEAKDPSCLGDGYVLIKEGELISGVIDDNII 622
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 600 EMTKKNISKLINSCYRKLGLKDTVIFADQLMYLGFRQATRSGVSVGMEDMLIPptkqviiDKAETEVREIEQQFEQGFVT 679
Cdd:PRK14977 623 GALVEEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIP-------DEAKQEIEDDIQGMKDEVSD 695
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 680 AGERYNKVVDIWA-RTNDQVAKAMMDN--LSYTLVKNKQGEDEKQKSF--------NSIYMMSDSGARGSAAQIRQLAGM 748
Cdd:PRK14977 696 LIDQRKITRKITIyKGKEELLRGMKEEeaLEADIVNELDKARDKAGSSandcidadNAGKIMAKTGARGSMANLAQIAGA 775
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 749 RGLMA-KPDGSIIETP---------------------------IKANFREGLTVLQYFISTHGARKGLADTALKTANSGY 800
Cdd:PRK14977 776 LGQQKrKTRIGFVLTGgrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGLIDKARRTEDSGY 855
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 801 LTRRLVDVAQDLVIT--EPDCGTAGGLVMtpFIQGGDVIEPLR---------DRVLGRVTAEDV-RRASDDEV------- 861
Cdd:PRK14977 856 FQRRLANALEDIRLEydETVRDPHGHIIQ--FKFGEDGIDPQKldhgeafnlERIIEKQKIEDRgKGASKDEIeelakey 933
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 862 ---VLPRGTLI--DEKIAAQLEEAGVDEvkvrsviacestfgVCARcyGRDLARGHLVNPGESVGVMAAQSIGEPGTQLT 936
Cdd:PRK14977 934 tktFNANLPKLlaDAIHGAELKEDELEA--------------ICAE--GKEGFEKAKVEPGQAIGIISAQSIAEPGTQMT 997
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 937 MRTFHVGGAASRtSAANSVQvRNKGTVRFHNVKTVQHAKGHL---VSVSRSGEIGIADDLGREReryklpygASILIKDG 1013
Cdd:PRK14977 998 LRTFHAAGIKAM-DVTHGLE-RFIELVDARAKPSTPTMDIYLddeCKEDIEKAIEIARNLKELK--------VRALIADS 1067
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1014 ESVEAGGIVaTWDPHTHPLVTEVAGKARFSQIadgVTATSKTDDATGMTTVEILPVTARPASGKDLRPAIVLDTTdggeq 1093
Cdd:PRK14977 1068 AIDNANEIK-LIKPDKRALENGCIPMERFAEI---EAALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIAIR----- 1138
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1094 fYFLPQNTIVTVRDGETIGVgdvigrvpqetsrtrditgglprvaDLFEARKPKEHAIlaevsgvvsfgkETKGKNrlvi 1173
Cdd:PRK14977 1139 -NKILDKPVKGVPDIERAWV-------------------------ELVEKDGRDEWII------------QTSGSN---- 1176
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1174 tpddgseiyeelipkwrQINVFEGEHVNRGETISDgpqNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVV 1253
Cdd:PRK14977 1177 -----------------LAAVLEMKCIDIANTITN---DCFEIAGTLGIEAARNAIFNELASILEDQGLEVDNRYIMLVA 1236
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1254 RQMLRKvditdggdtsfikgeqvDYIRVVQENQAVLAQNKFPAKferqlmgitkaslstDSFISAASFQETTRVLTEAAV 1333
Cdd:PRK14977 1237 DIMCSR-----------------GTIEAIGLQAAGVRHGFAGEK---------------DSPLAKAAFEITTHTIAHAAL 1284
|
1450 1460
....*....|....*....|....*
gi 480084187 1334 TGKEDDLRGLKENVVVGRLIPAGTG 1358
Cdd:PRK14977 1285 GGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
912-1359 |
2.54e-81 |
|
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: 265.55 E-value: 2.54e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 912 HLVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASrtsaansvqvrnkgtvrfhnvktvqhakghlvsvsrsgeigiad 991
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-------------------------------------------- 36
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 992 dlgrereryklpygasilikdgesveaggivatwdphthplvtevagkarfsqiadgvtatsktddatgmttveilpvta 1071
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1072 rpasgkdlrpaivldttdggeqfyflpqntivtvrdgetigvgdvigrvpqetsrtrDITGGLPRVADLFEARKPkehai 1151
Cdd:cd02655 37 ---------------------------------------------------------DITQGLPRVEELFEARKI----- 54
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1152 laevsgvvsfgketkgknrlvitpddgseiyeelipkwrqinvfegehvnrgetisdgpqNPHDILRLK--GEVALTNYI 1229
Cdd:cd02655 55 ------------------------------------------------------------NPHDLLRIKflGPEAVQKYL 74
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1230 VNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQENQAVLAQNKFPAKFERQLMGITKAS 1309
Cdd:cd02655 75 VEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPVLLGITKAS 154
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|
gi 480084187 1310 LSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGL 1359
Cdd:cd02655 155 LNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1007-1380 |
4.46e-81 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 293.44 E-value: 4.46e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1007 SILIKDGESVEAGGIVATwdphTHPLVTEvAGKARfsQIADGVTATSK----------TDDATGMTTVEilpVTARPASG 1076
Cdd:PRK02597 844 ELLVKDGQQIKPGDVVAR----TQILCKE-AGEVR--GIRVGGEAVRRllverdedtiTIPLSGKPTVK---VGDLVVAG 913
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1077 KDLRPAI-------VLDTTDGGEQF-----YFLPQNTIVTVRDGETIGVGDVIGRVPQETSRTRDITGGLPRVADLFEAR 1144
Cdd:PRK02597 914 DELAPGVpapesgeVEAVSGGSVTLrlgrpYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEAR 993
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1145 KPKEHAILAEVSGVVSFGKETKGKNRLVITPDDGSeIYEELIPKWRQINVFEGEHVNRGETISDGPQNPHDILR------ 1218
Cdd:PRK02597 994 KPKESCILAKKPGTVQIKYGDDESVDVKVIESDGT-ITEYPILPGQNVMVSDGQQVDAGEPLTDGPINPHELLEiffedl 1072
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1219 ----------LKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQENQAV 1288
Cdd:PRK02597 1073 rdrkglyeaaLEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAM 1152
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1289 LAQNKFPAKFERQLMGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGLAYHLERRRQ 1368
Cdd:PRK02597 1153 AITGGAPAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELSA 1232
|
410
....*....|..
gi 480084187 1369 EAEAAEFELHND 1380
Cdd:PRK02597 1233 EAGPHPDILAED 1244
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1007-1364 |
1.93e-71 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 262.48 E-value: 1.93e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1007 SILIKDGESVEAGGIVATwdphthplvTEVAGKARfsQIADGVTATSKT------DDATGMTTVEI-----LPVTARPAS 1075
Cdd:TIGR02388 842 SLLVKDGDLIKPGAVIAR---------TQILCKEA--GVVQGIDSGGESirrllvERNSDRLKVNIkakpvVKTGDLVVA 910
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1076 GKDLRPAIVLDTTD-----GGEQF-------YFLPQNTIVTVRDGETIGVGDVIGRVPQETSRTRDITGGLPRVADLFEA 1143
Cdd:TIGR02388 911 GDELAKGVKAEESGeieevASDYVilrigrpYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEA 990
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1144 RKPKEHAILAEVSGV--VSFGKETKGKNRLVITPDDGSEIYEeLIPKwRQINVFEGEHVNRGETISDGPQNPHDILR--- 1218
Cdd:TIGR02388 991 RKPKEACILAKRPGVvqVKYGTDDESVSIKVIERDGTISEYP-LLPG-QNIMVSDGQQVTGGEPLTDGPINPHDILDvff 1068
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1219 -------------LKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSFIKGEQVDYIRVVQEN 1285
Cdd:TIGR02388 1069 syykdqdglyeaaQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVN 1148
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 480084187 1286 QAVLAQNKFPAKFERQLMGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGLAYHLE 1364
Cdd:TIGR02388 1149 EAMAITGGAPAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYEE 1227
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
23-814 |
1.18e-66 |
|
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: 241.29 E-value: 1.18e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 23 DRIRIGLASPEMIKSWSHGEVKKPETINyRTFKPERDGLfcakifgpvKDyeclcgkyKRMkykGVI-----CEKCGvev 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGL---------ND--------PRM---GTIdrnsrCQTCG--- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 98 ttakvrrERM-------GHIDLASPVAHIWFLkslpsriglllDMTLRDIERVLYfesyvvtdpgmtpfekyQLLTDEEY 170
Cdd:cd02733 57 -------GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILRCVCK-----------------RELSAERV 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 171 YNALEEHGDEFTAKMGaeavqdllkdidleaeiarlreeipqttsetklkkaskrlklmeaFKDSNNKPEWMVMNVLPVL 250
Cdd:cd02733 102 LEIFKRISDEDCRILG---------------------------------------------FDPKFSRPDWMILTVLPVP 136
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 251 PPDLRPLVPLEGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQESVDALLDNGRRG--RAITGSnKRP 328
Cdd:cd02733 137 PPAVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQKS-GRP 215
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 329 LKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMAL-----ELFKPFIFAKLQ---ASGQATTIK 400
Cdd:cd02733 216 LKSIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLQelvRNGPNEYPG 295
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 401 AakKMVERETPEVWDvlasvIRQHP----------------------VMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLV 458
Cdd:cd02733 296 A--KYIIRDDGERID-----LRYLKkasdlhlqygyiverhlqdgdvVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSV 368
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 459 CAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPI--IVpsQDVVLGLYYIT-RDAVNAKGEGM---VF 532
Cdd:cd02733 369 TTPYNADFDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTkRDTFLEKDQVMnllMW 446
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 533 ADTHEVN---------RALATGKVAIHARVKVRVHQTVIDENGEREQQTIivdtTPGRCLLweVVPQGLsfdMINLEMTK 603
Cdd:cd02733 447 LPDWDGKipqpailkpKPLWTGKQIFSLIIPKINNLIRSSSHHDGDKKWI----SPGDTKV--IIENGE---LLSGILCK 517
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 604 KNISK----LINSCYRKLGLKDTVIFADQ--------LMYLGFrqatrsgvSVGMEDMLIPP----TKQVIIDKAETEVR 667
Cdd:cd02733 518 KTVGAssggLIHVIWLEYGPEAARDFIGNiqrvvnnwLLHNGF--------SIGIGDTIADKetmkKIQETIKKAKRDVI 589
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 668 EIEQQFEQGfvtagerynkvvdiwaRTNDQVAKAMMDNLSY--TLVKNK---QGEDEKQKS---FNSIYMMSDSGARGSA 739
Cdd:cd02733 590 KLIEKAQNG----------------ELEPQPGKTLRESFENkvNRILNKardKAGKSAQKSlseDNNFKAMVTAGSKGSF 653
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 740 AQIRQLAG-----------------MRGL--MAKPDGSIIETP-IKANFREGLTVLQYFISTHGARKGLADTALKTANSG 799
Cdd:cd02733 654 INISQIIAcvgqqnvegkripfgfrRRTLphFIKDDYGPESRGfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETG 733
|
890
....*....|....*
gi 480084187 800 YLTRRLVDVAQDLVI 814
Cdd:cd02733 734 YIQRRLVKAMEDVMV 748
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1095-1371 |
3.91e-58 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 220.97 E-value: 3.91e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1095 YFLPQNTIVTVRDGETIGVGDVIGRVPQETSRTRDITGGLPRVADLFEARKpkehailaevsgvvsfgketkgKNRLVIT 1174
Cdd:CHL00117 1096 YLATPGATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARS----------------------IDSISMN 1153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1175 PddgseiyEELIPKWrqinvfegehvnrgetisdgpqnPHDILRLKGE-------VALT-----NYIVNEVQDVYRLQGV 1242
Cdd:CHL00117 1154 L-------EKRLEGW-----------------------NERITRILGIpwgfligAELSiaqsqISLVNKIQKVYRSQGV 1203
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1243 KINDKHIEVVVRQMLRKVDITDGGDTS-FIKGEQVDYIRVVQENQAVlaqnKFPAKFERQLMGITKASLSTDSFISAASF 1321
Cdd:CHL00117 1204 QISDKHIEIIVRQMTSKVLVSEDGMSNvFLPGELIGLLRAERINRAL----EEAICYRPILLGITKASLNTQSFISEASF 1279
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 480084187 1322 QETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGLAYHLERRRQEAE 1371
Cdd:CHL00117 1280 QETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSKQHKN 1329
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
86-814 |
6.15e-56 |
|
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: 210.10 E-value: 6.15e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 86 KGVICEKCGvevttaKVRRERMGH---IDLASPVAHIWFLKSlpsrIGLLLDMTLRDIERVLyfesyvvtdpgmtpfeky 162
Cdd:cd02583 42 KDGICETCG------LNLADCVGHfgyIKLELPVFHIGYFKA----IINILQCICKTCSRVL------------------ 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 163 qlLTDEE---YYNALEEHGDEFTAKMGaeavqdllkdidLEAEIARLREEIPQTTSETKLKKAS------KRLKLMEAFK 233
Cdd:cd02583 94 --LPEEEkrkFLKRLRRPNLDNLQKKA------------LKKKILEKCKKVRKCPHCGLLKKAQedlnplKVLNLFKNIP 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 234 DSN----------NKPEWMVMNVLPVLPPDLRPLVPLEGGrfATSDLNDL---YRRVINRNNRLKRLLDLAAPDIIVRNE 300
Cdd:cd02583 160 PEDvelllmnplaGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMED 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 301 KRMLQESVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALE 380
Cdd:cd02583 238 WDFLQLQCALYINSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKI 317
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 381 LFKP-----FIFAKLQA-------------------SGQATTIKAAKKMVERETPEVWDVlasvIRQH-----PVMLNRA 431
Cdd:cd02583 318 LTYPervtrYNIEKLRKlvlngpdvhpganfvikrdGGKKKFLKYGNRRKIARELKIGDI----VERHledgdIVLFNRQ 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 432 PTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDV 511
Cdd:cd02583 394 PSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDF 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 512 VLGLYYIT-RDavnakgegmVFADTHEVNRALAtgkvaiharvkvrvhqTVIDENGERE--QQTIIvdtTPGRclLW--- 585
Cdd:cd02583 474 LTASYLLTsKD---------VFFDRAQFCQLCS----------------YMLDGEIKIDlpPPAIL---KPVE--LWtgk 523
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 586 -----EVVPQGLSFDMINLEMTKKNISKLINS--------CYRK-------LGlKDTV-------IFADQLMYLGFRQAT 638
Cdd:cd02583 524 qifslLLRPNKKSPVLVNLEAKEKSYTKKSPDmcpndgyvVIRNsellcgrLD-KSTLgsgsknsLFYVLLRDYGPEAAA 602
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 639 RS---------------GVSVGMEDMLIPPT----KQVIIDKAETEVREIEQQFEQGFVTAGERYN-------KVVDIWA 692
Cdd:cd02583 603 AAmnrlaklssrwlsnrGFSIGIDDVTPSKEllkkKEELVDNGYAKCDEYIKQYKKGKLELQPGCTaeqtleaKISGELS 682
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 693 RTNDQVAKAMMDNLSYtlvknkqgedekqksFNSIYMMSDSGARGSAAQIRQ---------LAGMRglmaKPDGSI---- 759
Cdd:cd02583 683 KIREDAGKACLKELHK---------------SNSPLIMALCGSKGSNINISQmiacvgqqiISGKR----IPNGFEdrtl 743
|
810 820 830 840 850 860
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 480084187 760 ------IETP-----IKANFREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVI 814
Cdd:cd02583 744 phfprnSKTPaakgfVANSFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSV 809
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
349-490 |
2.73e-45 |
|
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: 160.93 E-value: 2.73e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 349 GKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKPFIFAKL-----------------------QASGQATTIKAAKKM 405
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYnikrlrqlvengpnvypganyiiRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 406 VERETPEVWDVLASVIRQHPVMLNRAPTLHRLGLQAFEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEA 485
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 480084187 486 RALMM 490
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 ... |
228-806 |
9.92e-42 |
|
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: 165.82 E-value: 9.92e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 228 LMEAFKDSNNKPEWMVMNVLPVLPPDLRPLVPLEGGRFaTSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRM---- 303
Cdd:cd01435 116 LLVEAAELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLASMRQAESQSKLDLIsgkt 194
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 304 -----------LQESVDALLDNGrrgraitgSNKRPLKSLADMIKG----KQGRFRQNLLGKRVDYSGRSVITVGPTLRL 368
Cdd:cd01435 195 nseklinawlqLQSAVNELFDST--------KAPKSGKKSPPGIKQllekKEGLFRMNMMGKRVNYAARSVISPDPFIET 266
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 369 HQCGLPKKMALEL-F----KPFIFAKLQA------------------SGQaTTIKAAKKMVERETPEVWDVLASVIRQHP 425
Cdd:cd01435 267 NEIGIPLVFAKKLtFpepvTPFNVEELRQavingpdvypganaiedeDGR-LILLSALSEERRKALAKLLLLLSSAKLLL 345
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 426 ---------------VMLNRAPTLHRLGLQA-FEPILIEGKAIRLHPLVCAAFNADFDGDQMAVHVPLTLEAQLEARALM 489
Cdd:cd01435 346 ngpkkvyrhlldgdvVLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIA 425
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 490 MSTNNILSPANGEPI---IvpsQDVVLG-------LYYITRD-----AVNAKGEGMVFADTHEVN---------RALATG 545
Cdd:cd01435 426 STDNQYLVPTDGKPLrglI---QDHVVSgvlltsrDTFFTREeyqqlVYAALRPLFTSDKDGRIKllppailkpKPLWTG 502
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 546 KVAIH-------------------ARVKVRVHQTVIDENGErEQQTIIVDTTpgrcLLwevvpQGLsFDminlemtKKNI 606
Cdd:cd01435 503 KQVIStilknlipgnapllnlsgkKKTKKKVGGGKWGGGSE-ESQVIIRNGE----LL-----TGV-LD-------KSQF 564
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 607 SK----LINSCYRKLGLKDtvifADQLM---------YLGFRqatrsGVSVGMEDMLIPPT----KQVIIDKAETEVREI 669
Cdd:cd01435 565 GAsaygLVHAVYELYGGET----AGKLLsalgrlftaYLQMR-----GFTCGIEDLLLTPKadekRRKILRKAKKLGLEA 635
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 670 EQQFeqgfvtAGERYNKVvdiwarTNDQVAKAMMDNLsytlvknkqgedEKQKSFNSIYMMSDSGARGS---AAQI---- 742
Cdd:cd01435 636 AAEF------LGLKLNKV------TSSIIKACLPKGL------------LKPFPENNLQLMVQSGAKGSmvnASQIscll 691
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 480084187 743 --RQLAGMR-GLMAK----PDGSIIETPIKAN------FREGLTVLQYFISTHGARKGLADTALKTANSGYLTRRLV 806
Cdd:cd01435 692 gqQELEGRRvPLMVSgktlPSFPPYDTSPRAGgfitdrFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
494-649 |
1.43e-35 |
|
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: 132.75 E-value: 1.43e-35
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 494 NILSPANGEPIIVPSQDVVLGLYYITRDAVnakgegmvFADTHEVNRALATGKVAIHARVKVRVhqtvidengeREQQTI 573
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDT--------FFDREEVMQLLMYGIVLPHPAILKPI----------KPLWTG 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 574 ivDTTPGRCLLWEVVPQGL------------SFDMINLEMTK----------KNISKLINSCYRKLGLKDTVIFADQLMY 631
Cdd:pfam04983 63 --KQTFSRLLPNEINPKGKpktneedlcendSYVLINNGELIsgvidkktvgKSLGSLIHIIYKEYGPEETAKFLDRLQK 140
|
170
....*....|....*...
gi 480084187 632 LGFRQATRSGVSVGMEDM 649
Cdd:pfam04983 141 LGFRYLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1212-1359 |
4.23e-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: 100.18 E-value: 4.23e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1212 NPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDitdggdtsfikgeqvdyirvvqenqavlaq 1291
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSGG------------------------------ 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1292 nkfpakferqLMGITKASL--STDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTGL 1359
Cdd:cd00630 99 ----------LRGVTRSGFraSKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTGS 158
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
678-769 |
5.97e-24 |
|
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: 97.82 E-value: 5.97e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 678 VTAGERYNKVVDIWARTNDQVAKAMMDNLSYTLVKN-KQGEDEKQKSFNSIYMMSDSGARGSAAQIRQLAGMRGLMAKPD 756
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKARDPaGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 480084187 757 GSI---------------IETPIKANFR 769
Cdd:pfam05000 81 KRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
343-523 |
4.06e-21 |
|
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 100.17 E-value: 4.06e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 343 FRQNLLGKRVDYSGRSVITVGPTLRLHQCGLPKKMALELFKP-----FIFAKLQASGQATTIKAAKKMVERETPEVWdvl 417
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVServssWNRERLQEYCDLTLLLKGVIGVRRNGRLVG--- 282
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 418 asvIRQHP-----------------VMLNRAPTLHRLGLQAFEPILIE-GKAIRLHPLVCAAFNADFDGDQMAVHVPLTL 479
Cdd:cd10506 283 ---VRSHNtlqigdvihrplvdgdvVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRGDFDGDCLHGYIPQSL 359
|
170 180 190 200
....*....|....*....|....*....|....*....|....
gi 480084187 480 EAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYITRDAV 523
Cdd:cd10506 360 QARAELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGV 403
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
857-1358 |
2.18e-17 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 86.05 E-value: 2.18e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 857 SDDEVVLPRgtLIDEKIAAQLEEAGVDEVKVRSVI-ACEstfgvcaRCYGRDLarghlVNPGESVGVMAAQSIGEPGTQL 935
Cdd:PRK04309 12 EDASLELPQ--KLKEELREKLEERKLTEEEVEEIIeEVV-------REYLRSL-----VEPGEAVGVVAAQSIGEPGTQM 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 936 TMRTFHVGGAAsrtsaansvqvrnkgtvrfhnvktvqhakghlvsvsrsgEIGIAddLGREReryklpygasiLIkdgES 1015
Cdd:PRK04309 78 TMRTFHYAGVA---------------------------------------EINVT--LGLPR-----------LI---EI 102
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1016 VEAGGIVATW-------DPHTH--PLVTEVAGK---ARFSQIADGVTatskTDDATGMTTVEILPVTARpasGKDLRPAI 1083
Cdd:PRK04309 103 VDARKEPSTPmmtiylkDEYAYdrEKAEEVARKieaTTLENLAKDIS----VDLANMTIIIELDEEMLE---DRGLTVDD 175
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1084 VLDTtdggeqfyfLPQNTIVTVRDGETIGVgdvigrvpqetsrtrdITGGLPRVADLFEAR-KPKEHAIlaevSGVvsfg 1162
Cdd:PRK04309 176 VKEA---------IEKKKGGEVEIEGNTLI----------------ISPKEPSYRELRKLAeKIRNIKI----KGI---- 222
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1163 ketKGKNRLVITPD--------DGSEIYEelipkwrqinVFEGEHVNRGETISDgpqNPHDILRLKGEVALTNYIVNEVQ 1234
Cdd:PRK04309 223 ---KGIKRVIIRKEgdeyviytEGSNLKE----------VLKVEGVDATRTTTN---NIHEIEEVLGIEAARNAIIEEIK 286
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1235 DVYRLQGVKINDKHIEVVVRQMlrkvdITDGgdtsfiKGEQVDYIRVVQENQAVLAQnkfpakferqlmgitkaslstds 1314
Cdd:PRK04309 287 NTLEEQGLDVDIRHIMLVADMM-----TWDG------EVRQIGRHGVSGEKASVLAR----------------------- 332
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 480084187 1315 fisaASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTG 1358
Cdd:PRK04309 333 ----AAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1228-1362 |
3.64e-16 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 84.44 E-value: 3.64e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1228 YIVNEV--QDVYRLQGVkINDKHIEVVVRQMLRKVDI------------------TDGGDTSFIKGEQVDYIR---VVQE 1284
Cdd:COG0086 560 YLVNEIlpQEVPFYNQV-INKKHIEVIIRQMYRRCGLketvifldrlkklgfkyaTRAGISIGLDDMVVPKEKqeiFEEA 638
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1285 NQAVLAQNK--------FPAKFERQLMGITKASLSTDSFISAA-SFQETTRVLTEAAVTGKEDDL------RGLKEN--- 1346
Cdd:COG0086 639 NKEVKEIEKqyaeglitEPERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLrqlagmRGLMAKpsg 718
|
170 180
....*....|....*....|
gi 480084187 1347 ----VVVGRLIPAGTGLAYH 1362
Cdd:COG0086 719 niieTPIGSNFREGLGVLEY 738
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
868-1358 |
1.20e-15 |
|
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: 80.37 E-value: 1.20e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 868 LIDEKIAAQLEEAGVDEVKVRSVIAcestfgVCARCYGRDLarghlVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAAS 947
Cdd:cd06528 2 LLKEKLEEVLKEHGLTLSEAEEIIK------EVLREYLRSL-----IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 948 RtsaaNSVQvrnkGTVRFhnVKTVQHAKGHlvsVSRSGEIGIADDLGRERERYKlpygasilikdgesveaggivatwdp 1027
Cdd:cd06528 71 I----NVTL----GLPRL--IEIVDARKEP---STPTMTIYLEEEYKYDREKAE-------------------------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1028 hthplvtEVAGKARFSQIADgVTATSKTDDATGMTTVEILPvtaRPASGKDLRPAIVLdttdggeqfyflpqNTIVTVRD 1107
Cdd:cd06528 112 -------EVARKIEETTLEN-LAEDISIDLFNMRITIELDE---EMLEDRGITVDDVL--------------KAIEKLKK 166
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1108 GETIGVGDVIGRVPQEtsrtrditgGLPRVADLfeaRKPKEHAILAEVSGVvsfgketKGKNRLVITPDDGseiyeELIP 1187
Cdd:cd06528 167 GKVGEEGDVTLIVLKA---------EEPSIKEL---RKLAEKILNTKIKGI-------KGIKRVIVRKEED-----EYVI 222
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1188 KWRQIN---VFEGEHVNRGETISDgpqNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMlrkvditd 1264
Cdd:cd06528 223 YTEGSNlkaVLKVEGVDPTRTTTN---NIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIM-------- 291
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1265 ggdTSFIKGEQVDYIRVVQENQAVLAQnkfpakferqlmgitkaslstdsfisaASFQETTRVLTEAAVTGKEDDLRGLK 1344
Cdd:cd06528 292 ---TYDGEVRQIGRHGIAGEKPSVLAR---------------------------AAFEVTVKHLLDAAVRGEVDELRGVI 341
|
490
....*....|....
gi 480084187 1345 ENVVVGRLIPAGTG 1358
Cdd:cd06528 342 ENIIVGQPIPLGTG 355
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
862-1358 |
9.71e-15 |
|
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: 77.79 E-value: 9.71e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 862 VLPRgTLIDEKIAAQLEEAGVDEVKVRSVIAcestfgVCARCYGRDLarghlVNPGESVGVMAAQSIGEPGTQLTMRTFH 941
Cdd:TIGR02389 1 VLPE-KLLKELEETVKKREISDKEELDEIIK------RVEEEYLRSL-----IDPGEAVGIVAAQSIGEPGTQMTMRTFH 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 942 VGGAAsrtsaanSVQVrNKGTVRFhnVKTVQHAKghlVSVSRSGEIGIADDLGRERERyklpygasilikdgesveaggi 1021
Cdd:TIGR02389 69 YAGVA-------ELNV-TLGLPRL--IEIVDARK---TPSTPSMTIYLEDEYEKDREK---------------------- 113
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1022 vatwdphthplVTEVAGKARFSQIADGVTATSkTDDAtgmttveilpvtarpasgkDLRPAIVLDTtdggEQFyflpQNT 1101
Cdd:TIGR02389 114 -----------AEEVAKKIEATKLEDVAKDIS-IDLA-------------------DMTVIIELDE----EQL----KER 154
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1102 IVTVRDGETIGVGDVIGRVPQETSRTRDITGGL--PRVADLFEaRKPKEHAIlaEVSGVVSFGKE--TKGKNRLVITpDD 1177
Cdd:TIGR02389 155 GITVDDVEKAIKKAKLGKVIEIDMDNNTITIKPgnPSLKELRK-LKEKIKNL--HIKGIKGIKRVviRKEGDEYVIY-TE 230
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1178 GSEIYEelipkwrqinVFEGEHVNRGETISDgpqNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMl 1257
Cdd:TIGR02389 231 GSNLKE----------VLKLEGVDKTRTTTN---DIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLM- 296
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1258 rkvdITDGgdtsfiKGEQVDYIRVVQENQAVLAQnkfpakferqlmgitkaslstdsfisaASFQETTRVLTEAAVTGKE 1337
Cdd:TIGR02389 297 ----TWDG------EVRQIGRHGISGEKASVLAR---------------------------AAFEVTVKHLLDAAIRGEV 339
|
490 500
....*....|....*....|.
gi 480084187 1338 DDLRGLKENVVVGRLIPAGTG 1358
Cdd:TIGR02389 340 DELKGVIENIIVGQPIPLGTG 360
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
913-1358 |
1.47e-13 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 75.23 E-value: 1.47e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 913 LVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGaasrtsaansvqvrnkgtVRFHNVKtvqhakghlvsvsrsgeigiadd 992
Cdd:PRK14897 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAG------------------VAEMNVT----------------------- 216
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 993 LGREReryklpygasiLIkdgESVEAGGIVATwdP----HTHPLVTEVAGKARfsQIADGVTATSKTDDATGMTTVEILP 1068
Cdd:PRK14897 217 LGLPR-----------LI---EIVDARKKPST--PtmtiYLKKDYREDEEKVR--EVAKKIENTTLIDVADIITDIAEMS 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1069 VTARPASGKdlrpaivldttdggeqfyflpqntivtvRDGETIGVGDVIGRVPQETSRTRDITGGLPRVadlfearKPKE 1148
Cdd:PRK14897 279 VVVELDEEK----------------------------MKERLIEYDDILAAISKLTFKTVEIDDGIIRL-------KPQQ 323
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1149 HAI-----LAE------VSGVVSFGK---ETKGKNRLVITPDDGSEIYEelipkwrqinVFEGEHVNRGETISDgpqNPH 1214
Cdd:PRK14897 324 PSFkklylLAEkvksltIKGIKGIKRaiaRKENDERRWVIYTQGSNLKD----------VLEIDEVDPTRTYTN---DII 390
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1215 DILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMLRKVDITDGGDTSfIKGEQvdyirvvqenQAVLAQnkf 1294
Cdd:PRK14897 391 EIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIGRHG-ISGEK----------SSVLAR--- 456
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 480084187 1295 pakferqlmgitkaslstdsfisaASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTG 1358
Cdd:PRK14897 457 ------------------------AAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
917-948 |
1.35e-10 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 61.28 E-value: 1.35e-10
10 20 30
....*....|....*....|....*....|..
gi 480084187 917 GESVGVMAAQSIGEPGTQLTMRTFHVGGAASR 948
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASM 32
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
913-944 |
1.57e-10 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 64.14 E-value: 1.57e-10
10 20 30
....*....|....*....|....*....|..
gi 480084187 913 LVNPGESVGVMAAQSIGEPGTQLTMRTFHVGG 944
Cdd:cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
913-947 |
2.83e-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: 63.01 E-value: 2.83e-10
10 20 30
....*....|....*....|....*....|....*
gi 480084187 913 LVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAAS 947
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVAS 40
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
913-949 |
6.87e-10 |
|
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: 62.99 E-value: 6.87e-10
10 20 30
....*....|....*....|....*....|....*..
gi 480084187 913 LVNPGESVGVMAAQSIGEPGTQLTMRTFHVGGAASRT 949
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKN 59
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1135-1358 |
2.24e-07 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 55.67 E-value: 2.24e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1135 PRVADLFEaRKPKEHAIL----AEVSGVVSFGKETKGKNRLVITpDDGSEIYEelipkwrqinVFEGEHVNRGETISDgp 1210
Cdd:PRK14898 668 PSYKALRK-RIPKIKNIVlkgiPGIERVLVKKEEHENDEEYVLY-TQGSNLRE----------VFKIEGVDTSRTTTN-- 733
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 480084187 1211 qNPHDILRLKGEVALTNYIVNEVQDVYRLQGVKINDKHIEVVVRQMlrkvdiTDGGDTSFIkgeqvdyirvvqenqavla 1290
Cdd:PRK14898 734 -NIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIM------TADGEVKPI------------------- 787
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 480084187 1291 qnkfpakferqlmGITKASLSTDSFISAASFQETTRVLTEAAVTGKEDDLRGLKENVVVGRLIPAGTG 1358
Cdd:PRK14898 788 -------------GRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
913-937 |
7.49e-04 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 44.11 E-value: 7.49e-04
10 20
....*....|....*....|....*
gi 480084187 913 LVNPGESVGVMAAQSIGEPGTQLTM 937
Cdd:PRK14898 53 LVEPYEAVGIVAAQSIGEPGTQMSL 77
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