|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
26-1382 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2383.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 26 EFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEKCGVELALA 105
Cdd:PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 106 KVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPGMTELERGQLLNDEAYLDAMEQYGDE 185
Cdd:PRK00566 86 KVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGDE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 186 FDARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKITKRLKLLEAFYDSGNKPEWMIMDVLPVLPPDLRPLVPL 265
Cdd:PRK00566 166 FVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 266 DGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKGKQ 345
Cdd:PRK00566 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQ 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 346 GRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKKMVEREESVVWDILDDV 425
Cdd:PRK00566 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEV 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 426 IREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPAS 505
Cdd:PRK00566 406 IKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 506 GEPIIVPSQDVVLGLYYLTREKVNALGEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKEneaghHLVETTVGRAILAQI 585
Cdd:PRK00566 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSK-----KLVETTVGRVIFNEI 560
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 586 LPKGMSFVQINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNEVR 665
Cdd:PRK00566 561 LPEGLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIEEAEKEVA 640
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 666 EIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKIATeqvanvkgeliRQESFNPIFMMADSGARGSAAQIRQLAG 745
Cdd:PRK00566 641 EIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLSK-----------DQESFNPIYMMADSGARGSASQIRQLAG 709
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 746 MRGLMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGVLM 825
Cdd:PRK00566 710 MRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCGTDRGIEV 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 826 QPLIEGGDIVEPLHERVLGRVVAADVYIPNHSEPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRFGLCAKCYGRD 905
Cdd:PRK00566 790 TAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVCAKCYGRD 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 906 LARGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAasrataanniqiktkgvirlhniktvthenknlvavsrsgev 985
Cdd:PRK00566 870 LATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV------------------------------------------ 907
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 986 tivdefgrererykvpygavitvqdnsnveagqiiatwdphthpvisevggylkfvdlfdgitmnrqtdeltglsnivvi 1065
Cdd:PRK00566 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1066 dakqrssagrdlrpmvklvtetgeDIylagtnvpaqyylpvdaivnfedgghvgigdviaripqersktrdiTGGLPRVA 1145
Cdd:PRK00566 908 ------------------------DI----------------------------------------------TGGLPRVA 917
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1146 DLFEARKPKDSAVMAEVSGMVSFGKETKGKRRLIINVSEDQCHEELIPKWRHISVFEGEHVERGEIIAEGALNPHDILRL 1225
Cdd:PRK00566 918 ELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSIDPHDILRV 997
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1226 LGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESVLLQENDKLIAEGKQVARGI 1305
Cdd:PRK00566 998 LGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEGKEPATGR 1077
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 269987147 1306 PILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTGYAYHQGRKIKRAKAAAGE 1382
Cdd:PRK00566 1078 PVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAVDEEEA 1154
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
24-1202 |
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: 1914.91 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 24 SEEFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEKCGVELA 103
Cdd:COG0086 4 VEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 104 LAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPGMTELERGQLLNDEAYLDAMEQYG 183
Cdd:COG0086 84 LSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 184 DEFDARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKITKRLKLLEAFYDSGNKPEWMIMDVLPVLPPDLRPLV 263
Cdd:COG0086 164 DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 264 PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKG 343
Cdd:COG0086 244 PLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 344 KQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKKMVEREESVVWDILD 423
Cdd:COG0086 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 424 DVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSP 503
Cdd:COG0086 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 504 ASGEPIIVPSQDVVLGLYYLTREKVNALGEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKENEAGHHLVETTVGRAILA 583
Cdd:COG0086 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGEQVGKIVETTVGRYLVN 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 584 QILPKGMSFvqINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNE 663
Cdd:COG0086 564 EILPQEVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIFEEANKE 641
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 664 VREIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKIAteqvanvkgelirqeSFNPIFMMADSGARGSAAQIRQL 743
Cdd:COG0086 642 VKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS---------------SQNTTYMMADSGARGSADQLRQL 706
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 744 AGMRGLMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGV 823
Cdd:COG0086 707 AGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDCGTDRGI 786
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 824 LMQPLIEGGDIVEPLHERVLGRVVAADVYIPNHSEPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRFGLCAKCYG 903
Cdd:COG0086 787 TVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGVCAKCYG 866
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 904 RDLARGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRATAANNIQIKTKGVIRLHNIKTVTHENKNLVAVSRSG 983
Cdd:COG0086 867 RDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGVVVSRNS 946
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 984 EVTIVDEFGRERERYKVPYGAVITVQDNSNVEAGQIIATWDPHTHPVISEVGGYLKFVDLFDGITMNRQTDELTGLSNIV 1063
Cdd:COG0086 947 ELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEETGGLSIV 1026
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1064 VIDAKQRSSAGRDLRPMVKLVTETGEDIYLAGTNVPAQYYLPVDAIVNFEDGGHVGIGDVIARIPQERSKTRDITGGLPR 1143
Cdd:COG0086 1027 VEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDGTGGLAR 1106
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*....
gi 269987147 1144 VADLFEARKPKDSAVMAEVSGMVSFGKETKGKRRLIINVSEDQCHEELIPKWRHISVFE 1202
Cdd:COG0086 1107 VAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
29-1369 |
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: 1852.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 29 AIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEKCGVELALAKVR 108
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 109 RERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPGMTELERGQLLNDEAYLDAMEQYGDEFDA 188
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 189 RMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKITKRLKLLEAFYDSGNKPEWMIMDVLPVLPPDLRPLVPLDGG 268
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 269 RFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKGKQGRF 348
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 349 RQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKKMVEREESVVWDILDDVIRE 428
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 429 HPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEP 508
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 509 IIVPSQDVVLGLYYLTREKVNALGEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKEneaghhLVETTVGRAILAQILPK 588
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSGE------ILETTVGRVIFNEILPE 554
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 589 GMSFVQINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNEVREIE 668
Cdd:TIGR02386 555 GFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADKEVAKIQ 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 669 AQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKIATEQVanvkgelirqeSFNPIFMMADSGARGSAAQIRQLAGMRG 748
Cdd:TIGR02386 635 KFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLKKDTY-----------KFNPIFMMADSGARGNISQFRQLAGMRG 703
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 749 LMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGVLMQPL 828
Cdd:TIGR02386 704 LMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEGIEVEAI 783
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 829 IEGGD-IVEPLHERVLGRVVAADVYIPNHSEPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRFGLCAKCYGRDLA 907
Cdd:TIGR02386 784 VEGKDeIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKCYGRDLA 863
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 908 RGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRataanniqiktkgvirlhniktvthenknlvavsrsgevti 987
Cdd:TIGR02386 864 TGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGA----------------------------------------- 902
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 988 vdefgrererykvpygavitvqdnsnveagqiiatwdphthpvisevggylkfvdlfdgitmnrqtdeltglsnivvida 1067
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1068 kqrssagrdlrpmvklvtetgediylagtnvpaqyylpvdaivnfedgghvgigdviaripqerskTRDITGGLPRVADL 1147
Cdd:TIGR02386 903 ------------------------------------------------------------------SGDITQGLPRVKEL 916
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1148 FEARKPKDSAVMAEVSGMVSFGKET-KGKRRLIINVSEDQCHEELIPKWRHISVFEGEHVERGEIIAEGALNPHDILRLL 1226
Cdd:TIGR02386 917 FEARTPKDKAVIAEVDGTVEIIEDIvKNKRVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPHDLLRIK 996
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1227 GVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESVLLQENDKLIAEGKQVARGIP 1306
Cdd:TIGR02386 997 GIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKKPASAIP 1076
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 269987147 1307 ILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTGYAYHQ 1369
Cdd:TIGR02386 1077 QLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYK 1139
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
24-1364 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1601.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 24 SEEFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEKCGVELA 103
Cdd:PRK14844 1445 AQSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVT 1524
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 104 LAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPGMTELERGQLLNDEAYLDAMEQYG 183
Cdd:PRK14844 1525 SSKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYG 1604
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 184 -DEFDARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKITKRLKLLEAFYDSGNKPEWMIMDVLPVLPPDLRPL 262
Cdd:PRK14844 1605 iDSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPL 1684
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 263 VPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGraiTGTNKRPL----KSLA 338
Cdd:PRK14844 1685 VSLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRN---ALVNKAGAvgykKSIS 1761
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 339 DMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKKMVEREESVV 418
Cdd:PRK14844 1762 DMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEV 1841
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 419 WDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTN 498
Cdd:PRK14844 1842 WDMLEEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTN 1921
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 499 NILSPASGEPIIVPSQDVVLGLYYLTREKVNAlGEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKENEAG---HHLVET 575
Cdd:PRK14844 1922 NVLSPSNGRPIIVPSKDIVLGIYYLTLQEPKE-DDLPSFGAFCEVEHSLSDGTLHIHSSIKYRMEYINSSGethYKTICT 2000
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 576 TVGRAILAQILPK--GMSFVQINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDK 653
Cdd:PRK14844 2001 TPGRLILWQIFPKheNLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETK 2080
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 654 ASIIDHAYNEVREIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKIATEQvanvkgeliRQESFNPIFMMADSGA 733
Cdd:PRK14844 2081 ATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIYD---------GNSKYNSVYMMVNSGA 2151
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 734 RGSAAQIRQLAGMRGLMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVIT 813
Cdd:PRK14844 2152 RGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVT 2231
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 814 EDDCGVDTGVLMQPLIEGGDIVEPLHERVLGRVVAADVYIPNHSEPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQT 893
Cdd:PRK14844 2232 KHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEI 2311
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 894 RFGLCAKCYGRDLARGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRATAANNIQIKTKGVIRLHNIKTVTHEN 973
Cdd:PRK14844 2312 SPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKN 2391
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 974 KNLVAVSRSGEVTIVDEFGRERERYKVPYGAVITVQDNSNVEAGQIIATWDPHTHPVISEVGGYLKFVDLFDGITMNRQT 1053
Cdd:PRK14844 2392 GNKIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEVM 2471
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1054 DELTGLSNIVVIDAKQRsSAGRDLRPMVKLVTETGEDIYLAgTNVPAQYYLPVDAIVNFEDGGHVGIGDVIARIPQERSK 1133
Cdd:PRK14844 2472 DESTGISSKVVKDWKLY-SGGANLRPRIVLLDDNGKVMTLA-SGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESVK 2549
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1134 TRDITGGLPRVADLFEARKPKDSAVMAEVSGMVSFG-KETKGKRRLIINVSEDQCH--EELIPKWRHISVFEGEHVERGE 1210
Cdd:PRK14844 2550 TRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDEQISpvEYLVSRSKHVIVNEGDFVRKGD 2629
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1211 IIAEGALNPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESVLLQE 1290
Cdd:PRK14844 2630 LLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRE 2709
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 269987147 1291 NDKLIAEGKQVARGIPILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:PRK14844 2710 NDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTG 2783
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
17-1364 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1586.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 17 ILKQQGQSEEFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGV-IC 95
Cdd:PRK09603 1386 VIKEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTC 1465
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 96 EKCGVELALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPG--------MTELERG 167
Cdd:PRK09603 1466 EKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGeaaydnegTKLVMKY 1545
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 168 QLLNDEAYLDAMEQYGDE-FDARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKITKRLKLLEAFYDSGNKPEW 246
Cdd:PRK09603 1546 DILNEEQYQNISRRYEDRgFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEW 1625
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 247 MIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAI 326
Cdd:PRK09603 1626 MMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAV 1705
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 327 TGTNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKA 406
Cdd:PRK09603 1706 KGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQ 1785
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 407 AKKMVEREESVVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEA 486
Cdd:PRK09603 1786 AKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEA 1865
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 487 QLEARSLMMSTNNILSPASGEPIIVPSQDVVLGLYYLTREKVNALGEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKen 566
Cdd:PRK09603 1866 IAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQG-- 1943
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 567 eaghHLVETTVGRAILAQILPKGMSFVQINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDD 646
Cdd:PRK09603 1944 ----NIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGISISMED 2019
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 647 MEIPDDKASIIDHAYNEVREIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKIATEqvanvkgelirQESFNPIF 726
Cdd:PRK09603 2020 IITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKD-----------KEGFNSIY 2088
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 727 MMADSGARGSAAQIRQLAGMRGLMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDV 806
Cdd:PRK09603 2089 MMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLTRKLIDV 2168
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 807 AQDVVITEDDCGVDTGVLMQPLIEGGDIVEPLHERVLGRVVAADVYIPNHSEPVVTAGTLLDEAWVEKLEKQGVDQILVR 886
Cdd:PRK09603 2169 SQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGIKSITIR 2248
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 887 SPITCQTRFGLCAKCYGRDLARGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRATAANNIQIKTKGVIRLHNI 966
Cdd:PRK09603 2249 TPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGFVRFYNL 2328
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 967 KTVTH-ENKNLVAVSRSGEVTIVD-----EF-------------------GRERERY----------------------- 998
Cdd:PRK09603 2329 RTYTNkEGKNIIANRRNASILVVEpkikaPFdgelrietvyeevvvsvknGDQEAKFvlrrsdivkpselagvggkiegk 2408
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 999 -----------------------------KVPYGAVITVQDNS----------------------------NVEAGQ--- 1018
Cdd:PRK09603 2409 vylpyasghkvhkggsiadiiqegwnvpnRIPYASELLVKDNDpiaqdvyakekgiikyyvleanhlerthGIKKGDivs 2488
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1019 --------------------------------------------------IIATWDPHTHPVISEVGGYLKFVDLFDGIT 1048
Cdd:PRK09603 2489 ekglfaviaddngreaarhyiargseiliddnsevsansviskpttntfkTIATWDPYNTPIIADFKGKVSFVDIIAGVT 2568
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1049 MNRQTDELTGLSNIVVIDAKQRSsagrdLRPMVKLVTETGEDIylagtnvpaQYYLPVDAIVNFEDGGHVGIGDVIARIP 1128
Cdd:PRK09603 2569 VAEKEDENTGITSLVVNDYIPSG-----YKPSLFLEGANGEEI---------RYFLEPKTSIAISDGSSVEQAEVLAKIP 2634
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1129 QERSKTRDITGGLPRVADLFEAR--KPKDSAVMAEVSGMVSFGKETKGKRRLIINVSEDQCHEELIPKWRHISVFEGEHV 1206
Cdd:PRK09603 2635 KATVKSRDITGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVDKGKQILVHADEFV 2714
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1207 ERGEIIAEGALNPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESV 1286
Cdd:PRK09603 2715 HAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGDLVSKKL 2794
|
1450 1460 1470 1480 1490 1500 1510
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 269987147 1287 LLQENDKLIAEGKQVARGIPILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:PRK09603 2795 FKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIPVGTG 2872
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
25-816 |
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: 1329.07 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 25 EEFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEKCGVELAL 104
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 105 AKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFeafvvvdpgmtelergqllndeayldameqygd 184
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 185 efdarmgaeairdllrqvdledeirslreelpttnsetkikkitkrlkLLEAFYDSGNKPEWMIMDVLPVLPPDLRPLVP 264
Cdd:cd01609 128 ------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQ 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 265 LDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKGK 344
Cdd:cd01609 160 LDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGK 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 345 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKKMVEREESVVWDILDD 424
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 425 VIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPA 504
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 505 SGEPIIVPSQDVVLGLYYLTREKVNALGEGKIfvsaqeaqnfyeaghldihakikirmpkeneaghhlvETTVGRAILAQ 584
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTKERKGDKGEGII-------------------------------------ETTVGRVIFNE 442
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 585 ILPKGMSFvqINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNEV 664
Cdd:cd01609 443 ILPEGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEAEEKV 520
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 665 REIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMskiateqvanvkgELIRQESFNPIFMMADSGARGSAAQIRQLA 744
Cdd:cd01609 521 KEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMM-------------KNLDKDPFNPIYMMADSGARGSKSQIRQLA 587
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 269987147 745 GMRGLMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDD 816
Cdd:cd01609 588 GMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
24-1369 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1319.49 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 24 SEEFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEKCGVELA 103
Cdd:PRK14906 6 VTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVT 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 104 LAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVV--------------------------- 156
Cdd:PRK14906 86 RAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleeld 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 157 --------------------------------------VDPGMTEL---------------------ERGQLLNDEAYLD 177
Cdd:PRK14906 166 aerdrlieatrrlsvdyvpeddefvddigdderltaeeVRAEVADIyeeynerkalrreafdafmqiEPKQLISDEALYR 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 178 AMEQ-YGDEFDARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKItKRLKLLEAFYDSGNKPEWMIMDVLPVLP 256
Cdd:PRK14906 246 EMRLnYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRAIIANGKGQKREKAV-KRLKVVDAFLKSGNDPADMILDVIPVIP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 257 PDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKS 336
Cdd:PRK14906 325 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKS 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 337 LADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKKMVEREES 416
Cdd:PRK14906 405 LADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 417 VVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMS 496
Cdd:PRK14906 485 YVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLS 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 497 TNNILSPASGEPIIVPSQDVVLGLYYLTREKVNALGEGKIFVSAQEAQNFYEA-GHLDIHAKIKIRMPK----------- 564
Cdd:PRK14906 565 SNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDArADLDLQAKIVVRLSRdmtvrgsygdl 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 565 -ENEAGHHlVETTVGRAILAQILPKGMSFvqINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIG 643
Cdd:PRK14906 645 eETKAGER-IETTVGRIIFNQVLPEDYPY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVS 721
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 644 IDDMEIPDDKASIIDHAYNEVREIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKIAteqvanvkgelirqeSFN 723
Cdd:PRK14906 722 VYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFD---------------EDN 786
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 724 PIFMMADSGARGSAAQIRQLAGMRGLMAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRL 803
Cdd:PRK14906 787 PIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRL 866
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 804 VDVAQDVVITEDDCGVDTGVLMQPLIEGGDIVEPLhervLGRVVAADVYIPNhSEPVVTAG---TLLDEawVEKLEKQGV 880
Cdd:PRK14906 867 VDVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDPN-GEVLLSAGdyiESMDD--LKRLVEAGV 939
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 881 DQILVRSPITCQTRFGLCAKCYGRDLARGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAAsrataanniqiktkgv 960
Cdd:PRK14906 940 TKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGVA---------------- 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 961 irlhniktvthenknlvavsrsgevtivdefgrererykvpygavitvqdnsnveagqiiatwdphthpvisevggylkf 1040
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1041 vdlfdgitmnrqtdeltglsnivvidakqrssagrdlrpmvklvtetgediylagtnvpaqyylpvdaivnfedgghvgi 1120
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1121 GDviaripqersktrDITGGLPRVADLFEARKPKDSAVMAEVSGMVSFGKETKGKrRLIINVSEDQCHEELIPKWRHI-- 1198
Cdd:PRK14906 1004 GD-------------DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEK-TLTIHDQDGNSREYVVSARVQFmp 1069
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1199 SVFEGEHVERGEIIAEGALNPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLV 1278
Cdd:PRK14906 1070 GVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLP 1149
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1279 GEQIEESVLLQENDKLIAEGKQVARGIPILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRL 1358
Cdd:PRK14906 1150 GRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKP 1229
|
1450
....*....|..
gi 269987147 1359 IPAGTGY-AYHQ 1369
Cdd:PRK14906 1230 IPAGTGLsRYRD 1241
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
23-574 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 822.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 23 QSEEFDAIKIALASPELIRSWS---------YGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGV 93
Cdd:PRK02625 5 TENRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 94 ICEKCGVELALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPG-MTELERGQLLND 172
Cdd:PRK02625 85 VCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGnHKNLKYKQLLTE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 173 EAYLDAMEQ--------YGDEFdARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKItKRLKLLEAFYDSGNKP 244
Cdd:PRK02625 165 DQWLEIEDQiyaedselEGEEV-VGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQKRAKLI-KRLRVIDNFIATGSRP 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 245 EWMIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGR 324
Cdd:PRK02625 243 EWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGR 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 325 AITGTNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTI 404
Cdd:PRK02625 323 TVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNI 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 405 KAAKKMVEREESVVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTL 484
Cdd:PRK02625 403 KAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSL 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 485 EAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLGLYYLTREKVNAL-GEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMP 563
Cdd:PRK02625 483 EAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAQkGAGRYFASLEDVIMAFEQGRIDLHAWVWVRFN 562
|
570
....*....|.
gi 269987147 564 KENEAGHHLVE 574
Cdd:PRK02625 563 GEVEDDDEDTE 573
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
27-610 |
0e+00 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 811.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 27 FDAIKIALASPELIRSWS---------YGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKRLKHRGVICEK 97
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 98 CGVELALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVVVDPG-MTELERGQLLNDEAYL 176
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGnAKNLKYKQLLTEDQWL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 177 DAMEQ-YGDEFD------ARMGAEAIRDLLRQVDLEDEIRSLREELPTTNSETKIKKItKRLKLLEAFYDSGNKPEWMIM 249
Cdd:TIGR02387 162 EIEDQiYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQKRAKLI-KRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 250 DVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRGRAITGT 329
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 330 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATTIKAAKK 409
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 410 MVEREESVVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLE 489
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 490 ARSLMMSTNNILSPASGEPIIVPSQDVVLGLYYLTREKVNAL-GEGKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKENEA 568
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAEkGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVET 560
|
570 580 590 600
....*....|....*....|....*....|....*....|..
gi 269987147 569 GHHLVETTVGRAILAQILPKGMSFVQINRTMTKKVITKVIDT 610
Cdd:TIGR02387 561 NDPLDEPIKSEDLSDGTRIEQWTYRRDRFDEDGALISQYILT 602
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
26-586 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 798.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 26 EFDAIKIALASPELIRSWSY---------GEVKKPETINYRTFKPERDGLFCAKTFGPVKDYECLCGKYKR---LKHRGV 93
Cdd:CHL00018 6 KHQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVigdEKEDPK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 94 ICEKCGVELALAKVRRERMGHIELASPVAHIWFLKSLPSRIGLLLDMTLRDIERVLYFEAFVV--VDPGMTELERGQLLN 171
Cdd:CHL00018 86 FCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRLRGLFE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 172 DEA----YLDAMEQYGDEFDARM------GAEAIRDLLRQVDLED-------EIRSLREELPTTN--SETKIKK----IT 228
Cdd:CHL00018 166 YEIqswkYSIPLFFSTQGFDTFRnreistGAGAIREQLADLDLRIiidnslvEWKELGEEGSTGNewEDRKIGRrkdfLV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 229 KRLKLLEAFYDSGNKPEWMIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLN--APDIIVRNEK 306
Cdd:CHL00018 246 RRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQK 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 307 RMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALEL 386
Cdd:CHL00018 326 KLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 387 FKPFIFSKLEFRGLATTIKAAKKMVEREESVVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTA 466
Cdd:CHL00018 406 FQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 467 YNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLGLYYLTREKVNAL-------------GE 533
Cdd:CHL00018 486 FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRGIyanrynpcnrknsTK 565
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 534 GKIFVSAQEAQNFYEAGHLDIHA------KIKIRMPKENEA----------------GHHLVE-------------TTVG 578
Cdd:CHL00018 566 EPYFSNSYDALGAYRQKRINLDSplwlrwRLDQRIIASREVpievqyeslgtyheiyEHYLIVksrkkeilsiyirTTVG 645
|
....*...
gi 269987147 579 RAILAQIL 586
Cdd:CHL00018 646 RILFNREI 653
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
35-815 |
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: 586.32 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 35 ASPELIRSWSYGEVKKPETINYRTFKPERDGlfcaktfgpvkdyeclcgKYKRLKHRGVICEKCGVELALAKVRRERMGH 114
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 115 IELASPVAHIWFLKSLPSRIGllldmtlrdiervlyfeafvvvdpgmtelergqllndeayldameqygdefdarmgaea 194
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 195 irdllrqvdledeirslreelpttnsetkikkitkrlklleafydsgnkPEWMIMDVLPVLPPDLRPLVpldggrfatsd 274
Cdd:cd00399 84 -------------------------------------------------PEWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 275 lndlyrrvinrnnrlkrlldlnapdiIVRNEKRMLQESVDALLDNGRRGRAITGTNKRPLKSLADMIKGKQGRFRQNLLG 354
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 355 KRVDYSGRSVIVVGPTLKLHQCGLPKKMALELfkpfifsklefrglattikaakkmvereesvvwdilddviREHPILLN 434
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 435 RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQ 514
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 515 DVVLGLYYLTRekvnalgegkifvsaqeaqnfyeaghldihakikirmpkeneaghhlvettvGRAILAQILPKGMSFvq 594
Cdd:cd00399 278 DTLLGAYLLTL----------------------------------------------------GKQIVSAALPGGLLH-- 303
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 595 inrtmtkkvitkvidTCYRTFGLKETVIFADKLMYTGFKYATRSGASIG----IDDMEIPDDKASIIDHAYNEVREIEAQ 670
Cdd:cd00399 304 ---------------TVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGigdvIDDGVIPEEKTELIEEAKKKVDEVEEA 368
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 671 FRSGLVTNGER-------YNKVIDIWSRTNELVAKSMMSkiateqvanvkgELIRQESFNPIFMMADSGARGSAAQIRQL 743
Cdd:cd00399 369 FQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASV------------NLDLVSKFNSIYVMAMSGAKGSFINIRQM 436
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 744 AGMRGLMAAPDGSI--------------------IETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRL 803
Cdd:cd00399 437 SACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESGYLQRRL 516
|
810
....*....|..
gi 269987147 804 VDVAQDVVITED 815
Cdd:cd00399 517 VKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
245-521 |
3.62e-159 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 480.48 E-value: 3.62e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 245 EWMIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNG--RR 322
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 323 GRAITGtnkRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLE------ 396
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 397 ------------FRGLATTIKAAKKM-VEREESVVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV 463
Cdd:smart00663 158 lvrngpngakyiIRGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 269987147 464 CTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLGLY 521
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
769-1274 |
2.58e-137 |
|
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: 431.39 E-value: 2.58e-137
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 769 GLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGVLMQPLIEGGDIVEPLHERVLGRVVA 848
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 849 ADVYIPN-HSEPVVTAGTLLDEAWV--------------------------------EKLEKQGVDQILVRSPITCQTRF 895
Cdd:pfam04998 81 EFSDLKLeDKFKNDLLDDLLLLSEFslsykkeilvrdsklgrdrlskeaqeratllfELLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 896 GLCAKCYGRDLARGHLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRATaanniqikTKGVIRLHNIKTVTHENKn 975
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNV--------TLGVPRLKEIINVSKNIK- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 976 lvavSRSGEVTIVDEFGRERERYKVPYGAVITVQDNSNVEAGQIIATWDPHTHPVISEVGGYLKFVDLFDGITMNRQTDE 1055
Cdd:pfam04998 232 ----SPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEIDP 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1056 LTGLSNIVVIDAKQRSSAGRDlrpmvklvtetgediylagtnvPAQYYLPVDAIVNFEDGGHVGIGDVIARIPQERS-KT 1134
Cdd:pfam04998 308 ETGLLILVIRLLKILNKSIKK----------------------VVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISkKI 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1135 RDITGGLPRVADLFEARKPKDSAVMAEVSGmVSFGKETKGKRRLIINVSED-------QCHEELIPKWRHISVFegEHVE 1207
Cdd:pfam04998 366 RQDTGGLRRVDELFMEEDPKLAILVASLLG-NITLRGIPGIKRILVNEDDKgkvepdwVLETEGVNLLRVLLVP--GFVD 442
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 269987147 1208 RGEIIAEgalNPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDS 1274
Cdd:pfam04998 443 AGRILSN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRH 506
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
590-1043 |
2.18e-128 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 430.96 E-value: 2.18e-128
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 590 MSFvqINRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNEVREIEA 669
Cdd:PRK02597 1 PIF--RNRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 670 QFRSGLVTNGERYNKVIDIWSRTNElvaksmmskiatEQVANVKGELIRQESFNPIFMMADSGARGSAAQIRQLAGMRGL 749
Cdd:PRK02597 79 RYRRGEITEVERFQKVIDTWNETNE------------RLKDEVVKNFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGL 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 750 MAAPDGSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGVLMQPLI 829
Cdd:PRK02597 147 MANPQGEIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMD 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 830 EGGDIVEPLHERVLGRVVAADVYIPNhSEPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRFGLCAKCYGRDLARG 909
Cdd:PRK02597 227 DGDRVLIPLGDRLLGRVLAEDVVDPE-GEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHN 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 910 HLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGaASRATAANNIQIKTKGVIRL-HNIKTVTH-----ENKNLVAVsrSG 983
Cdd:PRK02597 306 HLVDLGEAVGIIAAQSIGEPGTQLTMRTFHTGG-VFTGEVARQVRSPFAGTVEFgKKLRTRPYrtrhgVEALQAEV--DF 382
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 269987147 984 EVTIVDEFGRERERYKVPYGAVITVQDNSNVEAGQIIA---------TWDPHTHPVISEVGGYLKFVDL 1043
Cdd:PRK02597 383 DLVLKPSGKGKPQKIEITQGSLLFVDDGQTVEADQLLAevaagavkkSTEKATKDVICDLAGEVRFADL 451
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
595-1021 |
3.85e-121 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 411.25 E-value: 3.85e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 595 INRTMTKKVITKVIDTcyrtFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNEVREIEAQFRSG 674
Cdd:CHL00117 14 IDKTALKRLISWLIDH----FGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYG 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 675 LVTNGERYNKVIDIWSRTNELVAKSMmskiateqVANVKgeliRQESFNPIFMMADSGARGSAAQIRQLAGMRGLMAAPD 754
Cdd:CHL00117 90 NVHAVEKLRQSIEIWYATSEYLKQEM--------NPNFR----MTDPLNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQ 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 755 GSIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGVLMQPLiEGGDI 834
Cdd:CHL00117 158 GQIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPR-NGMMI 236
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 835 VEPLHERVLGRVVAADVYIPNHSepVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRFGLCAKCYGRDLARGHLVNT 914
Cdd:CHL00117 237 ERILIQTLIGRVLADDIYIGSRC--IATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVEL 314
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 915 GEAVGIIAAQSIGEPGTQLTMRTFHIGG-----AASRATAANNIQIKTkgvirlhniktvtheNKNLVAVSRS--GE--- 984
Cdd:CHL00117 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGvftggTAEQVRAPFNGKIKF---------------NEDLVHPTRTrhGHpaf 379
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 269987147 985 -------VTIvdEFGRERERYKVPYGAVITVQDNSNVEAGQIIA 1021
Cdd:CHL00117 380 lckidlyVTI--ESEDIIHNVNIPPKSLLLVQNDQYVESEQVIA 421
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
596-1137 |
3.04e-117 |
|
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: 397.68 E-value: 3.04e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 596 NRTMTKKVITKVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPDDKASIIDHAYNEVREIEAQFRSGL 675
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 676 VTNGERYNKVIDIWSRTNElvaksmmskiatEQVANVKGELIRQESFNPIFMMADSGARGSAAQIRQLAGMRGLMAAPDG 755
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNE------------ELKDEVVNNFRQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 756 SIIETPITANFREGLNVFQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDTGVLMQPLIEGGDIV 835
Cdd:TIGR02388 152 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 836 EpLHERVLGRVVAADVYIPNhSEPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRFGLCAKCYGRDLARGHLVNTG 915
Cdd:TIGR02388 232 S-LGDRLLGRLVAEDVLHPE-GEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLG 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 916 EAVGIIAAQSIGEPGTQLTMRTFHIGGaASRATAANNIQIKTKGVIRL-HNIKTVTHENKNLV---AVSRSGEVTIVDEF 991
Cdd:TIGR02388 310 EAVGIIAAQSIGEPGTQLTMRTFHTGG-VFTGEVARQVRSKIDGTVEFgKKLRTRGYRTRHGEdakQVEVAGLLIIKPTG 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 992 GR--ERERYKVPYGAVITVQDNSNVEAGQIIA---------TWDPHTHPVISEVGGYLKFVDLFDGITMNRQtdeltglS 1060
Cdd:TIGR02388 389 SItnKAQEIEVTQGSLLFVEDGQTVDAGQLLAeialgavrkSTEKATKDVASDLAGEVKFDKVVPEEKTDRQ-------G 461
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1061 NIVVIDAKQ-----RSSAGRDLRPMVKLVTETGEDIYLAGtnvpaqyyLPVDAIVNFEDGGHVgigdviaRIPQERSKTR 1135
Cdd:TIGR02388 462 NTTRIAQRGgliwvLSGEVYNLPPGAEPVVKNGDRVEQGT--------VLAETKLSTEHGGVV-------RLPESVGDSR 526
|
..
gi 269987147 1136 DI 1137
Cdd:TIGR02388 527 EV 528
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
25-352 |
6.34e-107 |
|
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: 341.58 E-value: 6.34e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 25 EEFDAIKIALASPELIRSWSYGEVKKPETINYRTFKPERDGLFCAKTFGPVKDYEC-LCGKYKRlkhrgviceKCGVela 103
Cdd:pfam04997 2 KKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG--- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 104 lakvrreRMGHIELASPVAHIWFLKslpsrigllldMTLRDIERVLYFEAFVVVDPGmteleRGQLLNDEAYLDAMEQYg 183
Cdd:pfam04997 70 -------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENL- 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 184 defdaRMGAEAIRDLLRQVDL------------------EDEIRSLREELPTTNSE--------TKIKKITKRLK----L 233
Cdd:pfam04997 126 -----KMGAKAILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKKSKEEeekeilnpEKVLKIFKRISdedvE 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 234 LEAFYDSGNKPEWMIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESV 313
Cdd:pfam04997 201 ILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEHV 280
|
330 340 350 360
....*....|....*....|....*....|....*....|
gi 269987147 314 DALLDNGRRG-RAITGTNKRPLKSLADMIKGKQGRFRQNL 352
Cdd:pfam04997 281 ATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
28-837 |
8.46e-107 |
|
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: 359.64 E-value: 8.46e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 28 DAIKIALASPELIRSWSYGEVKKPETinYrtfkpERDGLfcaktfgPVK----DyeclcgkyKRLkhrGVI-----CEKC 98
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY-------PIEgglmD--------PRL---GVIepglrCKTC 59
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 99 GvelALAKVRRERMGHIELASPVAHIWFLKslpsRIGLLLDMTLRDIERVLyfeafvvvdpgMTELERgqllndEAYLDA 178
Cdd:cd02582 60 G---NTAGECPGHFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEI------EKYLER 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 179 MEQYG--DEFDARMGAEAIRDLLRQVDL----EDEIRSLREELPTTNSETKIKKITK------RLKL-------LEAF-Y 238
Cdd:cd02582 116 IRRLKekWPELVKRVIEKVKKKAKKRKVcphcGAPQYKIKLEKPTTFYEEKEEGEVKltpseiRERLekipdedLELLgI 195
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 239 DSGN-KPEWMIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALL 317
Cdd:cd02582 196 DPKTaRPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYF 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 318 DNgrrgrAITG------TNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFI 391
Cdd:cd02582 276 DN-----EIPGipparhRSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPER 350
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 392 FSKLefrglatTIKAAKKMVE-------------REESVVWDILD-------------DVIREH-----PILLNRAPTLH 440
Cdd:cd02582 351 VTEW-------NIEKMRKLVLngpdkwpganyviRPDGRRIRLRYvnreelaerlepgWIVERHlidgdIVLFNRQPSLH 423
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 441 RLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLGL 520
Cdd:cd02582 424 RMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGA 503
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 521 YYLTREkvNALgegkifVSAQEAqnfyeaghLDIHAKIKIRMPKENEAGHHLVETTVGRAILAQILPKGMSFVQINRTMT 600
Cdd:cd02582 504 YLLTRK--TTL------FTKEEA--------LQLLSAAGYDGLLPEPAILEPKPLWTGKQLFSLFLPKDLNFEGKAKVCS 567
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 601 KK--------------VIT--------------------KVIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDD 646
Cdd:cd02582 568 GCseckdedcpndgyvVIKngkllegvidkkaigaeqpgSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDD 647
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 647 MEIP----DDKASIIDHAYNEVREIEAQFRSGLVtngerynKVIDIWSRTNELVAKSM--MSKIATEqvanvKGELIRQ- 719
Cdd:cd02582 648 EDIPeearKEIEEIIKEAEKKVYELIEQYKNGEL-------EPLPGRTLEETLEMKIMqvLGKARDE-----AGKVASKy 715
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 720 -ESFNPIFMMADSGARGSAAQIRQLAGMRGLMAAPDGSIIE-----TP---------------ITANFREGLNVFQYFIS 778
Cdd:cd02582 716 lDPFNNAVIMARTGARGSMLNLTQMAACLGQQSVRGERINRgyrnrTLphfkpgdlgpeargfVRSSFRDGLSPTEFFFH 795
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 779 THGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDT-GVLMQpLIEGGDIVEP 837
Cdd:cd02582 796 AMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYDGTVRDSrGNIIQ-FKYGEDGVDP 854
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
29-837 |
3.82e-94 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 324.50 E-value: 3.82e-94
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 29 AIKIALASPELIRSWSYGEVKKPETinYrtfkpERDGLfcaktfgPVK----DyeclcgkyKRLkhrGVI-----CEKCG 99
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY-------PIDgglmD--------PRL---GVIdpglrCKTCG 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 100 velalaKVRRE---RMGHIELASPVAHIWFLKslpsRIGLLLDMTLRDIERVLyfeafvvvdpgMTELERgqllndEAYL 176
Cdd:PRK08566 66 ------GRAGEcpgHFGHIELARPVIHVGFAK----LIYKLLRATCRECGRLK-----------LTEEEI------EEYL 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 177 DAMEQYGDE-FDARMGAEAIRDLLRQVDL----EDEIRSLREELPTTNSETKIKKITK------RLKL-------LEAF- 237
Cdd:PRK08566 119 EKLERLKEWgSLADDLIKEVKKEAAKRMVcphcGEKQYKIKFEKPTTFYEERKEGLVKltpsdiRERLekipdedLELLg 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 238 YDSGN-KPEWMIMDVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDAL 316
Cdd:PRK08566 199 INPEVaRPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTY 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 317 LDNgrrgrAITGT------NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPF 390
Cdd:PRK08566 279 FDN-----EIPGIpparhrSGRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPE 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 391 IFS-------------------------KLEFRGLATTIKAAKKMVEREESvvwdilDDVIREH-----PILLNRAPTLH 440
Cdd:PRK08566 354 RVTewnieelreyvlngpekhpganyviRPDGRRIKLTDKNKEELAEKLEP------GWIVERHlidgdIVLFNRQPSLH 427
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 441 RLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLGL 520
Cdd:PRK08566 428 RMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGA 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 521 YYLTRekvnalgEGKIFvSAQEAQNFYEAGHLDihakikiRMPKENEAGHHLVETTVGRAILAQILPKGMSFVQ------ 594
Cdd:PRK08566 508 YLLTR-------KSTLF-TKEEALDLLRAAGID-------ELPEPEPAIENGKPYWTGKQIFSLFLPKDLNLEFkakics 572
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 595 ------------------INRTMTKKVITK---------VIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDM 647
Cdd:PRK08566 573 gcdeckkedcehdayvviKNGKLLEGVIDKkaigaeqgsILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTGIDDE 652
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 648 EIPDDKAS----IIDHAYNEVREIEAQFRSGLV------TNGE-RYNKVIDIWSRtnelvAKSMMSKIATEQVAnvkgel 716
Cdd:PRK08566 653 DIPEEAKEeideIIEEAEKRVEELIEAYENGELeplpgrTLEEtLEMKIMQVLGK-----ARDEAGEIAEKYLG------ 721
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 717 irqeSFNPIFMMADSGARGSAAQIRQLAGMRGLMAAPDGSIIE------TP--------------ITANFREGLNVFQYF 776
Cdd:PRK08566 722 ----LDNPAVIMARTGARGSMLNLTQMAACVGQQSVRGERIRRgyrdrtLPhfkpgdlgaeargfVRSSYKSGLTPTEFF 797
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 269987147 777 ISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDDCGVDT-GVLMQpLIEGGDIVEP 837
Cdd:PRK08566 798 FHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYDGTVRDTrGNIVQ-FKYGEDGVDP 858
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
28-1364 |
1.01e-83 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 301.56 E-value: 1.01e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 28 DAIKIALASPELIRSWSYGEVKKPETInyrtfkpERDGLfcaktfgPVKDyECLCGKYKRLKHRgvicEKCGVELALAKV 107
Cdd:PRK14977 10 DGIIFGLISPADARKIGFAEITAPEAY-------DEDGL-------PVQG-GLLDGRLGTIEPG----QKCLTCGNLAAN 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 108 RRERMGHIELASPVAHIWFLKslpsRIGLLLDMTLRDIERVLYFEAFVVVDPGMTELERGQLLNDEAYLDA--MEQYGDE 185
Cdd:PRK14977 71 CPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDeiIEEVRDQ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 186 FDARM---------GAEAIRDLLRQV-----DLEDEIRSLreeLPTTNSEtKIKKITKRLKLLEAFYDSGNKPEWMIMDV 251
Cdd:PRK14977 147 VKVYAkkakecphcGAPQHELEFEEPtifieKTEIEEHRL---LPIEIRD-IFEKIIDDDLELIGFDPKKARPEWAVLQA 222
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 252 LPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRG--RAITGT 329
Cdd:PRK14977 223 FLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHHKG 302
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 330 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFS--------KLEFRG-- 399
Cdd:PRK14977 303 SGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNenniekmkELVINGpd 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 400 ---------LATTIKAAKKMVEREESVVWDIL------DDVIREH-----PILLNRAPTLHRLGIQAFEPVLIEGKAIQL 459
Cdd:PRK14977 383 efpganairKGDGTKIRLDFLEDKGKDALREAaeqleiGDIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPGATFRL 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 460 HPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLGLYYLTREKVnalgegkiFVS 539
Cdd:PRK14977 463 HPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDDA--------LFD 534
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 540 AQEAQNFYE-AGHLDIHAKIKIRmPKENEAghhlvetTVGRAILAQILPKGMSFVQINRTMTKK---------------- 602
Cdd:PRK14977 535 KNEASNIAMlAGITDPLPEPAIK-TKDGPA-------WTGKQLFSLFLPKDFNFEGIAKWSAGKageakdpsclgdgyvl 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 603 ---------VITK------------VIDTCYRTFGLKETVIFADKLMYTGFKYATRSGASIGIDDMEIPD-DKASIID-- 658
Cdd:PRK14977 607 ikegelisgVIDDniigalveepesLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDeAKQEIEDdi 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 659 -HAYNEVREIEAQFRSGLVTNGERYNKVIDIWSRTNELVAKSMMSKI--ATEQVANVKGELIRQESFNPIfmMADSGARG 735
Cdd:PRK14977 687 qGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELdkARDKAGSSANDCIDADNAGKI--MAKTGARG 764
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 736 SAAQIRQLAGMRGLMAAPDGSIIETP----------------------------ITANFREGLNVFQYFISTHGARKGLA 787
Cdd:PRK14977 765 SMANLAQIAGALGQQKRKTRIGFVLTggrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGLI 844
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 788 DTALKTANSGYLTRRLVDVAQDVVITEDDCGVDT-GVLMQPLIeGGDIVEPLH---------ERVLGRVVAADVYIPNHS 857
Cdd:PRK14977 845 DKARRTEDSGYFQRRLANALEDIRLEYDETVRDPhGHIIQFKF-GEDGIDPQKldhgeafnlERIIEKQKIEDRGKGASK 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 858 EPVVTAGTLLDEAWVEKLEKQGVDQILVRSPITCQTRfGLCAKcyGRDLARGHLVNTGEAVGIIAAQSIGEPGTQLTMRT 937
Cdd:PRK14977 924 DEIEELAKEYTKTFNANLPKLLADAIHGAELKEDELE-AICAE--GKEGFEKAKVEPGQAIGIISAQSIAEPGTQMTLRT 1000
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 938 FHIGGAASRATaanniqikTKGVIRLhniktvthenKNLVAVSRSGEVTIVDefgrererykvpygavITVQDNSNVEAG 1017
Cdd:PRK14977 1001 FHAAGIKAMDV--------THGLERF----------IELVDARAKPSTPTMD----------------IYLDDECKEDIE 1046
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1018 QIIatwdphthpvisEVGGYLKFVDLFDGITmNRQTDELTglsNIVVIDAKQRSSAgRDLRPMVKlvtetgediylagtn 1097
Cdd:PRK14977 1047 KAI------------EIARNLKELKVRALIA-DSAIDNAN---EIKLIKPDKRALE-NGCIPMER--------------- 1094
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1098 vpaqyylpvdaivnfedgghvgIGDVIARIPQERSKTRDITGGLPRVADLFEARKPKDSAVMAEVSGMVsFGKETKG--- 1174
Cdd:PRK14977 1095 ----------------------FAEIEAALAKGKKFEMELEDDLIILDLVEAADRDKPLATLIAIRNKI-LDKPVKGvpd 1151
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1175 -KRRLIINVSEDQCHEELIPKWRH--ISVFEGEHVERGEIIAEgalNPHDILRLLGVGALANYIVNEVQDVYRLQGVKIN 1251
Cdd:PRK14977 1152 iERAWVELVEKDGRDEWIIQTSGSnlAAVLEMKCIDIANTITN---DCFEIAGTLGIEAARNAIFNELASILEDQGLEVD 1228
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1252 DKHIevivrqMLRKRVITFAGdskflVGEQIeesvllqendKLIAEGkqVARGIpillgitkaSLATESFISAASFQETT 1331
Cdd:PRK14977 1229 NRYI------MLVADIMCSRG-----TIEAI----------GLQAAG--VRHGF---------AGEKDSPLAKAAFEITT 1276
|
1450 1460 1470
....*....|....*....|....*....|...
gi 269987147 1332 RVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:PRK14977 1277 HTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
910-1365 |
2.27e-80 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 262.85 E-value: 2.27e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 910 HLVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasrataanniqiktkgvirlhniktvthenknlvavsrsgevtivd 989
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGG----------------------------------------------- 33
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 990 efgrererykvpygavitvqdnsnveagqiIATwdphthpvisevggylkfvdlfdgitmnrqtdeltglsnivvidakq 1069
Cdd:cd02655 34 ------------------------------VAT----------------------------------------------- 36
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1070 rssagrdlrpmvklvtetgediylagtnvpaqyylpvdaivnfedgghvgigdviaripqersktrDITGGLPRVADLFE 1149
Cdd:cd02655 37 ------------------------------------------------------------------DITQGLPRVEELFE 50
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1150 ARKPkdsavmaevsgmvsfgketkgkrrliinvsedqcheelipkwrhisvfegehvergeiiaegalNPHDILRLLGVG 1229
Cdd:cd02655 51 ARKI----------------------------------------------------------------NPHDLLRIKFLG 66
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1230 --ALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESVLLQENDKLIAEGKQVARGIPI 1307
Cdd:cd02655 67 peAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPV 146
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 269987147 1308 LLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTGY 1365
Cdd:cd02655 147 LLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1008-1369 |
1.81e-74 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 273.02 E-value: 1.81e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1008 VQDNSNVEAGQIIATwdphTHPVISEVG---GYLKFVDLFDGITMNRQTDELT-GLSNIVVIDAKQRSSAGRDLRPMVKl 1083
Cdd:PRK02597 847 VKDGQQIKPGDVVAR----TQILCKEAGevrGIRVGGEAVRRLLVERDEDTITiPLSGKPTVKVGDLVVAGDELAPGVP- 921
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1084 VTETGEDIYLAGTNVPAQ----YYLPVDAIVNFEDGGHVGIGDVIARIPQERSKTRDITGGLPRVADLFEARKPKDSAVM 1159
Cdd:PRK02597 922 APESGEVEAVSGGSVTLRlgrpYRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCIL 1001
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1160 AEVSGMVSFgkETKGKRRLIINVSE-DQCHEE--LIPKwRHISVFEGEHVERGEIIAEGALNPHDILR------------ 1224
Cdd:PRK02597 1002 AKKPGTVQI--KYGDDESVDVKVIEsDGTITEypILPG-QNVMVSDGQQVDAGEPLTDGPINPHELLEiffedlrdrkgl 1078
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1225 ----LLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESVLLQENDKLIAEGKQ 1300
Cdd:PRK02597 1079 yeaaLEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGA 1158
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 269987147 1301 VARGIPILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTGYAYHQ 1369
Cdd:PRK02597 1159 PAEYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFE 1227
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1008-1369 |
1.09e-72 |
|
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: 266.72 E-value: 1.09e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1008 VQDNSNVEAGQIIATWDphthpVISEVGGYLKFVD----LFDGITMNRQTDELT-GLSNIVVIDAKQRSSAGRDLRPMVK 1082
Cdd:TIGR02388 845 VKDGDLIKPGAVIARTQ-----ILCKEAGVVQGIDsggeSIRRLLVERNSDRLKvNIKAKPVVKTGDLVVAGDELAKGVK 919
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1083 LvTETGEDIYLAGTNVPAQ----YYLPVDAIVNFEDGGHVGIGDVIARIPQERSKTRDITGGLPRVADLFEARKPKDSAV 1158
Cdd:TIGR02388 920 A-EESGEIEEVASDYVILRigrpYRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARKPKEACI 998
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1159 MAEVSGMVSFgKETKGKRRLIINVSEDQ---CHEELIPKwRHISVFEGEHVERGEIIAEGALNPHDILRLL--------- 1226
Cdd:TIGR02388 999 LAKRPGVVQV-KYGTDDESVSIKVIERDgtiSEYPLLPG-QNIMVSDGQQVTGGEPLTDGPINPHDILDVFfsyykdqdg 1076
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1227 -------GVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVITFAGDSKFLVGEQIEESVLLQENDKLIAEGK 1299
Cdd:TIGR02388 1077 lyeaaqeSLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGG 1156
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1300 QVARGIPILLGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTGYAYHQ 1369
Cdd:TIGR02388 1157 APAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYE 1226
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
28-812 |
1.94e-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: 240.52 E-value: 1.94e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 28 DAIKIALASPELIRSWSYGEVKKPETINyRTFKPERDGLFCAKtFGPVKdyeclcgkykrlkhRGVICEKCGvelalakv 107
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPR-MGTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 108 rrERM-------GHIELASPVAHIWFLkslpsriglllDMTLRDIERVlyfeafvvvdpgmtelergqllnDEAYLdame 180
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILRCV-----------------------CKREL---- 96
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 181 qygdefdarmGAEAIRDLLRQVDLEDeirslreelpttnseTKIKKITKRLKlleafydsgnKPEWMIMDVLPVLPPDLR 260
Cdd:cd02733 97 ----------SAERVLEIFKRISDED---------------CRILGFDPKFS----------RPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 261 PLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQESVDALLDNGRRG--RAITGtNKRPLKSLA 338
Cdd:cd02733 142 PSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQK-SGRPLKSIR 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 339 DMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMAL-----ELFKPFIFSKLEF---RGLATTIKAakKM 410
Cdd:cd02733 221 QRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLQElvrNGPNEYPGA--KY 298
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 411 VEREESVVWD----------ILD--DVIREH-----PILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDG 473
Cdd:cd02733 299 IIRDDGERIDlrylkkasdlHLQygYIVERHlqdgdVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNADFDG 378
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 474 DQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPI--IVpsQDVVLGLYYLTREKVnalgegkiFVSAQEAQNF----- 546
Cdd:cd02733 379 DEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTKRDT--------FLEKDQVMNLlmwlp 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 547 YEAGHLDIHAKIKirmPKeneaghhlvETTVGRAILAQILPKGMSFVQ--------------------------INRTMT 600
Cdd:cd02733 449 DWDGKIPQPAILK---PK---------PLWTGKQIFSLIIPKINNLIRssshhdgdkkwispgdtkviiengelLSGILC 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 601 KKVITK----VIDTCYRTFGLKETVIFADK--------LMYTGFkyatrsgaSIGIDDMeIPD-----DKASIIDHAYNE 663
Cdd:cd02733 517 KKTVGAssggLIHVIWLEYGPEAARDFIGNiqrvvnnwLLHNGF--------SIGIGDT-IADketmkKIQETIKKAKRD 587
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 664 VREIEAQFRSG---------LVTNGERY-NKVIDiwsrtnelVAKSMMSKIATEQVAnvkgelirqeSFNPIFMMADSGA 733
Cdd:cd02733 588 VIKLIEKAQNGelepqpgktLRESFENKvNRILN--------KARDKAGKSAQKSLS----------EDNNFKAMVTAGS 649
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 734 RGSAAQIRQLAG-----------------MRGLmaaP-----DGSIIETP-ITANFREGLNVFQYFISTHGARKGLADTA 790
Cdd:cd02733 650 KGSFINISQIIAcvgqqnvegkripfgfrRRTL---PhfikdDYGPESRGfVENSYLRGLTPQEFFFHAMGGREGLIDTA 726
|
890 900
....*....|....*....|..
gi 269987147 791 LKTANSGYLTRRLVDVAQDVVI 812
Cdd:cd02733 727 VKTAETGYIQRRLVKAMEDVMV 748
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
94-816 |
6.03e-65 |
|
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: 237.45 E-value: 6.03e-65
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 94 ICEKCGVELAlakvrrERMGH---IELASPVAHIWFLKSlpsrIGLLLDMTLRDIERVLyfeafvvvdpgMTELERgqll 170
Cdd:cd02583 45 ICETCGLNLA------DCVGHfgyIKLELPVFHIGYFKA----IINILQCICKTCSRVL-----------LPEEEK---- 99
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 171 ndEAYLDAMEQYGDEFDARMG-AEAIRDLLRQVDL----------EDEIRSLreelpttnsetKIKKITKR-----LKLL 234
Cdd:cd02583 100 --RKFLKRLRRPNLDNLQKKAlKKKILEKCKKVRKcphcgllkkaQEDLNPL-----------KVLNLFKNippedVELL 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 235 EAFYDSGNkPEWMIMDVLPVLPPDLRPLVPLDGGrfATSDLNDL---YRRVINRNNRLKRLLDLNAPDIIVRNEKRMLQE 311
Cdd:cd02583 167 LMNPLAGR-PENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQL 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 312 SVDALLDNGRRGRAITGTNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKP-- 389
Cdd:cd02583 244 QCALYINSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPer 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 390 ------------------------FIFSKLEfrGLATTIKAAKKMVEREESVVWDILD------DVIrehpiLLNRAPTL 439
Cdd:cd02583 324 vtrynieklrklvlngpdvhpganFVIKRDG--GKKKFLKYGNRRKIARELKIGDIVErhledgDIV-----LFNRQPSL 396
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 440 HRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPIIVPSQDVVLG 519
Cdd:cd02583 397 HRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTA 476
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 520 LYYLTREKVnalgegkiFVSAQEaqnFYEAGHLDIHAKIKIRMPKenEAGHHLVETTVGRAILAQIL-PKGMSFVQIN-R 597
Cdd:cd02583 477 SYLLTSKDV--------FFDRAQ---FCQLCSYMLDGEIKIDLPP--PAILKPVELWTGKQIFSLLLrPNKKSPVLVNlE 543
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 598 TMTKKVITKVIDTCYR--------------TFGlKETV-------IFADKLMYTGFKYATRS---------------GAS 641
Cdd:cd02583 544 AKEKSYTKKSPDMCPNdgyvvirnsellcgRLD-KSTLgsgsknsLFYVLLRDYGPEAAAAAmnrlaklssrwlsnrGFS 622
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 642 IGIDDM----EIPDDKASIIDHAYNEVREIEAQFRSGLVTNGERYNKvidiwSRTNELVAKSMMSKIaTEQVANV-KGEL 716
Cdd:cd02583 623 IGIDDVtpskELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTA-----EQTLEAKISGELSKI-REDAGKAcLKEL 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 717 irqESFNPIFMMADSGARGSAAQIRQ---------LAGMRglmaAPDGSI----------IETPIT----AN-FREGLNV 772
Cdd:cd02583 697 ---HKSNSPLIMALCGSKGSNINISQmiacvgqqiISGKR----IPNGFEdrtlphfprnSKTPAAkgfvANsFYSGLTP 769
|
810 820 830 840
....*....|....*....|....*....|....*....|....
gi 269987147 773 FQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEDD 816
Cdd:cd02583 770 TEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDG 813
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1121-1365 |
4.08e-59 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 224.43 E-value: 4.08e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1121 GDVIARIPQERSKTRDITGGLPRVADLFEARKpKDSavmaevsgmvsfgketkgkrrliINVSedqcHEELIPKWrhisv 1200
Cdd:CHL00117 1115 GDTLVTLIYEKSRSGDITQGLPKVEQLLEARS-IDS-----------------------ISMN----LEKRLEGW----- 1161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1201 fegehvergeiiaegalnPHDILRLLGV------GA---LAN---YIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKRVI 1268
Cdd:CHL00117 1162 ------------------NERITRILGIpwgfliGAelsIAQsqiSLVNKIQKVYRSQGVQISDKHIEIIVRQMTSKVLV 1223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1269 TFAGDS-KFLVGEQIEesvLLQ-E--NDKLiaegKQVARGIPILLGITKASLATESFISAASFQETTRVLTEAAVSGKID 1344
Cdd:CHL00117 1224 SEDGMSnVFLPGELIG---LLRaEriNRAL----EEAICYRPILLGITKASLNTQSFISEASFQETTRVLAKAALRGRID 1296
|
250 260
....*....|....*....|.
gi 269987147 1345 DLRGLKENVMVGRLIPAGTGY 1365
Cdd:CHL00117 1297 WLKGLKENVILGGLIPAGTGF 1317
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
354-495 |
4.41e-46 |
|
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: 163.24 E-value: 4.41e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 354 GKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEF-----------------------RGLATTIKAAKKM 410
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNIkrlrqlvengpnvypganyiiriNGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 411 VEREESVVWDILDDVIREHPILLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQLEA 490
Cdd:pfam00623 81 LDKELEIGDIVERHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 269987147 491 RSLMM 495
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 ... |
220-804 |
6.45e-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: 166.21 E-value: 6.45e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 220 SETKIKKITKRLKLLE-----AFYDSGNKPEWMIMDVLPVLPPDLRPLVPLDGGRFaTSDLNDLYRRVINRNNRLKRLLD 294
Cdd:cd01435 98 SKWEVKLFVAKLKLLDkgllvEAAELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLA 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 295 LNAPDIIVRNEKRM---------------LQESVDALLDNGrrgraitgTNKRPLKSLADMIKG----KQGRFRQNLLGK 355
Cdd:cd01435 177 SMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDST--------KAPKSGKKSPPGIKQllekKEGLFRMNMMGK 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 356 RVDYSGRSVIVVGPTLKLHQCGLPKKMALEL-----------------------------------FKPFIFSKLEFRGL 400
Cdd:cd01435 249 RVNYAARSVISPDPFIETNEIGIPLVFAKKLtfpepvtpfnveelrqavingpdvypganaiededGRLILLSALSEERR 328
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 401 ATTIKAAKKMVEREES-----VVW-DILD-DVIrehpiLLNRAPTLHRLGIQA-FEPVLIEGKAIQLHPLVCTAYNADFD 472
Cdd:cd01435 329 KALAKLLLLLSSAKLLlngpkKVYrHLLDgDVV-----LLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNADFD 403
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 473 GDQMAVHVPLTLEAQLEARSLMMSTNNILSPASGEPI---IvpsQDVVLGLYYLT-REKvnalgegkiFVSAQEAQNF-Y 547
Cdd:cd01435 404 GDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLrglI---QDHVVSGVLLTsRDT---------FFTREEYQQLvY 471
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 548 EA----GHLDIHAKIK-----IRMPKENEAGHHLVETtvgraILAQILPKGMSFvqINRTMTKKVITKVIDTCYRTFGLK 618
Cdd:cd01435 472 AAlrplFTSDKDGRIKllppaILKPKPLWTGKQVIST-----ILKNLIPGNAPL--LNLSGKKKTKKKVGGGKWGGGSEE 544
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 619 ETVIF----------------------------------ADKLMyTGF-----KYATRSGASIGIDDMEIpddkasiidh 659
Cdd:cd01435 545 SQVIIrngelltgvldksqfgasayglvhavyelyggetAGKLL-SALgrlftAYLQMRGFTCGIEDLLL---------- 613
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 660 ayneVREIEAQfRSGLVtngERYNKVIDIWSRTNelvAKSMMSKIATEQVAN--VKGeLIRQESFNPIFMMADSGARGS- 736
Cdd:cd01435 614 ----TPKADEK-RRKIL---RKAKKLGLEAAAEF---LGLKLNKVTSSIIKAclPKG-LLKPFPENNLQLMVQSGAKGSm 681
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 737 --AAQI------RQLAGMR-GLMA--------AP-DGSiietP-----ITANFREGLNVFQYFISTHGARKGLADTALKT 793
Cdd:cd01435 682 vnASQIscllgqQELEGRRvPLMVsgktlpsfPPyDTS----PraggfITDRFLTGIRPQEYFFHCMAGREGLIDTAVKT 757
|
730
....*....|.
gi 269987147 794 ANSGYLTRRLV 804
Cdd:cd01435 758 SRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
499-647 |
8.64e-38 |
|
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: 139.30 E-value: 8.64e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 499 NILSPASGEPIIVPSQDVVLGLYYLTREkvnalgegKIFVSAQEAQNFYEAGHLDIHAKIKIRMPKENeaghhLVETTVG 578
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRE--------DTFFDREEVMQLLMYGIVLPHPAILKPIKPLW-----TGKQTFS 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 579 RAILAQILPKGM------------SFVQINRTMTKK-VITK---------VIDTCYRTFGLKETVIFADKLMYTGFKYAT 636
Cdd:pfam04983 68 RLLPNEINPKGKpktneedlcendSYVLINNGELISgVIDKktvgkslgsLIHIIYKEYGPEETAKFLDRLQKLGFRYLT 147
|
170
....*....|.
gi 269987147 637 RSGASIGIDDM 647
Cdd:pfam04983 148 KSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1216-1364 |
7.00e-25 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 102.11 E-value: 7.00e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1216 ALNPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVRQMlrkrviTFAGDskflvgeqieesvllqendkli 1295
Cdd:cd00630 47 AASIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVM------TYSGG---------------------- 98
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 269987147 1296 aegkqvargipiLLGITKASLA--TESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:cd00630 99 ------------LRGVTRSGFRasKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
676-767 |
7.10e-23 |
|
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: 94.74 E-value: 7.10e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 676 VTNGERYNKVIDIWSRTNELVAKSMMSKIATEQVaNVKGELIRQE--SFNPIFMMADSGARGSAAQIRQLAGMRGLMA-- 751
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNILNKAR-DPAGNIASKSldPNNSIYMMADSGAKGSIINISQIAGCRGQQNve 79
|
90 100
....*....|....*....|....*....
gi 269987147 752 ---APDG----------SIIETPITANFR 767
Cdd:pfam05000 80 gkrIPFGfsgrtlphfkKDDEGPESRGFV 108
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
348-528 |
5.35e-20 |
|
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 96.32 E-value: 5.35e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 348 FRQNLLGKRVDYSGRSVIVVGPTLKLHQCGLPKKMALELFKPFIFSKLEFRGLATtiKAAKKMVEREESVV--WDILDDV 425
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVSERVSSWNRERLQE--YCDLTLLLKGVIGVrrNGRLVGV 283
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 426 IREHP----------------ILLNRAPTLHRLGIQAFE-PVLIEGKAIQLHPLVCTAYNADFDGDQMAVHVPLTLEAQL 488
Cdd:cd10506 284 RSHNTlqigdvihrplvdgdvVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARA 363
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 269987147 489 EARSLMMSTNNILSPASGEPIIVPSQDVVLGLYYLTREKV 528
Cdd:cd10506 364 ELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGV 403
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
911-1364 |
1.60e-18 |
|
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: 89.34 E-value: 1.60e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASrataannIQIkTKGVIRLhnIKTVtheNKNLVAVSRSGEVTIVDE 990
Cdd:TIGR02389 40 LIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAE-------LNV-TLGLPRL--IEIV---DARKTPSTPSMTIYLEDE 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 991 FGRERER-----YKVPYGAVITVQDNSNVEAGQIIATWDPHTHPVISEvggylkfvdlfdGITMNRQTDELTGLSNIVVI 1065
Cdd:TIGR02389 107 YEKDREKaeevaKKIEATKLEDVAKDISIDLADMTVIIELDEEQLKER------------GITVDDVEKAIKKAKLGKVI 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1066 DAKQRSSAgrdlrpmvkLVTETGEDIYlagtnvpAQYYLPVDAIVNFEDGGHVGIGDVIaripqersktrditgglprva 1145
Cdd:TIGR02389 175 EIDMDNNT---------ITIKPGNPSL-------KELRKLKEKIKNLHIKGIKGIKRVV--------------------- 217
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1146 dlfeARKPKDSAVmaevsgMVSFGKETKGkrrliinvsedqcheelipkwrhisVFEGEHVERGEIIAEgalNPHDILRL 1225
Cdd:TIGR02389 218 ----IRKEGDEYV------IYTEGSNLKE-------------------------VLKLEGVDKTRTTTN---DIHEIAEV 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1226 LGVGALANYIVNEVQDVYRLQGVKINDKHIevivrqMLRKRVITFAGdskflvgeqieesvllqendkliaEGKQVARgi 1305
Cdd:TIGR02389 260 LGIEAARNAIIEEIKRTLEEQGLDVDIRHL------MLVADLMTWDG------------------------EVRQIGR-- 307
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 269987147 1306 pilLGIT--KASLatesfISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:TIGR02389 308 ---HGISgeKASV-----LARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTG 360
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
911-1364 |
4.71e-18 |
|
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: 87.69 E-value: 4.71e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRataanNIqikTKGVIRLHNI-----KTVThenknlvavsRSGEV 985
Cdd:cd06528 36 LIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEI-----NV---TLGLPRLIEIvdarkEPST----------PTMTI 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 986 TIVDEFGRERERykvpygaVITVqdnsnveAGQIIATwdpHTHPVISEVGgylkfVDLFDGitmnrqtdeltglSNIVVI 1065
Cdd:cd06528 98 YLEEEYKYDREK-------AEEV-------ARKIEET---TLENLAEDIS-----IDLFNM-------------RITIEL 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1066 DAKQRSSAGrdlrpmvklvtetgediylagtnvpaqyyLPVDaivnfedgghvgigDVIARIPQERSKTRDITGG----- 1140
Cdd:cd06528 143 DEEMLEDRG-----------------------------ITVD--------------DVLKAIEKLKKGKVGEEGDvtliv 179
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1141 -LPRVADLFEARKPKDSAVMAEVSGMvsfgketKGKRRLIINVSEDqcheELIpkwrhI--------SVFEGEHVERGEI 1211
Cdd:cd06528 180 lKAEEPSIKELRKLAEKILNTKIKGI-------KGIKRVIVRKEED----EYV-----IytegsnlkAVLKVEGVDPTRT 243
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1212 IAEgalNPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIevivrqMLRKRVITFAGdskflvgeqieesvllqen 1291
Cdd:cd06528 244 TTN---NIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHI------MLVADIMTYDG------------------- 295
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 269987147 1292 dkliaEGKQVAR-GIpillGITKASLatesfISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:cd06528 296 -----EVRQIGRhGI----AGEKPSV-----LARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
911-1364 |
5.23e-18 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 87.98 E-value: 5.23e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASrataannIQIkTKGVIRL-------HNIKTVTHenknlvavsrsg 983
Cdd:PRK04309 55 LVEPGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAE-------INV-TLGLPRLieivdarKEPSTPMM------------ 114
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 984 EVTIVDEFGRERERYKvpygaviTVqdnsnveAGQIIATwdphthpVISEVGGYLKfVDLFDGITmnrqtdeltglsnIV 1063
Cdd:PRK04309 115 TIYLKDEYAYDREKAE-------EV-------ARKIEAT-------TLENLAKDIS-VDLANMTI-------------II 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1064 VIDAKQRSSAGRDLRPMVKLVTE-TGEDIYLAGTNVpaqyylpvdaIVNFEDgghvgigDVIARIPQERSKTRDITgglp 1142
Cdd:PRK04309 160 ELDEEMLEDRGLTVDDVKEAIEKkKGGEVEIEGNTL----------IISPKE-------PSYRELRKLAEKIRNIK---- 218
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1143 rvadlfearkpkdsavmaeVSGMvsfgketKGKRRLIINVSEDqcheelipkwrhisvfegEHVergeIIAEG-AL---- 1217
Cdd:PRK04309 219 -------------------IKGI-------KGIKRVIIRKEGD------------------EYV----IYTEGsNLkevl 250
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1218 -------------NPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIevivrqMLRKRVITFAGdskflvgeqiee 1284
Cdd:PRK04309 251 kvegvdatrtttnNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHI------MLVADMMTWDG------------ 312
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1285 svllqendkliaEGKQVARgipilLGIT--KASLatesfISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAG 1362
Cdd:PRK04309 313 ------------EVRQIGR-----HGVSgeKASV-----LARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLG 370
|
..
gi 269987147 1363 TG 1364
Cdd:PRK04309 371 TG 372
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1234-1372 |
1.59e-17 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 89.06 E-value: 1.59e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1234 YIVNEV--QDVYRLQGVkINDKHIEVIVRQMLRK------------------RVITFAGDSKFLVGEQIEES---VLLQE 1290
Cdd:COG0086 560 YLVNEIlpQEVPFYNQV-INKKHIEVIIRQMYRRcglketvifldrlkklgfKYATRAGISIGLDDMVVPKEkqeIFEEA 638
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1291 NDKLIAEGKQVARGI--------PILLGITKASLATESFISAA-SFQETTRVLTEAAVSGKIDDLRGL----------KE 1351
Cdd:COG0086 639 NKEVKEIEKQYAEGLiteperynKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmakpSG 718
|
170 180
....*....|....*....|....*....
gi 269987147 1352 NVM---VGRLIPAGTG-----YAYHQGRK 1372
Cdd:COG0086 719 NIIetpIGSNFREGLGvleyfISTHGARK 747
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
911-1364 |
2.85e-16 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 83.70 E-value: 2.85e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRataanNIqikTKGVIRLhniktvthenknlvavsrsgeVTIVDE 990
Cdd:PRK14897 178 RVDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEM-----NV---TLGLPRL---------------------IEIVDA 228
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 991 fgrererYKVPYGAVITVqdnsnveagqiiatwdphthpvisevggYLKfvdlfDGITMNRQT--DELTGLSNIVVIDAK 1068
Cdd:PRK14897 229 -------RKKPSTPTMTI----------------------------YLK-----KDYREDEEKvrEVAKKIENTTLIDVA 268
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1069 QRSSAGRDLRPMVKLVTETGEDiylagtnvpaqyylpvdaivnfedgGHVGIGDVIARIPQERSKTRDITGGLPRVadlf 1148
Cdd:PRK14897 269 DIITDIAEMSVVVELDEEKMKE-------------------------RLIEYDDILAAISKLTFKTVEIDDGIIRL---- 319
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1149 eaRKPKDS----AVMAE-VSGMVSFGkeTKGKRRLIINVSEDQCHEELIPKWRHI-SVFEGEHVERGEIIAEgalNPHDI 1222
Cdd:PRK14897 320 --KPQQPSfkklYLLAEkVKSLTIKG--IKGIKRAIARKENDERRWVIYTQGSNLkDVLEIDEVDPTRTYTN---DIIEI 392
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1223 LRLLGVGALANYIVNEVQDVYRLQGVKINDKHIevivrqMLRKRVITFAGdskflvgeqieeSVllqendkliaegKQVA 1302
Cdd:PRK14897 393 ATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHI------MLVADMMTFDG------------SV------------KAIG 442
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 269987147 1303 R-GIpillgitkaSLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:PRK14897 443 RhGI---------SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
911-1364 |
1.51e-14 |
|
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: 77.63 E-value: 1.51e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRataanNIqikTKGVIRLHNIKTVThenKNLvavsRSGEVTI--V 988
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAK-----NV---TLGVPRLKEIINVA---KNI----KTPSLTVylE 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 989 DEFGRERERYKVPYGAV--ITVQDnsNVEAGQIIATWDPhTHPVISEVGgylKFVDLFdgITMNRQTDELTGLSNIVvid 1066
Cdd:cd02584 88 PGFAKDEEKAKKIQSRLehTTLKD--VTAATEIYYDPDP-QNTVIEEDK---EFVESY--FEFPDEDVEQDRLSPWL--- 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1067 akqrssagrdLRPMV--KLVTETGEDIYLAGTNVPAQYYLPVDAIVNFEDGGHVgigdVIA-RIPQErSKTRDITGGLPR 1143
Cdd:cd02584 157 ----------LRIELdrKKMTDKKLSMEQIAKKIKEEFKDDLNVIFSDDNAEKL----VIRiRIIND-DEEKEEDSEDDV 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1144 VADLFEARKPKDSAVMAEVSGMVSFGKETKGKRRLIINVSEDQCHEelipkWrhisVFEGEHVERGEIIAEGALNPH--- 1220
Cdd:cd02584 222 FLKKIESNMLSDMTLKGIEGIRKVFIREENKKKVDIETGEFKKREE-----W----VLETDGVNLREVLSHPGVDPTrtt 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1221 -----DILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIEVIVrqmlrkRVITFAGdskflvgeqieesvllqendKLI 1295
Cdd:cd02584 293 sndivEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHLALLC------DVMTQRG--------------------HLM 346
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 269987147 1296 AegkqVARgipilLGITKASLATesfISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:cd02584 347 A----ITR-----HGINRQDTGP---LMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTG 403
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
915-1364 |
3.38e-14 |
|
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: 74.95 E-value: 3.38e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 915 GEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRataanNIqikTKGVIRLHNIktvthenknlvavsrsgevtivdefgre 994
Cdd:cd02736 10 GTAVGAIAAQSIGEPGTQMTLKTFHFAGVASM-----NI---TLGVPRIKEI---------------------------- 53
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 995 rerykvpygavitvqdnsnVEAGQIIATwdphthPVISevggylkfVDLFDgitmnrQTDEltglsnivvidAKQRSSAG 1074
Cdd:cd02736 54 -------------------INASKNIST------PIIT--------AKLEN------DRDE-----------KSARIVKG 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1075 RDLRPMVKLVTETGEDIYLagtnvPAQYYLPVDAIVNFEDGGHVGIGDVIARIPQERSKtrditggLPRVadlfearkpk 1154
Cdd:cd02736 84 RIEKTYLGEVASYIEEVYS-----PDDCYILIKLDKKIIEKLQLSKSNLYFLLQSLKRK-------LPDV---------- 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1155 dsavmaEVSGMvsfgketKGKRRLIINVSED-QCHEELIPKWRHISVFEGEhvergEIIAEGALNPH--DILRLLGVGAL 1231
Cdd:cd02736 142 ------VVSGI-------PEVKRAVINKDKKkGKYKLLVEGYGLRAVMNTP-----GVIGTRTTSNHimEVEKVLGIEAA 203
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1232 ANYIVNEVQDVYRLQGVKINDKHIevivrqMLRKRVITFAGDskflvgeqieesvllqendkliaegkqvargipiLLGI 1311
Cdd:cd02736 204 RSTIINEIQYTMKSHGMSIDPRHI------MLLADLMTFKGE----------------------------------VLGI 243
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 269987147 1312 TKASLA--TESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:cd02736 244 TRFGIAkmKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
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| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
915-990 |
1.08e-11 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 64.36 E-value: 1.08e-11
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 269987147 915 GEAVGIIAAQSIGEPGTQLTMRTFHIGGAASRataanNIqikTKGVIRLHNIKTV--THENKNLVAVsRSGEVTIVDE 990
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASM-----NV---TLGLPRLKEILNAasIHEMLEALGI-EAARETIIRE 69
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| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
911-968 |
1.18e-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: 64.52 E-value: 1.18e-10
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTMRTFHIGGAAsratAANNiqikTKGVIRL--------HNIKT 968
Cdd:cd02735 6 LVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRG----EMNV----TLGIPRLreilmtasKNIKT 63
|
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| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1218-1364 |
3.29e-08 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 58.37 E-value: 3.29e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987147 1218 NPHDILRLLGVGALANYIVNEVQDVYRLQGVKINDKHIevivrqMLRKRVITFAGDSKflvgeqieesvllqendkliae 1297
Cdd:PRK14898 734 NIIEIQEVLGIEAARNAIINEMMNTLEQQGLEVDIRHL------MLVADIMTADGEVK---------------------- 785
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 269987147 1298 gkqvargiPIllGITKASLATESFISAASFQETTRVLTEAAVSGKIDDLRGLKENVMVGRLIPAGTG 1364
Cdd:PRK14898 786 --------PI--GRHGVAGEKGSVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
911-935 |
1.04e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.73 E-value: 1.04e-03
10 20
....*....|....*....|....*
gi 269987147 911 LVNTGEAVGIIAAQSIGEPGTQLTM 935
Cdd:PRK14898 53 LVEPYEAVGIVAAQSIGEPGTQMSL 77
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