|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
16-1382 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2382.83 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 16 EFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQT 95
Cdd:PRK00566 6 DFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTRS 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 96 KVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVEGGMTSLERSQILTEEQYLDALEEFGDE 175
Cdd:PRK00566 86 KVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGDE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 176 FDAKMGAEAIQALLKAMDLEQEVENLREELNETNSETKRKKLTKRIKLLEAFIQSGNKPEWMILTVLPVLPPDLRPLVPL 255
Cdd:PRK00566 166 FVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQL 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 256 DGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ 335
Cdd:PRK00566 246 DGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGKQ 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 336 GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV 415
Cdd:PRK00566 326 GRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEEV 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 416 IREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAS 495
Cdd:PRK00566 406 IKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPAN 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 496 GDPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLNGSTEAERVYRAGHASLHARVKVRITEEVkdgegnitkrtsMIDTTVG 575
Cdd:PRK00566 486 GKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRITSKK------------LVETTVG 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 576 RAILWRIVPRGLPYSLVNQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGIIA 655
Cdd:PRK00566 554 RVIFNEILPEGLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 656 EAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMENLSvetvvnrdgeeEQQVSFNSIFMMADSGARGSAA 735
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNLS-----------KDQESFNPIYMMADSGARGSAS 702
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 736 QIRQLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDCG 815
Cdd:PRK00566 703 QIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCG 782
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 816 THEGIVMTPVIEGGDVKEPLRDRVLGRVAAEDILKPGTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCETDFGVC 895
Cdd:PRK00566 783 TDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVC 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 896 AKCYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHiggaasraaaessiqvrnkgtlklfnakfimnsagklvi 975
Cdd:PRK00566 863 AKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFH--------------------------------------- 903
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 976 tsrntelrlidefgrtkesykvpygaqlskgdgeavnggetvanwdphtmpvvsevsgiirftdmhdgqtitrqtdelTG 1055
Cdd:PRK00566 904 ------------------------------------------------------------------------------TG 905
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1056 lsslvvldsaerttsakemrpalkivdaqgndvlipntdmpaayflpgkaivqlddGVaitagdtlaripqesvgtkDIT 1135
Cdd:PRK00566 906 --------------------------------------------------------GV-------------------DIT 910
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1136 GGLPRVADLFEARRPKEPAILAEISGIISFGKETKGKRRLVITPIDGsDPYEEMIPKWRQLNVFEGEMVERGDVVSDGPE 1215
Cdd:PRK00566 911 GGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDG-EEREYLIPKGKHLLVQEGDHVEAGDKLTDGSI 989
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1216 SPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEGEQVEYARVKVANRLLEQE 1295
Cdd:PRK00566 990 DPHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAE 1069
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1296 GKIPATFERDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGFAYHQDRIRRRHL 1375
Cdd:PRK00566 1070 GKEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARYRNIKVEPAV 1149
|
....*..
gi 490362540 1376 AETAEAA 1382
Cdd:PRK00566 1150 DEEEAEA 1156
|
|
| 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: 1901.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 14 TEEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVT 93
Cdd:COG0086 4 VEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 94 QTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVEGGMTSLERSQILTEEQYLDALEEFG 173
Cdd:COG0086 84 LSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 174 DEFDAKMGAEAIQALLKAMDLEQEVENLREELNETNSETKRKKLTKRIKLLEAFIQSGNKPEWMILTVLPVLPPDLRPLV 253
Cdd:COG0086 164 DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 254 PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKG 333
Cdd:COG0086 244 PLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 334 KQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILD 413
Cdd:COG0086 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 414 EVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSP 493
Cdd:COG0086 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 494 ASGDPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLNGSTEAERVYRAGHASLHARVKVRITEEVKdgegnitKRTSMIDTT 573
Cdd:COG0086 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGE-------QVGKIVETT 556
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 574 VGRAILWRIVPRGLPYslVNQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGI 653
Cdd:COG0086 557 VGRYLVNEILPQEVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEI 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 654 IAEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMENLSvetvvnrdgeeeqqvSFNSIFMMADSGARGS 733
Cdd:COG0086 635 FEEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS---------------SQNTTYMMADSGARGS 699
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 734 AAQIRQLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDD 813
Cdd:COG0086 700 ADQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 779
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 814 CGTHEGIVMTPVIEGGDVKEPLRDRVLGRVAAEDILKPGTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCETDFG 893
Cdd:COG0086 780 CGTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGG 859
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 894 VCAKCYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVRNKGTLKLFNAKFIMNSAGKL 973
Cdd:COG0086 860 VCAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKG 939
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 974 VITSRNTELRLIDEFGRTKESYKVPYGAQLSKGDGEAVNGGETVANWDPHTMPVVSEVSGIIRFTDMHDGQTITRQTDEL 1053
Cdd:COG0086 940 VVVSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEE 1019
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1054 TGLSSLVVLDSAERTTSAKEMRPALKIVDAQGNDVLIPNTDMPAAYFLPGKAIVQLDDGVAITAGDTLARIPQESVGTKD 1133
Cdd:COG0086 1020 TGGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRD 1099
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490362540 1134 ITGGLPRVADLFEARRPKEPAILAEISGIISFGKETKGKRRLVITPIDGSDPYEEMIPKWRQLNVF 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: 1800.01 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 19 AIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVR 98
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 99 RERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVEGGMTSLERSQILTEEQYLDALEEFGDEFDA 178
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 179 KMGAEAIQALLKAMDLEQEVENLREELNETNSETKRKKLTKRIKLLEAFIQSGNKPEWMILTVLPVLPPDLRPLVPLDGG 258
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 259 RFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRF 338
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 339 RQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIRE 418
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 419 HPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDP 498
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 499 IIVPSQDVVLGLYYMTRDCVNAKGEGMVLNGSTEAERVYRAGHASLHARVKVRITEEVkdgegnitkrtsmIDTTVGRAI 578
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRTSGEI-------------LETTVGRVI 547
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 579 LWRIVPRGLPYSLVNQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGIIAEAE 658
Cdd:TIGR02386 548 FNEILPEGFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEAD 627
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 659 AEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMENLSvetvvnrdgeeEQQVSFNSIFMMADSGARGSAAQIR 738
Cdd:TIGR02386 628 KEVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLLK-----------KDTYKFNPIFMMADSGARGNISQFR 696
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 739 QLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDCGTHE 818
Cdd:TIGR02386 697 QLAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEE 776
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 819 GIVMTPVIEGGD-VKEPLRDRVLGRVAAEDILKPGTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCETDFGVCAK 897
Cdd:TIGR02386 777 GIEVEAIVEGKDeIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQK 856
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 898 CYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaessiqvrnkgtlklfnakfimnsagklvits 977
Cdd:TIGR02386 857 CYGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGG-------------------------------------- 898
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 978 rntelrlidefgrtkesykvpygaqlskgdgeavnggetvanwdphtmpvvsevsgiirftdmhdgqtitrqtdeltgls 1057
Cdd:TIGR02386 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1058 slvvldsaerttsakemrpalkivdaqgndvlipntdmpaayflpgkaivqlddgvaiTAGDtlaripqesvgTKDITGG 1137
Cdd:TIGR02386 899 ----------------------------------------------------------VAGA-----------SGDITQG 909
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1138 LPRVADLFEARRPKEPAILAEISGIISFGKET-KGKRRLVITpiDGSDPYEE-MIPKWRQLNVFEGEMVERGDVVSDGPE 1215
Cdd:TIGR02386 910 LPRVKELFEARTPKDKAVIAEVDGTVEIIEDIvKNKRVVVIK--DENDEEKKyTIPFGAQLRVKDGDSVSAGDKLTEGSI 987
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1216 SPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEGEQVEYARVKVANRLLEQE 1295
Cdd:TIGR02386 988 DPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQ 1067
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490362540 1296 GKIPATFERDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGFAYHQD 1368
Cdd:TIGR02386 1068 GKKPASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGLKTYKE 1140
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1369 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1543.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 15 EEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQ 94
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 95 TKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVEGGMTSLERSQILTEEQYLDALEEFG- 173
Cdd:PRK14844 1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGi 1605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 174 DEFDAKMGAEAIQALLKAMDLEQEVENLREELNETNSETKRKKLTKRIKLLEAFIQSGNKPEWMILTVLPVLPPDLRPLV 253
Cdd:PRK14844 1606 DSFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLV 1685
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 254 PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLK-SLADMIK 332
Cdd:PRK14844 1686 SLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLK 1765
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 333 GKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDIL 412
Cdd:PRK14844 1766 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDML 1845
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 413 DEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILS 492
Cdd:PRK14844 1846 EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 493 PASGDPIIVPSQDVVLGLYYMTRDcvNAKGEGMVLNGS-TEAERVYRAGHASLHARVKVRIteEVKDGEGNITKRTsmID 571
Cdd:PRK14844 1926 PSNGRPIIVPSKDIVLGIYYLTLQ--EPKEDDLPSFGAfCEVEHSLSDGTLHIHSSIKYRM--EYINSSGETHYKT--IC 1999
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 572 TTVGRAILWRIVPR--GLPYSLVNQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEK 649
Cdd:PRK14844 2000 TTPGRLILWQIFPKheNLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPET 2079
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 650 KAGIIAEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMENLSVEtvvnrdgeeEQQVSFNSIFMMADSG 729
Cdd:PRK14844 2080 KATHVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIY---------DGNSKYNSVYMMVNSG 2150
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 730 ARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVI 809
Cdd:PRK14844 2151 ARGSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIV 2230
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 810 TEDDCGTHEGIVMTPVIEGGDVKEPLRDRVLGRVAAEDILKPGTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCE 889
Cdd:PRK14844 2231 TKHDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCE 2310
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 890 TDFGVCAKCYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVRNKGTLKLFNAKFIMNS 969
Cdd:PRK14844 2311 ISPGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDK 2390
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 970 AGKLVITSRNTELRLIDEFGRTKESYKVPYGAQLSKGDGEAVNGGETVANWDPHTMPVVSEVSGIIRFTDMHDGQTITRQ 1049
Cdd:PRK14844 2391 NGNKIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEV 2470
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1050 TDELTGLSSLVVLDSAERTTSAKeMRPALKIVDAQGNdVLIPNTDMPAAYFLPGKAIVQLDDGVAITAGDTLARIPQESV 1129
Cdd:PRK14844 2471 MDESTGISSKVVKDWKLYSGGAN-LRPRIVLLDDNGK-VMTLASGVEACYFIPIGAVLNVQDGQKVHAGDVITRTPRESV 2548
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1130 GTKDITGGLPRVADLFEARRPKEPAILAEISGIISFG-KETKGKRRLVITPIDGS-DPYEEMIPKWRQLNVFEGEMVERG 1207
Cdd:PRK14844 2549 KTRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDEQiSPVEYLVSRSKHVIVNEGDFVRKG 2628
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1208 DVVSDGPESPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEGEQVEYARVKV 1287
Cdd:PRK14844 2629 DLLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDR 2708
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1288 ANRLLEQEGKIPATFERDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGFAYHQ 1367
Cdd:PRK14844 2709 ENDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLIMNK 2788
|
..
gi 490362540 1368 DR 1369
Cdd:PRK14844 2789 VR 2790
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
8-1380 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1520.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 8 LKAQTKTEEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGV-ICE 86
Cdd:PRK09603 1387 IKEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTCE 1466
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 87 KCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVEGGMTSLE--------RSQ 158
Cdd:PRK09603 1467 KCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGEAAYDnegtklvmKYD 1546
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 159 ILTEEQYLDALEEFGDE-FDAKMGAEAIQALLKAMDLEQEVENLREELNETNSETKRKKLTKRIKLLEAFIQSGNKPEWM 237
Cdd:PRK09603 1547 ILNEEQYQNISRRYEDRgFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEWM 1626
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 238 ILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAIT 317
Cdd:PRK09603 1627 MLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAVK 1706
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 318 GSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAA 397
Cdd:PRK09603 1707 GANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQA 1786
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 398 KKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQ 477
Cdd:PRK09603 1787 KRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEAI 1866
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 478 LEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLNGSTEAERVYRAGHASLHARVKVriteevk 557
Cdd:PRK09603 1867 AECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRV------- 1939
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 558 dgegniTKRTSMIDTTVGRAILWRIVPRGLPYSLVNQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGA 637
Cdd:PRK09603 1940 ------LDQGNIIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGI 2013
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 638 SVGIDDMVIPEKKAGIIAEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMEnlsvetVVNRDGEeeqqv 717
Cdd:PRK09603 2014 SISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMT------AIAKDKE----- 2082
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 718 SFNSIFMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLT 797
Cdd:PRK09603 2083 GFNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLT 2162
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 798 RRLVDVAQDLVITEDDCGTHEGIVMTPVIEGGDVKEPLRDRVLGRVAAEDILKPGTADILIPRNTLLHEKQCDLLEENSV 877
Cdd:PRK09603 2163 RKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGI 2242
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 878 DSVKVRSVVSCETDFGVCAKCYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVRNKGT 957
Cdd:PRK09603 2243 KSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGF 2322
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 958 LKLFNAKFIMNSAGKLVITSRNT----------------ELR--------LIDEFGRTKES------------------- 994
Cdd:PRK09603 2323 VRFYNLRTYTNKEGKNIIANRRNasilvvepkikapfdgELRietvyeevVVSVKNGDQEAkfvlrrsdivkpselagvg 2402
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 995 --------------YKV--------------------PYGAQLSKGD--------------------------------- 1007
Cdd:PRK09603 2403 gkiegkvylpyasgHKVhkggsiadiiqegwnvpnriPYASELLVKDndpiaqdvyakekgiikyyvleanhlerthgik 2482
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1008 -GEAV------------NGGE-----------------------------------TVANWDPHTMPVVSEVSGIIRFTD 1039
Cdd:PRK09603 2483 kGDIVsekglfaviaddNGREaarhyiargseiliddnsevsansviskpttntfkTIATWDPYNTPIIADFKGKVSFVD 2562
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1040 MHDGQTITRQTDELTGLSSLVVLDSAerTTSAKemrPALKIVDAQGNDVlipntdmpaAYFLPGKAIVQLDDGVAITAGD 1119
Cdd:PRK09603 2563 IIAGVTVAEKEDENTGITSLVVNDYI--PSGYK---PSLFLEGANGEEI---------RYFLEPKTSIAISDGSSVEQAE 2628
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1120 TLARIPQESVGTKDITGGLPRVADLFEAR--RPKEPAILAEISGIISFGKETKGKRRLVITPIDGSDpYEEMIPKWRQLN 1197
Cdd:PRK09603 2629 VLAKIPKATVKSRDITGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRS-MDYFVDKGKQIL 2707
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1198 VFEGEMVERGDVVSDGPESPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEG 1277
Cdd:PRK09603 2708 VHADEFVHAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEG 2787
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1278 EQVEYARVKVANRLLEQEGKIPATFERDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLI 1357
Cdd:PRK09603 2788 DLVSKKLFKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMI 2867
|
1530 1540
....*....|....*....|...
gi 490362540 1358 PAGTGFaYHQDRIRRRHLAETAE 1380
Cdd:PRK09603 2868 PVGTGM-YKNKKIVLRTLEDDPK 2889
|
|
| 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: 1304.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 15 EEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQ 94
Cdd:cd01609 1 LDFDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 95 TKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFesyvvveggmtslersqilteeqyldaleefgd 174
Cdd:cd01609 81 SKVRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF--------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 175 efdakmgaeaiqallkamdleqevenlreelnetnsetkrkkltkrikLLEAFIQSGNKPEWMILTVLPVLPPDLRPLVP 254
Cdd:cd01609 128 ------------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQ 159
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 255 LDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGK 334
Cdd:cd01609 160 LDGGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGK 239
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 335 QGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE 414
Cdd:cd01609 240 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEE 319
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 415 VIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Cdd:cd01609 320 VIKGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 399
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 495 SGDPIIVPSQDVVLGLYYMTRDCVNAKGEGmvlngsteaervyraghaslharvkvriteevkdgegnitkrtsMIDTTV 574
Cdd:cd01609 400 SGKPIVTPSQDMVLGLYYLTKERKGDKGEG--------------------------------------------IIETTV 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 575 GRAILWRIVPRGLPYslVNQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGII 654
Cdd:cd01609 436 GRVIFNEILPEGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEII 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 655 AEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMENLSvetvvnrdgeeeqQVSFNSIFMMADSGARGSA 734
Cdd:cd01609 514 KEAEEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLD-------------KDPFNPIYMMADSGARGSK 580
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490362540 735 AQIRQLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDD 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: 1282.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 14 TEEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVT 93
Cdd:PRK14906 6 VTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVT 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 94 QTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVV--------------------------- 146
Cdd:PRK14906 86 RAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleeld 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 147 --------------------------------------VEGGMTSLERSqiLTEEQYL--DALEEF-------------- 172
Cdd:PRK14906 166 aerdrlieatrrlsvdyvpeddefvddigdderltaeeVRAEVADIYEE--YNERKALrrEAFDAFmqiepkqlisdeal 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 173 --------GDEFDAKMGAEAIQALLKAMDLEQEVENLREeLNETNSETKRKKLTKRIKLLEAFIQSGNKPEWMILTVLPV 244
Cdd:PRK14906 244 yremrlnySIYFKGGMGAEAVRDLLDAIDLEKEAEELRA-IIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPV 322
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 245 LPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPL 324
Cdd:PRK14906 323 IPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPL 402
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 325 KSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVERE 404
Cdd:PRK14906 403 KSLADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRG 482
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 405 EAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALM 484
Cdd:PRK14906 483 ASYVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLM 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 485 MSTNNILSPASGDPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLNGSTEAERVYRA-GHASLHARVKVRITEEVKD----G 559
Cdd:PRK14906 563 LSSNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDArADLDLQAKIVVRLSRDMTVrgsyG 642
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 560 EGNITKRTSMIDTTVGRAILWRIVPRGLPYslVNQPLGKKAISKMLNTC---YRILGLKPTVifaDQIMYTGFAYAARSG 636
Cdd:PRK14906 643 DLEETKAGERIETTVGRIIFNQVLPEDYPY--LNYKMVKKDIGRLVNDCcnrYSTAEVEPIL---DGIKKTGFHYATRAG 717
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 637 ASVGIDDMVIPEKKAGIIAEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANERVAKAMMENLSvetvvnrdgeeeqq 716
Cdd:PRK14906 718 LTVSVYDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFD-------------- 783
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 717 vSFNSIFMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYL 796
Cdd:PRK14906 784 -EDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYL 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 797 TRRLVDVAQDLVITEDDCGTHEGIVMTPVIEGGDVKEPLrdrvLGRVAAEDILKPGTADILIPRNTLLHEKQCDLLEENS 876
Cdd:PRK14906 863 TRRLVDVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDPNGEVLLSAGDYIESMDDLKRLVEAG 938
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 877 VDSVKVRSVVSCETDFGVCAKCYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaessiqvrnkg 956
Cdd:PRK14906 939 VTKVQIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGG----------------- 1001
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 957 tlklfnakfimnsagklvitsrntelrlidefgrtkesykvpygaqlskgdgeavnggetvanwdphtmpvvsevsgiir 1036
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1037 ftdmhdgqtitrqtdeltglsslvvldsaerttsakemrpalkivdaqgndvlipntdmpaayflpgkaivqlddgvaiT 1116
Cdd:PRK14906 1002 -------------------------------------------------------------------------------V 1002
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1117 AGDtlaripqesvgtkDITGGLPRVADLFEARRPKEPAILAEISGIISFGKETKGKrrlVITPIDGSDPYEEMIPKWR-- 1194
Cdd:PRK14906 1003 AGD-------------DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEK---TLTIHDQDGNSREYVVSARvq 1066
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1195 -QLNVFEGEMVERGDVVSDGPESPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSE 1273
Cdd:PRK14906 1067 fMPGVEDGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSD 1146
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1274 FLEGEQVE-YARVKVANRLLeQEGKIPATFERDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVI 1352
Cdd:PRK14906 1147 YLPGRQVNrYEFEDTANNLI-LEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVI 1225
|
1450
....*....|....*.
gi 490362540 1353 VGRLIPAGTGFAYHQD 1368
Cdd:PRK14906 1226 IGKPIPAGTGLSRYRD 1241
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
12-560 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 846.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 12 TKTEE-FDAIKIGLASPDMIRSWS---------FGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHR 81
Cdd:PRK02625 3 LRTENrFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHR 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 82 GVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVE-GGMTSLERSQIL 160
Cdd:PRK02625 83 GIVCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDpGNHKNLKYKQLL 162
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 161 TEEQYLDALE-------EFGDEFDAKMGAEAIQALLKAMDLEQEVENLREELNETNSEtKRKKLTKRIKLLEAFIQSGNK 233
Cdd:PRK02625 163 TEDQWLEIEDqiyaedsELEGEEVVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGSR 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 234 PEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG 313
Cdd:PRK02625 242 PEWMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRG 321
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 314 RAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATT 393
Cdd:PRK02625 322 RTVVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNN 401
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 394 IKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLT 473
Cdd:PRK02625 402 IKAAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLS 481
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 474 LEAQLEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRDCVNA-KGEGMVLNGSTEAERVYRAGHASLHARVKVRI 552
Cdd:PRK02625 482 LEAQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGAqKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRF 561
|
....*...
gi 490362540 553 TEEVKDGE 560
Cdd:PRK02625 562 NGEVEDDD 569
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
17-594 |
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: 829.23 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 17 FDAIKIGLASPDMIRSWS---------FGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEK 87
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 88 CGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVVE-GGMTSLERSQILTEEQYL 166
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNpGNAKNLKYKQLLTEDQWL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 167 DALEE-FGDEFD------AKMGAEAIQALLKAMDLEQEVENLREELNETNSEtKRKKLTKRIKLLEAFIQSGNKPEWMIL 239
Cdd:TIGR02387 162 EIEDQiYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 240 TVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGS 319
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 320 NKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKK 399
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 400 MVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLE 479
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 480 ARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRDCVNA-KGEGMVLNGSTEAERVYRAGHASLHARVKVRITEEVKD 558
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGAeKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRFNGEVET 560
|
570 580 590
....*....|....*....|....*....|....*...
gi 490362540 559 GE--GNITKRTSMIDTTVGRAILWRIVPRGLPYSLVNQ 594
Cdd:TIGR02387 561 NDplDEPIKSEDLSDGTRIEQWTYRRDRFDEDGALISQ 598
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
16-514 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 824.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 16 EFDAIKIGLASPDMIRSWS---------FGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKR---LKHRGV 83
Cdd:CHL00018 6 KHQQLRIGLASPQQIRAWAerilpngeiVGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVigdEKEDPK 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 84 ICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVV--VEGGMTSLERSQILT 161
Cdd:CHL00018 86 FCEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRLRGLFE 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 162 EE----QYLDALEEFGDEFDAKM------GAEAIQALLKAMDLEQEVENLR---EELNETNS----------ETKRKKLT 218
Cdd:CHL00018 166 YEiqswKYSIPLFFSTQGFDTFRnreistGAGAIREQLADLDLRIIIDNSLvewKELGEEGStgnewedrkiGRRKDFLV 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 219 KRIKLLEAFIQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLA--APDIIVRNEK 296
Cdd:CHL00018 246 RRIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQK 325
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 297 RMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALEL 376
Cdd:CHL00018 326 KLLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIEL 405
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 377 FKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAA 456
Cdd:CHL00018 406 FQPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKG 485
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|....*...
gi 490362540 457 YNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMT 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: 616.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 25 ASPDMIRSWSFGEVKKPETINYRTFKPERDGlfcarifgpvkdyeclcgKYKRLKHRGVICEKCGVEVTQTKVRRERMGH 104
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 105 IELASPTAHIWFLKSLPSRIGllldmplrdiervlyfesyvvveggmtslersqilteeqyldaleefgdefdakmgaea 184
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 185 iqallkamdleqevenlreelnetnsetkrkkltkriklleafiqsgnkPEWMILTVLPVLPPDLRPLVpldggrfatsd 264
Cdd:cd00399 84 -------------------------------------------------PEWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 265 lndlyrrvinrnnrlkrlldlaapdiIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLG 344
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 345 KRVDYSGRSVITVGPYLRLHQCGLPKKMALELfkpfiygklelrglattikaakkmvereeavvwdildeviREHPVLLN 424
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 425 RAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPIIVPSQ 504
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 505 DVVLGLYYMTRdcvnakgegmvlngsteaervyraghaslharvkvriteevkdgegnitkrtsmidttvgraiLWRIVP 584
Cdd:cd00399 278 DTLLGAYLLTL---------------------------------------------------------------GKQIVS 294
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 585 RGLPYSlvnqplgkkaiskMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG----IDDMVIPEKKAGIIAEAEAE 660
Cdd:cd00399 295 AALPGG-------------LLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVGigdvIDDGVIPEEKTELIEEAKKK 361
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 661 VAEIQEQFQSGLVTAGER-------YNKVIDIWAAANERVAKAMMENLsvetvvnrdgeeEQQVSFNSIFMMADSGARGS 733
Cdd:cd00399 362 VDEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASVNL------------DLVSKFNSIYVMAMSGAKGS 429
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 734 AAQIRQLAGMRGLMAKPDGSI--------------------IETPITANFREGLDVLQYFISTHGARKGLADTALKTANS 793
Cdd:cd00399 430 FINIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAES 509
|
810
....*....|....*....
gi 490362540 794 GYLTRRLVDVAQDLVITED 812
Cdd:cd00399 510 GYLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
235-511 |
4.64e-160 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 482.79 E-value: 4.64e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 235 EWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNG--RR 312
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEglPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 313 GRAITGsnkRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLE------ 386
Cdd:smart00663 81 ANQKSG---RPLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLNidklrk 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 387 ------------LRGLATTIKAAKKM-VEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLV 453
Cdd:smart00663 158 lvrngpngakyiIRGKKTNLKLAKKSkIANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLV 237
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 490362540 454 CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPIIVPSQDVVLGLY 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 |
7.35e-129 |
|
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: 408.67 E-value: 7.35e-129
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 766 GLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDCGTHEGIVMTPVIEGGDVKEPLRDRVLGRVAA 845
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 846 EDILKPGTADILIPRNTLLHEKQCD---------------------------------LLEENSVDSVKVRSVVSCETDF 892
Cdd:pfam04998 81 EFSDLKLEDKFKNDLLDDLLLLSEFslsykkeilvrdsklgrdrlskeaqeratllfeLLLKSGLESKRVRSELTCNSKA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 893 GVCAKCYGRDLARGHIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASraaaessiqvRNK--GTLKLFNAKFimnsa 970
Cdd:pfam04998 161 FVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVAS----------KNVtlGVPRLKEIIN----- 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 971 GKLVITSRNTELRLIDEFGRTKESYKVPYGAQLSKGDGEAVNGGETVANWDPHTMPVVSEVSGIIRFTDMHDGQTITRQT 1050
Cdd:pfam04998 226 VSKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEI 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1051 DELTGLSSLVVLDSAERTTSAKEMRpalkivdaqgndvlipntdmpaAYFLPGKAIVQLDDGVAITAGDTLARIPQESV- 1129
Cdd:pfam04998 306 DPETGLLILVIRLLKILNKSIKKVV----------------------KSEVIPRSIRNKVDEGRDIAIGEITAFIIKISk 363
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1130 GTKDITGGLPRVADLFEARRPKEPAILAEISGIISFgKETKGKRRLVITPIDGSDPYE------EMIPKWRQLNVFegEM 1203
Cdd:pfam04998 364 KIRQDTGGLRRVDELFMEEDPKLAILVASLLGNITL-RGIPGIKRILVNEDDKGKVEPdwvletEGVNLLRVLLVP--GF 440
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490362540 1204 VERGDVVSDgpeSPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAG 1270
Cdd:pfam04998 441 VDAGRILSN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIG 504
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
593-1048 |
6.34e-112 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 384.73 E-value: 6.34e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 593 NQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGIIAEAEAEVAEIQEQFQSGL 672
Cdd:PRK02597 5 NRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 673 VTAGERYNKVIDIWAAANERVAKAMMENLsvetvvnrdgeeEQQVSFNSIFMMADSGARGSAAQIRQLAGMRGLMAKPDG 752
Cdd:PRK02597 85 ITEVERFQKVIDTWNETNERLKDEVVKNF------------RQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 753 SIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDCGTHEGIVMTPVIEGGDVK 832
Cdd:PRK02597 153 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 833 EPLRDRVLGRVAAEDILKPgTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCETDFGVCAKCYGRDLARGHIINAG 912
Cdd:PRK02597 233 IPLGDRLLGRVLAEDVVDP-EGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLG 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 913 EAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAEssiQVRNK--GTLKlFNAK--------------FIMNSAGKLVIT 976
Cdd:PRK02597 312 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVAR---QVRSPfaGTVE-FGKKlrtrpyrtrhgveaLQAEVDFDLVLK 387
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 977 SRNtelrlidefGRTKESYKVPYGAQLSKGDGEAVNGGETVA---------NWDPHTMPVVSEVSGIIRFTDM-----HD 1042
Cdd:PRK02597 388 PSG---------KGKPQKIEITQGSLLFVDDGQTVEADQLLAevaagavkkSTEKATKDVICDLAGEVRFADLipeekTD 458
|
....*..
gi 490362540 1043 GQ-TITR 1048
Cdd:PRK02597 459 RQgNTTR 465
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-342 |
1.91e-108 |
|
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Pssm-ID: 398595 Cd Length: 320 Bit Score: 345.81 E-value: 1.91e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 14 TEEFDAIKIGLASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYEC-LCGKYKRlkhrgviceKCGVev 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 93 tqtkvrreRMGHIELASPTAHIWFLKSLpsrigllldmpLRDIERVLYFESYVVVEGGmtsleRSQILTEEQYLDALEEF 172
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFKKT-----------LKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 173 gdefdaKMGAEAIQALLKAMDL------------------EQEVENLREELNETNSE--------TKRKKLTKRIK---- 222
Cdd:pfam04997 126 ------KMGAKAILELCKKKDLcehcggkngvcgsqqpvsRKEGLKLKAAIKKSKEEeekeilnpEKVLKIFKRISdedv 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 223 LLEAFIQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEA 302
Cdd:pfam04997 200 EILGFNPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEH 279
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 490362540 303 VDALLDNGRRG-RAITGSNKRPLKSLADMIKGKQGRFRQNL 342
Cdd:pfam04997 280 VATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
593-1049 |
3.20e-107 |
|
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: 369.18 E-value: 3.20e-107
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 593 NQPLGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGIIAEAEAEVAEIQEQFQSGL 672
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 673 VTAGERYNKVIDIWAAANERVAKAMMENLsvetvvnrdgeeEQQVSFNSIFMMADSGARGSAAQIRQLAGMRGLMAKPDG 752
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTNEELKDEVVNNF------------RQTDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 753 SIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDCGTHEGIVMTPVIEGGDVK 832
Cdd:TIGR02388 152 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDKKI 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 833 EpLRDRVLGRVAAEDILKPgTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCETDFGVCAKCYGRDLARGHIINAG 912
Cdd:TIGR02388 232 S-LGDRLLGRLVAEDVLHP-EGEVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVDLG 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 913 EAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAEssiQVRNK--GTLKLFNA-------------KFIMNSAGKLVITS 977
Cdd:TIGR02388 310 EAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVAR---QVRSKidGTVEFGKKlrtrgyrtrhgedAKQVEVAGLLIIKP 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 978 RNtelrlidEFGRTKESYKVPYGAQLSKGDGEAVNGGETVA---------NWDPHTMPVVSEVSGIIRFTDMHDGQTITR 1048
Cdd:TIGR02388 387 TG-------SITNKAQEIEVTQGSLLFVEDGQTVDAGQLLAeialgavrkSTEKATKDVASDLAGEVKFDKVVPEEKTDR 459
|
.
gi 490362540 1049 Q 1049
Cdd:TIGR02388 460 Q 460
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
593-939 |
6.04e-101 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 353.47 E-value: 6.04e-101
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 593 NQPLGKKAISKMLN---TCYrilGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKAGIIAEAEAEVAEIQEQFQ 669
Cdd:CHL00117 11 NKVIDKTALKRLISwliDHF---GMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYH 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 670 SGLVTAGERYNKVIDIWAAANERVAKAMMENLSvetvvNRDgeeeqqvSFNSIFMMADSGARGSAAQIRQLAGMRGLMAK 749
Cdd:CHL00117 88 YGNVHAVEKLRQSIEIWYATSEYLKQEMNPNFR-----MTD-------PLNPVYMMSFSGARGNASQVHQLVGMRGLMSD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 750 PDGSIIETPITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDCGTHEGIVMTPvIEGG 829
Cdd:CHL00117 156 PQGQIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSP-RNGM 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 830 DVKEPLRDRVLGRVAAEDILKpgTADILIPRNTLLHEKQCDLLEENSVDSVKVRSVVSCETDFGVCAKCYGRDLARGHII 909
Cdd:CHL00117 235 MIERILIQTLIGRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLV 312
|
330 340 350
....*....|....*....|....*....|
gi 490362540 910 NAGEAVGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:CHL00117 313 ELGEAVGIIAGQSIGEPGTQLTLRTFHTGG 342
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
18-812 |
1.92e-91 |
|
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: 316.50 E-value: 1.92e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 18 DAIKIGLASPDMIRSWSFGEVKKPETinYrtfkpERDGLfcaRIFGPVKDyeclcgkyKRLkhrGVI-----CEKCGVev 92
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GVIepglrCKTCGN-- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 93 tqtkvRRER----MGHIELASPTAHIWFLKslpsRIGLLLDMPLRDIERVLyfesyvvveggMTSLERSQILteeQYLDA 168
Cdd:cd02582 62 -----TAGEcpghFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEIEKYL---ERIRR 118
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 169 LEEFGDEFDAKMGAEAIQALLKAM----------DLEQE-----VENLREELNETNSETKRKKLTK----RIKLLeAFIQ 229
Cdd:cd02582 119 LKEKWPELVKRVIEKVKKKAKKRKvcphcgapqyKIKLEkpttfYEEKEEGEVKLTPSEIRERLEKipdeDLELL-GIDP 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 230 SGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDN 309
Cdd:cd02582 198 KTARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTYFDN 277
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 310 GRRG--RAITGSnKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLel 387
Cdd:cd02582 278 EIPGipPARHRS-GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTEW-- 354
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 388 rglatTIKAAKKMVE-------------REEAVVWDILDE-------------VIREH-----PVLLNRAPTLHRLGIQA 436
Cdd:cd02582 355 -----NIEKMRKLVLngpdkwpganyviRPDGRRIRLRYVnreelaerlepgwIVERHlidgdIVLFNRQPSLHRMSIMA 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 437 FEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRD 516
Cdd:cd02582 430 HRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYLLTRK 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 517 cvNAKGEgmvlngSTEAERVYRAghaslhARVKVRITEE-VKDGEGNITkrtsmidttvGRAILWRIVPRGLPYS----- 590
Cdd:cd02582 510 --TTLFT------KEEALQLLSA------AGYDGLLPEPaILEPKPLWT----------GKQLFSLFLPKDLNFEgkakv 565
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 591 ------------------------LVNQPLGKKAI-----SKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGI 641
Cdd:cd02582 566 csgcseckdedcpndgyvvikngkLLEGVIDKKAIgaeqpGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGI 645
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 642 DDMVIPEKKAGIIAEAEAEVAEIQ----EQFQSGLVTA--GERY-----NKVIDIWAAANERVAKAMMENLSVetvvnrd 710
Cdd:cd02582 646 DDEDIPEEARKEIEEIIKEAEKKVyeliEQYKNGELEPlpGRTLeetleMKIMQVLGKARDEAGKVASKYLDP------- 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 711 geeeqqvsFNSIFMMADSGARGSAAQIRQLAGM------------RGLMAKP--------DGSIIETPITANFREGLDVL 770
Cdd:cd02582 719 --------FNNAVIMARTGARGSMLNLTQMAAClgqqsvrgerinRGYRNRTlphfkpgdLGPEARGFVRSSFRDGLSPT 790
|
890 900 910 920
....*....|....*....|....*....|....*....|..
gi 490362540 771 QYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITED 812
Cdd:cd02582 791 EFFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLYVEYD 832
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
907-1363 |
3.54e-81 |
|
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; Bacterial RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. This family also includes the eukaryotic plastid-encoded RNAP beta" subunit. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure with two pincers defining a central cleft. Beta' and beta, the largest and the second largest subunits of bacterial RNAP, each makes up one pincer and part of the base of the cleft. The C-terminal domain includes a G loop that forms part of the floor of the downstream DNA-binding cavity. The position of the G loop may determine the switch of the bridge helix between flipped-out and normal alpha-helical conformations.
Pssm-ID: 132721 [Multi-domain] Cd Length: 204 Bit Score: 265.16 E-value: 3.54e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 907 HIINAGEAVGVIAAQSIGEPGTQLTMRTFHIGgaasraaaessiqvrnkgtlklfnakfimnsagklvitsrntelrlid 986
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTG------------------------------------------------ 32
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 987 efgrtkesykvpygaqlskgdgeavnggetvanwdphtmpvvsevsgiirftdmhdgqtitrqtdeltglsslvvldsae 1066
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1067 rttsakemrpalkivdaqgndvlipntdmpaayflpgkaivqlddGVAitagdtlaripqesvgtKDITGGLPRVADLFE 1146
Cdd:cd02655 33 ---------------------------------------------GVA-----------------TDITQGLPRVEELFE 50
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1147 ARRPkepailaeisgiisfgketkgkrrlvitpidgsdpyeemipkwrqlnvfegemvergdvvsdgpeSPHDILRLR-- 1224
Cdd:cd02655 51 ARKI-----------------------------------------------------------------NPHDLLRIKfl 65
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1225 GVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEGEQVEYARVKVANRLLEQEGKIPATFER 1304
Cdd:cd02655 66 GPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEP 145
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*....
gi 490362540 1305 DLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGF 1363
Cdd:cd02655 146 VLLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
19-816 |
1.63e-80 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 285.21 E-value: 1.63e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 19 AIKIGLASPDMIRSWSFGEVKKPETinYrtfkpERDGLfcaRIFGPVKDyeclcgkyKRLkhrGVI-----CEKCGvevt 93
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVIdpglrCKTCG---- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 94 qtKVRRE---RMGHIELASPTAHIWFLKslpsRIGLLLDMPLRDIERVLyfesyvvveggMTSLERSQILTEEQYLDALE 170
Cdd:PRK08566 66 --GRAGEcpgHFGHIELARPVIHVGFAK----LIYKLLRATCRECGRLK-----------LTEEEIEEYLEKLERLKEWG 128
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 171 EFGDEFDAKMGAEAIQALL------KAMDLEQE-----VENLREELNETNSETKRKKLTK----RIKLLeAFIQSGNKPE 235
Cdd:PRK08566 129 SLADDLIKEVKKEAAKRMVcphcgeKQYKIKFEkpttfYEERKEGLVKLTPSDIRERLEKipdeDLELL-GINPEVARPE 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 236 WMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDN---G-- 310
Cdd:PRK08566 208 WMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNeipGip 287
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 311 ----RRGRaitgsnkrPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYG--- 383
Cdd:PRK08566 288 parhRSGR--------PLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVPERVTewn 359
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 384 -----KLELRG-----------------LATTIKAAKKMVEREEavvwdILDEVIReH-----PVLLNRAPTLHRLGIQA 436
Cdd:PRK08566 360 ieelrEYVLNGpekhpganyvirpdgrrIKLTDKNKEELAEKLE-----PGWIVER-HlidgdIVLFNRQPSLHRMSIMA 433
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 437 FEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRD 516
Cdd:PRK08566 434 HRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYLLTRK 513
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 517 CVN-AKGEGMVLNGST------EAERVYRAGHASLHAR----------VKVRITEEVKDGEGNITKRTSMIDTTVgrail 579
Cdd:PRK08566 514 STLfTKEEALDLLRAAgidelpEPEPAIENGKPYWTGKqifslflpkdLNLEFKAKICSGCDECKKEDCEHDAYV----- 588
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 580 wrIVPRGlpySLVNQPLGKKAIS----KMLNTCYRILGLKPTVIFADQ--------IMYTGFayaarsgaSVGIDDMVIP 647
Cdd:PRK08566 589 --VIKNG---KLLEGVIDKKAIGaeqgSILDRIVKEYGPERARRFLDSvtrlairfIMLRGF--------TTGIDDEDIP 655
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 648 EKkagiiaeaeaevaeIQEQFQSGLVTAGERYNKVIDIWAAANERVA--KAMMENLSVE--TVVNRDGEEEQQVS----- 718
Cdd:PRK08566 656 EE--------------AKEEIDEIIEEAEKRVEELIEAYENGELEPLpgRTLEETLEMKimQVLGKARDEAGEIAekylg 721
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 719 -FNSIFMMADSGARGSAAQIRQLAGM------------RGLMAK-----PDGSIieTP-----ITANFREGLDVLQYFIS 775
Cdd:PRK08566 722 lDNPAVIMARTGARGSMLNLTQMAACvgqqsvrgerirRGYRDRtlphfKPGDL--GAeargfVRSSYKSGLTPTEFFFH 799
|
890 900 910 920
....*....|....*....|....*....|....*....|.
gi 490362540 776 THGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDdcGT 816
Cdd:PRK08566 800 AMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYD--GT 838
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1099-1400 |
8.46e-75 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 273.80 E-value: 8.46e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1099 YFLPGKAIVQLDDGVAITAGDTLARIPQESVGTKDITGGLPRVADLFEARRPKEPAILAEISGI--ISFGKETKgkrrLV 1176
Cdd:PRK02597 944 YRVSPGAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCILAKKPGTvqIKYGDDES----VD 1019
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1177 ITPIDGSDPYEEM-IPKWRQLNVFEGEMVERGDVVSDGPESPHDILR----------------LRGVNAVARYIANEVQE 1239
Cdd:PRK02597 1020 VKVIESDGTITEYpILPGQNVMVSDGQQVDAGEPLTDGPINPHELLEiffedlrdrkglyeaaLEALQKLQRFLVNEVQN 1099
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1240 VYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEGEQVEYARVKVANRLLEQEGKIPATFERDLLGITKASLATESF 1319
Cdd:PRK02597 1100 VYQSQGVDISDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSF 1179
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1320 ISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGFAYHQDRIRrrhlaetAEAAPQQVSADEATANLAELL 1399
Cdd:PRK02597 1180 ISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSGFEEELS-------AEAGPHPDILAEDPAGYRRMQ 1252
|
.
gi 490362540 1400 N 1400
Cdd:PRK02597 1253 N 1253
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
18-939 |
5.37e-72 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 264.97 E-value: 5.37e-72
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 18 DAIKIGLASPDMIRSWSFGEVKKPETInyrtfkpERDGLfcarifgPVKDyECLCGKYKRLKHRgvicEKCGVEVTQTKV 97
Cdd:PRK14977 10 DGIIFGLISPADARKIGFAEITAPEAY-------DEDGL-------PVQG-GLLDGRLGTIEPG----QKCLTCGNLAAN 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 98 RRERMGHIELASPTAHIWFLKslpsRIGLLLDMPLRDIERVLYFESYVVVEGGMTSLERSQILTEEQYLDA--LEEFGDE 175
Cdd:PRK14977 71 CPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLPQEDLNVFKLIEEAHAAARDIPEKRIDDeiIEEVRDQ 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 176 FD--AKMGAEAIQALLKAMDLEQE-----VENLREELNETNSETKRKKLTKRIK---LLEAFIQSGNKPEWMILTVLPVL 245
Cdd:PRK14977 147 VKvyAKKAKECPHCGAPQHELEFEeptifIEKTEIEEHRLLPIEIRDIFEKIIDddlELIGFDPKKARPEWAVLQAFLVP 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 246 PPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSNKRP 323
Cdd:PRK14977 227 PLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFDNATAGipQAHHKGSGRP 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 324 LKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYG--------KLELRG------ 389
Cdd:PRK14977 307 LKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIVNenniekmkELVINGpdefpg 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 390 -----LATTIKAAKKMVEREEAVVWDILDE------VIREH-----PVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLV 453
Cdd:PRK14977 387 anairKGDGTKIRLDFLEDKGKDALREAAEqleigdIVERHladgdIVIFNRQPSLHKLSILAHRVKVLPGATFRLHPAV 466
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 454 CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRD----CVNAKGEGMVLNG 529
Cdd:PRK14977 467 CPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKDdalfDKNEASNIAMLAG 546
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 530 STEA----------ERVYRA---------------GHASLHARVKVRITEEVKDGEGNITKRTSmidttvgrAILWRIVP 584
Cdd:PRK14977 547 ITDPlpepaiktkdGPAWTGkqlfslflpkdfnfeGIAKWSAGKAGEAKDPSCLGDGYVLIKEG--------ELISGVID 618
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 585 RGLPYSLVNQPLgkkaisKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKkagiiaeaeaevaeI 664
Cdd:PRK14977 619 DNIIGALVEEPE------SLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDE--------------A 678
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 665 QEQFQSGLVTAGERYNKVID--------IWAAANERVAKAMMENLSVET-VVNRDGEEEQQVSF---------NSIFMMA 726
Cdd:PRK14977 679 KQEIEDDIQGMKDEVSDLIDqrkitrkiTIYKGKEELLRGMKEEEALEAdIVNELDKARDKAGSsandcidadNAGKIMA 758
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 727 DSGARGSAAQIRQLAGMRGLMA-KPDGSIIETP---------------------------ITANFREGLDVLQYFISTHG 778
Cdd:PRK14977 759 KTGARGSMANLAQIAGALGQQKrKTRIGFVLTGgrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMG 838
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 779 ARKGLADTALKTANSGYLTRRLVDVAQDLVITEDDC--GTHEGIVMtpVIEGGDVKEPLR---------DRVLGRVAAED 847
Cdd:PRK14977 839 GREGLIDKARRTEDSGYFQRRLANALEDIRLEYDETvrDPHGHIIQ--FKFGEDGIDPQKldhgeafnlERIIEKQKIED 916
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 848 ILKPGTADILiprNTLLHEKQCDL---LEENSVDSVKVRSVVSCETDfGVCAKcyGRDLARGHIINAGEAVGVIAAQSIG 924
Cdd:PRK14977 917 RGKGASKDEI---EELAKEYTKTFnanLPKLLADAIHGAELKEDELE-AICAE--GKEGFEKAKVEPGQAIGIISAQSIA 990
|
1050
....*....|....*
gi 490362540 925 EPGTQLTMRTFHIGG 939
Cdd:PRK14977 991 EPGTQMTLRTFHAAG 1005
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1007-1368 |
6.06e-70 |
|
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: 257.86 E-value: 6.06e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1007 DGEAVNGGETVAnwdphTMPVVSEVSGIIRFTDmHDGQTITR-----QTDELT-GLSSLVVLDSAERTTSAKEMRPALKI 1080
Cdd:TIGR02388 847 DGDLIKPGAVIA-----RTQILCKEAGVVQGID-SGGESIRRllverNSDRLKvNIKAKPVVKTGDLVVAGDELAKGVKA 920
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1081 -----VDAQGNDVLIPNTDMPaaYFLPGKAIVQLDDGVAITAGDTLARIPQESVGTKDITGGLPRVADLFEARRPKEPAI 1155
Cdd:TIGR02388 921 eesgeIEEVASDYVILRIGRP--YRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARKPKEACI 998
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1156 LAEISGIISFgKETKGKRRLVITPIDGSDPYEE--MIPKwRQLNVFEGEMVERGDVVSDGPESPHDILR----------- 1222
Cdd:TIGR02388 999 LAKRPGVVQV-KYGTDDESVSIKVIERDGTISEypLLPG-QNIMVSDGQQVTGGEPLTDGPINPHDILDvffsyykdqdg 1076
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1223 -----LRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVTITSAGSSEFLEGEQVEYARVKVANRLLEQEGK 1297
Cdd:TIGR02388 1077 lyeaaQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGG 1156
|
330 340 350 360 370 380 390
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490362540 1298 IPATFERDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGFAYHQD 1368
Cdd:TIGR02388 1157 APAQYTPVLLGITKASLNTDSFISAASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGFSSYEE 1227
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
18-809 |
5.42e-67 |
|
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: 242.06 E-value: 5.42e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 18 DAIKIGLASPDMIRSWSFGEVKKPETINyRTFKPERDGLFCARIfGPVKdyeclcgkykrlkhRGVICEKCGvevtqtkv 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 98 rrERM-------GHIELASPTAHIWFLKSlpsrigllldmplrdIERVLyfesyvvveggmtsleRS---QILTEEQYLD 167
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFLTK---------------ILKIL----------------RCvckRELSAERVLE 103
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 168 ALEEFGDEFDAKMGaeaiqallkamdleqevenlreeLNETNSetkrkkltkriklleafiqsgnKPEWMILTVLPVLPP 247
Cdd:cd02733 104 IFKRISDEDCRILG-----------------------FDPKFS----------------------RPDWMILTVLPVPPP 138
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 248 DLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG--RAITGSnKRPLK 325
Cdd:cd02733 139 AVRPSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQKS-GRPLK 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 326 SLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMAL-----ELFKPFIYGKL-EL--RGLATTIKAa 397
Cdd:cd02733 218 SIRQRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLqELvrNGPNEYPGA- 296
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 398 kKMVEREEAVVWD------ILDEVIRE------H-----PVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNAD 460
Cdd:cd02733 297 -KYIIRDDGERIDlrylkkASDLHLQYgyiverHlqdgdVVLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNAD 375
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 461 FDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPI--IVpsQDVVLGLYYMT-RDCVNAKGEGM-VLNGSTEAErv 536
Cdd:cd02733 376 FDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTkRDTFLEKDQVMnLLMWLPDWD-- 451
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 537 yraGHASLHARVKVR---------------ITEEVKDGEGNITKRT--SMIDTTVgrailwrIVPRGLpysLVNQPLGKK 599
Cdd:cd02733 452 ---GKIPQPAILKPKplwtgkqifsliipkINNLIRSSSHHDGDKKwiSPGDTKV-------IIENGE---LLSGILCKK 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 600 AISK----MLNTCYRILGLKPTVIFADQI--------MYTGFayaarsgaSVGIDDMVIPEKkagiiaeaeaevaeIQEQ 667
Cdd:cd02733 519 TVGAssggLIHVIWLEYGPEAARDFIGNIqrvvnnwlLHNGF--------SIGIGDTIADKE--------------TMKK 576
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 668 FQSGLVTAGERYNKVIDIW-AAANERVA-KAMMENLsvETVVNR-------DGEEEQQVS---FNSIFMMADSGARGSAA 735
Cdd:cd02733 577 IQETIKKAKRDVIKLIEKAqNGELEPQPgKTLRESF--ENKVNRilnkardKAGKSAQKSlseDNNFKAMVTAGSKGSFI 654
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 736 QIRQLAG-----------------MRGL--MAKPDGSIIETP-ITANFREGLDVLQYFISTHGARKGLADTALKTANSGY 795
Cdd:cd02733 655 NISQIIAcvgqqnvegkripfgfrRRTLphFIKDDYGPESRGfVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGY 734
|
890
....*....|....
gi 490362540 796 LTRRLVDVAQDLVI 809
Cdd:cd02733 735 IQRRLVKAMEDVMV 748
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1099-1373 |
1.99e-59 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 225.20 E-value: 1.99e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1099 YFLPGKAIVQLDDGVAITAGDTLARIPQESVGTKDITGGLPRVADLFEARRpkepailaeisgiisfgketkgkrrlvIT 1178
Cdd:CHL00117 1096 YLATPGATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARS---------------------------ID 1148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1179 PIdgSDPYEEMIPKWrqlnvfegemvergdvvsdgpesPHDILRLRGVN-----AVARYIA-------NEVQEVYRLQGV 1246
Cdd:CHL00117 1149 SI--SMNLEKRLEGW-----------------------NERITRILGIPwgfliGAELSIAqsqislvNKIQKVYRSQGV 1203
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1247 KINDKHIEVIVRQMLRKVTITSAG-SSEFLEGEQVEYARVKVANRLLEQegkiPATFERDLLGITKASLATESFISAASF 1325
Cdd:CHL00117 1204 QISDKHIEIIVRQMTSKVLVSEDGmSNVFLPGELIGLLRAERINRALEE----AICYRPILLGITKASLNTQSFISEASF 1279
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 490362540 1326 QETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGFAYHQDRIRRR 1373
Cdd:CHL00117 1280 QETTRVLAKAALRGRIDWLKGLKENVILGGLIPAGTGFKGLVHRSKQH 1327
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
215-813 |
5.33e-54 |
|
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: 204.32 E-value: 5.33e-54
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 215 KKLTKRIK----LLEAFIQSGNKPEWMILTVLPVLPPDLRPLVPLDGGrfATSDLNDL---YRRVINRNNRLKRLLDLAA 287
Cdd:cd02583 152 LNLFKNIPpedvELLLMNPLAGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGA 229
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 288 PDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCG 367
Cdd:cd02583 230 KTQKIMEDWDFLQLQCALYINSELPGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVG 309
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 368 LPKKMALELFKP--------------------------FIYGKLElrGLATTIKAAKKM-----------VEREeavvwd 410
Cdd:cd02583 310 VPEHVAKILTYPervtrynieklrklvlngpdvhpganFVIKRDG--GKKKFLKYGNRRkiarelkigdiVERH------ 381
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 411 ILDEVIrehpVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNI 490
Cdd:cd02583 382 LEDGDI----VLFNRQPSLHRLSIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNL 457
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 491 LSPASGDPIIVPSQDVVLGLYYMT-RDCVNAKGE-----GMVLNGSTEAE-----------------------RVYRAGH 541
Cdd:cd02583 458 VTPRNGEPLIAATQDFLTASYLLTsKDVFFDRAQfcqlcSYMLDGEIKIDlpppailkpvelwtgkqifslllRPNKKSP 537
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 542 ASLHARVKVRI----TEEVKDGEGNITKRTS-MIDTTVGRAILWRIVPRGLPYSLVNqPLGKKAISKMLNtcyRIlglkp 616
Cdd:cd02583 538 VLVNLEAKEKSytkkSPDMCPNDGYVVIRNSeLLCGRLDKSTLGSGSKNSLFYVLLR-DYGPEAAAAAMN---RL----- 608
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 617 TVIFADQIMYTGFayaarsgaSVGIDDmVIPEKKagiiaeaeaevaeiQEQFQSGLVTAGerYNKVIDIWAAANERVAKA 696
Cdd:cd02583 609 AKLSSRWLSNRGF--------SIGIDD-VTPSKE--------------LLKKKEELVDNG--YAKCDEYIKQYKKGKLEL 663
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 697 -----MMENLsvETVVN------RD--GEEEQQV--SFNSIFMMADSGARGSAAQIRQ---------LAGMRglmaKPDG 752
Cdd:cd02583 664 qpgctAEQTL--EAKISgelskiREdaGKACLKElhKSNSPLIMALCGSKGSNINISQmiacvgqqiISGKR----IPNG 737
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490362540 753 SI----------IETPIT----AN-FREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVITEDD 813
Cdd:cd02583 738 FEdrtlphfprnSKTPAAkgfvANsFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDG 813
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
344-485 |
1.42e-45 |
|
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 161.70 E-value: 1.42e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 344 GKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFI---YGKLELRGL----------ATTIK---------AAKKMV 401
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIvtpYNIKRLRQLvengpnvypgANYIIringarrdlRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 402 EREEAVVWDILDE-VIREHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA 480
Cdd:pfam00623 81 LDKELEIGDIVERhVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 490362540 481 RALMM 485
Cdd:pfam00623 161 EELML 165
|
|
| RNAP_I_RPA1_N |
cd01435 |
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the ... |
210-801 |
3.55e-42 |
|
Largest subunit (RPA1) of eukaryotic RNA polymerase I (RNAP I), N-terminal domain; RPA1 is the largest subunit of the eukaryotic RNA polymerase I (RNAP I). RNAP I is a multi-subunit protein complex responsible for the synthesis of rRNA precursors. RNAP I consists of at least 14 different subunits, the largest being homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. The yeast member of this family is known as Rpb190. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shaped structure. The N-terminal domain of Rpb1, the largest subunit of RNAP II in yeast, forms part of the active site. It makes up the head and core of one clamp, as well as the pore and funnel structures of RNAP II. The strong homology between RPA1 and Rpb1 suggests a similar functional and structural role.
Pssm-ID: 259844 [Multi-domain] Cd Length: 779 Bit Score: 167.36 E-value: 3.55e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 210 SETKRKKLTKRIKLLE-----AFIQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFaTSDLNDLYRRVINRNNRLKRLLD 284
Cdd:cd01435 98 SKWEVKLFVAKLKLLDkgllvEAAELDFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDLLA 176
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 285 LAAPDIIVRNEKRM---------------LQEAVDALLDNGrrgraitgSNKRPLKSLADMIKG----KQGRFRQNLLGK 345
Cdd:cd01435 177 SMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDST--------KAPKSGKKSPPGIKQllekKEGLFRMNMMGK 248
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 346 RVDYSGRSVITVGPYLRLHQCGLPKKMAL--------------ELFKPFIYGK--------LELRGLATTIKAAKKMVER 403
Cdd:cd01435 249 RVNYAARSVISPDPFIETNEIGIPLVFAKkltfpepvtpfnveELRQAVINGPdvypganaIEDEDGRLILLSALSEERR 328
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 404 EEA------------------VVW------DIldevirehpVLLNRAPTLHRLGIQA-FEPILIEGKAIQLHPLVCAAYN 458
Cdd:cd01435 329 KALaklllllssaklllngpkKVYrhlldgDV---------VLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYN 399
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 459 ADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPASGDPI---IvpsQDVVLGLYYMT-RDCVNAKGEGMVLngsteae 534
Cdd:cd01435 400 ADFDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLrglI---QDHVVSGVLLTsRDTFFTREEYQQL------- 469
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 535 rVYRAGHASLHARVKVRIteevkdgegnitkrtsmidTTVGRAILWrivPRGLpYSlvnqplGKKAISKMLNTCyrILGL 614
Cdd:cd01435 470 -VYAALRPLFTSDKDGRI-------------------KLLPPAILK---PKPL-WT------GKQVISTILKNL--IPGN 517
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 615 KP--------------------------TVIFADQIMYTGF--------------------------------------A 630
Cdd:cd01435 518 APllnlsgkkktkkkvgggkwgggseesQVIIRNGELLTGVldksqfgasayglvhavyelyggetagkllsalgrlftA 597
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 631 YAARSGASVGIDDMVIPEKkagiiaeaeaevaeiqeqfqsglvtAGERYNKVIDiwaAANERVAKAMMENLSVET----- 705
Cdd:cd01435 598 YLQMRGFTCGIEDLLLTPK-------------------------ADEKRRKILR---KAKKLGLEAAAEFLGLKLnkvts 649
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 706 -VVN---RDGeeeQQVSF--NSIFMMADSGARGS---AAQI------RQLAGMR-GLMA--------KP-DGSiietP-- 758
Cdd:cd01435 650 sIIKaclPKG---LLKPFpeNNLQLMVQSGAKGSmvnASQIscllgqQELEGRRvPLMVsgktlpsfPPyDTS----Pra 722
|
730 740 750 760
....*....|....*....|....*....|....*....|....*.
gi 490362540 759 ---ITANFREGLDVLQYFISTHGARKGLADTALKTANSGYLTRRLV 801
Cdd:cd01435 723 ggfITDRFLTGIRPQEYFFHCMAGREGLIDTAVKTSRSGYLQRCLI 768
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
489-644 |
2.20e-32 |
|
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: 123.89 E-value: 2.20e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 489 NILSPASGDPIIVPSQDVVLGLYYMTRDCVnakgegmvLNGSTEAERVYRAGHASLHARVKVRITEevkdgegnitKRTs 568
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTREDT--------FFDREEVMQLLMYGIVLPHPAILKPIKP----------LWT- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 569 mIDTTVGRAILWRIVPRGLPYS------------------LVNQPLGKKA----ISKMLNTCYRILGLKPTVIFADQIMY 626
Cdd:pfam04983 62 -GKQTFSRLLPNEINPKGKPKTneedlcendsyvlinngeLISGVIDKKTvgksLGSLIHIIYKEYGPEETAKFLDRLQK 140
|
170
....*....|....*...
gi 490362540 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 ... |
1216-1362 |
1.02e-25 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 104.81 E-value: 1.02e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1216 SPHDILRLRGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMLRKVtitsagsseflegeqveyarvkvanrlleqe 1295
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYSG------------------------------- 97
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490362540 1296 gkipatferDLLGITKASLA--TESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:cd00630 98 ---------GLRGVTRSGFRasKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
673-764 |
8.96e-23 |
|
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 94.35 E-value: 8.96e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 673 VTAGERYNKVIDIWAAANERVAKAMMENLSvETVVNRDGE--EEQQVSFNSIFMMADSGARGSAAQIRQLAGMRGLMAKP 750
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNIL-NKARDPAGNiaSKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
90 100
....*....|....*....|....*....
gi 490362540 751 DGSI---------------IETPITANFR 764
Cdd:pfam05000 80 GKRIpfgfsgrtlphfkkdDEGPESRGFV 108
|
|
| RNAP_IV_RPD1_N |
cd10506 |
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 ... |
338-518 |
4.66e-20 |
|
Largest subunit (NRPD1) of higher plant RNA polymerase IV, N-terminal domain; NRPD1 and NRPE1 are the largest subunits of plant DNA-dependent RNA polymerase IV and V that, together with second largest subunits (NRPD2 and NRPE2), form the active site region of the DNA entry and RNA exit channel. Higher plants have five multi-subunit nuclear RNA polymerases; RNAP I, RNAP II and RNAP III, which are essential for viability, plus the two isoforms of the non-essential polymerase RNAP IV and V, which specialize in small RNA-mediated gene silencing pathways. RNAP IV and/or V might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. The subunit compositions of RNAP IV and V reveal that they evolved from RNAP II.
Pssm-ID: 259849 [Multi-domain] Cd Length: 744 Bit Score: 96.70 E-value: 4.66e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 338 FRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKP-------------FIYGKLELRGL-----ATTIKAAKK 399
Cdd:cd10506 206 MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCEIAERLTVServsswnrerlqeYCDLTLLLKGVigvrrNGRLVGVRS 285
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 400 MVEREeavVWDILDEVIRE-HPVLLNRAPTLHRLGIQAFEPILIE-GKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQ 477
Cdd:cd10506 286 HNTLQ---IGDVIHRPLVDgDVVLVNRPPSIHQHSLIALSVKVLPtNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQAR 362
|
170 180 190 200
....*....|....*....|....*....|....*....|.
gi 490362540 478 LEARALMMSTNNILSPASGDPIIVPSQDVVLGLYYMTRDCV 518
Cdd:cd10506 363 AELEELVALPKQLISSQSGQNLLSLTQDSLLAAHLMTERGV 403
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1229-1379 |
3.02e-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: 94.46 E-value: 3.02e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1229 VARYIANEV--QEVYRLQGVkINDKHIEVIVRQM---------------LRKVTI---TSAGSSEFLEGEQVEYARVKV- 1287
Cdd:COG0086 557 VGRYLVNEIlpQEVPFYNQV-INKKHIEVIIRQMyrrcglketvifldrLKKLGFkyaTRAGISIGLDDMVVPKEKQEIf 635
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1288 --ANRLLE------QEGKI--PATFERDLLGITKASLATESFISAA-SFQETTRVLTEAAVAGKRDELRGL--------- 1347
Cdd:COG0086 636 eeANKEVKeiekqyAEGLItePERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLRQLagmrglmak 715
|
170 180 190
....*....|....*....|....*....|....*...
gi 490362540 1348 -KENVI---VGRLIPAGTGFAYHQDRIR--RRHLAETA 1379
Cdd:COG0086 716 pSGNIIetpIGSNFREGLGVLEYFISTHgaRKGLADTA 753
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
909-1362 |
1.01e-13 |
|
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: 74.70 E-value: 1.01e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 909 INAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVrnkgTLKLFNAKFIMNSagKLVITSRNTELRLIDEF 988
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAG-------VAELNV----TLGLPRLIEIVDA--RKTPSTPSMTIYLEDEY 107
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 989 GRTKESYKvpygaqlskgdgEAVNGGETVANWDphtmpVVSEVSgiirfTDMHDGqTITRQTDELTGLSSLVVLDSAERt 1068
Cdd:TIGR02389 108 EKDREKAE------------EVAKKIEATKLED-----VAKDIS-----IDLADM-TVIIELDEEQLKERGITVDDVEK- 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1069 tSAKEMRPALKIVDAQGNDVLI--PNTDMPAAYFLPGKAIvqlddgvaitagdtlaripqesvgtKDITgglprvadlfe 1146
Cdd:TIGR02389 164 -AIKKAKLGKVIEIDMDNNTITikPGNPSLKELRKLKEKI-------------------------KNLH----------- 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1147 arrpkepailaeISGIisfgketKGKRRLVITPIDgsdpyEEMIPKWRQLNVFEGEMVERGDVVSDGPESPHDILRLRGV 1226
Cdd:TIGR02389 207 ------------IKGI-------KGIKRVVIRKEG-----DEYVIYTEGSNLKEVLKLEGVDKTRTTTNDIHEIAEVLGI 262
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1227 NAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMlrkvtiTSAGSseflegeqveyarvkvanrlLEQEGKipatferdl 1306
Cdd:TIGR02389 263 EAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLM------TWDGE--------------------VRQIGR--------- 307
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 490362540 1307 LGIT--KASLatesfISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:TIGR02389 308 HGISgeKASV-----LARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTG 360
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
909-1362 |
2.42e-13 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 74.46 E-value: 2.42e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 909 INAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVrnkgTLKLFNAKFIMNSagKLVITSRNTELRLIDEF 988
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAG-------VAEMNV----TLGLPRLIEIVDA--RKKPSTPTMTIYLKKDY 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 989 GRTKEsykvpygaqlskgdgeavnggetvanwdphtmpVVSEVSGIIRFTDMHDGQTITRQTDEltgLSSLVVLDsaERT 1068
Cdd:PRK14897 246 REDEE---------------------------------KVREVAKKIENTTLIDVADIITDIAE---MSVVVELD--EEK 287
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1069 TsakemrpalkivdaqgNDVLIPNTDMPAAYFLPGKAIVQLDDGVAITagdtlaRIPQESvgtkditgglprVADLFEAR 1148
Cdd:PRK14897 288 M----------------KERLIEYDDILAAISKLTFKTVEIDDGIIRL------KPQQPS------------FKKLYLLA 333
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1149 RPKEPAILAEISGIISFGKETKGKRRLVITPIDGSDPYEemipkwrqlnVFEGEMVergDVVSDGPESPHDILRLRGVNA 1228
Cdd:PRK14897 334 EKVKSLTIKGIKGIKRAIARKENDERRWVIYTQGSNLKD----------VLEIDEV---DPTRTYTNDIIEIATVLGIEA 400
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1229 VARYIANEVQEVYRLQGVKINDKHIevivrqMLRKVTITSAGSseflegeqveyarVKVANRlleqegkipatferdlLG 1308
Cdd:PRK14897 401 ARNAIIHEAKRTLQEQGLNVDIRHI------MLVADMMTFDGS-------------VKAIGR----------------HG 445
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 490362540 1309 ItkaSLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK14897 446 I---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTG 496
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
908-1363 |
4.43e-13 |
|
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: 73.01 E-value: 4.43e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 908 IINAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaessiqVRNKG-TLKLFNAKFIMNSAGKlvITSRNTELRLID 986
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG------------VSAKNvTLGVPRLKEIINVAKN--IKTPSLTVYLEP 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 987 EFGRTKESYKVpYGAQLskgdgEAVNGGETVAN----WDPHTMPVVSE-----VSGIIRFTDmhdgqtitrQTDELTGLS 1057
Cdd:cd02584 89 GFAKDEEKAKK-IQSRL-----EHTTLKDVTAAteiyYDPDPQNTVIEedkefVESYFEFPD---------EDVEQDRLS 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1058 SLV---VLDSAERTTSAKEM-RPALKIVDAQGNDVLIPNTDMPAayflpGKAIVQLddgvaitagdtlaRIPQESvGTKD 1133
Cdd:cd02584 154 PWLlriELDRKKMTDKKLSMeQIAKKIKEEFKDDLNVIFSDDNA-----EKLVIRI-------------RIINDD-EEKE 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1134 ITGGLPRVADLFEARRPKEPaILAEISGI-ISFGKETKGKRrlVITPIDGSDPYEEmipkWrqlnVFEGEMVergdvvsd 1212
Cdd:cd02584 215 EDSEDDVFLKKIESNMLSDM-TLKGIEGIrKVFIREENKKK--VDIETGEFKKREE----W----VLETDGV-------- 275
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1213 gpeSPHDILRLRGVNAVaRYIANEVQEVYRLQGvkindkhIE----VIVRQMlRKVtITSAGSSeflegeqVEYARVKVA 1288
Cdd:cd02584 276 ---NLREVLSHPGVDPT-RTTSNDIVEIFEVLG-------IEaarkALLKEL-RNV-ISFDGSY-------VNYRHLALL 335
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490362540 1289 NRLLEQEGKIPAtFERDllGITKASLATesfISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGF 1363
Cdd:cd02584 336 CDVMTQRGHLMA-ITRH--GINRQDTGP---LMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQLAPIGTGC 404
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
909-1362 |
5.92e-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: 72.28 E-value: 5.92e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 909 INAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVrnkgTLKLFNAKFIMNSAGKLVITSRNTELRliDEF 988
Cdd:cd06528 37 IEPGEAVGIVAAQSIGEPGTQMTLRTFHYAG-------VAEINV----TLGLPRLIEIVDARKEPSTPTMTIYLE--EEY 103
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 989 GRTKESYKvpygaqlskgdgeavnggetvanwdphtmpvvsEVSGIIRFTDMHDgqtitrqtdeltglsslvvlDSAERT 1068
Cdd:cd06528 104 KYDREKAE---------------------------------EVARKIEETTLEN--------------------LAEDIS 130
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1069 TSAKEMRPALKivdaqgndvliPNTDMpaayfLPGKAIvQLDDGVAITAGDTLARIPQESVGTKDITG-GLPRVADLFEA 1147
Cdd:cd06528 131 IDLFNMRITIE-----------LDEEM-----LEDRGI-TVDDVLKAIEKLKKGKVGEEGDVTLIVLKaEEPSIKELRKL 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1148 RrpkePAIL-AEISGIisfgketKGKRRLVITPIDGsdpyeEMIPKWRQLN---VFEGEMVERGDVVSDgpeSPHDILRL 1223
Cdd:cd06528 194 A----EKILnTKIKGI-------KGIKRVIVRKEED-----EYVIYTEGSNlkaVLKVEGVDPTRTTTN---NIHEIEEV 254
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1224 RGVNAVARYIANEVQEVYRLQGVKINDKHIevivrqMLrkvtitsagsseflegeqveyarvkVANRLleqegkipaTFE 1303
Cdd:cd06528 255 LGIEAARNAIINEIKRTLEEQGLDVDIRHI------ML-------------------------VADIM---------TYD 294
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490362540 1304 RDLLGITKASLATE--SFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:cd06528 295 GEVRQIGRHGIAGEkpSVLARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTG 355
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
909-1362 |
1.79e-11 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 67.56 E-value: 1.79e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 909 INAGEAVGVIAAQSIGEPGTQLTMRTFHIGGaasraaaESSIQVrnkgTLKLFNAKFIMNsAGKlVITSRNTELRLIDEF 988
Cdd:PRK04309 56 VEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG-------VAEINV----TLGLPRLIEIVD-ARK-EPSTPMMTIYLKDEY 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 989 GRTKESYKvpygaqlskgdgEAVNGGE--TVANwdphtmpVVSEVSgiirfTDMHDGQTItrqtdeltglsslVVLDS-- 1064
Cdd:PRK04309 123 AYDREKAE------------EVARKIEatTLEN-------LAKDIS-----VDLANMTII-------------IELDEem 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1065 -AERTTSAKEMRPALKivDAQGNDVLIpntdmpaayflpgkaivqldDGVAITagdtlaripqesvgtkdITGGLPRVAD 1143
Cdd:PRK04309 166 lEDRGLTVDDVKEAIE--KKKGGEVEI--------------------EGNTLI-----------------ISPKEPSYRE 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1144 LFEaRRPKEPAILaeISGIisfgketKGKRRLVITPiDGsdpyEEMIPKWRQLNVFEGEMVERGDVVSDGPESPHDILRL 1223
Cdd:PRK04309 207 LRK-LAEKIRNIK--IKGI-------KGIKRVIIRK-EG----DEYVIYTEGSNLKEVLKVEGVDATRTTTNNIHEIEEV 271
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1224 RGVNAVARYIANEVQEVYRLQGVKINDKHIEVIVRQMlrkvtitsagsseflegeqveyarvkvanrlleqegkipaTFE 1303
Cdd:PRK04309 272 LGIEAARNAIIEEIKNTLEEQGLDVDIRHIMLVADMM----------------------------------------TWD 311
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490362540 1304 RDLLGITKASLATE--SFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK04309 312 GEVRQIGRHGVSGEkaSVLARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTG 372
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
912-939 |
3.61e-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: 60.12 E-value: 3.61e-10
10 20
....*....|....*....|....*...
gi 490362540 912 GEAVGVIAAQSIGEPGTQLTMRTFHIGG 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 |
1.46e-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: 61.08 E-value: 1.46e-09
10 20 30
....*....|....*....|....*....|..
gi 490362540 908 IINAGEAVGVIAAQSIGEPGTQLTMRTFHIGG 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 |
2.19e-09 |
|
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132722 [Multi-domain] Cd Length: 309 Bit Score: 60.67 E-value: 2.19e-09
10 20 30
....*....|....*....|....*....|.
gi 490362540 909 INAGEAVGVIAAQSIGEPGTQLTMRTFHIGG 939
Cdd:cd02735 7 VEPGEAVGLLAAQSIGEPSTQMTLNTFHFAG 37
|
|
| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1219-1362 |
3.11e-08 |
|
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 56.84 E-value: 3.11e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1219 DILRLRGVNAvARY-IANEVQEVYRLQGVKINDKHIEVIVRQMlrkvtitsagsseflegeqveyarvkvanrlleqegk 1297
Cdd:cd02736 193 EVEKVLGIEA-ARStIINEIQYTMKSHGMSIDPRHIMLLADLM------------------------------------- 234
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490362540 1298 ipaTFERDLLGITKASLA--TESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:cd02736 235 ---TFKGEVLGITRFGIAkmKESVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1149-1362 |
2.18e-05 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 49.12 E-value: 2.18e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1149 RPKEPAILA------EISGIISFGKEtkGKRRLVITPiDGSDPYEEMIPKWRQLNVFEGEMVERGDVVSDGPESPHDILR 1222
Cdd:PRK14898 664 KPKTPSYKAlrkripKIKNIVLKGIP--GIERVLVKK-EEHENDEEYVLYTQGSNLREVFKIEGVDTSRTTTNNIIEIQE 740
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1223 LRGVNAVARYIANEVQEVYRLQGVKINDKHIevivrqMLrkvtitsagsseflegeqveYARVKVANRLLEQEGKIPATF 1302
Cdd:PRK14898 741 VLGIEAARNAIINEMMNTLEQQGLEVDIRHL------ML--------------------VADIMTADGEVKPIGRHGVAG 794
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|
gi 490362540 1303 ERDllgitkaslateSFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
Cdd:PRK14898 795 EKG------------SVLARAAFEETVKHLYDAAEHGEVDKLKGVIENVIVGKPIKLGTG 842
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
913-932 |
4.88e-03 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 41.42 E-value: 4.88e-03
|
| |
