|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
16-1381 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2409.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 16 EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQT 95
Cdd:PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 96 KVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDE 175
Cdd:PRK00566 86 KVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGDE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 176 FDAKMGAEAIQALLKSMDLEQECETLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPL 255
Cdd:PRK00566 166 FVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 256 DGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ 335
Cdd:PRK00566 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQ 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 336 GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV 415
Cdd:PRK00566 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEV 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 416 IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN 495
Cdd:PRK00566 406 IKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 496 GEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERIYRAGLASLHARVKVRITEYEkdengefvaktsLKDTTVG 575
Cdd:PRK00566 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSKK------------LVETTVG 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 576 RAILWMIVPKGLPFSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEIIS 655
Cdd:PRK00566 554 RVIFNEILPEGLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 656 EAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLqtetvinrdgvEEQQVSFNSIYMMADSGARGSAA 735
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNL-----------SKDQESFNPIYMMADSGARGSAS 702
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 736 QIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG 815
Cdd:PRK00566 703 QIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCG 782
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 816 TLEGITMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCDTDFGVC 895
Cdd:PRK00566 783 TDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVC 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 896 AHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFhiggaasraaaessiqvknkgsirlsnaksvvnssgklvi 975
Cdd:PRK00566 863 AKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTF---------------------------------------- 902
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 976 tsrntelklidefgrtkesykvpygsvmakgdgeqvaggetvanwdpHTmpvitevsgfvrftdmidgqtitrqtdeltg 1055
Cdd:PRK00566 903 -----------------------------------------------HT------------------------------- 904
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1056 lsslvvldsaertaggkdlrpalkivdaqgndvlipgtdmpaqyflpgkaivqledgvqissgdtlarvpqesGGTkDIT 1135
Cdd:PRK00566 905 -------------------------------------------------------------------------GGV-DIT 910
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1136 GGLPRVADLFEARRPKEPAILAEISGIISFGKETKGKRRLVITPVDGsEPYEEMIPKWRQLNVFEGERVERGDVVSDGPE 1215
Cdd:PRK00566 911 GGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDG-EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSI 989
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1216 APHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEGEQVEYSRVKIANRELEAN 1295
Cdd:PRK00566 990 DPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAE 1069
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1296 GKVGATFSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAA 1375
Cdd:PRK00566 1070 GKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAV 1149
|
....*.
gi 489923573 1376 GELPAA 1381
Cdd:PRK00566 1150 DEEEAE 1155
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
14-1199 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 1941.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 14 TEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVT 93
Cdd:COG0086 4 VEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 94 QTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFG 173
Cdd:COG0086 84 LSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 174 DEFDAKMGAEAIQALLKSMDLEQECETLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV 253
Cdd:COG0086 164 DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 254 PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKG 333
Cdd:COG0086 244 PLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 334 KQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILD 413
Cdd:COG0086 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 414 EVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSP 493
Cdd:COG0086 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 494 ANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERIYRAGLASLHARVKVRITEYEKDengefvaKTSLKDTT 573
Cdd:COG0086 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGEQ-------VGKIVETT 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 574 VGRAILWMIVPKGLPFsiVNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEI 653
Cdd:COG0086 557 VGRYLVNEILPQEVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEI 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 654 ISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQtetvinrdgveeqqvSFNSIYMMADSGARGS 733
Cdd:COG0086 635 FEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS---------------SQNTTYMMADSGARGS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 734 AAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDD 813
Cdd:COG0086 700 ADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 814 CGTLEGITMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCDTDFG 893
Cdd:COG0086 780 CGTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGG 859
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 894 VCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIRLSNAKSVVNSSGKL 973
Cdd:COG0086 860 VCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKG 939
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 974 VITSRNTELKLIDEFGRTKESYKVPYGSVMAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDEL 1053
Cdd:COG0086 940 VVVSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEE 1019
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1054 TGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARVPQESGGTKD 1133
Cdd:COG0086 1020 TGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRD 1099
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489923573 1134 ITGGLPRVADLFEARRPKEPAILAEISGIISFGKETKGKRRLVITPVDGSEPYEEMIPKWRQLNVF 1199
Cdd:COG0086 1100 GTGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
19-1368 |
0e+00 |
|
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274103 [Multi-domain] Cd Length: 1140 Bit Score: 1808.87 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 19 AIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVR 98
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 99 RERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDA 178
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 179 KMGAEAIQALLKSMDLEQECETLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGG 258
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 259 RFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRF 338
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 339 RQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIRE 418
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 419 HPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEP 498
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 499 IIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERIYRAGLASLHARVKVRIteyekdengefvaKTSLKDTTVGRAI 578
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRT-------------SGEILETTVGRVI 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 579 LWMIVPKGLPFSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAE 658
Cdd:TIGR02386 548 FNEILPEGFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEAD 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 659 AEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLqtetvinrdgvEEQQVSFNSIYMMADSGARGSAAQIR 738
Cdd:TIGR02386 628 KEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLL-----------KKDTYKFNPIFMMADSGARGNISQFR 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 739 QLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTLE 818
Cdd:TIGR02386 697 QLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEE 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 819 GITMTPVIEGGD-VKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCDTDFGVCAH 897
Cdd:TIGR02386 777 GIEVEAIVEGKDeIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQK 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 898 CYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAasraaaessiqvknkgsirlsnaksvvnssgklvits 977
Cdd:TIGR02386 857 CYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGGV------------------------------------- 899
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 978 rntelklidefgrtkesykvpygsvmakgdgeqvaggetvanwdphtmpvitevsgfvrftdmidgqtitrqtdeltgls 1057
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1058 slvvldsaertaggkdlrpalkivdaqgndvlipgtdmpaqyflpgkaivqledgvqissgdtlarvpqeSGGTKDITGG 1137
Cdd:TIGR02386 900 ----------------------------------------------------------------------AGASGDITQG 909
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1138 LPRVADLFEARRPKEPAILAEISGIISFGKET-KGKRRLVITPvDGSEPYEEMIPKWRQLNVFEGERVERGDVVSDGPEA 1216
Cdd:TIGR02386 910 LPRVKELFEARTPKDKAVIAEVDGTVEIIEDIvKNKRVVVIKD-ENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSID 988
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1217 PHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEGEQVEYSRVKIANRELEANG 1296
Cdd:TIGR02386 989 PHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQG 1068
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489923573 1297 KVGATFSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQD 1368
Cdd:TIGR02386 1069 KKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYKE 1140
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1529.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 15 EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQ 94
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 95 TKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFG- 173
Cdd:PRK14844 1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGi 1605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 174 DEFDAKMGAEAIQALLKSMDLEQECETLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV 253
Cdd:PRK14844 1606 DSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLV 1685
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 254 PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLK-SLADMIK 332
Cdd:PRK14844 1686 SLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLK 1765
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 333 GKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDIL 412
Cdd:PRK14844 1766 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDML 1845
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 413 DEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILS 492
Cdd:PRK14844 1846 EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 493 PANGEPIIVPSQDVVLGLYYMTRDcvNAKGEGMVLTGP-KEAERIYRAGLASLHARVKVRItEYEKDEnGEFVAKTSLkd 571
Cdd:PRK14844 1926 PSNGRPIIVPSKDIVLGIYYLTLQ--EPKEDDLPSFGAfCEVEHSLSDGTLHIHSSIKYRM-EYINSS-GETHYKTIC-- 1999
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 572 TTVGRAILWMIVPK--GLPFSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEK 649
Cdd:PRK14844 2000 TTPGRLILWQIFPKheNLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPET 2079
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 650 KHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQtetvinrdgVEEQQVSFNSIYMMADSG 729
Cdd:PRK14844 2080 KATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAIS---------IYDGNSKYNSVYMMVNSG 2150
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 730 ARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVV 809
Cdd:PRK14844 2151 ARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIV 2230
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 810 TEDDCGTLEGITMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCD 889
Cdd:PRK14844 2231 TKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCE 2310
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 890 TDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIRLSNAKSVVNS 969
Cdd:PRK14844 2311 ISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDK 2390
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 970 SGKLVITSRNTELKLIDEFGRTKESYKVPYGSVMAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQ 1049
Cdd:PRK14844 2391 NGNKIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEV 2470
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1050 TDELTGLSSLVVLDsAERTAGGKDLRPALKIVDAQGNdVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARVPQESG 1129
Cdd:PRK14844 2471 MDESTGISSKVVKD-WKLYSGGANLRPRIVLLDDNGK-VMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESV 2548
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1130 GTKDITGGLPRVADLFEARRPKEPAILAEISGIISFG-KETKGKRRLVITPVDGS-EPYEEMIPKWRQLNVFEGERVERG 1207
Cdd:PRK14844 2549 KTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDEQiSPVEYLVSRSKHVIVNEGDFVRKG 2628
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1208 DVVSDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEGEQVEYSRVKI 1287
Cdd:PRK14844 2629 DLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDR 2708
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489923573 1288 ANRELEANGKVGATFSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK14844 2709 ENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTG 2783
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
8-1377 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1517.53 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 8 LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGV-ICE 86
Cdd:PRK09603 1387 IKEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCE 1466
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 87 KCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQ--------Q 158
Cdd:PRK09603 1467 KCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDNEgtklvmkyD 1546
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 159 ILTEEQYLDALEEFGDE-FDAKMGAEAIQALLKSMDLEQECETLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWM 237
Cdd:PRK09603 1547 ILNEEQYQNISRRYEDRgFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWM 1626
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 238 ILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAIT 317
Cdd:PRK09603 1627 MLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVK 1706
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 318 GSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAA 397
Cdd:PRK09603 1707 GANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQA 1786
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 398 KKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQ 477
Cdd:PRK09603 1787 KRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAI 1866
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 478 LEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERIYRAGLASLHARVKVriteyek 557
Cdd:PRK09603 1867 AECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRV------- 1939
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 558 dengefVAKTSLKDTTVGRAILWMIVPKGLPFSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGA 637
Cdd:PRK09603 1940 ------LDQGNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGI 2013
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 638 SVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMdnlqtetvinrDGVEEQQV 717
Cdd:PRK09603 2014 SISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMM-----------TAIAKDKE 2082
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 718 SFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLT 797
Cdd:PRK09603 2083 GFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLT 2162
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 798 RRLVDVAQDLVVTEDDCGTLEGITMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSV 877
Cdd:PRK09603 2163 RKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGI 2242
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 878 DSVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGS 957
Cdd:PRK09603 2243 KSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGF 2322
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 958 IRLSNAKSVVNSSGKLVITSRNT----------------ELK--------LIDEFGRTKES------------------- 994
Cdd:PRK09603 2323 VRFYNLRTYTNKEGKNIIANRRNasilvvepkikapfdgELRietvyeevVVSVKNGDQEAkfvlrrsdivkpselagvg 2402
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 995 --------------YKV--------------------PYGS--------------------------------------- 1001
Cdd:PRK09603 2403 gkiegkvylpyasgHKVhkggsiadiiqegwnvpnriPYASellvkdndpiaqdvyakekgiikyyvleanhlerthgik 2482
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1002 ------------VMAKGDGEQ-----VAGGE-------------------------TVANWDPHTMPVITEVSGFVRFTD 1039
Cdd:PRK09603 2483 kgdivsekglfaVIADDNGREaarhyIARGSeiliddnsevsansviskpttntfkTIATWDPYNTPIIADFKGKVSFVD 2562
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1040 MIDGQTITRQTDELTGLSSLVVLDSAerTAGGKdlrPALKIVDAQGNDVlipgtdmpaQYFLPGKAIVQLEDGVQISSGD 1119
Cdd:PRK09603 2563 IIAGVTVAEKEDENTGITSLVVNDYI--PSGYK---PSLFLEGANGEEI---------RYFLEPKTSIAISDGSSVEQAE 2628
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1120 TLARVPQESGGTKDITGGLPRVADLFEAR--RPKEPAILAEISGIISFGKETKGKRRLVITPVDGSEpYEEMIPKWRQLN 1197
Cdd:PRK09603 2629 VLAKIPKATVKSRDITGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRS-MDYFVDKGKQIL 2707
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1198 VFEGERVERGDVVSDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEG 1277
Cdd:PRK09603 2708 VHADEFVHAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEG 2787
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1278 EQVEYSRVKIANRELEANGKVGATFSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLI 1357
Cdd:PRK09603 2788 DLVSKKLFKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMI 2867
|
1530 1540
....*....|....*....|
gi 489923573 1358 PAGTGYaYHQDRMRRRAAGE 1377
Cdd:PRK09603 2868 PVGTGM-YKNKKIVLRTLED 2886
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
15-813 |
0e+00 |
|
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; Beta' is the largest subunit of bacterial DNA-dependent RNA polymerase (RNAP). This family also includes the eukaryotic plastid-encoded RNAP beta' subunit. Bacterial RNAP is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. Structure studies suggest that RNA polymerase complexes from different organisms share a crab-claw-shaped structure with two "pincers" defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. Beta' contains part of the active site and binds two zinc ions that have a structural role in the formation of the active polymerase.
Pssm-ID: 259845 [Multi-domain] Cd Length: 659 Bit Score: 1331.77 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 15 EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQ 94
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 95 TKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFesyvvieggmtnlerqqilteeqyldaleefgd 174
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 175 efdakmgaeaiqallksmdleqecetlreelnetnsetkrkkltkrikLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVP 254
Cdd:cd01609 128 ------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQ 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 255 LDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGK 334
Cdd:cd01609 160 LDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGK 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 335 QGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE 414
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 415 VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 495 NGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVltgpkeaeriyraglaslharvkvriteyekdengefvaktslkDTTV 574
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTKERKGDKGEGII--------------------------------------------ETTV 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 575 GRAILWMIVPKGLPFsiVNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEII 654
Cdd:cd01609 436 GRVIFNEILPEGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEII 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 655 SEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLqtetvinrdgveeQQVSFNSIYMMADSGARGSA 734
Cdd:cd01609 514 KEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNL-------------DKDPFNPIYMMADSGARGSK 580
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489923573 735 AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDD 813
Cdd:cd01609 581 SQIRQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
14-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1279.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 14 TEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVT 93
Cdd:PRK14906 6 VTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVT 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 94 QTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVV--------------------------- 146
Cdd:PRK14906 86 RAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleeld 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 147 --------------------------------------IEGGMTNLE----------------------RQQILTEEQYL 166
Cdd:PRK14906 166 aerdrlieatrrlsvdyvpeddefvddigdderltaeeVRAEVADIYeeynerkalrreafdafmqiepKQLISDEALYR 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 167 DALEEFGDEFDAKMGAEAIQALLKSMDLEQECETLREeLNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLP 246
Cdd:PRK14906 246 EMRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEELRA-IIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 247 PDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKS 326
Cdd:PRK14906 325 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKS 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 327 LADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEA 406
Cdd:PRK14906 405 LADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 407 VVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMS 486
Cdd:PRK14906 485 YVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLS 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 487 TNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERIYRA-GLASLHARVKVRIT----------EY 555
Cdd:PRK14906 565 SNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDArADLDLQAKIVVRLSrdmtvrgsygDL 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 556 EKDENGEFVaktslkDTTVGRAILWMIVPKGLPFsiVNQALGKKAISKMLNTC---YRILGLKPTVifaDQTMYTGFAYA 632
Cdd:PRK14906 645 EETKAGERI------ETTVGRIIFNQVLPEDYPY--LNYKMVKKDIGRLVNDCcnrYSTAEVEPIL---DGIKKTGFHYA 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 633 ARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQtetvinrdgv 712
Cdd:PRK14906 714 TRAGLTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFD---------- 783
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 713 eeqqvSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTAN 792
Cdd:PRK14906 784 -----EDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTAD 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 793 SGYLTRRLVDVAQDLVVTEDDCGTLEGITMTPVIEGGDVKEPLrdrvLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLL 872
Cdd:PRK14906 859 SGYLTRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDPNGEVLLSAGDYIESMDDLKRL 934
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 873 EENSVDSVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaessiqv 952
Cdd:PRK14906 935 VEAGVTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGG------------- 1001
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 953 knkgsirlsnaksvvnssgklvitsrntelklidefgrtkesykvpygsvmakgdgeqVAGgetvanwdphtmpvitevs 1032
Cdd:PRK14906 1002 ----------------------------------------------------------VAG------------------- 1004
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1033 gfvrftdmidgqtitrqtdeltglsslvvldsaertaggkdlrpalkivdaqgndvlipgtdmpaqyflpgkaivqledg 1112
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1113 vqissgdtlarvpqesggtKDITGGLPRVADLFEARRPKEPAILAEISGIISFGKETKGKrrlVITPVDGSEPYEEMIPK 1192
Cdd:PRK14906 1005 -------------------DDITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEK---TLTIHDQDGNSREYVVS 1062
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1193 WR---QLNVFEGERVERGDVVSDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESA 1269
Cdd:PRK14906 1063 ARvqfMPGVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNP 1142
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1270 GSSDFLEGEQVEYSRVKIANRELEANGKVGATFSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKE 1349
Cdd:PRK14906 1143 GDSDYLPGRQVNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKE 1222
|
1450
....*....|....*....
gi 489923573 1350 NVIVGRLIPAGTGYAYHQD 1368
Cdd:PRK14906 1223 NVIIGKPIPAGTGLSRYRD 1241
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
12-574 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 845.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 12 TKTEE-FDAIKIALASPDMIRSWS---------FGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHR 81
Cdd:PRK02625 3 LRTENrFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 82 GVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIE-GGMTNLERQQIL 160
Cdd:PRK02625 83 GIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDpGNHKNLKYKQLL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 161 TEEQYLDALE-------EFGDEFDAKMGAEAIQALLKSMDLEQECETLREELNETNSEtKRKKLTKRIKLLEAFVQSGNK 233
Cdd:PRK02625 163 TEDQWLEIEDqiyaedsELEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGSR 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 234 PEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG 313
Cdd:PRK02625 242 PEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRG 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 314 RAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATT 393
Cdd:PRK02625 322 RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNN 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 394 IKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLT 473
Cdd:PRK02625 402 IKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLS 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 474 LEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNA-KGEGMVLTGPKEAERIYRAGLASLHARVKVRI 552
Cdd:PRK02625 482 LEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAqKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRF 561
|
570 580
....*....|....*....|....
gi 489923573 553 T-EYEKDENGEFVAKT-SLKDTTV 574
Cdd:PRK02625 562 NgEVEDDDEDTEPLKTeTLEDGTR 585
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
17-574 |
0e+00 |
|
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Pssm-ID: 131440 [Multi-domain] Cd Length: 619 Bit Score: 827.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 17 FDAIKIALASPDMIRSWS---------FGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEK 87
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 88 CGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIE-GGMTNLERQQILTEEQYL 166
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNpGNAKNLKYKQLLTEDQWL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 167 DALEE-FGDEFD------AKMGAEAIQALLKSMDLEQECETLREELNETNSEtKRKKLTKRIKLLEAFVQSGNKPEWMIL 239
Cdd:TIGR02387 162 EIEDQiYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 240 TVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGS 319
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 320 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKK 399
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 400 MVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE 479
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 480 ARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNA-KGEGMVLTGPKEAERIYRAGLASLHARVKVRITEYEKD 558
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAeKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVET 560
|
570
....*....|....*...
gi 489923573 559 EN--GEFVAKTSLKDTTV 574
Cdd:TIGR02387 561 NDplDEPIKSEDLSDGTR 578
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
16-514 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 824.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 16 EFDAIKIALASPDMIRSWS---------FGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKR---LKHRGV 83
Cdd:CHL00018 6 KHQQLRIGLASPQQIRAWAerilpngeiVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVigdEKEDPK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 84 ICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVV--IEGGMTNLERQQILT 161
Cdd:CHL00018 86 FCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRLRGLFE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 162 EE----QYLDALEEFGDEFDAKM------GAEAIQALLKSMDLEQECETLR---EELNETNS----------ETKRKKLT 218
Cdd:CHL00018 166 YEiqswKYSIPLFFSTQGFDTFRnreistGAGAIREQLADLDLRIIIDNSLvewKELGEEGStgnewedrkiGRRKDFLV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 219 KRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLA--APDIIVRNEK 296
Cdd:CHL00018 246 RRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQK 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 297 RMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALEL 376
Cdd:CHL00018 326 KLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 377 FKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAA 456
Cdd:CHL00018 406 FQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 485
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 489923573 457 YNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT 514
Cdd:CHL00018 486 FNADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLT 543
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
25-812 |
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: 657.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 25 ASPDMIRSWSFGEVKKPETINYRTFKPERDGlfcarifgpvkdyeclcgKYKRLKHRGVICEKCGVEVTQTKVRRERMGH 104
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 105 IELASPTAHIWFLKSLPSRIGllldmplrdiervlyfesyvvieggmtnlerqqilteeqyldaleefgdefdakmgaea 184
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 185 iqallksmdleqecetlreelnetnsetkrkkltkriklleafvqsgnkPEWMILTVLPVLPPDLRPLVpldggrfatsd 264
Cdd:cd00399 84 -------------------------------------------------PEWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 265 lndlyrrvinrnnrlkrlldlaapdiIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLG 344
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 345 KRVDYSGRSVITVGPYLRLHQCGLPKKMALELfkpfiygklelrglattikaakkmvereeavvwdildeviREHPVLLN 424
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 425 RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ 504
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 505 DVVLGLYYMTRdcvnakgegmvltgpkeaeriyraglaslharvkvriteyekdengefvaktslkdttvgraiLWMIVP 584
Cdd:cd00399 278 DTLLGAYLLTL---------------------------------------------------------------GKQIVS 294
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 585 KGLPfsivnqalgkkaiSKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVG----IDDMVIPEKKHEIISEAEAE 660
Cdd:cd00399 295 AALP-------------GGLLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGigdvIDDGVIPEEKTELIEEAKKK 361
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 661 VAEIQEQFQSGLVTAGER-------YNKVIDIWAAANDRVSKAMMDNLQTetvinrdgveeqQVSFNSIYMMADSGARGS 733
Cdd:cd00399 362 VDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNLDL------------VSKFNSIYVMAMSGAKGS 429
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 734 AAQIRQLAGMRGLMAKPDGSI--------------------IETPITANFREGLNVLQYFISTHGARKGLADTALKTANS 793
Cdd:cd00399 430 FINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAES 509
|
810
....*....|....*....
gi 489923573 794 GYLTRRLVDVAQDLVVTED 812
Cdd:cd00399 510 GYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
235-511 |
1.10e-161 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 487.03 E-value: 1.10e-161
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 235 EWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNG--RR 312
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 313 GRAITGsnkRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLE------ 386
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 387 ------------LRGLATTIKAAKKM-VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV 453
Cdd:smart00663 158 lvrngpngakyiIRGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 489923573 454 CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLY 511
Cdd:smart00663 238 CSPYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
766-1270 |
1.30e-124 |
|
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: 397.49 E-value: 1.30e-124
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 766 GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTLEGITMTPVIEGGDVKEPLRDRVLGRVTA 845
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 846 EDVLKPGTADILVPRNTLLHEQWCD---------------------------------LLEENSVDSVKVRSVVSCDTDF 892
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFslsykkeilvrdsklgrdrlskeaqeratllfeLLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 893 GVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASraaaessiqvKNK--GSIRLSNAKSVvnss 970
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVAS----------KNVtlGVPRLKEIINV---- 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 971 gKLVITSRNTELKLIDEFGRTKESYKVPYGSVMAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQT 1050
Cdd:pfam04998 227 -SKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEI 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1051 DELTGLSSLVVLDsaertaggkdlrpaLKIVDAQGNDVLIPgtdmpaqYFLPGKAIVQLEDGVQISSGDTLARVPQESGG 1130
Cdd:pfam04998 306 DPETGLLILVIRL--------------LKILNKSIKKVVKS-------EVIPRSIRNKVDEGRDIAIGEITAFIIKISKK 364
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1131 TKDITGGLPRVADLFEARRPKEPAILAEISGIISFgKETKGKRRLVITPVDGSEPYE------EMIPKWRQLNVFegERV 1204
Cdd:pfam04998 365 IRQDTGGLRRVDELFMEEDPKLAILVASLLGNITL-RGIPGIKRILVNEDDKGKVEPdwvletEGVNLLRVLLVP--GFV 441
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489923573 1205 ERGDVVSDgpeAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAG 1270
Cdd:pfam04998 442 DAGRILSN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIG 504
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
593-1049 |
7.37e-121 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 409.77 E-value: 7.37e-121
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 593 NQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGL 672
Cdd:PRK02597 5 NRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 673 VTAGERYNKVIDIWAAANDRVSKAMMDNLQtetvinrdgveeQQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDG 752
Cdd:PRK02597 85 ITEVERFQKVIDTWNETNERLKDEVVKNFR------------QNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 753 SIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTLEGITMTPVIEGGDVK 832
Cdd:PRK02597 153 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 833 EPLRDRVLGRVTAEDVLKPgTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKG 912
Cdd:PRK02597 233 IPLGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLG 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 913 EAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAEssiQVKNK--GSIRLSNAKSV-------------VNSSGKLVITS 977
Cdd:PRK02597 312 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVAR---QVRSPfaGTVEFGKKLRTrpyrtrhgvealqAEVDFDLVLKP 388
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 978 RNtelklidefGRTKESYKVPYGSVMAKGDGEQVAGGETVA---------NWDPHTMPVITEVSGFVRFTDMIDGQTITR 1048
Cdd:PRK02597 389 SG---------KGKPQKIEITQGSLLFVDDGQTVEADQLLAevaagavkkSTEKATKDVICDLAGEVRFADLIPEEKTDR 459
|
.
gi 489923573 1049 Q 1049
Cdd:PRK02597 460 Q 460
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
593-1049 |
5.05e-114 |
|
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: 388.82 E-value: 5.05e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 593 NQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGL 672
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 673 VTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINrdgveeqqvsfnSIYMMADSGARGSAAQIRQLAGMRGLMAKPDG 752
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNFRQTDPLN------------SVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 753 SIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTLEGITMTPVIEGGDVK 832
Cdd:TIGR02388 152 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 833 EpLRDRVLGRVTAEDVLKPgTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKG 912
Cdd:TIGR02388 232 S-LGDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLG 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 913 EAIGVIAAQSIGEPGTQLTMRTFHIGGaASRAAAESSIQVKNKGSIRLSNAKSV-------------VNSSGKLVITSRN 979
Cdd:TIGR02388 310 EAVGIIAAQSIGEPGTQLTMRTFHTGG-VFTGEVARQVRSKIDGTVEFGKKLRTrgyrtrhgedakqVEVAGLLIIKPTG 388
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489923573 980 telklidEFGRTKESYKVPYGSVMAKGDGEQVAGGETVA---------NWDPHTMPVITEVSGFVRFTDMIDGQTITRQ 1049
Cdd:TIGR02388 389 -------SITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAeialgavrkSTEKATKDVASDLAGEVKFDKVVPEEKTDRQ 460
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-342 |
1.20e-109 |
|
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: 349.28 E-value: 1.20e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 14 TEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYEC-LCGKYKRlkhrgviceKCGVev 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 93 tqtkvrreRMGHIELASPTAHIWFLKSLpsrigllldmpLRDIERVLYFESYVVIeggmtNLERQQILTEEQYLDALEEF 172
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFKKT-----------LKILECVCKYCSKLLL-----DPGKPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 173 gdefdaKMGAEAIQALLKSMDL------------------EQECETLREELNETNSE--------TKRKKLTKRIK---- 222
Cdd:pfam04997 126 ------KMGAKAILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKKSKEEeekeilnpEKVLKIFKRISdedv 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 223 LLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEA 302
Cdd:pfam04997 200 EILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEH 279
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 489923573 303 VDALLDNGRRG-RAITGSNKRPLKSLADMIKGKQGRFRQNL 342
Cdd:pfam04997 280 VATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
581-939 |
1.20e-106 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 370.04 E-value: 1.20e-106
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 581 MIVPKGLPFSivNQALGKKAISKMLN---TCYrilGLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKHEIISEA 657
Cdd:CHL00117 1 MAERANLVFH--NKVIDKTALKRLISwliDHF---GMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDA 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 658 EAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQtetviNRDgveeqqvSFNSIYMMADSGARGSAAQI 737
Cdd:CHL00117 76 EQQSLILEKHYHYGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFR-----MTD-------PLNPVYMMSFSGARGNASQV 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 738 RQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTL 817
Cdd:CHL00117 144 HQLVGMRGLMSDPQGQIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTT 223
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 818 EGITMTPvIEGGDVKEPLRDRVLGRVTAEDVLKpgTADILVPRNTLLHEQWCDLLEENSVDSVKVRSVVSCDTDFGVCAH 897
Cdd:CHL00117 224 RGISVSP-RNGMMIERILIQTLIGRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQL 300
|
330 340 350 360
....*....|....*....|....*....|....*....|..
gi 489923573 898 CYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:CHL00117 301 CYGWSLAHGDLVELGEAVGIIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
18-812 |
2.88e-104 |
|
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: 352.70 E-value: 2.88e-104
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 18 DAIKIALASPDMIRSWSFGEVKKPETinYrtfkpERDGLfcaRIFGPVKDyeclcgkyKRLkhrGVI-----CEKCGVev 92
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTCGN-- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 93 tqtkvRRER----MGHIELASPTAHIWFLKslpsRIGLLLDMPLRDIERVLyfesyvvieggmtnLERQQIlteEQYLDA 168
Cdd:cd02582 62 -----TAGEcpghFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL--------------LPEEEI---EKYLER 115
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 169 LEEfGDEFDAKMGAEAIQALLKSMDLEQEC-------------------ETLREELNETNSETKRKKLTK----RIKLLe 225
Cdd:cd02582 116 IRR-LKEKWPELVKRVIEKVKKKAKKRKVCphcgapqykiklekpttfyEEKEEGEVKLTPSEIRERLEKipdeDLELL- 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 226 AFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDA 305
Cdd:cd02582 194 GIDPKTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTT 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 306 LLDNGRRG--RAITGSnKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYG 383
Cdd:cd02582 274 YFDNEIPGipPARHRS-GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVT 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 384 KLelrglatTIKAAKKMVE-------------REEAVVWDILDE-------------VIREH-----PVLLNRAPTLHRL 432
Cdd:cd02582 353 EW-------NIEKMRKLVLngpdkwpganyviRPDGRRIRLRYVnreelaerlepgwIVERHlidgdIVLFNRQPSLHRM 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 433 GIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY 512
Cdd:cd02582 426 SIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYL 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 513 MTRDcvnakgeGMVLTgPKEAERIYRAglaslhARVKVRITEYEKDENGEFVAktslkdttvGRAILWMIVPKGLPFS-- 590
Cdd:cd02582 506 LTRK-------TTLFT-KEEALQLLSA------AGYDGLLPEPAILEPKPLWT---------GKQLFSLFLPKDLNFEgk 562
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 591 ----------------------IVN----------QALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGFAYAARSGAS 638
Cdd:cd02582 563 akvcsgcseckdedcpndgyvvIKNgkllegvidkKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFT 642
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 639 VGIDDMVIPEKKH----EIISEAEAEVAEIQEQFQSGLVTA--GERY-----NKVIDIWAAANDRVSKAMMDNLQTetvi 707
Cdd:cd02582 643 IGIDDEDIPEEARkeieEIIKEAEKKVYELIEQYKNGELEPlpGRTLeetleMKIMQVLGKARDEAGKVASKYLDP---- 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 708 nrdgveeqqvsFNSIYMMADSGARGSAAQIRQLAGM------------RGLMAKP--------DGSIIETPITANFREGL 767
Cdd:cd02582 719 -----------FNNAVIMARTGARGSMLNLTQMAAClgqqsvrgerinRGYRNRTlphfkpgdLGPEARGFVRSSFRDGL 787
|
890 900 910 920
....*....|....*....|....*....|....*....|....*
gi 489923573 768 NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED 812
Cdd:cd02582 788 SPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYD 832
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
19-816 |
4.09e-92 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 318.72 E-value: 4.09e-92
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 19 AIKIALASPDMIRSWSFGEVKKPETinYrtfkpERDGLfcaRIFGPVKDyeclcgkyKRLkhrGVI-----CEKCGvevt 93
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTCG---- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 94 qtKVRRE---RMGHIELASPTAHIWFLKslpsRIGLLLDMPLRDIERVLyfesyvvieggMTNLERQQILTEEQYLDALE 170
Cdd:PRK08566 66 --GRAGEcpgHFGHIELARPVIHVGFAK----LIYKLLRATCRECGRLK-----------LTEEEIEEYLEKLERLKEWG 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 171 EFGDEFDAKMGAEAIQAllksmdleQEC-------------------ETLREELNETNSETKRKKLTK----RIKLLeAF 227
Cdd:PRK08566 129 SLADDLIKEVKKEAAKR--------MVCphcgekqykikfekpttfyEERKEGLVKLTPSDIRERLEKipdeDLELL-GI 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 228 VQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALL 307
Cdd:PRK08566 200 NPEVARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYF 279
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 308 DN---G------RRGRaitgsnkrPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFK 378
Cdd:PRK08566 280 DNeipGipparhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTV 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 379 PFIYG--------KLELRG-----------------LATTIKAAKKMVEREEavvwdILDEVIReH-----PVLLNRAPT 428
Cdd:PRK08566 352 PERVTewnieelrEYVLNGpekhpganyvirpdgrrIKLTDKNKEELAEKLE-----PGWIVER-HlidgdIVLFNRQPS 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 429 LHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVL 508
Cdd:PRK08566 426 LHRMSIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHIS 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 509 GLYYMTRDcvnakgeGMVLTgPKEAERIYRAglaslhARVKVRITEYEKDENGefvaktslKDTTVGRAILWMIVPKGLP 588
Cdd:PRK08566 506 GAYLLTRK-------STLFT-KEEALDLLRA------AGIDELPEPEPAIENG--------KPYWTGKQIFSLFLPKDLN 563
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 589 FS------------------------IVN-----QALGKKAIS----KMLNTCYRILGLKPTVIFADQT--------MYT 627
Cdd:PRK08566 564 LEfkakicsgcdeckkedcehdayvvIKNgklleGVIDKKAIGaeqgSILDRIVKEYGPERARRFLDSVtrlairfiMLR 643
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 628 GFayaarsgaSVGIDDMVIP----EKKHEIISEAEAEVAEIQEQFQSGLV------TAGE-RYNKVIDIWAAANDRVSKA 696
Cdd:PRK08566 644 GF--------TTGIDDEDIPeeakEEIDEIIEEAEKRVEELIEAYENGELeplpgrTLEEtLEMKIMQVLGKARDEAGEI 715
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 697 MMDNLQtetvinrdgveeqqvSFNSIYMMADSGARGSAAQIRQLAGM------------RGLMAK-----PDGSIieTP- 758
Cdd:PRK08566 716 AEKYLG---------------LDNPAVIMARTGARGSMLNLTQMAACvgqqsvrgerirRGYRDRtlphfKPGDL--GAe 778
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489923573 759 ----ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDdcGT 816
Cdd:PRK08566 779 argfVRSSYKSGLTPTEFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYD--GT 838
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
907-1363 |
4.69e-81 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 264.77 E-value: 4.69e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 907 HIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaessiqvknkgsirlsnaksvvnssgklvitsrntelklid 986
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGG----------------------------------------------- 33
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 987 efgrtkesykvpygsvmakgdgeqVAGgetvanwdphtmpvitevsgfvrftdmidgqtitrqtdeltglsslvvldsae 1066
Cdd:cd02655 34 ------------------------VAT----------------------------------------------------- 36
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1067 rtaggkdlrpalkivdaqgndvlipgtdmpaqyflpgkaivqledgvqissgdtlarvpqesggtkDITGGLPRVADLFE 1146
Cdd:cd02655 37 ------------------------------------------------------------------DITQGLPRVEELFE 50
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1147 ARRPKepailaeisgiisfgketkgkrrlvitpvdgsepyeemipkwrqlnvfegervergdvvsdgpeaPHDILRLR-- 1224
Cdd:cd02655 51 ARKIN-----------------------------------------------------------------PHDLLRIKfl 65
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1225 GVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEGEQVEYSRVKIANRELEANGKVGATFSR 1304
Cdd:cd02655 66 GPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEP 145
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*....
gi 489923573 1305 DLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGY 1363
Cdd:cd02655 146 VLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
18-1362 |
6.52e-76 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 277.29 E-value: 6.52e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 18 DAIKIALASPDMIRSWSFGEVKKPETInyrtfkpERDGLfcarifgPVKDyECLCGKYKRLKHRgvicEKCGVEVTQTKV 97
Cdd:PRK14977 10 DGIIFGLISPADARKIGFAEITAPEAY-------DEDGL-------PVQG-GLLDGRLGTIEPG----QKCLTCGNLAAN 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 98 RRERMGHIELASPTAHIWFLKslpsRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDA--LEEFGDE 175
Cdd:PRK14977 71 CPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDeiIEEVRDQ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 176 FD--AKMGAEAIQALLKSMDLEQECETLREELNETNSE-----TKRKKLTKRIK---LLEAFVQSGNKPEWMILTVLPVL 245
Cdd:PRK14977 147 VKvyAKKAKECPHCGAPQHELEFEEPTIFIEKTEIEEHrllpiEIRDIFEKIIDddlELIGFDPKKARPEWAVLQAFLVP 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 246 PPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSNKRP 323
Cdd:PRK14977 227 PLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHHKGSGRP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 324 LKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYG--------KLELRG------ 389
Cdd:PRK14977 307 LKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNenniekmkELVINGpdefpg 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 390 -----LATTIKAAKKMVEREEAVVWDILDE------VIREH-----PVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV 453
Cdd:PRK14977 387 anairKGDGTKIRLDFLEDKGKDALREAAEqleigdIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAV 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 454 CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDcvnakgeGMVLTgPKEA 533
Cdd:PRK14977 467 CPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKD-------DALFD-KNEA 538
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 534 ERI-YRAGLASLHARVKVRITE-------------YEKDENGEFVAKTS------LKDTTVGRAILWMIVPKGLPFSIVN 593
Cdd:PRK14977 539 SNIaMLAGITDPLPEPAIKTKDgpawtgkqlfslfLPKDFNFEGIAKWSagkageAKDPSCLGDGYVLIKEGELISGVID 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 594 QALGKKAISKMLNTCYRIL---GLKPTVIFADQTMYTGFAYAARSGASVGIDDMVIPEKKH----EIISEAEAEVAEIQE 666
Cdd:PRK14977 619 DNIIGALVEEPESLIDRIAkdyGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAKqeieDDIQGMKDEVSDLID 698
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 667 QFQSGLVTAGERYNK---------------VIDIWAAANDRVSKAMMDNLQTEtvinrdgveeqqvsfNSIYMMADSGAR 731
Cdd:PRK14977 699 QRKITRKITIYKGKEellrgmkeeealeadIVNELDKARDKAGSSANDCIDAD---------------NAGKIMAKTGAR 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 732 GSAAQIRQLAGMRGLMA-KPDGSIIETP---------------------------ITANFREGLNVLQYFISTHGARKGL 783
Cdd:PRK14977 764 GSMANLAQIAGALGQQKrKTRIGFVLTGgrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGGREGL 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 784 ADTALKTANSGYLTRRLVDVAQDLVVTEDdcGTLEGiTMTPVIE---GGDVKEPLR---------DRVLGRVTAEDVLKP 851
Cdd:PRK14977 844 IDKARRTEDSGYFQRRLANALEDIRLEYD--ETVRD-PHGHIIQfkfGEDGIDPQKldhgeafnlERIIEKQKIEDRGKG 920
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 852 GTADILvprNTLLHEQWCDL---LEENSVDSVKvRSVVSCDTDFGVCAHcyGRDLARGHIINKGEAIGVIAAQSIGEPGT 928
Cdd:PRK14977 921 ASKDEI---EELAKEYTKTFnanLPKLLADAIH-GAELKEDELEAICAE--GKEGFEKAKVEPGQAIGIISAQSIAEPGT 994
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 929 QLTMRTFHIGGAASRAAaessiqvknkgSIRLSNAKSVVNSSGKLVITSRNTELKliDEFGRTKESYKVPYGSVMAkgdg 1008
Cdd:PRK14977 995 QMTLRTFHAAGIKAMDV-----------THGLERFIELVDARAKPSTPTMDIYLD--DECKEDIEKAIEIARNLKE---- 1057
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1009 eqvaggetvanwdphtmpvitevsgfVRFTDMIDGQTITRQTDELTGLSslvvlDSAERTAGGKDLRPALKIVDAQGNDV 1088
Cdd:PRK14977 1058 --------------------------LKVRALIADSAIDNANEIKLIKP-----DKRALENGCIPMERFAEIEAALAKGK 1106
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1089 lipgtdmpaqyflpgKAIVQLEDGVQIssgdtlarvpqesggtkditgglprvADLFE-ARRPKEPAILAEISGIIsFGK 1167
Cdd:PRK14977 1107 ---------------KFEMELEDDLII--------------------------LDLVEaADRDKPLATLIAIRNKI-LDK 1144
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1168 ETKGKR---RLVITPV--DGSEPYEEMIPKWRQLNVFEGERVERGDVVSDGPEaphDILRLRGVHAVTRYIVNEVQDVYR 1242
Cdd:PRK14977 1145 PVKGVPdieRAWVELVekDGRDEWIIQTSGSNLAAVLEMKCIDIANTITNDCF---EIAGTLGIEAARNAIFNELASILE 1221
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1243 LQGVKINDKHIEVIVRQMLRKATIESAGssdflegeqveysrvkianreLEANGKVGATFSrdllgitkaslATESFISA 1322
Cdd:PRK14977 1222 DQGLEVDNRYIMLVADIMCSRGTIEAIG---------------------LQAAGVRHGFAG-----------EKDSPLAK 1269
|
1450 1460 1470 1480
....*....|....*....|....*....|....*....|
gi 489923573 1323 ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK14977 1270 AAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSG 1309
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1099-1388 |
1.60e-74 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 273.02 E-value: 1.60e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1099 YFLPGKAIVQLEDGVQISSGDTLARVPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGI--ISFGKETKgkrrLV 1176
Cdd:PRK02597 944 YRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCILAKKPGTvqIKYGDDES----VD 1019
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1177 ITPV--DGSEPYEEMIPKwRQLNVFEGERVERGDVVSDGPEAPHDILR----------------LRGVHAVTRYIVNEVQ 1238
Cdd:PRK02597 1020 VKVIesDGTITEYPILPG-QNVMVSDGQQVDAGEPLTDGPINPHELLEiffedlrdrkglyeaaLEALQKLQRFLVNEVQ 1098
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1239 DVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEGEQVEYSRVKIANRELEANGKVGATFSRDLLGITKASLATES 1318
Cdd:PRK02597 1099 NVYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDS 1178
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1319 FISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDrmrrRAAGELPAAPQVTAED 1388
Cdd:PRK02597 1179 FISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEE----ELSAEAGPHPDILAED 1244
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
18-809 |
1.32e-71 |
|
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: 255.92 E-value: 1.32e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 18 DAIKIALASPDMIRSWSFGEVKKPETINyRTFKPERDGLFCARIfGPVKdyeclcgkykrlkhRGVICEKCGvevtqtkv 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 98 rrERM-------GHIELASPTAHIWFLKSlpsrigllldmplrdIERVLyfesyvvieggmtnleR---QQILTEEQYLD 167
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFLTK---------------ILKIL----------------RcvcKRELSAERVLE 103
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 168 ALEEFGDEFDAKMGaeaiqallksmdleqecetlreeLNETNSetkrkkltkriklleafvqsgnKPEWMILTVLPVLPP 247
Cdd:cd02733 104 IFKRISDEDCRILG-----------------------FDPKFS----------------------RPDWMILTVLPVPPP 138
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 248 DLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSnKRPLK 325
Cdd:cd02733 139 AVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQKS-GRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 326 SLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMAL-----ELFKPFIYGKL-EL--RGLATTIKAa 397
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLqELvrNGPNEYPGA- 296
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 398 kKMVEREEAVVWD------ILDEVIRE------H-----PVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNAD 460
Cdd:cd02733 297 -KYIIRDDGERIDlrylkkASDLHLQYgyiverHlqdgdVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNAD 375
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 461 FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPI--IVpsQDVVLGLYYMT-RDCVNAKGEGMVL-------TG- 529
Cdd:cd02733 376 FDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTkRDTFLEKDQVMNLlmwlpdwDGk 453
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 530 -PKEAerIYRAG-------LASLhARVKVRITEYEKDENGEFVAKTSLKDTTVgrailwmIVPKGLPFS-IVNQALGKKA 600
Cdd:cd02733 454 iPQPA--ILKPKplwtgkqIFSL-IIPKINNLIRSSSHHDGDKKWISPGDTKV-------IIENGELLSgILCKKTVGAS 523
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 601 ISKMLNTCYRILGLKPTVIFADQT--------MYTGFayaarsgaSVGIDDMVIP----EKKHEIISEAEAEVAEIQEQF 668
Cdd:cd02733 524 SGGLIHVIWLEYGPEAARDFIGNIqrvvnnwlLHNGF--------SIGIGDTIADketmKKIQETIKKAKRDVIKLIEKA 595
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 669 QSGLV--TAGERY-----NKVIDIWAAANDRVSKAMMDNLQtetvinrdgveeqqvSFNSIYMMADSGARGSAAQIRQLA 741
Cdd:cd02733 596 QNGELepQPGKTLresfeNKVNRILNKARDKAGKSAQKSLS---------------EDNNFKAMVTAGSKGSFINISQII 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 742 G-----------------MRGL--MAKPDGSIIETP-ITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLV 801
Cdd:cd02733 661 AcvgqqnvegkripfgfrRRTLphFIKDDYGPESRGfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLV 740
|
....*...
gi 489923573 802 DVAQDLVV 809
Cdd:cd02733 741 KAMEDVMV 748
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1007-1368 |
2.68e-71 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 262.09 E-value: 2.68e-71
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1007 DGEQVAGGETVANWDPHTMPViTEVSGFVRFTDMIDGQTITRQTDELT-GLSSLVVLDSAERTAGGKDLRPALKI----- 1080
Cdd:TIGR02388 847 DGDLIKPGAVIARTQILCKEA-GVVQGIDSGGESIRRLLVERNSDRLKvNIKAKPVVKTGDLVVAGDELAKGVKAeesge 925
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1081 VDAQGNDVLIPGTDMPaqYFLPGKAIVQLEDGVQISSGDTLARVPQESGGTKDITGGLPRVADLFEARRPKEPAILAEIS 1160
Cdd:TIGR02388 926 IEEVASDYVILRIGRP--YRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARKPKEACILAKRP 1003
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1161 GIISFgKETKGKRRLVITPV--DGSEPYEEMIPKwRQLNVFEGERVERGDVVSDGPEAPHDILR---------------- 1222
Cdd:TIGR02388 1004 GVVQV-KYGTDDESVSIKVIerDGTISEYPLLPG-QNIMVSDGQQVTGGEPLTDGPINPHDILDvffsyykdqdglyeaa 1081
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1223 LRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSSDFLEGEQVEYSRVKIANRELEANGKVGATF 1302
Cdd:TIGR02388 1082 QESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQY 1161
|
330 340 350 360 370 380
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489923573 1303 SRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQD 1368
Cdd:TIGR02388 1162 TPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYEE 1227
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
103-813 |
1.82e-63 |
|
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 (C160) subunit forms part of the active site region of RNAP III. RNAP III is one of the three distinct classes of nuclear RNAP in eukaryotes that is responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA genes, and some others. RNAP III is the largest nuclear RNA polymerase with 17 subunits. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site, making up the head and core of the one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between Rpc1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259847 [Multi-domain] Cd Length: 816 Bit Score: 232.82 E-value: 1.82e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 103 GHIELASPTAHIWFLKSlpsrIGLLLDMPLRDIERVLyfesyvvieggmtnLERQQIlteEQYLDALEEFGDEFDAKMG- 181
Cdd:cd02583 61 GYIKLELPVFHIGYFKA----IINILQCICKTCSRVL--------------LPEEEK---RKFLKRLRRPNLDNLQKKAl 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 182 AEAIQALLKSMDLEQECETLR---EELNETnsetKRKKLTKRIK----LLEAFVQSGNKPEWMILTVLPVLPPDLRPLVP 254
Cdd:cd02583 120 KKKILEKCKKVRKCPHCGLLKkaqEDLNPL----KVLNLFKNIPpedvELLLMNPLAGRPENLILTRIPVPPLCIRPSVV 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 255 LDGGrfATSDLNDL---YRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMI 331
Cdd:cd02583 196 MDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQCALYINSELPGLPLSMQPKKPIRGFCQRL 273
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 332 KGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP--------------------------FIYGKL 385
Cdd:cd02583 274 KGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPervtrynieklrklvlngpdvhpganFVIKRD 353
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 386 ElrGLATTIKAAKKM-----------VEREeavvwdILDEVIrehpVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVC 454
Cdd:cd02583 354 G--GKKKFLKYGNRRkiarelkigdiVERH------LEDGDI----VLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVC 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 455 AAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT-RD----------CVNAKGE 523
Cdd:cd02583 422 TPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYLLTsKDvffdraqfcqLCSYMLD 501
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 524 GMVL---------------TG---------PKEAERIyraglaSLHARVKVRITEYEKDE-----------NGEFVA--- 565
Cdd:cd02583 502 GEIKidlpppailkpvelwTGkqifslllrPNKKSPV------LVNLEAKEKSYTKKSPDmcpndgyvvirNSELLCgrl 575
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 566 -KTSLKDTTvgrailwmivpKGLPFSIVNQALGKKAISKMLNTCYRIlglkptvifadqtmytGFAYAARSGASVGIDDm 644
Cdd:cd02583 576 dKSTLGSGS-----------KNSLFYVLLRDYGPEAAAAAMNRLAKL----------------SSRWLSNRGFSIGIDD- 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 645 VIP-----EKKHEIISEAEAEVAEIQEQFQSGLVTAGERYN-------KVIDIWAAANDRVSKAMMDNLQtetvinrdgv 712
Cdd:cd02583 628 VTPskellKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCTaeqtleaKISGELSKIREDAGKACLKELH---------- 697
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 713 eeqqvSFNSIYMMADSGARGSAAQIRQ---------LAGMRglmaKPDGSI----------IETPIT----AN-FREGLN 768
Cdd:cd02583 698 -----KSNSPLIMALCGSKGSNINISQmiacvgqqiISGKR----IPNGFEdrtlphfprnSKTPAAkgfvANsFYSGLT 768
|
810 820 830 840
....*....|....*....|....*....|....*....|....*
gi 489923573 769 VLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDD 813
Cdd:cd02583 769 PTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDG 813
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1099-1373 |
1.95e-55 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 212.49 E-value: 1.95e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1099 YFLPGKAIVQLEDGVQISSGDTLARVPQESGGTKDITGGLPRVADLFEARrPKEPailaeisgiISFGKETKgkrrlvit 1178
Cdd:CHL00117 1096 YLATPGATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEAR-SIDS---------ISMNLEKR-------- 1157
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1179 pvdgsepyeemIPKWrqlnvfegervergdvvsdgpeaPHDILRLRGV-----HAVTR-------YIVNEVQDVYRLQGV 1246
Cdd:CHL00117 1158 -----------LEGW-----------------------NERITRILGIpwgflIGAELsiaqsqiSLVNKIQKVYRSQGV 1203
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1247 KINDKHIEVIVRQMLRKATIESAG-SSDFLEGEQVEYSRVKIANRELeangKVGATFSRDLLGITKASLATESFISAASF 1325
Cdd:CHL00117 1204 QISDKHIEIIVRQMTSKVLVSEDGmSNVFLPGELIGLLRAERINRAL----EEAICYRPILLGITKASLNTQSFISEASF 1279
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 489923573 1326 QETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRR 1373
Cdd:CHL00117 1280 QETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSKQH 1327
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
198-801 |
1.60e-47 |
|
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: 183.92 E-value: 1.60e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 198 CETLREelnetnSETKRKKLTKRIKLLE-----AFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFaTSDLNDLYRRV 272
Cdd:cd01435 92 CHRFRI------SKWEVKLFVAKLKLLDkgllvEAAELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKI 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 273 INRNNRLKRLLDLAAPDIIVRNEKRM---------------LQEAVDALLDNGrrgraitgSNKRPLKSLADMIKG---- 333
Cdd:cd01435 165 LKDNQQIRDLLASMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDST--------KAPKSGKKSPPGIKQllek 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 334 KQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMAL--------------ELFKPFIYGK--------LELRGLA 391
Cdd:cd01435 237 KEGLFRMNMMGKRVNYAARSVISPDPFIETNEIGIPLVFAKkltfpepvtpfnveELRQAVINGPdvypganaIEDEDGR 316
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 392 TTIKAAKKMVEREEA------------------VVW------DIldevirehpVLLNRAPTLHRLGIQA-FEPVLIEGKA 446
Cdd:cd01435 317 LILLSALSEERRKALaklllllssaklllngpkKVYrhlldgDV---------VLLNRQPTLHKPSIMAhKVRVLPGEKT 387
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 447 IQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPI---IvpsQDVVLGLYYMT-RDCVNAKG 522
Cdd:cd01435 388 LRLHYANCKSYNADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLrglI---QDHVVSGVLLTsRDTFFTRE 464
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 523 EGMVLtgpkeaerIYRAGLASLHARVKVRIteyekdengEFVAKTSLKDttvgrAILWM-----------IVPKGLPFSi 591
Cdd:cd01435 465 EYQQL--------VYAALRPLFTSDKDGRI---------KLLPPAILKP-----KPLWTgkqvistilknLIPGNAPLL- 521
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 592 vNQALGKKAISKMLNTCYRILGLKPTVIFADQTMYTGF--------------------------------------AYAA 633
Cdd:cd01435 522 -NLSGKKKTKKKVGGGKWGGGSEESQVIIRNGELLTGVldksqfgasayglvhavyelyggetagkllsalgrlftAYLQ 600
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 634 RSGASVGIDDMVI-PE---KKHEIISEAEAEVAEIQEQFqsglvtAGERYNKVidiwaaANDRVSKAMMDNLQTetvinr 709
Cdd:cd01435 601 MRGFTCGIEDLLLtPKadeKRRKILRKAKKLGLEAAAEF------LGLKLNKV------TSSIIKACLPKGLLK------ 662
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 710 dgveeqQVSFNSIYMMADSGARGS---AAQI------RQLAGMR-GLMA--------KP-DGSiietP-----ITANFRE 765
Cdd:cd01435 663 ------PFPENNLQLMVQSGAKGSmvnASQIscllgqQELEGRRvPLMVsgktlpsfPPyDTS----PraggfITDRFLT 732
|
730 740 750
....*....|....*....|....*....|....*.
gi 489923573 766 GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLV 801
Cdd:cd01435 733 GIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
344-485 |
2.94e-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: 163.63 E-value: 2.94e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 344 GKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFI---YGKLELRGL----------ATTIK---------AAKKMV 401
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpYNIKRLRQLvengpnvypgANYIIringarrdlRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 402 EREEAVVWDILDE-VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA 480
Cdd:pfam00623 81 LDKELEIGDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 489923573 481 RALMM 485
Cdd:pfam00623 161 EELML 165
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
489-644 |
1.23e-34 |
|
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Pssm-ID: 461507 Cd Length: 158 Bit Score: 130.06 E-value: 1.23e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 489 NILSPANGEPIIVPSQDVVLGLYYMTRDCvnakgegmVLTGPKEAERIYRAGLASLHARVKVRITEYEkdengefvakts 568
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHPAILKPIKPLW------------ 60
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 569 LKDTTVGRAILWMIVPKGLP------------FSIVNQALGK----------KAISKMLNTCYRILGLKPTVIFADQTMY 626
Cdd:pfam04983 61 TGKQTFSRLLPNEINPKGKPktneedlcendsYVLINNGELIsgvidkktvgKSLGSLIHIIYKEYGPEETAKFLDRLQK 140
|
170
....*....|....*...
gi 489923573 627 TGFAYAARSGASVGIDDM 644
Cdd:pfam04983 141 LGFRYLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1217-1362 |
1.91e-26 |
|
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: 106.73 E-value: 1.91e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1217 PHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMlrkatiesagssdflegeqveysrvkianreleang 1296
Cdd:cd00630 50 IHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVM------------------------------------ 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489923573 1297 kvgaTFSRDLLGITKASLA--TESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:cd00630 94 ----TYSGGLRGVTRSGFRasKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
673-764 |
6.01e-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: 95.12 E-value: 6.01e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 673 VTAGERYNKVIDIWAAANDRVSKAMMDN-LQTETVINRDGVEEQQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPD 751
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNiLNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVEG 80
|
90 100
....*....|....*....|....*...
gi 489923573 752 GSI---------------IETPITANFR 764
Cdd:pfam05000 81 KRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
338-518 |
2.11e-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: 97.86 E-value: 2.11e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 338 FRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP-------------FIYGKLELRGL-----ATTIKAAKK 399
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVServsswnrerlqeYCDLTLLLKGVigvrrNGRLVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 400 MVEREeavVWDILDEVIRE-HPVLLNRAPTLHRLGIQAFE-PVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQ 477
Cdd:cd10506 286 HNTLQ---IGDVIHRPLVDgDVVLVNRPPSIHQHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQAR 362
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 489923573 478 LEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCV 518
Cdd:cd10506 363 AELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGV 403
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1231-1362 |
4.74e-19 |
|
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: 94.07 E-value: 4.74e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1231 RYIVNEV--QDVYRLQGVkINDKHIEVIVRQMLRKATIES------------------AGSSDFLEGEQVEYSRVKI--- 1287
Cdd:COG0086 559 RYLVNEIlpQEVPFYNQV-INKKHIEVIIRQMYRRCGLKEtvifldrlkklgfkyatrAGISIGLDDMVVPKEKQEIfee 637
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1288 ANRELE------ANGKV--GATFSRDLLGITKASLATESFISAA-SFQETTRVLTEAAVAGKRDELRGL----------K 1348
Cdd:COG0086 638 ANKEVKeiekqyAEGLItePERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmakpS 717
|
170
....*....|....*..
gi 489923573 1349 ENVI---VGRLIPAGTG 1362
Cdd:COG0086 718 GNIIetpIGSNFREGLG 734
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
909-1362 |
2.67e-14 |
|
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274105 [Multi-domain] Cd Length: 367 Bit Score: 76.25 E-value: 2.67e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVkNKGSIRLSnakSVVNSsgKLVITSRNTELKLIDEF 988
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAG-------VAELNV-TLGLPRLI---EIVDA--RKTPSTPSMTIYLEDEY 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 989 grtkesykvpygsvmaKGDGEQVaggETVANWDPHT--MPVITEVSgfvrfTDMIDGQTITRQTDELT---GLSSLVVLD 1063
Cdd:TIGR02389 108 ----------------EKDREKA---EEVAKKIEATklEDVAKDIS-----IDLADMTVIIELDEEQLkerGITVDDVEK 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1064 SAERTAGGKDlrpalkIVDAQGNDVLI--PGTDMPaqyflpgKAIVQLEDGVqissgdtlarvpqesggtKDITgglprv 1141
Cdd:TIGR02389 164 AIKKAKLGKV------IEIDMDNNTITikPGNPSL-------KELRKLKEKI------------------KNLH------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1142 adlfearrpkepailaeISGIisfgketKGKRRLVITpvdgsEPYEEMIPKWRQLNVFEGERVERGDVVSDGPEAPHDIL 1221
Cdd:TIGR02389 207 -----------------IKGI-------KGIKRVVIR-----KEGDEYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIA 257
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1222 RLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGssdflegeqveysRVKIANREleangkvgat 1301
Cdd:TIGR02389 258 EVLGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG-------------RHGISGEK---------- 314
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489923573 1302 fsrdllgitkaslatESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:TIGR02389 315 ---------------ASVLARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTG 360
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
909-1362 |
1.10e-13 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 74.21 E-value: 1.10e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVkNKGSIRLsnaKSVVNSSGKLVITSRNTELKliDEF 988
Cdd:cd06528 37 IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAG-------VAEINV-TLGLPRL---IEIVDARKEPSTPTMTIYLE--EEY 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 989 GRTKESykvpygsvmakgdGEQVA---GGETVANwdphtmpVITEVSgfvrfTDMIDGQTItrqtdeltglsslVVLDsa 1065
Cdd:cd06528 104 KYDREK-------------AEEVArkiEETTLEN-------LAEDIS-----IDLFNMRIT-------------IELD-- 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1066 ERTAGGKDLRPalkivdaqgNDVLipgtdmpaqyflpgKAIVQLEDGVQISSGDtlarvpqesGGTKDITGGLPRVADLF 1145
Cdd:cd06528 144 EEMLEDRGITV---------DDVL--------------KAIEKLKKGKVGEEGD---------VTLIVLKAEEPSIKELR 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1146 EARrpkePAIL-AEISGIisfgketKGKRRLVITPVDGsepyeEMIPKWRQLN---VFEGERVERGDVVSDGpeaPHDIL 1221
Cdd:cd06528 192 KLA----EKILnTKIKGI-------KGIKRVIVRKEED-----EYVIYTEGSNlkaVLKVEGVDPTRTTTNN---IHEIE 252
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1222 RLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGssdflegeqveysRVKIANREleangkvgat 1301
Cdd:cd06528 253 EVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYDGEVRQIG-------------RHGIAGEK---------- 309
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489923573 1302 fsrdllgitkaslatESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:cd06528 310 ---------------PSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
909-1362 |
3.53e-12 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 70.61 E-value: 3.53e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVkNKGSIRLsnaksvvnssgklvitsrnteLKLIDef 988
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAG-------VAEMNV-TLGLPRL---------------------IEIVD-- 227
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 989 GRTKESykVPYGSVMAKGDGEQvaggetvaNWDphtmpVITEVSGFVRFTDMIDGQTITRQTDEltgLSSLVVLD---SA 1065
Cdd:PRK14897 228 ARKKPS--TPTMTIYLKKDYRE--------DEE-----KVREVAKKIENTTLIDVADIITDIAE---MSVVVELDeekMK 289
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1066 ERtaggkdlrpalkivdaqgndvlipgtdmpaqyflpgkaivqledgvQISSGDTLARVPQESGGTKDITGGLPRVadlf 1145
Cdd:PRK14897 290 ER----------------------------------------------LIEYDDILAAISKLTFKTVEIDDGIIRL---- 319
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1146 earRPKEPAI-----LAE------ISGIisfgketKGKRRlVITPVDGSEPYEEMIPKWRQL-NVFEGERVergDVVSDG 1213
Cdd:PRK14897 320 ---KPQQPSFkklylLAEkvksltIKGI-------KGIKR-AIARKENDERRWVIYTQGSNLkDVLEIDEV---DPTRTY 385
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1214 PEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGssdflegeqveysRVKIANREle 1293
Cdd:PRK14897 386 TNDIIEIATVLGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIG-------------RHGISGEK-- 450
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489923573 1294 angkvgatfsrdllgitkaslatESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK14897 451 -----------------------SSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
908-1362 |
7.01e-12 |
|
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: 69.16 E-value: 7.01e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 908 IINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaessIQVKN--KGSIRLsnaKSVVNSSGKLvitsRNTELK-- 983
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG----------VSAKNvtLGVPRL---KEIINVAKNI----KTPSLTvy 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 984 LIDEFGRTKESYKV-----PYGSVmakgdGEQVAGGETvaNWDPHTM-PVITEVSGFVR-FTDMIDgqtitrQTDELTGL 1056
Cdd:cd02584 86 LEPGFAKDEEKAKKiqsrlEHTTL-----KDVTAATEI--YYDPDPQnTVIEEDKEFVEsYFEFPD------EDVEQDRL 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1057 SSLV---VLDSAERTagGKDLRP---ALKIVDAQGNDVLIPGTDMPAQyflpgKAIVQLedgvqissgdtlaRVPQESGG 1130
Cdd:cd02584 153 SPWLlriELDRKKMT--DKKLSMeqiAKKIKEEFKDDLNVIFSDDNAE-----KLVIRI-------------RIINDDEE 212
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1131 tKDITGGLPRVADLFEARRPKEPaILAEISGI-ISFGKETKGKRrlVITPVDGSEPYEEmipkWrqlnVFEGERVergdv 1209
Cdd:cd02584 213 -KEEDSEDDVFLKKIESNMLSDM-TLKGIEGIrKVFIREENKKK--VDIETGEFKKREE----W----VLETDGV----- 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1210 vsdgpeAPHDILRLRGVHAvTRYIVNEVQDVYRLQGvkindkhIEVIVRQMLR--KATIESAGSSdflegeqVEYsrvki 1287
Cdd:cd02584 276 ------NLREVLSHPGVDP-TRTTSNDIVEIFEVLG-------IEAARKALLKelRNVISFDGSY-------VNY----- 329
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1288 anRELeangkvgA------TFSRDLLGIT-----KASLATesfISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRL 1356
Cdd:cd02584 330 --RHL-------AllcdvmTQRGHLMAITrhginRQDTGP---LMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQL 397
|
....*.
gi 489923573 1357 IPAGTG 1362
Cdd:cd02584 398 APIGTG 403
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
909-1362 |
7.97e-12 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 68.72 E-value: 7.97e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVkNKGSIRLSNaksvvnssgklVITSRNT------EL 982
Cdd:PRK04309 56 VEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG-------VAEINV-TLGLPRLIE-----------IVDARKEpstpmmTI 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 983 KLIDEFGRTKEsykvpygsvMAkgdgEQVA---GGETVANwdphtmpVITEVSgfvrfTDMIDGQTItrqtdeltglssl 1059
Cdd:PRK04309 117 YLKDEYAYDRE---------KA----EEVArkiEATTLEN-------LAKDIS-----VDLANMTII------------- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1060 VVLDsaERTAGGKDLRPalkivdaqgNDVlipgtdmpaqyflpgKAIVQLEDGVQISsgdtlarvpqESGGTKDITGGLP 1139
Cdd:PRK04309 159 IELD--EEMLEDRGLTV---------DDV---------------KEAIEKKKGGEVE----------IEGNTLIISPKEP 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1140 RVADLFEaRRPKEPAILaeISGIisfgketKGKRRLVITP--------VDGSePYEEmipkwrqlnVFEGERVergDVVS 1211
Cdd:PRK04309 203 SYRELRK-LAEKIRNIK--IKGI-------KGIKRVIIRKegdeyviyTEGS-NLKE---------VLKVEGV---DATR 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1212 DGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIESAGSsdflegeqveysrvkianre 1291
Cdd:PRK04309 260 TTTNNIHEIEEVLGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMMTWDGEVRQIGR-------------------- 319
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489923573 1292 leaNGKVGatfsrdllgiTKASLatesfISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK04309 320 ---HGVSG----------EKASV-----LARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
912-939 |
7.14e-10 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 58.97 E-value: 7.14e-10
10 20
....*....|....*....|....*...
gi 489923573 912 GEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAG 28
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
908-939 |
9.44e-09 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 58.38 E-value: 9.44e-09
10 20 30
....*....|....*....|....*....|..
gi 489923573 908 IINKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAG 37
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
909-939 |
2.90e-08 |
|
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: 57.20 E-value: 2.90e-08
10 20 30
....*....|....*....|....*....|.
gi 489923573 909 INKGEAIGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1149-1362 |
1.27e-07 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 56.44 E-value: 1.27e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1149 RPKEPAILA------EISGIISFGKEtkGKRRLVITPvDGSEPYEEMIPKWRQLNVFEGERVERGDVVSDGPEAPHDILR 1222
Cdd:PRK14898 664 KPKTPSYKAlrkripKIKNIVLKGIP--GIERVLVKK-EEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQE 740
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1223 LRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMlrkatiesagssdflegeqveysrvkIANRELEANGKVGATF 1302
Cdd:PRK14898 741 VLGIEAARNAIINEMMNTLEQQGLEVDIRHLMLVADIM--------------------------TADGEVKPIGRHGVAG 794
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1303 SRDllgitkaslateSFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK14898 795 EKG------------SVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
1152-1362 |
3.68e-06 |
|
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: 50.65 E-value: 3.68e-06
10 20 30 40 50 60 70 80
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gi 489923573 1152 EPAILAEISGIISF--GKETKGKRRLVITPVDGSEPYEemipKWRQLNVFEGERVERGDVvsdgpeapHDILRLRGVHAV 1229
Cdd:cd02735 143 RKAVIREIPGITRCfvVEEDKGGKTKYLVITEGVNLAA----LWKFSDILDVNRIYTNDI--------HAMLNTYGIEAA 210
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90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489923573 1230 TRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIEsagssdflegeqveysrvkianreleangkvgaTFSRdlLGI 1309
Cdd:cd02735 211 RRAIVKEISNVFKVYGIAVDPRHLSLIADYMTFEGGYR---------------------------------PFNR--IGM 255
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170 180 190 200 210
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gi 489923573 1310 TKASlateSFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:cd02735 256 ESST----SPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTG 304
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