|
Name |
Accession |
Description |
Interval |
E-value |
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
15-1376 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 2216.04 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 15 QTFDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEKCGVEVTQ 94
Cdd:PRK00566 5 QDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTLKPERDGLFCERIFGPTKDYECLCGKYKRVRYKGIICERCGVEVTR 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 95 SKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPGMTTLKKGQLLSEEEYIEALEEFGN 174
Cdd:PRK00566 85 SKVRRERMGHIELAAPVAHIWFFKSLPSRIGLLLDMSLKDLERVLYFESYVVIDPGDTPLEKKQLLTEEEYREALEEYGD 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 175 DFDALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQIKLKRLTKRLKLAESLLKSGNRPEWMILKVLPVLPPDLRPLVP 254
Cdd:PRK00566 165 EFVAKMGAEAIKELLKNIDLEAEAEELREELKETGSEQKRKKALKRLKVVEAFRKSGNKPEWMILDVLPVIPPDLRPLVQ 244
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 255 LDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLKSLADMIKGK 334
Cdd:PRK00566 245 LDGGRFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGRPVTGPNNRPLKSLSDMLKGK 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 335 QGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKRLAEAEGPEIWDILDD 414
Cdd:PRK00566 325 QGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIMKKLVERGLATTIKSAKKMVEREDPEVWDVLEE 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 415 VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPA 494
Cdd:PRK00566 405 VIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPA 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 495 NGEPIIVPSQDVVLGLYYMTRERINDLGEGHIYADVTELQRAYDGGYVGLQAKVKLRIlrntepedesnVTHELVETTVG 574
Cdd:PRK00566 485 NGKPIIVPSQDMVLGLYYLTREREGAKGEGMVFSSPEEALRAYENGEVDLHARIKVRI-----------TSKKLVETTVG 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 575 RGLLSRIIPPELPYSAVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEILA 654
Cdd:PRK00566 554 RVIFNEILPEGLPFINVNKPLKKKEISKIINEVYRRYGLKETVIFLDKIKDLGFKYATRSGISIGIDDIVIPPEKKEIIE 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 655 GAERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLgreevedqagnKKIQPSFNSIFMMADSGARGSPA 734
Cdd:PRK00566 634 EAEKEVAEIEKQYRRGLITDGERYNKVIDIWSKATDEVAKAMMKNL-----------SKDQESFNPIYMMADSGARGSAS 702
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 735 QIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDCE 814
Cdd:PRK00566 703 QIRQLAGMRGLMAKPSGEIIETPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVREDDCG 782
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 815 TNKGLTVSTIVEGGAIVQGLGDRILGRFIAEPLIDREKNEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETKHGVC 894
Cdd:PRK00566 783 TDRGIEVTAIIEGGEVIEPLEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKIRSVLTCETRHGVC 862
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 895 VSCYGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaavnsievkndgkihlynvktikskdknlva 974
Cdd:PRK00566 863 AKCYGRDLATGKLVNIGEAVGVIAAQSIGEPGTQLTMRTFHTGG------------------------------------ 906
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 975 vsrsgeisvTDnygkeverykipygarITtkdgqkvkrgqiistwdphthpivaeaagiigfedfidgvtvteqvdeltg 1054
Cdd:PRK00566 907 ---------VD----------------IT--------------------------------------------------- 910
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1055 inntlimdsqkqsakskelrprarlhnakgkpiffsgtetpiiyafpsgaiiratdgakinagdviariplessktidit 1134
Cdd:PRK00566 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1135 GGLPRVADLFEARKPKDAAILAKYSGITSFGRETKGKVRLVITSEDGDVHEELILKTRRLNIYEGESIAKGEIIADGELS 1214
Cdd:PRK00566 911 GGLPRVAELFEARKPKGPAIIAEIDGTVSFGKETKGKRRIVITPDDGEEREYLIPKGKHLLVQEGDHVEAGDKLTDGSID 990
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1215 LHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKEQINKSDLLVVNETMQAED 1294
Cdd:PRK00566 991 PHDILRVLGVEAVQNYLVNEVQKVYRLQGVKINDKHIEVIVRQMLRKVRITDPGDTDFLPGELVDRSEFEEENRKLIAEG 1070
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1295 LEPATYRHILMGITKASLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFVQ----EIDETAI 1370
Cdd:PRK00566 1071 KEPATGRPVLLGITKASLATESFLSAASFQETTRVLTEAAIKGKVDPLRGLKENVIIGRLIPAGTGLARyrniKVEPAVD 1150
|
....*.
gi 297172930 1371 AEEEFA 1376
Cdd:PRK00566 1151 EEEAEA 1156
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
14-1198 |
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: 1785.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 14 TQTFDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEKCGVEVT 93
Cdd:COG0086 4 VEDFDAIKIGLASPEKIRSWSYGEVKKPETINYRTFKPERDGLFCERIFGPCKDYECYCGKYKRMVYKGVVCEKCGVEVT 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 94 QSKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPGMTTLKKGQLLSEEEYIEALEEFG 173
Cdd:COG0086 84 LSKVRRERMGHIELAMPVFHIWGLKSLPSRIGLLLDMSLRDLERVLYFESYVVIDPGDTPLEKGQLLTEDEYREILEEYG 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 174 NDFDALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQIKLKRLTKRLKLAESLLKSGNRPEWMILKVLPVLPPDLRPLV 253
Cdd:COG0086 164 DEFVAKMGAEAIKDLLGRIDLEKESEELREELKETTSEQKRKKLIKRLKVVEAFRESGNRPEWMILDVLPVIPPDLRPLV 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 254 PLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLKSLADMIKG 333
Cdd:COG0086 244 PLDGGRFATSDLNDLYRRVINRNNRLKRLLELKAPDIIVRNEKRMLQEAVDALFDNGRRGRAVTGANKRPLKSLSDMLKG 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 334 KQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKRLAEAEGPEIWDILD 413
Cdd:COG0086 324 KQGRFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKKMALELFKPFIYRKLEERGLATTIKSAKKMVEREEPEVWDILE 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 414 DVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSP 493
Cdd:COG0086 404 EVIKEHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARLLMLSTNNILSP 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 494 ANGEPIIVPSQDVVLGLYYMTRERINDLGEGHIYADVTELQRAYDGGYVGLQAKVKLRILRNTEPEdesnvtHELVETTV 573
Cdd:COG0086 484 ANGKPIIVPSQDMVLGLYYLTREREGAKGEGMIFADPEEVLRAYENGAVDLHARIKVRITEDGEQV------GKIVETTV 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 574 GRGLLSRIIPPELPYsaVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEIL 653
Cdd:COG0086 558 GRYLVNEILPQEVPF--YNQVINKKHIEVIIRQMYRRCGLKETVIFLDRLKKLGFKYATRAGISIGLDDMVVPKEKQEIF 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 654 AGAERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLGreevedqagnkkiqpSFNSIFMMADSGARGSP 733
Cdd:COG0086 636 EEANKEVKEIEKQYAEGLITEPERYNKVIDGWTKASLETESFLMAAFS---------------SQNTTYMMADSGARGSA 700
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 734 AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDC 813
Cdd:COG0086 701 DQLRQLAGMRGLMAKPSGNIIETPIGSNFREGLGVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEEDC 780
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 814 ETNKGLTVSTIVEGGAIVQGLGDRILGRFIAEPLIDREKNEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETKHGV 893
Cdd:COG0086 781 GTDRGITVTAIKEGGEVIEPLKERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVKVRSVLTCETRGGV 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 894 CVSCYGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASSSAAVNSIEVKNDGKIHLYNVKTIKSKDKNLV 973
Cdd:COG0086 861 CAKCYGRDLARGHLVNIGEAVGVIAAQSIGEPGTQLTMRTFHIGGAASRAAEESSIEAKAGGIVRLNNLKVVVNEEGKGV 940
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 974 AVSRSGEISVTDNYGKEVERYKIPYGARITTKDGQKVKRGQIISTWDPHTHPIVAEAAGIIGFEDFIDGVTVTEQVDELT 1053
Cdd:COG0086 941 VVSRNSELVIVDDGGRREEEYKVPYGGVLVVVGGGVVVGGGIVAEWDPHTPPIIEEVGGGVVFDDIVEGGVIVEKTDEET 1020
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1054 GINNTLIMDSQKQSAKSKELRPRARLHNAKGKPIFFSGTETPIIYAFPSGAIIRATDGAKINAGDVIARIPLESSKTIDI 1133
Cdd:COG0086 1021 GGLSIVVEDDKARRGGGKLLIRALKLLDAVGLSLLLGGTDAAAAGVIIGGLDVVLGDGVAIGVGAAIARIPGLSGGTRDG 1100
|
1130 1140 1150 1160 1170 1180
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 297172930 1134 TGGLPRVADLFEARKPKDAAILAKYSGITSFGRETKGKVRLVITSEDGDVHEELILKTRRLNIYE 1198
Cdd:COG0086 1101 TGGLARVAAAAEAKEAKEIAAGAEIIGGVGFGKKTKKKRRLVITEEDGSPIEEEVVKKKRILVVE 1165
|
|
| rpoC_TIGR |
TIGR02386 |
DNA-directed RNA polymerase, beta' subunit, predominant form; Bacteria have a single ... |
19-1361 |
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: 1756.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 19 AIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEKCGVEVTQSKVR 98
Cdd:TIGR02386 1 AIKISIASPDTIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECYCGKYKKIRYKGVVCERCGVEVTESKVR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 99 RERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPGMTTLKKGQLLSEEEYIEALEEFGNDFDA 178
Cdd:TIGR02386 81 RERMGHIELAAPVAHIWYFKGLPSRIGLLLDITAKELESVLYFENYVVLDPGDTKLDKKEVLDETEYREVLKRYGDGFRA 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 179 LMGAEAIHSVLKDVKLDDLINSIHQDMGATASQIKLKRLTKRLKLAESLLKSGNRPEWMILKVLPVLPPDLRPLVPLDGG 258
Cdd:TIGR02386 161 GMGAEAIKELLEKIDLDKEIEELKIQLRESKSDQKRKKLLKRLEIVEAFKDSGNRPEWMVLDVIPVIPPELRPMVQLDGG 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 259 RFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLKSLADMIKGKQGRF 338
Cdd:TIGR02386 241 RFATSDLNDLYRRVINRNNRLKRLLELGAPEIIVRNEKRMLQEAVDALFDNGRRGKPVVGKNNRPLKSLSDMLKGKQGRF 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 339 RQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKRLAEAEGPEIWDILDDVIRE 418
Cdd:TIGR02386 321 RQNLLGKRVDYSGRSVIVVGPELKMYQCGLPKKMALELFKPFIIKRLIDRELAANIKSAKKMIEQEDPEVWDVLEDVIKE 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 419 HPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEP 498
Cdd:TIGR02386 401 HPVLLNRAPTLHRLGIQAFEPVLVEGKAIRLHPLVCTAFNADFDGDQMAVHVPLSPEAQAEARALMLASNNILNPKDGKP 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 499 IIVPSQDVVLGLYYMTRERINDLGEGHIYADVTELQRAYDGGYVGLQAKVKLRIlrntepedesnvTHELVETTVGRGLL 578
Cdd:TIGR02386 481 IVTPSQDMVLGLYYLTTEKPGAKGEGKIFSNVDEAIRAYDNGKVHLHALIGVRT------------SGEILETTVGRVIF 548
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 579 SRIIPPELPYSAVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEILAGAER 658
Cdd:TIGR02386 549 NEILPEGFPYINDNEPLSKKEISSLIDLLYEVHGIEETAEMLDKIKALGFKYATKSGTTISASDIVVPDEKYEILKEADK 628
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 659 QVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLgreevedqagnKKIQPSFNSIFMMADSGARGSPAQIRQ 738
Cdd:TIGR02386 629 EVAKIQKFYNKGLITDEERYRKVVSIWSETKDKVTDAMMKLL-----------KKDTYKFNPIFMMADSGARGNISQFRQ 697
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 739 LAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDCETNKG 818
Cdd:TIGR02386 698 LAGMRGLMAKPSGDIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVVVREEDCGTEEG 777
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 819 LTVSTIVEGGA-IVQGLGDRILGRFIAEPLIDREKNEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETKHGVCVSC 897
Cdd:TIGR02386 778 IEVEAIVEGKDeIIESLKDRIVGRYSAEDVYDPDTGKLIAEANTLITEEIAEKIENSGIEKVKVRSVLTCESEHGVCQKC 857
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 898 YGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaavnsievkndgkihlynvktikskdknlvavsr 977
Cdd:TIGR02386 858 YGRDLATGKLVEIGEAVGVIAAQSIGEPGTQLTMRTFHTGG--------------------------------------- 898
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 978 sgeisvtdnygkeverykipygarittkdgqkvkrgqiistwdphthpiVAEAAGiigfedfidgvtvteqvdeltginn 1057
Cdd:TIGR02386 899 -------------------------------------------------VAGASG------------------------- 904
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1058 tlimdsqkqsakskelrprarlhnakgkpiffsgtetpiiyafpsgaiiratdgakinagdviariplessktiDITGGL 1137
Cdd:TIGR02386 905 --------------------------------------------------------------------------DITQGL 910
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1138 PRVADLFEARKPKDAAILAKYSGITSFGRET-KGKVRLVITSEDGDVHEELILKTRRLNIYEGESIAKGEIIADGELSLH 1216
Cdd:TIGR02386 911 PRVKELFEARTPKDKAVIAEVDGTVEIIEDIvKNKRVVVIKDENDEEKKYTIPFGAQLRVKDGDSVSAGDKLTEGSIDPH 990
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1217 DILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKEQINKSDLLVVNETMQAEDLE 1296
Cdd:TIGR02386 991 DLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQMLRKVRITDSGDSNLLPGELIDIHEFNEENRKLLEQGKK 1070
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 297172930 1297 PATYRHILMGITKASLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGF 1361
Cdd:TIGR02386 1071 PASAIPQLLGITKASLNTESFLSAASFQETTKVLTDAAIKGKVDYLLGLKENVIIGNLIPAGTGL 1135
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1519.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 15 QTFDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEKCGVEVTQ 94
Cdd:PRK14844 1446 QSFNEVSISIASPESIKRMSYGEIEDVSTANYRTFKVEKGGLFCPKIFGPVNDDECLCGKYKKRRHRGRICEKCGVEVTS 1525
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 95 SKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPGMTTLKKGQLLSEEEYIEALEEFGN 174
Cdd:PRK14844 1526 SKVRRERMGHIELASPVAHIWFLKSLPSRIGALLDMSLRDIENILYSDNYIVIDPLVSPFEKGEIISEKAYNEAKDSYGI 1605
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 175 D-FDALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQIKLKRLTKRLKLAESLLKSGNRPEWMILKVLPVLPPDLRPLV 253
Cdd:PRK14844 1606 DsFVAMQGVEAIRELLTRLDLHEIRKDLRLELESVASEIRRKKIIKRLRIVENFIKSGNRPEWMILTTIPILPPDLRPLV 1685
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 254 PLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLK-SLADMIK 332
Cdd:PRK14844 1686 SLESGRPAVSDLNHHYRTIINRNNRLRKLLSLNPPEIMIRNEKRMLQEAVDSLFDNSRRNALVNKAGAVGYKkSISDMLK 1765
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 333 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKRLAEAEGPEIWDIL 412
Cdd:PRK14844 1766 GKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLNQCGLPKRMALELFKPFVYSKLKMYGMAPTIKFASKLIRAEKPEVWDML 1845
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 413 DDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILS 492
Cdd:PRK14844 1846 EEVIKEHPVLLNRAPTLHRLGIQAFEPILIEGKAIQLHPLVCTAFNADFDGDQMAVHVPISLEAQLEARVLMMSTNNVLS 1925
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 493 PANGEPIIVPSQDVVLGLYYMTRERINDlGEGHIYADVTELQRAYDGGYVGLQAKVKLRIlrnTEPEDESNVTHELVETT 572
Cdd:PRK14844 1926 PSNGRPIIVPSKDIVLGIYYLTLQEPKE-DDLPSFGAFCEVEHSLSDGTLHIHSSIKYRM---EYINSSGETHYKTICTT 2001
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 573 VGRGLLSRIIPPE--LPYSAVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKE 650
Cdd:PRK14844 2002 PGRLILWQIFPKHenLGFDLINQVLTVKEITSIVDLVYRNCGQSATVAFSDKLMVLGFEYATFSGVSFSRCDMVIPETKA 2081
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 651 EILAGAERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLGREEvedqaGNKKiqpsFNSIFMMADSGAR 730
Cdd:PRK14844 2082 THVDHARGEIKKFSMQYQDGLITRSERYNKVIDEWSKCTDMIANDMLKAISIYD-----GNSK----YNSVYMMVNSGAR 2152
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 731 GSPAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTE 810
Cdd:PRK14844 2153 GSTSQMKQLAGMRGLMTKPSGEIIETPIISNFREGLNVFEYFNSTHGARKGLADTALKTANSGYLTRRLVDVSQNCIVTK 2232
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 811 DDCETNKGLTVSTIVEGGAIVQGLGDRILGRFIAEPLIDREKNEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETK 890
Cdd:PRK14844 2233 HDCKTKNGLVVRATVEGSTIVASLESVVLGRTAANDIYNPVTKELLVKAGELIDEDKVKQINIAGLDVVKIRSPLTCEIS 2312
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 891 HGVCVSCYGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASSSAAVNSIEVKNDGKIHLYNVKTIKSKDK 970
Cdd:PRK14844 2313 PGVCSLCYGRDLATGKIVSIGEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGVESSNIIASINAKIKLNNSNIIIDKNG 2392
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 971 NLVAVSRSGEISVTDNYGKEVERYKIPYGARITTKDGQKVKRGQIISTWDPHTHPIVAEAAGIIGFEDFIDGVTVTEQVD 1050
Cdd:PRK14844 2393 NKIVISRSCEVVLIDSLGSEKLKHSVPYGAKLYVDEGGSVKIGDKVAEWDPYTLPIITEKTGTVSYQDLKDGISITEVMD 2472
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1051 ELTGINNTLIMDSQKQSAKSKeLRPRARLHNAKGKPIFF-SGTETpiIYAFPSGAIIRATDGAKINAGDVIARIPLESSK 1129
Cdd:PRK14844 2473 ESTGISSKVVKDWKLYSGGAN-LRPRIVLLDDNGKVMTLaSGVEA--CYFIPIGAVLNVQDGQKVHAGDVITRTPRESVK 2549
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1130 TIDITGGLPRVADLFEARKPKDAAILAKYSGITSFG-RETKGKVRLVITSEDGDVH--EELILKTRRLNIYEGESIAKGE 1206
Cdd:PRK14844 2550 TRDITGGLPRVIELFEARRPKEHAIVSEIDGYVAFSeKDRRGKRSILIKPVDEQISpvEYLVSRSKHVIVNEGDFVRKGD 2629
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1207 IIADGELSLHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKEQINKSDLLVV 1286
Cdd:PRK14844 2630 LLMDGDPDLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQMLQKVEITDPGDTMYLVGESIDKLEVDRE 2709
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 297172930 1287 NETMQAEDLEPATYRHILMGITKASLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFV 1362
Cdd:PRK14844 2710 NDAMSNSGKRPAHYLPILQGITRASLETSSFISAASFQETTKVLTEAAFCGKSDPLSGLKENVIVGRLIPAGTGLI 2785
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
7-1360 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1499.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 7 IFKPKDQTQTFDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGV-VC 85
Cdd:PRK09603 1386 VIKEDDRPKDFSSFQLTLASPEKIHSWSYGEVKKPETINYRTLKPERDGLFCMKIFGPTKDYECLCGKYKKPRFKDIgTC 1465
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 86 EKCGVEVTQSKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPG--------MTTLKKG 157
Cdd:PRK09603 1466 EKCGVAITHSKVRRFRMGHIELATPVAHIWYVNSLPSRIGTLLGVKMKDLERVLYYEAYIVKEPGeaaydnegTKLVMKY 1545
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 158 QLLSEEEYIEALEEFGND-FDALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQIKLKRLTKRLKLAESLLKSGNRPEW 236
Cdd:PRK09603 1546 DILNEEQYQNISRRYEDRgFVAQMGGEAIKDLLEEIDLITLLQSLKEEVKDTNSDAKKKKLIKRLKVVESFLNSGNRPEW 1625
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 237 MILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAI 316
Cdd:PRK09603 1626 MMLTVLPVLPPDLRPLVALDGGKFAVSDVNELYRRVINRNQRLKRLMELGAPEIIVRNEKRMLQEAVDVLFDNGRSTNAV 1705
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 317 TGSNRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKA 396
Cdd:PRK09603 1706 KGANKRPLKSLSEIIKGKQGRFRQNLLGKRVDFSGRSVIVVGPNLKMDECGLPKNMALELFKPHLLSKLEERGYATTLKQ 1785
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 397 AKRLAEAEGPEIWDILDDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEA 476
Cdd:PRK09603 1786 AKRMIEQKSNEVWECLQEITEGYPVLLNRAPTLHKQSIQAFHPKLIDGKAIQLHPLVCSAFNADFDGDQMAVHVPLSQEA 1865
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 477 QLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRERINDLGEGHIYADVTELQRAYDGGYVGLQAKVKLRILRNt 556
Cdd:PRK09603 1866 IAECKVLMLSSMNILLPASGKAVAIPSQDMVLGLYYLSLEKSGVKGEHKLFSSVNEIITAIDTKELDIHAKIRVLDQGN- 1944
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 557 epedesnvtheLVETTVGRGLLSRIIPPELPYSAVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGV 636
Cdd:PRK09603 1945 -----------IIATSAGRMIIKSILPDFIPTDLWNRPMKKKDIGVLVDYVHKVGGIGITATFLDNLKTLGFRYATKAGI 2013
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 637 SICLDDMEVPEKKEEILAGAERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLGreevEDQAGnkkiqp 716
Cdd:PRK09603 2014 SISMEDIITPKDKQKMVEKAKVEVKKIQQQYDQGLLTDQERYNKIIDTWTEVNDKMSKEMMTAIA----KDKEG------ 2083
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 717 sFNSIFMMADSGARGSPAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLT 796
Cdd:PRK09603 2084 -FNSIYMMADSGARGSAAQIRQLSAMRGLMTKPDGSIIETPIISNFKEGLNVLEYFNSTHGARKGLADTALKTANAGYLT 2162
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 797 RRLVDVSQDLVVTEDDCETNKGLTVSTIVEGGAIVQGLGDRILGRFIAEPLIDREKNEILLESGTLIDEKNVHLLELHGI 876
Cdd:PRK09603 2163 RKLIDVSQNVKVVSDDCGTHEGIEITDIAVGSELIEPLEERIFGRVLLEDVIDPITNEILLYADTLIDEEGAKKVVEAGI 2242
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 877 ETISVRSPVTCETKHGVCVSCYGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASSSAAVNSIEVKNDGK 956
Cdd:PRK09603 2243 KSITIRTPVTCKAPKGVCAKCYGLNLGEGKMSYPGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRSQDEREIVASKEGF 2322
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 957 IHLYNVKTIKSKD-KNLVAVSRS---------------GEISVTDNY---------GKEVERY----------------- 994
Cdd:PRK09603 2323 VRFYNLRTYTNKEgKNIIANRRNasilvvepkikapfdGELRIETVYeevvvsvknGDQEAKFvlrrsdivkpselagvg 2402
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 995 -----------------------------------KIPYGARITTKD--------------------------------- 1006
Cdd:PRK09603 2403 gkiegkvylpyasghkvhkggsiadiiqegwnvpnRIPYASELLVKDndpiaqdvyakekgiikyyvleanhlerthgik 2482
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1007 -GQKVK----------------------RGQ-------------------------IISTWDPHTHPIVAEAAGIIGFED 1038
Cdd:PRK09603 2483 kGDIVSekglfaviaddngreaarhyiaRGSeiliddnsevsansviskpttntfkTIATWDPYNTPIIADFKGKVSFVD 2562
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1039 FIDGVTVTEQVDELTGINNTLIMDSQKQSAKskelrPRARLHNAKGKPIFfsgtetpiiYAFPSGAIIRATDGAKINAGD 1118
Cdd:PRK09603 2563 IIAGVTVAEKEDENTGITSLVVNDYIPSGYK-----PSLFLEGANGEEIR---------YFLEPKTSIAISDGSSVEQAE 2628
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1119 VIARIPLESSKTIDITGGLPRVADLFEAR--KPKDAAILAKYSGITSFGRETKGKVRLVITSEDGDVHEELILKTRRLNI 1196
Cdd:PRK09603 2629 VLAKIPKATVKSRDITGGLPRVSELFEARkpKPKDVAILSEVDGIVSFGKPIRNKEHIIVTSKDGRSMDYFVDKGKQILV 2708
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1197 YEGESIAKGEIIADGELSLHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKE 1276
Cdd:PRK09603 2709 HADEFVHAGEAMTDGVVSSHDILRISGEKELYKYIVSEVQQVYRRQGVSIADKHIEIIVSQMLRQVRILDSGDSKFIEGD 2788
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1277 QINKSDLLVVNETMQAEDLEPATYRHILMGITKASLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVP 1356
Cdd:PRK09603 2789 LVSKKLFKEENARVIALKGEPAIAEPVLLGITRAAIGSDSIISAASFQETTKVLTEASIAMKKDFLEDLKENVVLGRMIP 2868
|
....
gi 297172930 1357 AGTG 1360
Cdd:PRK09603 2869 VGTG 2872
|
|
| RNAP_beta'_N |
cd01609 |
Largest subunit (beta') of bacterial DNA-dependent RNA polymerase (RNAP), N-terminal domain; ... |
17-812 |
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: 1312.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 17 FDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEKCGVEVTQSK 96
Cdd:cd01609 3 FDAIRISLASPEQIRSWSHGEVTKPETINYRTLKPEKDGLFCERIFGPTKDYECACGKYKRIRYKGIICDRCGVEVTRSK 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 97 VRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFeaylvvepgmttlkkgqllseeeyiealeefgndf 176
Cdd:cd01609 83 VRRERMGHIELAAPVAHIWFFKGLPSRIGLLLDLSPKDLERVIYF----------------------------------- 127
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 177 dalmgaeaihsvlkdvklddlinsihqdmgatasqiklkrltkrlkLAESLLKSGNRPEWMILKVLPVLPPDLRPLVPLD 256
Cdd:cd01609 128 ----------------------------------------------VVESFRKSGNRPEWMILTVLPVIPPDLRPMVQLD 161
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 257 GGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLKSLADMIKGKQG 336
Cdd:cd01609 162 GGRFATSDLNDLYRRVINRNNRLKKLLELGAPEIIVRNEKRMLQEAVDALIDNGRRGKPVTGANNRPLKSLSDMLKGKQG 241
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 337 RFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKRLAEAEGPEIWDILDDVI 416
Cdd:cd01609 242 RFRQNLLGKRVDYSGRSVIVVGPELKLHQCGLPKEMALELFKPFVIRELIERGLAPNIKSAKKMIERKDPEVWDILEEVI 321
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 417 REHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANG 496
Cdd:cd01609 322 KGHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQAEARVLMLSSNNILSPASG 401
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 497 EPIIVPSQDVVLGLYYMTRERINDLGEGhiyadvtelqraydggyvglqakvklrilrntepedesnvtheLVETTVGRG 576
Cdd:cd01609 402 KPIVTPSQDMVLGLYYLTKERKGDKGEG-------------------------------------------IIETTVGRV 438
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 577 LLSRIIPPELPYsaVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEILAGA 656
Cdd:cd01609 439 IFNEILPEGLPF--INKTLKKKVLKKLINECYDRYGLEETAELLDDIKELGFKYATRSGISISIDDIVVPPEKKEIIKEA 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 657 ERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLGREEvedqagnkkiqpsFNSIFMMADSGARGSPAQI 736
Cdd:cd01609 517 EEKVKEIEKQYEKGLLTEEERYNKVIEIWTEVTEKVADAMMKNLDKDP-------------FNPIYMMADSGARGSKSQI 583
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 297172930 737 RQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDD 812
Cdd:cd01609 584 RQLAGMRGLMAKPSGKIIELPIKSNFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRRLVDVAQDVIVTEED 659
|
|
| PRK14906 |
PRK14906 |
DNA-directed RNA polymerase subunit beta'; |
14-1360 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta';
Pssm-ID: 184899 [Multi-domain] Cd Length: 1460 Bit Score: 1255.16 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 14 TQTFDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEKCGVEVT 93
Cdd:PRK14906 6 VTNFDALRISLASAEDIRSWSHGEVKKPETINYRTLKPEKDGLFCEKIFGPTKDWECACGKYKRIRFKGIVCERCGVEVT 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 94 QSKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLV--------------------------- 146
Cdd:PRK14906 86 RAKVRRERMGHIELAAPVSHIWYFKGSPSRLGYLLDIKPKDLEKVLYFASYIItsvdkeareedaddlrdelaadleeld 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 147 --------------------------------------VEPGMT---------------------TLKKGQLLSEEEY-I 166
Cdd:PRK14906 166 aerdrlieatrrlsvdyvpeddefvddigdderltaeeVRAEVAdiyeeynerkalrreafdafmQIEPKQLISDEALyR 245
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 167 EALEEFGNDFDALMGAEAIHSVLKDVKLDDLINSIhQDMGATASQIKLKRLTKRLKLAESLLKSGNRPEWMILKVLPVLP 246
Cdd:PRK14906 246 EMRLNYSIYFKGGMGAEAVRDLLDAIDLEKEAEEL-RAIIANGKGQKREKAVKRLKVVDAFLKSGNDPADMILDVIPVIP 324
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 247 PDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLKS 326
Cdd:PRK14906 325 PDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLLDLGAPEIIVNNEKRMLQEAVDSLFDNGRRGRPVTGPGNRPLKS 404
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 327 LADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKRLAEAEGP 406
Cdd:PRK14906 405 LADMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKLHQCGLPSAMALELFKPFVMKRLVELEYAANIKAAKRAVDRGAS 484
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 407 EIWDILDDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMS 486
Cdd:PRK14906 485 YVWDVLEEVIQDHPVLLNRAPTLHRLGIQAFEPVLVEGKAIKLHPLVCTAFNADFDGDQMAVHVPLSTQAQAEARVLMLS 564
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 487 TNNILSPANGEPIIVPSQDVVLGLYYMTRERINDLGEGHIYADVTELQRAYDG-GYVGLQAKVKLRILRNTEPE---DES 562
Cdd:PRK14906 565 SNNIKSPAHGRPLTVPTQDMIIGVYYLTTERDGFEGEGRTFADFDDALNAYDArADLDLQAKIVVRLSRDMTVRgsyGDL 644
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 563 NVTH--ELVETTVGRGLLSRIIPPELPYsaVNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICL 640
Cdd:PRK14906 645 EETKagERIETTVGRIIFNQVLPEDYPY--LNYKMVKKDIGRLVNDCCNRYSTAEVEPILDGIKKTGFHYATRAGLTVSV 722
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 641 DDMEVPEKKEEILAGAERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLGReevedqagnkkiqpsFNS 720
Cdd:PRK14906 723 YDATIPDDKPEILAEADEKVAAIDEDYEDGFLSERERHKQVVDIWTEATEEVGEAMLAGFDE---------------DNP 787
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 721 IFMMADSGARGSPAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLV 800
Cdd:PRK14906 788 IYMMADSGARGNIKQIRQLAGMRGLMADMKGEIIDLPIKANFREGLSVLEYFISTHGARKGLVDTALRTADSGYLTRRLV 867
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 801 DVSQDLVVTEDDCETNKGLTVSTIVEGGAIVQGLgdriLGRFIAEPLIDREkNEILLESGTLIDEK-NVHLLELHGIETI 879
Cdd:PRK14906 868 DVAQDVIVREEDCGTDEGVTYPLVKPKGDVDTNL----IGRCLLEDVCDPN-GEVLLSAGDYIESMdDLKRLVEAGVTKV 942
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 880 SVRSPVTCETKHGVCVSCYGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAasssaavnsievkndgkihl 959
Cdd:PRK14906 943 QIRTLMTCHAEYGVCQKCYGWDLATRRPVNIGTAVGIIAAQSIGEPGTQLTMRTFHSGGV-------------------- 1002
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 960 ynvktikskdknlvavsrsgeisvtdnygkeverykipygarittkdgqkvkrgqiistwdphthpivaeaagiigfedf 1039
Cdd:PRK14906 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1040 idgvtvteqvdeltginntlimdsqkqsakskelrprarlhnakgkpiffsgtetpiiyafpsgaiiratdgakinAGDv 1119
Cdd:PRK14906 1003 ----------------------------------------------------------------------------AGD- 1005
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1120 iariplessktiDITGGLPRVADLFEARKPKDAAILAKYSGITSFGRETKGKVrLVITSEDGDVHEELILKTRRL--NIY 1197
Cdd:PRK14906 1006 ------------DITQGLPRVAELFEARKPKGEAVLAEISGTLQITGDKTEKT-LTIHDQDGNSREYVVSARVQFmpGVE 1072
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1198 EGESIAKGEIIADGELSLHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKEQ 1277
Cdd:PRK14906 1073 DGVEVRVGQQITRGSVNPHDLLRLTDPNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQMLRKVAVTNPGDSDYLPGRQ 1152
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1278 INKSDLLVVNETMQAEDLEPATYRHILMGITKASLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPA 1357
Cdd:PRK14906 1153 VNRYEFEDTANNLILEGKQPPVGQPLLLGITKASLATDSWLSAASFQETTKVLTDAAIEGKVDHLAGLKENVIIGKPIPA 1232
|
...
gi 297172930 1358 GTG 1360
Cdd:PRK14906 1233 GTG 1235
|
|
| rpoC1 |
PRK02625 |
DNA-directed RNA polymerase subunit gamma; Provisional |
13-604 |
0e+00 |
|
DNA-directed RNA polymerase subunit gamma; Provisional
Pssm-ID: 235055 [Multi-domain] Cd Length: 627 Bit Score: 812.44 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 13 QTQTFDAIKIGLASPEMIRSWS---------YGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGV 83
Cdd:PRK02625 5 TENRFDYVKIGLASPERIRQWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGI 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 84 VCEKCGVEVTQSKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPG-MTTLKKGQLLSE 162
Cdd:PRK02625 85 VCERCGVEVTESRVRRHRMGFIKLAAPVTHVWYLKGIPSYVAILLDMPLRDVEQIVYFNCYVVLDPGnHKNLKYKQLLTE 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 163 EE-YIEALEEFGNDFD------ALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQiKLKRLTKRLKLAESLLKSGNRPE 235
Cdd:PRK02625 165 DQwLEIEDQIYAEDSElegeevVGIGAEALKRLLEDLNLEEEAEQLREEIANSKGQ-KRAKLIKRLRVIDNFIATGSRPE 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 236 WMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRA 315
Cdd:PRK02625 244 WMVLDVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRT 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 316 ITGSNRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIK 395
Cdd:PRK02625 324 VVGANNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIK 403
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 396 AAKRLAEAEGPEIWDILDDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIE 475
Cdd:PRK02625 404 AAKKLIQRADPEVWQVLEEVIEGHPVLLNRAPTLHRLGIQAFEPILVEGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLE 483
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 476 AQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRERIN-DLGEGHIYADVTELQRAYDGGYVGLQAKVKLRIlr 554
Cdd:PRK02625 484 AQAEARLLMLASNNILSPATGEPIVTPSQDMVLGCYYLTAENPGaQKGAGRYFASLEDVIMAFEQGRIDLHAWVWVRF-- 561
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|
gi 297172930 555 NTEPEDESNVTHELVETTVGRGLLSRiippELPYSAVNQTMDSKQISQLI 604
Cdd:PRK02625 562 NGEVEDDDEDTEPLKTETLEDGTRIE----QYRYRRDRFDEDGNLISQYI 607
|
|
| rpoC1_cyan |
TIGR02387 |
DNA-directed RNA polymerase, gamma subunit; The RNA polymerase gamma subunit, encoded by the ... |
17-604 |
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: 794.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 17 FDAIKIGLASPEMIRSWS---------YGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKRLKHRGVVCEK 87
Cdd:TIGR02387 2 FDYVKITIASPERVMEWGqrtlpngqvVGEVTKPETINYRTLKPEMDGLFCEKIFGPSKDWECHCGKYKRVRHRGIVCER 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 88 CGVEVTQSKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLVVEPG-MTTLKKGQLLSEEE-Y 165
Cdd:TIGR02387 82 CGVEVTESRVRRHRMGYIKLAAPVTHVWYLKGIPSYVSILLDMPLRDVEQIVYFNAYVVLNPGnAKNLKYKQLLTEDQwL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 166 IEALEEFGNDFD------ALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQiKLKRLTKRLKLAESLLKSGNRPEWMIL 239
Cdd:TIGR02387 162 EIEDQIYAEDSEleneevVGIGAEALKQLLADLNLEEVAEQLREEINGSKGQ-KRAKLIKRLRVIDNFIATSSRPEWMVL 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 240 KVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGRAITGS 319
Cdd:TIGR02387 241 DVIPVIPPDLRPMVQLDGGRFATSDLNDLYRRVINRNNRLARLQEILAPEIIVRNEKRMLQEAVDALIDNGRRGRTVVGA 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 320 NRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLIYQGEAGTIKAAKR 399
Cdd:TIGR02387 321 NNRPLKSLSDIIEGKQGRFRQNLLGKRVDYSGRSVIVVGPKLKMHQCGLPKEMAIELFQPFVIHRLIRQGIVNNIKAAKK 400
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 400 LAEAEGPEIWDILDDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLE 479
Cdd:TIGR02387 401 LIQRADDEIWSVLQEVITGHPVMLNRAPTLHRLGIQAFEPILVDGRAIQLHPLVCPAFNADFDGDQMAVHVPLSLEAQTE 480
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 480 SRALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRERIN-DLGEGHIYADVTELQRAYDGGYVGLQAKVKLRIlrNTEP 558
Cdd:TIGR02387 481 ARLLMLASNNVLSPATGEPIVTPSQDMVLGCYYLTALNPGaEKGRGRYFSSLEDAIHAYEDGRIDLHDWIWVRF--NGEV 558
|
570 580 590 600
....*....|....*....|....*....|....*....|....*.
gi 297172930 559 EDESNVTHELVETTVGRGLLSRiippELPYSAVNQTMDSKQISQLI 604
Cdd:TIGR02387 559 ETNDPLDEPIKSEDLSDGTRIE----QWTYRRDRFDEDGALISQYI 600
|
|
| rpoC1 |
CHL00018 |
RNA polymerase beta' subunit |
17-521 |
0e+00 |
|
RNA polymerase beta' subunit
Pssm-ID: 214336 [Multi-domain] Cd Length: 663 Bit Score: 788.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 17 FDAIKIGLASPEMIRSWSY---------GEVKKPETINYRTFRPERDGLFCAKIFGPVKDYECLCGKYKR---LKHRGVV 84
Cdd:CHL00018 7 HQQLRIGLASPQQIRAWAErilpngeivGEVTKPYTIHYKTNKPEKDGLFCERIFGPIKSGICACGNYRVigdEKEDPKF 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 85 CEKCGVEVTQSKVRRERMGHLELASPVAHIWFLKSLPSRIGLLLDMTLREIERVLYFEAYLV--VEPGMTTLKKGQLLSE 162
Cdd:CHL00018 87 CEQCGVEFTDSRVRRYRMGYIKLACPVTHVWYLKRLPSYIANLLDKPLKELEGLVYCDFSFArpIAKKPTFLRLRGLFEY 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 163 EEYIEALEEF----GNDFDALM------GAEAIHSVLKDVKLDDLINSIH---QDMGATAS----------QIKLKRLTK 219
Cdd:CHL00018 167 EIQSWKYSIPlffsTQGFDTFRnreistGAGAIREQLADLDLRIIIDNSLvewKELGEEGStgnewedrkiGRRKDFLVR 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 220 RLKLAESLLKSGNRPEWMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELN--APEIIVRNEKR 297
Cdd:CHL00018 247 RIKLAKHFIRTNIEPEWMVLCLLPVLPPELRPIIQLDGGKLMSSDLNELYRRVIYRNNTLTDLLTTSrsTPGELVMCQKK 326
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 298 MLQKSVDALLDNGRMGRAITGSNRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELF 377
Cdd:CHL00018 327 LLQEAVDALLDNGIRGQPMRDGHNKPYKSFSDVIEGKEGRFRENLLGKRVDYSGRSVIVVGPSLSLHQCGLPREIAIELF 406
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 378 KPFVFHKLIYQGEAGTIKAAKRLAEAEGPEIWDILDDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAF 457
Cdd:CHL00018 407 QPFVIRGLIRQHLASNIRAAKSKIREKEPIVWEILQEVMQGHPVLLNRAPTLHRLGIQAFQPILVEGRAICLHPLVCKGF 486
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 297172930 458 NADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRERINDL 521
Cdd:CHL00018 487 NADFDGDQMAVHVPLSLEAQAEARLLMFSHMNLLSPAIGDPISVPSQDMLLGLYVLTIGNRRGI 550
|
|
| RNAP_largest_subunit_N |
cd00399 |
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the ... |
25-811 |
0e+00 |
|
Largest subunit of RNA polymerase (RNAP), N-terminal domain; This region represents the N-terminal domain of the largest subunit of RNA polymerase (RNAP). RNAP is a large multi-protein complex responsible for the synthesis of RNA. It is the principle enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei; RNAP I transcribes the ribosomal RNA precursor, RNAP II the mRNA precursor, and RNAP III the 5S and tRNA genes. A single distinct RNAP complex is found in prokaryotes and archaea, respectively, which may be responsible for the synthesis of all RNAs. Structure studies reveal that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shaped structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. All RNAPs are metalloenzymes. At least one Mg2+ ion is bound in the catalytic center. In addition, all cellular RNAPs contain several tightly bound zinc ions to different subunits that vary between RNAPs from prokaryotic to eukaryotic lineages. This domain represents the N-terminal region of the largest subunit of RNAP, and includes part of the active site. In archaea and some of the photosynthetic organisms or cellular organelle, however, this domain exists as a separate subunit.
Pssm-ID: 259843 [Multi-domain] Cd Length: 528 Bit Score: 589.79 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 25 ASPEMIRSWSYGEVKKPETINYRTFRPERDGlfcakifgpvkdyeclcgKYKRLKHRGVVCEKCGVEVTQSKVRRERMGH 104
Cdd:cd00399 1 MSPEEIRKWSVAKVIKPETIDNRTLKAERGG------------------KYDPRLGSIDRCEKCGTCGTGLNDCPGHFGH 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 105 LELASPVAHIWFLKSLPSRIGllldmtlreiervlyfeaylvvepgmttlkkgqllseeeyiealeefgndfdalmgaea 184
Cdd:cd00399 63 IELAKPVFHVGFIKKVPSFLG----------------------------------------------------------- 83
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 185 ihsvlkdvklddlinsihqdmgatasqiklkrltkrlklaesllksgnrPEWMILKVLPVLPPDLRPLVpldggrfatsd 264
Cdd:cd00399 84 -------------------------------------------------PEWMILTCLPVPPPCLRPSV----------- 103
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 265 lndlyrrvinrnnrlqrllelnapeiIVRNEKRMLQKSVDALLDNGRMGRAITGSNRRPLKSLADMIKGKQGRFRQNLLG 344
Cdd:cd00399 104 --------------------------IIEERWRLLQEHVDTYLDNGIAGQPQTQKSGRPLRSLAQRLKGKEGRFRGNLMG 157
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 345 KRVDYSGRSVIVVGPTLKLHQCGIPKKMALELfkpfvfhkliyqgeagtikaakrlaeaegpeiwdilddviREHPVLLN 424
Cdd:cd00399 158 KRVDFSGRSVISPDPNLRLDQVGVPKSIALTL----------------------------------------DGDPVLFN 197
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 425 RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQ 504
Cdd:cd00399 198 RQPSLHKLSIMAHRVRVLPGSTFRLNPLVCSPYNADFDGDEMNLHVPQSEEARAEARELMLVPNNILSPQNGEPLIGLSQ 277
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 505 DVVLGLYYMTRerindlgeghiyadvtelqraydggyvglqakvklrilrntepedesnvthelvettvgrglLSRIIPP 584
Cdd:cd00399 278 DTLLGAYLLTL--------------------------------------------------------------GKQIVSA 295
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 585 ELPYSavnqtmdskqisqLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSI----CLDDMEVPEKKEEILAGAERQV 660
Cdd:cd00399 296 ALPGG-------------LLHTVTRELGPEKAAKLLSNLQRVGFVFLTTSGFSVgigdVIDDGVIPEEKTELIEEAKKKV 362
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 661 KNIQNQFSSGLLTQGER-------YNKVVDIWSRTNDLIANAMMEklgreevedqagNKKIQPSFNSIFMMADSGARGSP 733
Cdd:cd00399 363 DEVEEAFQAGLLTAQEGmtleeslEDNILDFLNEARDKAGSAASV------------NLDLVSKFNSIYVMAMSGAKGSF 430
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 734 AQIRQLAGMRGLMAKPDGSI--------------------IETPITANFREGLNVLQYFISTHGARKGLADTALKTANSG 793
Cdd:cd00399 431 INIRQMSACVGQQSVEGKRIprgfsdrtlphfskddyspeAKGFIRNSFLEGLTPLEYFFHAMGGREGLVDTAVKTAESG 510
|
810
....*....|....*...
gi 297172930 794 YLTRRLVDVSQDLVVTED 811
Cdd:cd00399 511 YLQRRLVKALEDLVVHYD 528
|
|
| RPOLA_N |
smart00663 |
RNA polymerase I subunit A N-terminus; |
235-511 |
1.14e-154 |
|
RNA polymerase I subunit A N-terminus;
Pssm-ID: 214767 [Multi-domain] Cd Length: 295 Bit Score: 468.54 E-value: 1.14e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 235 EWMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMGR 314
Cdd:smart00663 1 EWMILTVLPVPPPCLRPSVQLDGGRFAEDDLTHLLRDIIKRNNRLKRLLELGAPSIIIRNEKRLLQEAVDTLIDNEGLPR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 315 AITGSNRrPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKL--------- 385
Cdd:smart00663 81 ANQKSGR-PLKSLSQRLKGKEGRFRQNLLGKRVDFSARSVITPDPNLKLNEVGVPKEIALELTFPEIVTPLnidklrklv 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 386 ---------IYQGEAGTIKAAKRLA-EAEGPEIWDILDDVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCK 455
Cdd:smart00663 160 rngpngakyIIRGKKTNLKLAKKSKiANHLKIGDIVERHVIDGDVVLFNRQPTLHRMSIQAHRVRVLEGKTIRLNPLVCS 239
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*.
gi 297172930 456 AFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLY 511
Cdd:smart00663 240 PYNADFDGDEMNLHVPQSLEARAEARELMLVPNNILSPKNGKPIIGPIQDMLLGLY 295
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
592-1210 |
1.27e-123 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 417.47 E-value: 1.27e-123
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 592 NQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEILAGAERQVKNIQNQFSSGL 671
Cdd:PRK02597 5 NRVVDKKALKNLIAWAFKNYGTARTAQMADNLKDLGFRYATQAGVSISVDDLKVPPAKRDLLEQAEEEITATEERYRRGE 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 672 LTQGERYNKVVDIWSRTNDLIANAMMEklgreevedqagNKKIQPSFNSIFMMADSGARGSPAQIRQLAGMRGLMAKPDG 751
Cdd:PRK02597 85 ITEVERFQKVIDTWNETNERLKDEVVK------------NFRQNDPLNSVYMMAFSGARGNMSQVRQLVGMRGLMANPQG 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 752 SIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDCETNKGLTVSTIVEGGAIV 831
Cdd:PRK02597 153 EIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTTRGIVVEAMDDGDRVL 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 832 QGLGDRILGRFIAEPLIDrEKNEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETKHGVCVSCYGRDLGRGNIVNKG 911
Cdd:PRK02597 233 IPLGDRLLGRVLAEDVVD-PEGEVIAERNTAIDPDLAKKIEKAGVEEVMVRSPLTCEAARSVCRKCYGWSLAHNHLVDLG 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 912 EAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaaVNSIEV------KNDGKIHL------YNVKTIKSKDKNLVAVsrSG 979
Cdd:PRK02597 312 EAVGIIAAQSIGEPGTQLTMRTFHTGG-------VFTGEVarqvrsPFAGTVEFgkklrtRPYRTRHGVEALQAEV--DF 382
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 980 EISVTDNYGKEVERYKIPYGARITTKDGQKVKRGQII----------STwDPHTHPIVAEAAGIIGFEDfidgvTVTEQV 1049
Cdd:PRK02597 383 DLVLKPSGKGKPQKIEITQGSLLFVDDGQTVEADQLLaevaagavkkST-EKATKDVICDLAGEVRFAD-----LIPEEK 456
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1050 DELTGiNNTLImdSQKQsakskelrprarlhnakGKPIFFSGTetpiIYAFPSGAIIRATDGAKINAGDVIARiplesSK 1129
Cdd:PRK02597 457 TDRQG-NTTRK--AQRG-----------------GLLWVLSGD----VYNLPPGAEPVVSNGDRVEEGDVLAE-----TK 507
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1130 TIDITGGLPRVADLFEARKPKD---AAIL---AKYSGITSFGREtkgkvRLVITSEDGDVHeelilktrRLNIYEGESIA 1203
Cdd:PRK02597 508 LVSEHGGVVRLRESSGDSREVEiitASVLldqAKVLEESTHGRE-----QYNLETKDGQRF--------RLNATPGTKVQ 574
|
....*..
gi 297172930 1204 KGEIIAD 1210
Cdd:PRK02597 575 NGEVVAE 581
|
|
| RNA_pol_Rpb1_5 |
pfam04998 |
RNA polymerase Rpb1, domain 5; RNA polymerases catalyze the DNA dependent polymerization of ... |
765-1283 |
1.91e-119 |
|
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: 383.24 E-value: 1.91e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 765 GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDCETNKGLTVSTIVEGGAIVQGLGDRILGRFIA 844
Cdd:pfam04998 1 GLTPQEFFFHTMGGREGLIDTAVKTAESGYLQRRLVKALEDLVVTYDDTVRNSGGEIVQFLYGEDGLDPLKIEKQGRFTI 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 845 -------------------------------EPLIDREKNeILLESGTLIDEKNVHLLELH---GIETISVRSPVTCETK 890
Cdd:pfam04998 81 efsdlkledkfkndllddllllsefslsykkEILVRDSKL-GRDRLSKEAQERATLLFELLlksGLESKRVRSELTCNSK 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 891 HGVCVSCYGRDLGRGNIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaaVNSIEVKnDGKIHLYNVktiksKDK 970
Cdd:pfam04998 160 AFVCLLCYGRLLYQQSLINPGEAVGIIAAQSIGEPGTQMTLNTFHFAG-------VASKNVT-LGVPRLKEI-----INV 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 971 NLVAVSRSGEISVTDNYGKEVERYKIPYGARITTKDGQKVKRGQIISTWDPHTHPIVAEAAGIIGFEDFIDGVTVTEQVD 1050
Cdd:pfam04998 227 SKNIKSPSLTVYLFDEVGRELEKAKKVYGAIEKVTLGSVVESGEILYDPDPFNTPIISDVKGVVKFFDIIDEVTNEEEID 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1051 ELTGINNTLIMdsqkqsakskelrprarlhnaKGKPIFFSGTETPIIYAFPSGAIIRATDGAKINAGDVIARIPLESSKT 1130
Cdd:pfam04998 307 PETGLLILVIR---------------------LLKILNKSIKKVVKSEVIPRSIRNKVDEGRDIAIGEITAFIIKISKKI 365
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1131 IDITGGLPRVADLFEARKPKDAAILAKYSGITSFgRETKGKVRLVIT-SEDGDVHEELILKTRRLNIYE----GESIAKG 1205
Cdd:pfam04998 366 RQDTGGLRRVDELFMEEDPKLAILVASLLGNITL-RGIPGIKRILVNeDDKGKVEPDWVLETEGVNLLRvllvPGFVDAG 444
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 297172930 1206 EIIADgelSLHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAflnkeqINKSDL 1283
Cdd:pfam04998 445 RILSN---DIHEILEILGIEAARNALLNEIRNVYRFQGIYINDRHLELIADQMTRKGYIMAIGRHG------INKAEL 513
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
592-1210 |
9.87e-117 |
|
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 gene, a subunit of DNA-directed RNA polymerase of cyanobacteria and chloroplasts. RpoC2 corresponds largely to the C-terminal region of the RpoC (the beta' subunit) of other bacteria. Members of this family are designated beta'' in chloroplasts/plastids, and beta' (confusingly) in Cyanobacteria, where RpoC1 is called beta' in chloroplasts/plastids and gamma in Cyanobacteria. We prefer to name this family beta'', after its organellar members, to emphasize that this RpoC1 and RpoC2 together replace RpoC in other bacteria. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 274104 [Multi-domain] Cd Length: 1227 Bit Score: 396.14 E-value: 9.87e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 592 NQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEILAGAERQVKNIQNQFSSGL 671
Cdd:TIGR02388 4 NRVVDKKALKNLISWAYKTYGTARTAAMADKLKDLGFRYATRAGVSISVDDLKVPPAKQDLLEAAEKEIRATEERYRRGE 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 672 LTQGERYNKVVDIWSRTNdlianammeklgrEEVEDQAGN--KKIQPsFNSIFMMADSGARGSPAQIRQLAGMRGLMAKP 749
Cdd:TIGR02388 84 ITEVERFQKVIDTWNGTN-------------EELKDEVVNnfRQTDP-LNSVYMMAFSGARGNMSQVRQLVGMRGLMANP 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 750 DGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDCETNKGLTVSTIVEGGA 829
Cdd:TIGR02388 150 QGEIIDLPIKTNFREGLTVTEYVISSYGARKGLVDTALRTADSGYLTRRLVDVSQDVIVREEDCGTERSIVVRAMTEGDK 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 830 IVQgLGDRILGRFIAEPLIDREKnEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETKHGVCVSCYGRDLGRGNIVN 909
Cdd:TIGR02388 230 KIS-LGDRLLGRLVAEDVLHPEG-EVIVPKNTAIDPDLAKTIETAGISEVVVRSPLTCEAARSVCRKCYGWSLAHAHLVD 307
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 910 KGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASSSAAvNSIEVKNDGKIHL------YNVKTIKSKDKNLVAVSRSGEISV 983
Cdd:TIGR02388 308 LGEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEVA-RQVRSKIDGTVEFgkklrtRGYRTRHGEDAKQVEVAGLLIIKP 386
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 984 TDNYGKEVERYKIPYGARITTKDGQKVKRGQII-----STWDPHTHPIVAEAAGIIGFEDFIDGVtVTEQVDELTGiNNT 1058
Cdd:TIGR02388 387 TGSITNKAQEIEVTQGSLLFVEDGQTVDAGQLLaeialGAVRKSTEKATKDVASDLAGEVKFDKV-VPEEKTDRQG-NTT 464
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1059 LIMdsqkqsakskelrprarlhnAKGKPIFFSGTEtpiIYAFPSGAIIRATDGAKINAGDVIARIPLESsktidITGGLP 1138
Cdd:TIGR02388 465 RIA--------------------QRGGLIWVLSGE---VYNLPPGAEPVVKNGDRVEQGTVLAETKLST-----EHGGVV 516
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 297172930 1139 RVADLFEARKPKD---AAIL---AKYSGITSFGREtkgkvRLVITSEDGDVHeelilktrRLNIYEGESIAKGEIIAD 1210
Cdd:TIGR02388 517 RLPESVGDSREVEiitASVLldqAKVIEESSQGRE-----LYHIETADGQRF--------RLKAAPGTKVQNGQVVAE 581
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
592-1016 |
4.11e-112 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 385.45 E-value: 4.11e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 592 NQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKKEEILAGAERQVKNIQNQFSSGL 671
Cdd:CHL00117 11 NKVIDKTALKRLISWLIDHFGMAYTSHILDQLKTLGFQQATAAGISLGIDDLLTPPSKGWLVQDAEQQSLILEKHYHYGN 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 672 LTQGERYNKVVDIWSRTNDLIANAMMEKLgreevedqagnKKIQPsFNSIFMMADSGARGSPAQIRQLAGMRGLMAKPDG 751
Cdd:CHL00117 91 VHAVEKLRQSIEIWYATSEYLKQEMNPNF-----------RMTDP-LNPVYMMSFSGARGNASQVHQLVGMRGLMSDPQG 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 752 SIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDCETNKGLTVSTIVEGGaIV 831
Cdd:CHL00117 159 QIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTADAGYLTRRLVEVVQHIVVRETDCGTTRGISVSPRNGMM-IE 237
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 832 QGLGDRILGRFIAEPLIDreKNEILLESGTLIDEKNVHLLELHGIETISVRSPVTCETKHGVCVSCYGRDLGRGNIVNKG 911
Cdd:CHL00117 238 RILIQTLIGRVLADDIYI--GSRCIATRNQDIGIGLANRFITFRAQPISIRSPLTCRSTSWICQLCYGWSLAHGDLVELG 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 912 EAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaaVNSIEVKN------DGKIHlYNvktikskdKNLVAVSRS--GEI-- 981
Cdd:CHL00117 316 EAVGIIAGQSIGEPGTQLTLRTFHTGG-------VFTGGTAEqvrapfNGKIK-FN--------EDLVHPTRTrhGHPaf 379
|
410 420 430 440
....*....|....*....|....*....|....*....|.
gi 297172930 982 ------SVTDNYGKEVERYKIPYGARITTKDGQKVKRGQII 1016
Cdd:CHL00117 380 lckidlYVTIESEDIIHNVNIPPKSLLLVQNDQYVESEQVI 420
|
|
| RNAP_archeal_A' |
cd02582 |
A' subunit of archaeal RNA polymerase (RNAP); A' is the largest subunit of the archaeal RNA ... |
18-832 |
5.49e-97 |
|
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: 331.90 E-value: 5.49e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 18 DAIKIGLASPEMIRSWSYGEVKKPETinYrtfrpERDGLfcaKIFGPVKDyeclcgkyKRLkhrGV-----VCEKCGVev 92
Cdd:cd02582 5 KGIKFGLLSPEEIRKMSVVEIITPDT--Y-----DEDGY---PIEGGLMD--------PRL---GViepglRCKTCGN-- 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 93 tqskvRRER----MGHLELASPVAHIWFLKslpsRIGLLLDMTLREIERVLyfeaylvvepgMTTLKKGQLLSEEEYIEA 168
Cdd:cd02582 62 -----TAGEcpghFGHIELARPVIHVGFAK----HIYDLLRATCRSCGRIL-----------LPEEEIEKYLERIRRLKE 121
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 169 LeefgNDFDALMGAEAIH-------------SVLKDVKLDDLINSIHQDMGataSQIKLKRLTKRLKLA----ESLLKSG 231
Cdd:cd02582 122 K----WPELVKRVIEKVKkkakkrkvcphcgAPQYKIKLEKPTTFYEEKEE---GEVKLTPSEIRERLEkipdEDLELLG 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 232 -----NRPEWMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDAL 306
Cdd:cd02582 195 idpktARPEWMVLTVLPVPPVTVRPSITLETGERSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWDLLQYHVTTY 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 307 LDNGRMG--RAITGSnRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHK 384
Cdd:cd02582 275 FDNEIPGipPARHRS-GRPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEDIAKELTVPERVTE 353
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 385 LiyqgeagTIKAAKRLAEaEGPEIW--------------DILD-------------DVIREH-----PVLLNRAPTLHRL 432
Cdd:cd02582 354 W-------NIEKMRKLVL-NGPDKWpganyvirpdgrriRLRYvnreelaerlepgWIVERHlidgdIVLFNRQPSLHRM 425
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 433 GIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYY 512
Cdd:cd02582 426 SIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQSEEARAEARELMLVQEHILSPRYGGPIIGGIQDYISGAYL 505
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 513 MTR--------ERINDLGEGHIYADVTELQRAYDGGYV-GLQ---------------AKVKLRILRNTEPEDEsnvTHEL 568
Cdd:cd02582 506 LTRkttlftkeEALQLLSAAGYDGLLPEPAILEPKPLWtGKQlfslflpkdlnfegkAKVCSGCSECKDEDCP---NDGY 582
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 569 VETTVGRgLLSRIIPpelpysavNQTMDSKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPE- 647
Cdd:cd02582 583 VVIKNGK-LLEGVID--------KKAIGAEQPGSLLHRIAKEYGNEVARRFLDSVTRLAIRFIELRGFTIGIDDEDIPEe 653
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 648 ---KKEEILAGAERQVKNIQNQFSSGLLtQGERynkvvdiwSRT-NDLIANAMMEKLG--REEVEDQAgNKKIQPsFNSI 721
Cdd:cd02582 654 arkEIEEIIKEAEKKVYELIEQYKNGEL-EPLP--------GRTlEETLEMKIMQVLGkaRDEAGKVA-SKYLDP-FNNA 722
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 722 FMMADSGARGSPAQIRQLAGM------------RGLMAKP--------DGSIIETPITANFREGLNVLQYFISTHGARKG 781
Cdd:cd02582 723 VIMARTGARGSMLNLTQMAAClgqqsvrgerinRGYRNRTlphfkpgdLGPEARGFVRSSFRDGLSPTEFFFHAMGGREG 802
|
890 900 910 920 930
....*....|....*....|....*....|....*....|....*....|.
gi 297172930 782 LADTALKTANSGYLTRRLVDVSQDLVVTEDdcetnkgLTVSTivEGGAIVQ 832
Cdd:cd02582 803 LVDTAVRTSQSGYMQRRLINALQDLYVEYD-------GTVRD--SRGNIIQ 844
|
|
| RNA_pol_Rpb1_1 |
pfam04997 |
RNA polymerase Rpb1, domain 1; RNA polymerases catalyze the DNA dependent polymerization of ... |
14-342 |
3.63e-95 |
|
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: 309.22 E-value: 3.63e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 14 TQTFDAIKIGLASPEMIRSWSYGEVKKPETINYRTFRPERDGLFCAKIFGPVKDYEC-LCGKYKRlkhrgvvceKCGVev 92
Cdd:pfam04997 1 LKKIKEIQFGIASPEEIRKWSVGEVTKPETYNYGSLKPEEGGLLDERMGTIDKDYECeTCGKKKK---------DCPG-- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 93 tqskvrreRMGHLELASPVAHIWFLKslpsrigllldMTLREIERVLYFEAYLVVEPGmttlkKGQLLSEEEYIEALEEF 172
Cdd:pfam04997 70 --------HFGHIELAKPVFHIGFFK-----------KTLKILECVCKYCSKLLLDPG-----KPKLFNKDKKRLGLENL 125
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 173 GndfdalMGAEAIHSVLKDVKL--------------------------DDLINSIHQDMGATASQIKLKRLTKRLKLAES 226
Cdd:pfam04997 126 K------MGAKAILELCKKKDLcehcggkngvcgsqqpvsrkeglklkAAIKKSKEEEEKEILNPEKVLKIFKRISDEDV 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 227 LL----KSGNRPEWMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKS 302
Cdd:pfam04997 200 EIlgfnPSGSRPEWMILTVLPVPPPCIRPSVQLDGGRRAEDDLTHKLRDIIKRNNRLKKLLELGAPSHIIREEWRLLQEH 279
|
330 340 350 360
....*....|....*....|....*....|....*....|.
gi 297172930 303 VDALLDNGRMG-RAITGSNRRPLKSLADMIKGKQGRFRQNL 342
Cdd:pfam04997 280 VATLFDNEIPGlPPALQKSKRPLKSISQRLKGKEGRFRGNL 320
|
|
| PRK08566 |
PRK08566 |
DNA-directed RNA polymerase subunit A'; Validated |
19-832 |
2.29e-87 |
|
DNA-directed RNA polymerase subunit A'; Validated
Pssm-ID: 236292 [Multi-domain] Cd Length: 882 Bit Score: 304.86 E-value: 2.29e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 19 AIKIGLASPEMIRSWSYGEVKKPETinYrtfrpERDGLfcaKIFGPVKDyeclcgkyKRLkhrGV-----VCEKCGvevt 93
Cdd:PRK08566 11 SIKFGLLSPEEIRKMSVTKIITADT--Y-----DDDGY---PIDGGLMD--------PRL---GVidpglRCKTCG---- 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 94 qSKVRR--ERMGHLELASPVAHIWFLKslpsRIGLLLDMTLREIERVLyfeaylvvepgMTTLKKGQLLSEEEYIEALEE 171
Cdd:PRK08566 66 -GRAGEcpGHFGHIELARPVIHVGFAK----LIYKLLRATCRECGRLK-----------LTEEEIEEYLEKLERLKEWGS 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 172 FGNDFDALMGAEAI------H--SVLKDVKLDDLINSIHQDMGAtasqikLKRLT-----KRL-KLAESLLK------SG 231
Cdd:PRK08566 130 LADDLIKEVKKEAAkrmvcpHcgEKQYKIKFEKPTTFYEERKEG------LVKLTpsdirERLeKIPDEDLEllginpEV 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 232 NRPEWMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGR 311
Cdd:PRK08566 204 ARPEWMVLTVLPVPPVTVRPSITLETGQRSEDDLTHKLVDIIRINQRLKENIEAGAPQLIIEDLWELLQYHVTTYFDNEI 283
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 312 MG----RAITGsnrRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPfvfhkliy 387
Cdd:PRK08566 284 PGippaRHRSG---RPLKTLAQRLKGKEGRFRGNLSGKRVNFSARTVISPDPNLSINEVGVPEAIAKELTVP-------- 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 388 qgEAGT---IKAAKRLAeAEGPEIW--------------DILD-------------DVIREH-----PVLLNRAPTLHRL 432
Cdd:PRK08566 353 --ERVTewnIEELREYV-LNGPEKHpganyvirpdgrriKLTDknkeelaeklepgWIVERHlidgdIVLFNRQPSLHRM 429
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 433 GIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYY 512
Cdd:PRK08566 430 SIMAHRVRVLPGKTFRLNLAVCPPYNADFDGDEMNLHVPQTEEARAEARILMLVQEHILSPRYGGPIIGGIQDHISGAYL 509
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 513 MTRErindlgeghiYADVTELQRAYdggyvgLQAKVKLRILRNTEPEDESNvthelVETTVGRGLLSRIIPPEL------ 586
Cdd:PRK08566 510 LTRK----------STLFTKEEALD------LLRAAGIDELPEPEPAIENG-----KPYWTGKQIFSLFLPKDLnlefka 568
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 587 --------------PYSA---------VNQTMDSKQIS----QLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSIC 639
Cdd:PRK08566 569 kicsgcdeckkedcEHDAyvvikngklLEGVIDKKAIGaeqgSILDRIVKEYGPERARRFLDSVTRLAIRFIMLRGFTTG 648
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 640 LDDMEVP----EKKEEILAGAERQVKNIQNQFSSGLLTQgerynkvvdIWSRT-NDLIANAMMEKLG--REEVEDQAGnK 712
Cdd:PRK08566 649 IDDEDIPeeakEEIDEIIEEAEKRVEELIEAYENGELEP---------LPGRTlEETLEMKIMQVLGkaRDEAGEIAE-K 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 713 KIQPsFNSIFMMADSGARGSPAQIRQLAGM------------RGLMAK-----PDGSIieTP-----ITANFREGLNVLQ 770
Cdd:PRK08566 719 YLGL-DNPAVIMARTGARGSMLNLTQMAACvgqqsvrgerirRGYRDRtlphfKPGDL--GAeargfVRSSYKSGLTPTE 795
|
890 900 910 920 930 940
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 297172930 771 YFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDdcetnkgLTVSTivEGGAIVQ 832
Cdd:PRK08566 796 FFFHAMGGREGLVDTAVRTSQSGYMQRRLINALQDLKVEYD-------GTVRD--TRGNIVQ 848
|
|
| PRK14977 |
PRK14977 |
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional |
15-1362 |
2.18e-83 |
|
bifunctional DNA-directed RNA polymerase A'/A'' subunit; Provisional
Pssm-ID: 184940 [Multi-domain] Cd Length: 1321 Bit Score: 300.40 E-value: 2.18e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 15 QTFDAIKIGLASPEMIRSWSYGEVKKPETInyrtfrpERDGLfcaKIFGPVKDyeclcGKYKRLKHRgvvcEKCGVEVTQ 94
Cdd:PRK14977 7 KAIDGIIFGLISPADARKIGFAEITAPEAY-------DEDGL---PVQGGLLD-----GRLGTIEPG----QKCLTCGNL 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 95 SKVRRERMGHLELASPVAHIWFLKslpsRIGLLLDMTLREIERVLYFEAYLVVepgMTTLKKGQllseeeyiealEEFGN 174
Cdd:PRK14977 68 AANCPGHFGHIELAEPVIHIAFID----NIKDLLNSTCHKCAKLKLPQEDLNV---FKLIEEAH-----------AAARD 129
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 175 DFDALMGAEAIHSVLKDVKLDDLINSIHQDMGATASQIKLKRLTKRLKLAE----------------------SLLKSGN 232
Cdd:PRK14977 130 IPEKRIDDEIIEEVRDQVKVYAKKAKECPHCGAPQHELEFEEPTIFIEKTEieehrllpieirdifekiidddLELIGFD 209
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 233 ----RPEWMILKVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLD 308
Cdd:PRK14977 210 pkkaRPEWAVLQAFLVPPLTARPSIILETGERSEDDLTHILVDIIKANQKLKESKDAGAPPLIVEDEVDHLQYHTSTFFD 289
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 309 NGRMG--RAITGSNRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFV----- 381
Cdd:PRK14977 290 NATAGipQAHHKGSGRPLKSLFQRLKGKEGRFRGNLIGKRVDFSARTVISPDPMIDIDEVGVPEAIAMKLTIPEIvnenn 369
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 382 ---FHKLIYQG-----------EAGTIKAAKRLAEAEG----PEIWDILD--DVIREH-----PVLLNRAPTLHRLGIQA 436
Cdd:PRK14977 370 iekMKELVINGpdefpganairKGDGTKIRLDFLEDKGkdalREAAEQLEigDIVERHladgdIVIFNRQPSLHKLSILA 449
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 437 FEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR- 515
Cdd:PRK14977 450 HRVKVLPGATFRLHPAVCPPYNADFDGDEMNLHVPQIEDARAEAIELMGVKDNLISPRTGGPIIGALQDFITAAYLITKd 529
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 516 -------ERINDLGEGHIY------ADVTELQRAYDG------------GYVGLQakvKLRILRNTEPEDESNVTHELVE 570
Cdd:PRK14977 530 dalfdknEASNIAMLAGITdplpepAIKTKDGPAWTGkqlfslflpkdfNFEGIA---KWSAGKAGEAKDPSCLGDGYVL 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 571 TTVGRgLLSRIIPPELPYSAVnqtmdsKQISQLINKCYRDVGLKAAVILADKLMYMGFEYATKAGVSICLDDMEVPEKK- 649
Cdd:PRK14977 607 IKEGE-LISGVIDDNIIGALV------EEPESLIDRIAKDYGEAVAIEFLNKILIIAKKEILHYGFSNGPGDLIIPDEAk 679
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 650 ---EEILAGAERQVKNIQNQFSSGLLTQGERYNKVVDIWSRTNDLIANAMMEKLGREEVEDQAGNKKIQPSFNSIFMMAD 726
Cdd:PRK14977 680 qeiEDDIQGMKDEVSDLIDQRKITRKITIYKGKEELLRGMKEEEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAK 759
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 727 SGARGSPAQIRQLAGMRGLMA-KPDGSIIETP---------------------------ITANFREGLNVLQYFISTHGA 778
Cdd:PRK14977 760 TGARGSMANLAQIAGALGQQKrKTRIGFVLTGgrlhegykdralshfqegddnpdahgfVKNNYREGLNAAEFFFHAMGG 839
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 779 RKGLADTALKTANSGYLTRRLVDVSQDLVVTEDDcetnkglTVSTivEGGAIVQGL--GDRI------------LGRFIA 844
Cdd:PRK14977 840 REGLIDKARRTEDSGYFQRRLANALEDIRLEYDE-------TVRD--PHGHIIQFKfgEDGIdpqkldhgeafnLERIIE 910
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 845 EPLID-------REKNEILLESGTLIDEKNVHLL---ELHGIETisvrspvtceTKHGVCVSCY-GRDLGRGNIVNKGEA 913
Cdd:PRK14977 911 KQKIEdrgkgasKDEIEELAKEYTKTFNANLPKLladAIHGAEL----------KEDELEAICAeGKEGFEKAKVEPGQA 980
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 914 VGIIAAQSIGEPGTQLTMRTFHIGGaasssaavnsievkndgkihlynvktIKSKDKNLvAVSRSGEIsvtdnygkeVER 993
Cdd:PRK14977 981 IGIISAQSIAEPGTQMTLRTFHAAG--------------------------IKAMDVTH-GLERFIEL---------VDA 1024
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 994 YKIPYGARITTKDGQKVKrgqiistwdphthpivaeaagiigfEDFIDGVTVTEQVDELTgiNNTLIMDSQKQSAKS-KE 1072
Cdd:PRK14977 1025 RAKPSTPTMDIYLDDECK-------------------------EDIEKAIEIARNLKELK--VRALIADSAIDNANEiKL 1077
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1073 LRPRARLhnakgkpiffsgTETPIIYAFPSGAIIRATDGAKinagdviariplesSKTIDITGGLPRVaDLFEA---RKP 1149
Cdd:PRK14977 1078 IKPDKRA------------LENGCIPMERFAEIEAALAKGK--------------KFEMELEDDLIIL-DLVEAadrDKP 1130
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1150 KDAAILAKYSGITSFGRETKGKVRLVITSEDGDVHEELILKTRRLN---IYEGESIAKGEIIADgelslhDILEIQ---G 1223
Cdd:PRK14977 1131 LATLIAIRNKILDKPVKGVPDIERAWVELVEKDGRDEWIIQTSGSNlaaVLEMKCIDIANTITN------DCFEIAgtlG 1204
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1224 VQALSEYLVKEVQDVYRLQGVPINDKHIEVIirqmmrvvevenpgdtaflnkeqinkSDLLVVNETMQAEDLEPATYRHI 1303
Cdd:PRK14977 1205 IEAARNAIFNELASILEDQGLEVDNRYIMLV--------------------------ADIMCSRGTIEAIGLQAAGVRHG 1258
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....*....
gi 297172930 1304 LMGITKASLATtsfisaASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFV 1362
Cdd:PRK14977 1259 FAGEKDSPLAK------AAFEITTHTIAHAALGGEIEKIKGILDALIMGQNIPIGSGKV 1311
|
|
| RNAP_beta'_C |
cd02655 |
Largest subunit (beta') of Bacterial DNA-dependent RNA polymerase (RNAP), C-terminal domain; ... |
906-1361 |
6.55e-74 |
|
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: 244.36 E-value: 6.55e-74
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 906 NIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAasssaavnsievkndgkihlynvktikskdknlvavsrsgeisvtd 985
Cdd:cd02655 1 KLVELGEAVGIIAAQSIGEPGTQLTMRTFHTGGV---------------------------------------------- 34
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 986 nygkeverykipygarittkdgqkvkrgqiistwdphthpivaeaagiigfedfidgvtvteqvdeltginntlimdsqk 1065
Cdd:cd02655 --------------------------------------------------------------------------------
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1066 qsakskelrprarlhnakgkpiffsgtetpiiyafpsgaiirATDgakinagdviariplessktidITGGLPRVADLFE 1145
Cdd:cd02655 35 ------------------------------------------ATD----------------------ITQGLPRVEELFE 50
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1146 ARKPkdaailakysgitsfgretkgkvrlvitsedgdvheelilktrrlniyegesiakgeiiadgelSLHDILEIQ--G 1223
Cdd:cd02655 51 ARKI----------------------------------------------------------------NPHDLLRIKflG 66
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1224 VQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKEQINKSDLLVVNETMQAEDLEPATYRHI 1303
Cdd:cd02655 67 PEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMTSKVKIIDPGDSGFLPGELVDLNEFEEENKRLLLLGKKPAKYEPV 146
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*...
gi 297172930 1304 LMGITKASLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGF 1361
Cdd:cd02655 147 LLGITKASLNTESFISAASFQETTKVLTEAAIEGKIDWLRGLKENVILGRLIPAGTGL 204
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
1103-1374 |
6.52e-73 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 268.02 E-value: 6.52e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1103 GAIIRATDGAKINAGDVIARIPLESSKTIDITGGLPRVADLFEARKPKDAAILAKYSGITSFGRETKGKVRLVITSEDGD 1182
Cdd:PRK02597 949 GAVLHVRDGDLVQRGDNLALLVFERAKTGDIIQGLPRIEELLEARKPKESCILAKKPGTVQIKYGDDESVDVKVIESDGT 1028
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1183 VHEELILKTRRLNIYEGESIAKGEIIADGELSLHDILEI----------------QGVQALSEYLVKEVQDVYRLQGVPI 1246
Cdd:PRK02597 1029 ITEYPILPGQNVMVSDGQQVDAGEPLTDGPINPHELLEIffedlrdrkglyeaalEALQKLQRFLVNEVQNVYQSQGVDI 1108
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1247 NDKHIEVIIRQMMRVVEVENPGDTAFLNKEQINKSDLLVVNETMQAEDLEPATYRHILMGITKASLATTSFISAASFQET 1326
Cdd:PRK02597 1109 SDKHIEVIVRQMTSKVRIDDGGDTTMLPGELIELRQVEQVNEAMAITGGAPAEYTPVLLGITKASLNTDSFISAASFQET 1188
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 297172930 1327 TRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFvQEIDETAIAEEE 1374
Cdd:PRK02597 1189 TRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF-SGFEEELSAEAG 1235
|
|
| rpoC2_cyan |
TIGR02388 |
DNA-directed RNA polymerase, beta'' subunit; The family consists of the product of the rpoC2 ... |
1098-1361 |
7.23e-67 |
|
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: 248.23 E-value: 7.23e-67
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1098 YAFPSGAIIRATDGAKINAGDVIARIPLESSKTIDITGGLPRVADLFEARKPKDAAILAKYSGITSFGR-ETKGKVRLVI 1176
Cdd:TIGR02388 942 YRVSPGAVLHIEDGDLVQRGDNLALLVFERAKTGDIVQGLPRIEELLEARKPKEACILAKRPGVVQVKYgTDDESVSIKV 1021
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1177 TSEDGDVHEELILKTRRLNIYEGESIAKGEIIADGELSLHDILEI----------------QGVQALSEYLVKEVQDVYR 1240
Cdd:TIGR02388 1022 IERDGTISEYPLLPGQNIMVSDGQQVTGGEPLTDGPINPHDILDVffsyykdqdglyeaaqESLQKVQRFLVNEVQNVYQ 1101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1241 LQGVPINDKHIEVIIRQMMRVVEVENPGDTAFLNKEQINKSDLLVVNETMQAEDLEPATYRHILMGITKASLATTSFISA 1320
Cdd:TIGR02388 1102 SQGVDISDKHIEVIVRQMTSKVRIDDAGDTTLLPGELVELRQVEQVNEAMAITGGAPAQYTPVLLGITKASLNTDSFISA 1181
|
250 260 270 280
....*....|....*....|....*....|....*....|.
gi 297172930 1321 ASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGF 1361
Cdd:TIGR02388 1182 ASFQETTRVLTEAAIEGKSDWLRGLKENVIIGRLIPAGTGF 1222
|
|
| RNAP_III_RPC1_N |
cd02583 |
Largest subunit (RPC1) of eukaryotic RNA polymerase III (RNAP III), N-terminal domain; Rpc1 ... |
227-812 |
3.76e-62 |
|
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: 228.97 E-value: 3.76e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 227 LLKSGNRPEWMILKVLPVLPPDLRPLVPLDGGrfATSDLNDL---YRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSV 303
Cdd:cd02583 168 MNPLAGRPENLILTRIPVPPLCIRPSVVMDEK--SGTNEDDLtvkLSEIIFLNDVIKKHLEKGAKTQKIMEDWDFLQLQC 245
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 304 dALLDNGRM-GRAITGSNRRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKP--- 379
Cdd:cd02583 246 -ALYINSELpGLPLSMQPKKPIRGFCQRLKGKQGRFRGNLSGKRVDFSGRTVISPDPNLRIDQVGVPEHVAKILTYPerv 324
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 380 FVF-----HKLIYQGE-----AGTI-----------KAAKRLAEAEGPEIWDILD------DVirehpVLLNRAPTLHRL 432
Cdd:cd02583 325 TRYnieklRKLVLNGPdvhpgANFVikrdggkkkflKYGNRRKIARELKIGDIVErhledgDI-----VLFNRQPSLHRL 399
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 433 GIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLGLYY 512
Cdd:cd02583 400 SIMAHRAKVMPWRTFRFNECVCTPYNADFDGDEMNLHVPQTEEARAEALELMGVKNNLVTPRNGEPLIAATQDFLTASYL 479
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 513 MT-------RERINDL----GEGHIYADVTE------------------LQRAY--DGGYVGLQAKVKLRILRNTE--PE 559
Cdd:cd02583 480 LTskdvffdRAQFCQLcsymLDGEIKIDLPPpailkpvelwtgkqifslLLRPNkkSPVLVNLEAKEKSYTKKSPDmcPN 559
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 560 DESNVTH--ELV-----ETTVG----RGLLSRIIppelpysavnqtmdskqisqlinkcyRDVGLKAAVILADKLMYMGF 628
Cdd:cd02583 560 DGYVVIRnsELLcgrldKSTLGsgskNSLFYVLL--------------------------RDYGPEAAAAAMNRLAKLSS 613
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 629 EYATKAGVSICLDDM----EVPEKKEEILAGAERQVKNIQNQFSSGLLTQGERYNkvvdiwsrtndliANAMME-KLGRE 703
Cdd:cd02583 614 RWLSNRGFSIGIDDVtpskELLKKKEELVDNGYAKCDEYIKQYKKGKLELQPGCT-------------AEQTLEaKISGE 680
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 704 --EVEDQAGNKKIQ--PSFNSIFMMADSGARGSPAQIRQ---------LAGMRglmaKPDGSI----------IETPIT- 759
Cdd:cd02583 681 lsKIREDAGKACLKelHKSNSPLIMALCGSKGSNINISQmiacvgqqiISGKR----IPNGFEdrtlphfprnSKTPAAk 756
|
650 660 670 680 690
....*....|....*....|....*....|....*....|....*....|....*..
gi 297172930 760 ---AN-FREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVSQDLVVTEDD 812
Cdd:cd02583 757 gfvANsFYSGLTPTEFFFHTMSGREGLVDTAVKTAETGYMQRRLMKALEDLSVQYDG 813
|
|
| RNAP_II_RPB1_N |
cd02733 |
Largest subunit (Rpb1) of eukaryotic RNA polymerase II (RNAP II), N-terminal domain; The two ... |
18-808 |
1.26e-60 |
|
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: 223.18 E-value: 1.26e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 18 DAIKIGLASPEMIRSWSYGEVKKPETINyRTFRPERDGLFCAKIfGPVKdyeclcgkykrlkhRGVVCEKCGvevtqskv 97
Cdd:cd02733 1 KRVQFGILSPDEIRAMSVAEIEHPETYE-NGGGPKLGGLNDPRM-GTID--------------RNSRCQTCG-------- 56
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 98 rrERM-------GHLELASPVAHIWFLkslpsriglllDMTLREIERVLyfeaylvvepgmttlkkgqllseeeyieale 170
Cdd:cd02733 57 --GDMkecpghfGHIELAKPVFHIGFL-----------TKILKILRCVC------------------------------- 92
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 171 efgndfDALMGAEAIHSVLKDVKLDDLinsihqdmgatasqiklkrltKRLKLAESLLksgnRPEWMILKVLPVLPPDLR 250
Cdd:cd02733 93 ------KRELSAERVLEIFKRISDEDC---------------------RILGFDPKFS----RPDWMILTVLPVPPPAVR 141
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 251 PLVPLDGGRFATSDLNDLYRRVINRNNRLQRLLELNAPEIIVRNEKRMLQKSVDALLDNGRMG--RAITGSNRrPLKSLA 328
Cdd:cd02733 142 PSVVMDGSARSEDDLTHKLADIIKANNQLKRQEQNGAPAHIIEEDEQLLQFHVATYMDNEIPGlpQATQKSGR-PLKSIR 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 329 DMIKGKQGRFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKKMAL-----ELFKPFVFHKLIYQGEAGTIK--AAKRLA 401
Cdd:cd02733 221 QRLKGKEGRIRGNLMGKRVDFSARTVITPDPNLELDQVGVPRSIAMnltfpEIVTPFNIDRLQELVRNGPNEypGAKYII 300
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 402 EAEG--------PEIWDIL-------------DDVirehpVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNAD 460
Cdd:cd02733 301 RDDGeridlrylKKASDLHlqygyiverhlqdGDV-----VLFNRQPSLHKMSMMGHRVKVLPYSTFRLNLSVTTPYNAD 375
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 461 FDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPI--IVpsQDVVLGLYYMTRERindlgeghiyadvTELQR--- 535
Cdd:cd02733 376 FDGDEMNLHVPQSLETRAELKELMMVPRQIVSPQSNKPVmgIV--QDTLLGVRKLTKRD-------------TFLEKdqv 440
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 536 -------AYDGGYVGLQAKVKLRILrntepedesnvthelvetTVGRGLLSRIIP-----------PELPYSAVNQ---- 593
Cdd:cd02733 441 mnllmwlPDWDGKIPQPAILKPKPL------------------WTGKQIFSLIIPkinnlirssshHDGDKKWISPgdtk 502
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 594 -----------TMDSKQI--SQ--LINKCYRDVGLKAAVILADK--------LMYMGFeyatKAGVSICLDDMEVPEKKE 650
Cdd:cd02733 503 viiengellsgILCKKTVgaSSggLIHVIWLEYGPEAARDFIGNiqrvvnnwLLHNGF----SIGIGDTIADKETMKKIQ 578
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 651 EILAGAERQVKNIQNQFSSGLLTQgerynkvvdiwsrtndLIANAMME----KLGRE--EVEDQAGnKKIQPS---FNSI 721
Cdd:cd02733 579 ETIKKAKRDVIKLIEKAQNGELEP----------------QPGKTLREsfenKVNRIlnKARDKAG-KSAQKSlseDNNF 641
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 722 FMMADSGARGSPAQIRQLAG-----------------MRGL--MAKPDGSIIETP-ITANFREGLNVLQYFISTHGARKG 781
Cdd:cd02733 642 KAMVTAGSKGSFINISQIIAcvgqqnvegkripfgfrRRTLphFIKDDYGPESRGfVENSYLRGLTPQEFFFHAMGGREG 721
|
890 900
....*....|....*....|....*..
gi 297172930 782 LADTALKTANSGYLTRRLVDVSQDLVV 808
Cdd:cd02733 722 LIDTAVKTAETGYIQRRLVKAMEDVMV 748
|
|
| rpoC2 |
CHL00117 |
RNA polymerase beta'' subunit; Reviewed |
1098-1361 |
6.00e-59 |
|
RNA polymerase beta'' subunit; Reviewed
Pssm-ID: 214368 [Multi-domain] Cd Length: 1364 Bit Score: 223.66 E-value: 6.00e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1098 YAFPSGAIIRATDGAKINAGDVIARIPLESSKTIDITGGLPRVADLFEARKpkdaailakysgITSfgretkgkvrLVIT 1177
Cdd:CHL00117 1096 YLATPGATVHGHYGEILYEGDTLVTLIYEKSRSGDITQGLPKVEQLLEARS------------IDS----------ISMN 1153
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1178 SEDGDvheeLILKTRRLNIYEgesIAKGEIIAdGELSlhdILEIQGvqalseYLVKEVQDVYRLQGVPINDKHIEVIIRQ 1257
Cdd:CHL00117 1154 LEKRL----EGWNERITRILG---IPWGFLIG-AELS---IAQSQI------SLVNKIQKVYRSQGVQISDKHIEIIVRQ 1216
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1258 MMRVVEVENPGDT-AFLNKEQInksDLLvvnetmQAEDL-----EPATYRHILMGITKASLATTSFISAASFQETTRVLT 1331
Cdd:CHL00117 1217 MTSKVLVSEDGMSnVFLPGELI---GLL------RAERInraleEAICYRPILLGITKASLNTQSFISEASFQETTRVLA 1287
|
250 260 270
....*....|....*....|....*....|
gi 297172930 1332 EAAVRGSVDKLRGLKENVVVGRLVPAGTGF 1361
Cdd:CHL00117 1288 KAALRGRIDWLKGLKENVILGGLIPAGTGF 1317
|
|
| RNA_pol_Rpb1_2 |
pfam00623 |
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
344-485 |
4.96e-46 |
|
RNA polymerase Rpb1, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion.
Pssm-ID: 395498 Cd Length: 166 Bit Score: 163.24 E-value: 4.96e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 344 GKRVDYSGRSVIVVGPTLKLHQCGIPKKMALELFKPFVFHKLI--------------------YQGEAGTIKAAKRLAEA 403
Cdd:pfam00623 1 GKRVDFSARTVISPDPNLKLDEVGVPISFAKTLTFPEIVTPYNikrlrqlvengpnvypganyIIRINGARRDLRYQKRR 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 404 EGPEIW--DILD-DVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLES 480
Cdd:pfam00623 81 LDKELEigDIVErHVIDGDVVLFNRQPSLHRLSIMGHRVRVLPGKTFRLNLSVTTPYNADFDGDEMNLHVPQSEEARAEA 160
|
....*
gi 297172930 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 ... |
208-509 |
3.25e-38 |
|
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: 154.65 E-value: 3.25e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 208 TASQIKLKRLTKRLKLAESLLKSG-----NRPEWMILKVLPVLPPDLRPLVPLDGGRFaTSDLNDLYRRVINRNNRLQRL 282
Cdd:cd01435 96 RISKWEVKLFVAKLKLLDKGLLVEaaeldFGYDMFFLDVLLVPPNRFRPPSFLGDKVF-ENPQNVLLSKILKDNQQIRDL 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 283 LELNAPEIIVRNEKRM---------------LQKSVDALLDNGrmgraitgSNRRPLKSLADMIK----GKQGRFRQNLL 343
Cdd:cd01435 175 LASMRQAESQSKLDLIsgktnseklinawlqLQSAVNELFDST--------KAPKSGKKSPPGIKqlleKKEGLFRMNMM 246
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 344 GKRVDYSGRSVIVVGPTLKLHQCGIPKKMALEL-F----KPFVFHKL---------------IYQGEAGTI--------- 394
Cdd:cd01435 247 GKRVNYAARSVISPDPFIETNEIGIPLVFAKKLtFpepvTPFNVEELrqavingpdvypganAIEDEDGRLillsalsee 326
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 395 ----KAAKRLAEAE------GPEIW--DILD-DVirehpVLLNRAPTLHRLGIQA-FEPVLIEGKAIQLHPLVCKAFNAD 460
Cdd:cd01435 327 rrkaLAKLLLLLSSaklllnGPKKVyrHLLDgDV-----VLLNRQPTLHKPSIMAhKVRVLPGEKTLRLHYANCKSYNAD 401
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|..
gi 297172930 461 FDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPI---IvpsQDVVLG 509
Cdd:cd01435 402 FDGDEMNLHFPQSELARAEAYYIASTDNQYLVPTDGKPLrglI---QDHVVS 450
|
|
| RNA_pol_Rpb1_3 |
pfam04983 |
RNA polymerase Rpb1, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
489-643 |
4.10e-29 |
|
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: 114.26 E-value: 4.10e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 489 NILSPANGEPIIVPSQDVVLGLYYMTRERindlgeghIYADVTELQRAYDGGYVGLQAkvklRILRNTEPEdesnvthEL 568
Cdd:pfam04983 1 NILSPQNGKPIIGPSQDMVLGAYLLTRED--------TFFDREEVMQLLMYGIVLPHP----AILKPIKPL-------WT 61
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 569 VETTVGRGLLSRIIPPELPYSA------------VNQTMD----------SKQISQLINKCYRDVGLKAAVILADKLMYM 626
Cdd:pfam04983 62 GKQTFSRLLPNEINPKGKPKTNeedlcendsyvlINNGELisgvidkktvGKSLGSLIHIIYKEYGPEETAKFLDRLQKL 141
|
170
....*....|....*..
gi 297172930 627 GFEYATKAGVSICLDDM 643
Cdd:pfam04983 142 GFRYLTKSGFSIGIDDI 158
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
1214-1360 |
6.54e-25 |
|
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The region covered by this domain makes up part of the foot and jaw structures. In archaea, some photosynthetic organisms, and some organelles, this domain exists as a separate subunit, while it forms the C-terminal region of the RNAP largest subunit in eukaryotes and bacteria.
Pssm-ID: 132719 [Multi-domain] Cd Length: 158 Bit Score: 102.50 E-value: 6.54e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1214 SLHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMmrvvevenpgdtaflnkeqinksdllvvnetmqae 1293
Cdd:cd00630 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVM----------------------------------- 93
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 297172930 1294 dlepaTYRHILMGITKASLA--TTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTG 1360
Cdd:cd00630 94 -----TYSGGLRGVTRSGFRasKTSPLMRASFEKTTKHLLDAAAAGEKDELEGVSENIILGRPAPLGTG 157
|
|
| RNA_pol_Rpb1_4 |
pfam05000 |
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of ... |
672-763 |
3.50e-24 |
|
RNA polymerase Rpb1, domain 4; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors.
Pssm-ID: 398598 Cd Length: 108 Bit Score: 98.59 E-value: 3.50e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 672 LTQGERYNKVVDIWSRTNDLIANAMMEKLgREEVEDQAGN--KKIQPSFNSIFMMADSGARGSPAQIRQLAGMRGLMAKP 749
Cdd:pfam05000 1 ITDAERYGKLEDIWGMTLEESFEALINNI-LNKARDPAGNiaSKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQQNVE 79
|
90 100
....*....|....*....|....*....
gi 297172930 750 DGSI---------------IETPITANFR 763
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 ... |
214-516 |
7.65e-22 |
|
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: 102.48 E-value: 7.65e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 214 LKRLTKRL--KLAESLLKsgnRPEWMILKVLPVLPPDLRplVPLDGGRFATsdlndlyrrvinrnnrlqrllelnAPEII 291
Cdd:cd10506 124 VKKILKEIdpKLIAKGLP---RQEGLFLKCLPVPPNCHR--VTEFTHGFST------------------------GSRLI 174
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 292 VRNEKRMLQKSVDAlldngrmgraiTGSNRRplKSLADMIKGKQgrFRQNLLGKRVDYSGRSVIVVGPTLKLHQCGIPKK 371
Cdd:cd10506 175 FDERTRAYKKLVDF-----------IGTANE--SAASKKSGLKW--MKDLLLGKRSGHSFRSVVVGDPYLELNEIGIPCE 239
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 372 MALELFKP-------------FVFHKLIYQGEAGTIKAAK--RLAEAEGPEIWDIL------DDVirehpVLLNRAPTLH 430
Cdd:cd10506 240 IAERLTVServsswnrerlqeYCDLTLLLKGVIGVRRNGRlvGVRSHNTLQIGDVIhrplvdGDV-----VLVNRPPSIH 314
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 431 RLGIQAFE-PVLIEGKAIQLHPLVCKAFNADFDGDQMAVHVPLSIEAQLESRALMMSTNNILSPANGEPIIVPSQDVVLG 509
Cdd:cd10506 315 QHSLIALSvKVLPTNSVVSINPLCCSPFRGDFDGDCLHGYIPQSLQARAELEELVALPKQLISSQSGQNLLSLTQDSLLA 394
|
....*..
gi 297172930 510 LYYMTRE 516
Cdd:cd10506 395 AHLMTER 401
|
|
| RNAP_A'' |
cd06528 |
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial ... |
906-1362 |
2.92e-18 |
|
A'' subunit of Archaeal RNA Polymerase (RNAP); Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Pssm-ID: 132725 [Multi-domain] Cd Length: 363 Bit Score: 88.46 E-value: 2.92e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 906 NIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaaVNSIevkndgkihlyNVKTIKSKDKNLVAVSR-----SGE 980
Cdd:cd06528 35 SLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAG-------VAEI-----------NVTLGLPRLIEIVDARKepstpTMT 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 981 ISVTDNYGKEVERykipygARITTKDGQKVKRGQIIS--TWDPHTHPIVAEaagiigfedfidgvtvteqVDELTGINNT 1058
Cdd:cd06528 97 IYLEEEYKYDREK------AEEVARKIEETTLENLAEdiSIDLFNMRITIE-------------------LDEEMLEDRG 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1059 LIMDSQKQsakskelrprarlhnakgkpiffsgtetpiiyafpsgAIIRATDGAKINAGDVIariplesskTIDITGGLP 1138
Cdd:cd06528 152 ITVDDVLK-------------------------------------AIEKLKKGKVGEEGDVT---------LIVLKAEEP 185
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1139 RVADLFEAR-KPKDAAIlakySGItsfgretKGKVRLVITSEDGdvheELILKTRRLN---IYEGESIAKGEIIADgelS 1214
Cdd:cd06528 186 SIKELRKLAeKILNTKI----KGI-------KGIKRVIVRKEED----EYVIYTEGSNlkaVLKVEGVDPTRTTTN---N 247
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1215 LHDILEIQGVQALSEYLVKEVQDVYRLQGvpindkhIEVIIRQMMRVvevenpgdtaflnkeqinkSDLLvvneTMQAEd 1294
Cdd:cd06528 248 IHEIEEVLGIEAARNAIINEIKRTLEEQG-------LDVDIRHIMLV-------------------ADIM----TYDGE- 296
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 297172930 1295 LEPATyRHILMGiTKASLattsfISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFV 1362
Cdd:cd06528 297 VRQIG-RHGIAG-EKPSV-----LARAAFEVTVKHLLDAAVRGEVDELRGVIENIIVGQPIPLGTGDV 357
|
|
| RNA_pol_rpoA2 |
TIGR02389 |
DNA-directed RNA polymerase, subunit A''; This family consists of the archaeal A'' subunit of ... |
908-1362 |
1.39e-17 |
|
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: 86.26 E-value: 1.39e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 908 VNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaavnsievkndgkIHLYNVKT-----IKSKDKNLVAVSRSGEIS 982
Cdd:TIGR02389 41 IDPGEAVGIVAAQSIGEPGTQMTMRTFHYAG------------------VAELNVTLglprlIEIVDARKTPSTPSMTIY 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 983 VTDNYGKEVERykipygARITTKDGQKVKrgqiISTwdphthpiVAEAAGIigfeDFIDGvTVTEQVDELTGINNTLIMD 1062
Cdd:TIGR02389 103 LEDEYEKDREK------AEEVAKKIEATK----LED--------VAKDISI----DLADM-TVIIELDEEQLKERGITVD 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1063 SQKQSAKSKELrprarlhnakgkpiffsgtetpiiyafpsgaiiratdgakinaGDVIarIPLESSKTIDITGGLPRVAD 1142
Cdd:TIGR02389 160 DVEKAIKKAKL-------------------------------------------GKVI--EIDMDNNTITIKPGNPSLKE 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1143 LFEaRKPKDAAIlaKYSGItsfgretKGKVRLVITSEDgdvhEELILKTRRLNIYEgesIAKGEIIADGELSLHDILEIQ 1222
Cdd:TIGR02389 195 LRK-LKEKIKNL--HIKGI-------KGIKRVVIRKEG----DEYVIYTEGSNLKE---VLKLEGVDKTRTTTNDIHEIA 257
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1223 ---GVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGdtaflnkeqinksdllvvnetmqaedlepat 1299
Cdd:TIGR02389 258 evlGIEAARNAIIEEIKRTLEEQGLDVDIRHLMLVADLMTWDGEVRQIG------------------------------- 306
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 297172930 1300 yRHILMGiTKASLattsfISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFV 1362
Cdd:TIGR02389 307 -RHGISG-EKASV-----LARAAFEVTVKHLLDAAIRGEVDELKGVIENIIVGQPIPLGTGDV 362
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
1229-1381 |
1.14e-16 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 85.98 E-value: 1.14e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1229 EYLVKEV--QDV--YRlqgVPINDKHIEVIIRQMMRVVEVEN------------------PGDTAFLNKEQINKSDLLVV 1286
Cdd:COG0086 559 RYLVNEIlpQEVpfYN---QVINKKHIEVIIRQMYRRCGLKEtvifldrlkklgfkyatrAGISIGLDDMVVPKEKQEIF 635
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1287 NETMQ---------AEDL--EPATYRHILMGITKASLATTSFISAA-SFQETTRVLTEAAVRGSVDKL------RGLKEN 1348
Cdd:COG0086 636 EEANKevkeiekqyAEGLitEPERYNKVIDGWTKASLETESFLMAAfSSQNTTYMMADSGARGSADQLrqlagmRGLMAK 715
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 297172930 1349 -------VVVGRLVPAGTGFVQEIDETAIAEeefaKGLRD 1381
Cdd:COG0086 716 psgniieTPIGSNFREGLGVLEYFISTHGAR----KGLAD 751
|
|
| PRK04309 |
PRK04309 |
DNA-directed RNA polymerase subunit A''; Validated |
908-1363 |
7.34e-16 |
|
DNA-directed RNA polymerase subunit A''; Validated
Pssm-ID: 235277 [Multi-domain] Cd Length: 383 Bit Score: 81.43 E-value: 7.34e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 908 VNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaaVNSIevkndgkihlyNVKT-----IKSKDKNLVAVSRSGEIS 982
Cdd:PRK04309 56 VEPGEAVGVVAAQSIGEPGTQMTMRTFHYAG-------VAEI-----------NVTLglprlIEIVDARKEPSTPMMTIY 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 983 VTDNYGKEVERykipygARittkdgqKVKRgQIISTwdphthpivaeaagiiGFEDFIDGVTVTEqvdeltgINNTLIMD 1062
Cdd:PRK04309 118 LKDEYAYDREK------AE-------EVAR-KIEAT----------------TLENLAKDISVDL-------ANMTIIIE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1063 SQKQSAKSKELrprarlhnakgkpiffsgTETPIIyafpsgAIIRATDGAKINAGDVIARIPLESsktiditgglPRVAD 1142
Cdd:PRK04309 161 LDEEMLEDRGL------------------TVDDVK------EAIEKKKGGEVEIEGNTLIISPKE----------PSYRE 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1143 LFEAR-KPKDAAIlakySGItsfgretKGKVRLVITSEDgdvhEELILKTRRLNIyegESIAKGEIIADGELSLHDILEI 1221
Cdd:PRK04309 207 LRKLAeKIRNIKI----KGI-------KGIKRVIIRKEG----DEYVIYTEGSNL---KEVLKVEGVDATRTTTNNIHEI 268
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1222 Q---GVQALSEYLVKEVQDVYRLQGvpindkhIEVIIRQMMRVvevenpgdtaflnkeqinkSDLLvvneTMQAEdLEPA 1298
Cdd:PRK04309 269 EevlGIEAARNAIIEEIKNTLEEQG-------LDVDIRHIMLV-------------------ADMM----TWDGE-VRQI 317
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 297172930 1299 TyRHILMGiTKASLattsfISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFVQ 1363
Cdd:PRK04309 318 G-RHGVSG-EKASV-----LARAAFEVTVKHLLDAAVRGEVDELKGVTENIIVGQPIPLGTGDVE 375
|
|
| RNAP_II_Rpb1_C |
cd02584 |
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA ... |
907-1361 |
3.67e-14 |
|
Largest subunit (Rpb1) of Eukaryotic RNA polymerase II (RNAP II), C-terminal domain; RNA polymerase II (RNAP II) is a large multi-subunit complex responsible for the synthesis of mRNA. RNAP II consists of a 10-subunit core enzyme and a peripheral heterodimer of two subunits. The largest core subunit (Rpb1) of yeast RNAP II is the best characterized member of this family. Structure studies suggest that RNAP complexes from different organisms share a crab-claw-shape structure. In yeast, Rpb1 and Rpb2, the largest and the second largest subunits, each makes up one clamp, one jaw, and part of the cleft. Rpb1 interacts with Rpb2 to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis. The C-terminal domain of Rpb1 makes up part of the foot and jaw structures.
Pssm-ID: 132720 [Multi-domain] Cd Length: 410 Bit Score: 76.47 E-value: 3.67e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 907 IVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGaasssaaVNSIEV-------KndgkiHLYNV-KTIKSKdknlvavsrS 978
Cdd:cd02584 23 LVHPGEMVGTIAAQSIGEPATQMTLNTFHFAG-------VSAKNVtlgvprlK-----EIINVaKNIKTP---------S 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 979 GEISVTDNYGKEVERYK-----IPYgarITTKDgqKVKRGQIISTWDPhTHPIVAEAagiigfEDFIDgvTVTEQVDELT 1053
Cdd:cd02584 82 LTVYLEPGFAKDEEKAKkiqsrLEH---TTLKD--VTAATEIYYDPDP-QNTVIEED------KEFVE--SYFEFPDEDV 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1054 GINNT------LIMDSQKQSAKSKELRPRA-RLHNAKGKPIFfsgtetpIIYAFPsgaiiratdgakiNAGDVIARIPL- 1125
Cdd:cd02584 148 EQDRLspwllrIELDRKKMTDKKLSMEQIAkKIKEEFKDDLN-------VIFSDD-------------NAEKLVIRIRIi 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1126 ESSKTIDITGGLPRVADLFEARKPKDAaILAKYSGITS-FGRETKGKVRLVITSEDGDVhEELILKTrrlniyEGESIAk 1204
Cdd:cd02584 208 NDDEEKEEDSEDDVFLKKIESNMLSDM-TLKGIEGIRKvFIREENKKKVDIETGEFKKR-EEWVLET------DGVNLR- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1205 gEIIA----DGEL----SLHDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIeviirqmmrvvevenpgdtaflnke 1276
Cdd:cd02584 279 -EVLShpgvDPTRttsnDIVEIFEVLGIEAARKALLKELRNVISFDGSYVNYRHL------------------------- 332
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1277 qinksDLLVvnETMqaedlepaTYRHILMGITKASL--ATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRL 1354
Cdd:cd02584 333 -----ALLC--DVM--------TQRGHLMAITRHGInrQDTGPLMRCSFEETVDILLEAAAFGETDDLKGVSENIMLGQL 397
|
....*..
gi 297172930 1355 VPAGTGF 1361
Cdd:cd02584 398 APIGTGC 404
|
|
| PRK14897 |
PRK14897 |
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional |
908-1362 |
1.82e-12 |
|
unknown domain/DNA-directed RNA polymerase subunit A'' fusion protein; Provisional
Pssm-ID: 237853 [Multi-domain] Cd Length: 509 Bit Score: 71.38 E-value: 1.82e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 908 VNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAASSSAAV---NSIEVKNDGKIHLYNVKTIKSKdknlvavsrsGEISVT 984
Cdd:PRK14897 179 VDPYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLglpRLIEIVDARKKPSTPTMTIYLK----------KDYRED 248
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 985 DNYGKEVerykipygarittkdgqkVKRgqiistwdphthpivAEAAGIIGFEDFIDGV---TVTEQVDEltginntlim 1061
Cdd:PRK14897 249 EEKVREV------------------AKK---------------IENTTLIDVADIITDIaemSVVVELDE---------- 285
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1062 dsqkqsakskelrprarlhnakgkpiffsgtetpiiyafpsgaiiRATDGAKINAGDVIARIPLESSKTIDITGGLPRVa 1141
Cdd:PRK14897 286 ---------------------------------------------EKMKERLIEYDDILAAISKLTFKTVEIDDGIIRL- 319
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1142 dlfearKPKDAAILAKY-----------SGITSFGRetkgkvrlVITSEDGDVHEELilktrrlnIYEGESIAKGEIIAD 1210
Cdd:PRK14897 320 ------KPQQPSFKKLYllaekvksltiKGIKGIKR--------AIARKENDERRWV--------IYTQGSNLKDVLEID 377
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1211 G----ELSLHDILEIQ---GVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRVVEVENPGdtaflnkeqinksdl 1283
Cdd:PRK14897 378 EvdptRTYTNDIIEIAtvlGIEAARNAIIHEAKRTLQEQGLNVDIRHIMLVADMMTFDGSVKAIG--------------- 442
|
410 420 430 440 450 460 470
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 297172930 1284 lvvnetmqaedlepatyRHilmGItkaSLATTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFV 1362
Cdd:PRK14897 443 -----------------RH---GI---SGEKSSVLARAAFEITGKHLLRAGILGEVDKLAGVAENIIVGQPITLGTGAV 498
|
|
| RNAP_I_Rpa1_C |
cd02735 |
Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain; RNA ... |
906-1360 |
4.45e-11 |
|
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: 65.68 E-value: 4.45e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 906 NIVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGGAasssaavnsIEVkndgkihlyNVKtikskdknlVAVSRSGEISVTD 985
Cdd:cd02735 5 SLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGR---------GEM---------NVT---------LGIPRLREILMTA 57
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 986 NygkeverykipygARITT-------KDGQKVKRGQIIstwdphthpivAEAAGIIGFEDFIDGVTVTEqvdeltgINNT 1058
Cdd:cd02735 58 S-------------KNIKTpsmtlplKNGKSAERAETL-----------KKRLSRVTLSDVVEKVEVTE-------ILKT 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1059 LIMDSQKQSAKSKElrprarlhnakgkpiffsgtetpiiyafpsgaiiratdgakinagdVIARIPLESSKtIDITGGLP 1138
Cdd:cd02735 107 IERVFKKLLGKWCE----------------------------------------------VTIKLPLSSPK-LLLLSIVE 139
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1139 RvadlfEARKpkdaAILakysgitsfgRETKGKVRLVITSEDGDVHEELILKTRRLNIYegESIAKGEIIADGEL---SL 1215
Cdd:cd02735 140 K-----LARK----AVI----------REIPGITRCFVVEEDKGGKTKYLVITEGVNLA--ALWKFSDILDVNRIytnDI 198
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1216 HDILEIQGVQALSEYLVKEVQDVYRLQGVPINDKHIEVIIRQMMRvvevenPGDTAFLNKEQINKSdllvvnetmqaedl 1295
Cdd:cd02735 199 HAMLNTYGIEAARRAIVKEISNVFKVYGIAVDPRHLSLIADYMTF------EGGYRPFNRIGMESS-------------- 258
|
410 420 430 440 450 460
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 297172930 1296 epatyrhilmgitkaslatTSFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTG 1360
Cdd:cd02735 259 -------------------TSPLQKMSFETTLAFLKKATLNGDIDNLSSPSSRLVVGKPVNGGTG 304
|
|
| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
1173-1368 |
1.35e-10 |
|
DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 66.07 E-value: 1.35e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1173 RLVITSEDGDVHEELILKTRRLNIYEgesIAKGEIIADGELSLHDILEIQ---GVQALSEYLVKEVQDVYRLQGVPINDK 1249
Cdd:PRK14898 693 RVLVKKEEHENDEEYVLYTQGSNLRE---VFKIEGVDTSRTTTNNIIEIQevlGIEAARNAIINEMMNTLEQQGLEVDIR 769
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 297172930 1250 HIEVIIRQMMRVVEVENPGdtaflnkeqinksdllvvnetmqaedlepatyRHILMGITKASLATtsfisaASFQETTRV 1329
Cdd:PRK14898 770 HLMLVADIMTADGEVKPIG--------------------------------RHGVAGEKGSVLAR------AAFEETVKH 811
|
170 180 190 200
....*....|....*....|....*....|....*....|
gi 297172930 1330 LTEAAVRGSVDKLRGLKENVVVGRLVPAGTGFVQ-EIDET 1368
Cdd:PRK14898 812 LYDAAEHGEVDKLKGVIENVIVGKPIKLGTGCVDlRIDRE 851
|
|
| RNAP_largest_subunit_C |
cd00630 |
Largest subunit of RNA polymerase (RNAP), C-terminal domain; RNA polymerase (RNAP) is a large ... |
911-938 |
5.52e-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: 59.35 E-value: 5.52e-10
10 20
....*....|....*....|....*...
gi 297172930 911 GEAVGIIAAQSIGEPGTQLTMRTFHIGG 938
Cdd:cd00630 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAG 28
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| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
907-938 |
7.53e-09 |
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Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; Eukaryotic RNA polymerase III (RNAP III) is a large multi-subunit complex responsible for the synthesis of tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is also known as C160 in yeast. Structure studies suggest that different RNA polymerase complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Pssm-ID: 132723 [Multi-domain] Cd Length: 300 Bit Score: 58.77 E-value: 7.53e-09
10 20 30
....*....|....*....|....*....|..
gi 297172930 907 IVNKGEAVGIIAAQSIGEPGTQLTMRTFHIGG 938
Cdd:cd02736 6 KVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAG 37
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| RNAP_III_Rpc1_C |
cd02736 |
Largest subunit (Rpc1) of Eukaryotic RNA polymerase III (RNAP III), C-terminal domain; ... |
1299-1360 |
2.90e-06 |
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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: 50.68 E-value: 2.90e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 297172930 1299 TYRHILMGITKASLATT--SFISAASFQETTRVLTEAAVRGSVDKLRGLKENVVVGRLVPAGTG 1360
Cdd:cd02736 235 TFKGEVLGITRFGIAKMkeSVLMLASFEKTTDHLFNAALHGRKDSIEGVSECIIMGKPMPIGTG 298
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| PRK14898 |
PRK14898 |
DNA-directed RNA polymerase subunit A''; Provisional |
877-931 |
1.14e-03 |
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DNA-directed RNA polymerase subunit A''; Provisional
Pssm-ID: 237854 [Multi-domain] Cd Length: 858 Bit Score: 43.34 E-value: 1.14e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 297172930 877 ETISVRSPVTCETKHGV---CVSCYgrdlgRGNIVNKGEAVGIIAAQSIGEPGTQLTM 931
Cdd:PRK14898 25 EKLSKRDGVTEEMVEEIideVVSAY-----LNALVEPYEAVGIVAAQSIGEPGTQMSL 77
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