|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2204.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1 MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPknrEDIGLQAAFRSVFPIESYSGNAALEFVEYSLG 80
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPP---EDEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 81 KPEFDVRECILRGSTYAAPMRVKIRLIIKDretksIKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFD 160
Cdd:PRK00405 78 EPKYDVEECKERGLTYSAPLRVKLRLINKE-----TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 161 HDKGKThSSGKVLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYldmgsyq 240
Cdd:PRK00405 153 HDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 241 idlvperlrgemaqfdiadndgkviveqgkrinarhvrqmeaaglTKLSVPDEYLYERITAENITLRD-GEVIA-ANTLL 318
Cdd:PRK00405 225 ---------------------------------------------KEIEVPVEYLLGKVLAEDIVDEEtGEVLAeANDEI 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 319 SHEVmvklaeggvkqfnilftndidRGSFVADTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDL 398
Cdd:PRK00405 260 TEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDL 318
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 399 SPVGRMKFNRRLGRPYEvgtdqksrEVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLV 478
Cdd:PRK00405 319 SKVGRYKLNKKLGLDED--------EDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLS 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 479 RVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRD 558
Cdd:PRK00405 391 RMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRD 470
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 559 VHQTHYGRVCPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNL 638
Cdd:PRK00405 471 VHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRF 550
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 639 TEEFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVA 718
Cdd:PRK00405 551 VDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVA 630
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 719 RDSGVCVIANRGGAIEYVDASRIVIRVneDEMIAGEAGVDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPST 798
Cdd:PRK00405 631 RDSGAVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPST 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 799 DMGELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESG 878
Cdd:PRK00405 709 DNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESG 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 879 IVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRdglekddralaie 958
Cdd:PRK00405 789 IVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 959 kaqldayrkdlkeeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvf 1038
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1039 lkeksaeidekfaekkrkLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIV 1118
Cdd:PRK00405 856 ------------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIV 917
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1119 LNPLGVPSRMNVGQILETHLGMAAKGLGDKIekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlrag 1198
Cdd:PRK00405 918 LNPLGVPSRMNIGQILETHLGWAAKGLGIKF------------------------------------------------- 948
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1199 vplATPVFDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 1278
Cdd:PRK00405 949 ---ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPL 1025
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1279 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIEL 1358
Cdd:PRK00405 1026 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVEL 1105
|
....
gi 488043460 1359 KNGD 1362
Cdd:PRK00405 1106 LDED 1109
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1358 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 1824.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 8 KKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDVR 87
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 88 ECILRGSTYAAPMRVKIRLIIKdrETKSIKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGkTH 167
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINK--EEDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD-TT 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 168 SSGKVLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQilnlfyekvpvyldmgsyqidlvper 247
Cdd:TIGR02013 158 KSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDT-------------------------- 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 248 lrgemaqfdiadndgkviveqgkrinarhvrqmeaagltklsvpdeylyeritaenitlrdgeviaantllshevmvkla 327
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 328 eggvkqfniLFTNDIDRGSFVADTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFN 407
Cdd:TIGR02013 212 ---------LILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLN 282
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 408 RRLGRPyevgtdqkSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKER 487
Cdd:TIGR02013 283 KKLGLD--------VPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRER 354
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 488 LSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRV 567
Cdd:TIGR02013 355 MSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRI 434
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 568 CPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRV--TDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSV 645
Cdd:TIGR02013 435 CPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVA 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 646 RHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCV 725
Cdd:TIGR02013 515 RYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVI 594
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 726 IANRGGAIEYVDASRIVIRVNEDEMiAGEAGVDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELAL 805
Cdd:TIGR02013 595 VAKRGGVVEYVDAKRIVIRYDEDEE-EPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELAL 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 806 GQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAE 885
Cdd:TIGR02013 674 GRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAE 753
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 886 VTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGlekddralaiekaqlday 965
Cdd:TIGR02013 754 VKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQ------------------ 815
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 966 rkdlkeeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksae 1045
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1046 idekfaekkrklatGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVP 1125
Cdd:TIGR02013 816 --------------GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVP 881
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1126 SRMNVGQILETHLGMAAKGLGDKiekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlraGVPLATPV 1205
Cdd:TIGR02013 882 SRMNIGQILETHLGWAGKRLGRK-------------------------------------------------GVPIATPV 912
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1206 FDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFG 1285
Cdd:TIGR02013 913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488043460 1286 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIEL 1358
Cdd:TIGR02013 993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1362 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 1629.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 12 RKNFGKLPQVMDAPYLLSIQVDSYRTFLqdgktpknreDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDVRECIL 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 92 RGSTYAAPMRVKIRLIikDRETKSIKdvrEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKthsSGK 171
Cdd:COG0085 71 RDLTYAAPLYVKVRLV--NKETGEIK---EQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGK 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 172 VLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGY-NNEQILNLFYEKVPvyldmgsyqidlvperlrg 250
Cdd:COG0085 143 DLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLeTDEEILEAFGDDPI------------------- 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 251 emaqfdiadndgkviveqgkrinarhvrqmeaagltklsvpDEYLYEritaenitlrdgeviaantllshevmvklaegg 330
Cdd:COG0085 204 -----------------------------------------QEYILA--------------------------------- 209
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 331 vkqfnilftndidrgsfvadTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRL 410
Cdd:COG0085 210 --------------------TLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKL 269
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 411 GrpyeVGTDQKSRevegILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQ 490
Cdd:COG0085 270 G----LDVPPEDR----VLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT 341
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 491 AETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPI 570
Cdd:COG0085 342 QDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPI 421
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 571 ETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGE 650
Cdd:COG0085 422 ETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGE 501
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 651 FVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLvgtgmeanvardsgvcvianrg 730
Cdd:COG0085 502 EVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 731 gaieyvdasrivirvnedemiageagvDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMR 810
Cdd:COG0085 560 ---------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLL 612
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 811 VAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGD 890
Cdd:COG0085 613 VAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGD 692
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 891 ILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGlekddralaiekaqldayrkdlk 970
Cdd:COG0085 693 ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREE----------------------- 749
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 971 eeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekf 1050
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1051 aekkrklatGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNV 1130
Cdd:COG0085 750 ---------GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNV 820
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1131 GQILETHLGMAAKGLGDKIekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlragvplATPVFDGAE 1210
Cdd:COG0085 821 GQVLETHLGWAAALLGRRV----------------------------------------------------ATPVFDGAP 848
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1211 ESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG 1290
Cdd:COG0085 849 EEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFG 928
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488043460 1291 EMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362
Cdd:COG0085 929 EMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1359 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 876.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 27 LLSIQVDSYRTFLQDGktpknredigLQAAFRSVFPIESYS--GNAALEFVEYSLGKP---------EFDVRECILRGST 95
Cdd:cd00653 1 LVKQQIDSFNYFLNVG----------LQEIVKSIPPITDTDddGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 96 YAAPMRVKIRLIIKDREtksikDVREQEVYMGEIPLMTE------------------------NGTFVINGTERVIVSQL 151
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG-----KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 152 HRSPGVFFDHDkgkthSSGKVLYSARIIP----YRGSWLDFEFDAKDlvyvridrrrkllatvvlralgynneqilnlfy 227
Cdd:cd00653 146 QRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKK--------------------------------- 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 228 ekvpvyldmgsyqidlvperlrgemaqfdiadndgkviveqgKRINARHvrqmeaagltklsvpdeylyeritaenitlr 307
Cdd:cd00653 188 ------------------------------------------DRIYVRI------------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 308 dgeviaantllshevmvklaeggvkqfnilftnDIDRgsfvadtlradttagREEALVEIYKvmrpgepptkeaaenlfn 387
Cdd:cd00653 195 ---------------------------------DLKR---------------QEEALKYIGK------------------ 208
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 388 nlffsserydlspvgrmKFnrrlgrpyevgtdqksrevegilshEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGE 467
Cdd:cd00653 209 -----------------RF-------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGE 246
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 468 MTENQFRVGLVRVERAVKERLSQA--ETDNLSPQDLINAKPVAAAIKEFFGSSQ------------LSQFMDQNNPLSEI 533
Cdd:cd00653 247 LLQNLFRSGLKRLEREVKEKLQKQlsKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSEL 326
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 534 THKRRVSAlgpGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANdfGFLETPYRKVVdgrvtdave 613
Cdd:cd00653 327 SHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE--------- 392
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 614 ylsaieevgtviaqadsavdkdgnlteefvsvrhqgefvrmppEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSN 693
Cdd:cd00653 393 -------------------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSN 429
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 694 MQRQAVPT----------------LRADKPLVGTGMEANVARDsgvcvianrggaieyvdasrivirvnedemiageagv 757
Cdd:cd00653 430 MQKQAVGTpalnqqyrmdtklyllLYPQKPLVGTGIEEYIAFG------------------------------------- 472
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 758 diynlikytrsnqntcinqniivnlgdkvargdiladgpstdmgELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRL 837
Cdd:cd00653 473 --------------------------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFF 508
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 838 TSIHIQELSCVARDTKLGAEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTAGDILVGKVTPKGETQLTPeekllraIFG 916
Cdd:cd00653 509 RSIHYKKYEIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFG 581
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 917 EKAADVKDSSLRVPSGTKGTVIDVQVFTRdglekddralaiekaqldayrkdlkeeykifeeaarervirllkgqesngg 996
Cdd:cd00653 582 EKARDVRDTSLKYPGGEKGIVDDVKIFSR--------------------------------------------------- 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 997 gstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfaekkrklatgdELTTGVLKVVKVYLA 1076
Cdd:cd00653 611 -----------------------------------------------------------------ELNDGGNKLVKVYIR 625
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1077 VKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAkglgdkiekmlkeq 1156
Cdd:cd00653 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAG-------------- 691
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1157 rtvlelrefldkiynkvggeqedldsltdaevlALSGNLRAGvplatPVFDGAEESQIKDLLELAGISRTGQTVLFDGRT 1236
Cdd:cd00653 692 ---------------------------------ALLGKFGDA-----TPFDGAEEEDISELLGEAGLNYYGKEVLYDGRT 733
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1237 GEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1316
Cdd:cd00653 734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDD 813
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|...
gi 488043460 1317 VEGRTRIYKNIV----------DGNHYMDPGMPESFNVLTKEIRSLGINIELK 1359
Cdd:cd00653 814 VVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
726-1283 |
1.35e-161 |
|
RNA polymerase Rpb2, domain 6; 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 488.96 E-value: 1.35e-161
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 726 IANRGGAIEYVDASRIVIRVNEdemiaGEAGVDIYNLIKYTRSNQNT---CINQNIIVNLGdKVARGDiladgpstdMGE 802
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 803 LALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQElsCVARDTKLGA-EEITADIPNVGEAALSKLDESGIVY 881
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 882 IGAEVTAGDILVGKVtpkGETQLTpeeKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTrdglekddralaiekaq 961
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE----------------- 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 962 ldayrkdlkeeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflke 1041
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1042 ksaeidekfaekkrklatgdeLTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNP 1121
Cdd:pfam00562 201 ---------------------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1122 LGVPSRMNVGQILETHLGMAAKGLgdkiekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlraGVPL 1201
Cdd:pfam00562 260 HGVPSRMTIGQLLETHLGKAAALL----------------------------------------------------GVFV 287
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1202 ATPVFDGA--EESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG 1279
Cdd:pfam00562 288 DATPFDGAstEVEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLG 367
|
....
gi 488043460 1280 GKAQ 1283
Cdd:pfam00562 368 GRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2204.14 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1 MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPknrEDIGLQAAFRSVFPIESYSGNAALEFVEYSLG 80
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPP---EDEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 81 KPEFDVRECILRGSTYAAPMRVKIRLIIKDretksIKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFD 160
Cdd:PRK00405 78 EPKYDVEECKERGLTYSAPLRVKLRLINKE-----TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 161 HDKGKThSSGKVLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYldmgsyq 240
Cdd:PRK00405 153 HDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 241 idlvperlrgemaqfdiadndgkviveqgkrinarhvrqmeaaglTKLSVPDEYLYERITAENITLRD-GEVIA-ANTLL 318
Cdd:PRK00405 225 ---------------------------------------------KEIEVPVEYLLGKVLAEDIVDEEtGEVLAeANDEI 259
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 319 SHEVmvklaeggvkqfnilftndidRGSFVADTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDL 398
Cdd:PRK00405 260 TEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDL 318
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 399 SPVGRMKFNRRLGRPYEvgtdqksrEVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLV 478
Cdd:PRK00405 319 SKVGRYKLNKKLGLDED--------EDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLS 390
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 479 RVERAVKERLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRD 558
Cdd:PRK00405 391 RMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRD 470
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 559 VHQTHYGRVCPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNL 638
Cdd:PRK00405 471 VHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRF 550
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 639 TEEFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVA 718
Cdd:PRK00405 551 VDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVA 630
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 719 RDSGVCVIANRGGAIEYVDASRIVIRVneDEMIAGEAGVDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPST 798
Cdd:PRK00405 631 RDSGAVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPST 708
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 799 DMGELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESG 878
Cdd:PRK00405 709 DNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESG 788
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 879 IVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRdglekddralaie 958
Cdd:PRK00405 789 IVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 959 kaqldayrkdlkeeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvf 1038
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1039 lkeksaeidekfaekkrkLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIV 1118
Cdd:PRK00405 856 ------------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIV 917
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1119 LNPLGVPSRMNVGQILETHLGMAAKGLGDKIekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlrag 1198
Cdd:PRK00405 918 LNPLGVPSRMNIGQILETHLGWAAKGLGIKF------------------------------------------------- 948
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1199 vplATPVFDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 1278
Cdd:PRK00405 949 ---ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPL 1025
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1279 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIEL 1358
Cdd:PRK00405 1026 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVEL 1105
|
....
gi 488043460 1359 KNGD 1362
Cdd:PRK00405 1106 LDED 1109
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1358 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit of Bacterial RNA polymerase. The core enzyme consists of two alpha chains, one beta chain, and one beta' subunit. [Transcription, DNA-dependent RNA polymerase]
Pssm-ID: 273928 [Multi-domain] Cd Length: 1065 Bit Score: 1824.66 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 8 KKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQDGKTPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDVR 87
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 88 ECILRGSTYAAPMRVKIRLIIKdrETKSIKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGkTH 167
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINK--EEDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD-TT 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 168 SSGKVLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQilnlfyekvpvyldmgsyqidlvper 247
Cdd:TIGR02013 158 KSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDT-------------------------- 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 248 lrgemaqfdiadndgkviveqgkrinarhvrqmeaagltklsvpdeylyeritaenitlrdgeviaantllshevmvkla 327
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 328 eggvkqfniLFTNDIDRGSFVADTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFN 407
Cdd:TIGR02013 212 ---------LILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRYKLN 282
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 408 RRLGRPyevgtdqkSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKER 487
Cdd:TIGR02013 283 KKLGLD--------VPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRER 354
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 488 LSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRV 567
Cdd:TIGR02013 355 MSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRI 434
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 568 CPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRV--TDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSV 645
Cdd:TIGR02013 435 CPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVA 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 646 RHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCV 725
Cdd:TIGR02013 515 RYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVI 594
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 726 IANRGGAIEYVDASRIVIRVNEDEMiAGEAGVDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELAL 805
Cdd:TIGR02013 595 VAKRGGVVEYVDAKRIVIRYDEDEE-EPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELAL 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 806 GQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAE 885
Cdd:TIGR02013 674 GRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAE 753
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 886 VTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGlekddralaiekaqlday 965
Cdd:TIGR02013 754 VKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQ------------------ 815
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 966 rkdlkeeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksae 1045
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1046 idekfaekkrklatGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVP 1125
Cdd:TIGR02013 816 --------------GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVP 881
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1126 SRMNVGQILETHLGMAAKGLGDKiekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlraGVPLATPV 1205
Cdd:TIGR02013 882 SRMNIGQILETHLGWAGKRLGRK-------------------------------------------------GVPIATPV 912
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1206 FDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFG 1285
Cdd:TIGR02013 913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488043460 1286 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIEL 1358
Cdd:TIGR02013 993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1362 |
0e+00 |
|
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA polymerase, beta subunit/140 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439855 [Multi-domain] Cd Length: 1001 Bit Score: 1629.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 12 RKNFGKLPQVMDAPYLLSIQVDSYRTFLqdgktpknreDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDVRECIL 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 92 RGSTYAAPMRVKIRLIikDRETKSIKdvrEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKthsSGK 171
Cdd:COG0085 71 RDLTYAAPLYVKVRLV--NKETGEIK---EQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGK 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 172 VLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGY-NNEQILNLFYEKVPvyldmgsyqidlvperlrg 250
Cdd:COG0085 143 DLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLeTDEEILEAFGDDPI------------------- 203
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 251 emaqfdiadndgkviveqgkrinarhvrqmeaagltklsvpDEYLYEritaenitlrdgeviaantllshevmvklaegg 330
Cdd:COG0085 204 -----------------------------------------QEYILA--------------------------------- 209
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 331 vkqfnilftndidrgsfvadTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRL 410
Cdd:COG0085 210 --------------------TLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKL 269
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 411 GrpyeVGTDQKSRevegILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQ 490
Cdd:COG0085 270 G----LDVPPEDR----VLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTT 341
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 491 AETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPI 570
Cdd:COG0085 342 QDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPI 421
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 571 ETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGE 650
Cdd:COG0085 422 ETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGE 501
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 651 FVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLvgtgmeanvardsgvcvianrg 730
Cdd:COG0085 502 EVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL---------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 731 gaieyvdasrivirvnedemiageagvDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMR 810
Cdd:COG0085 560 ---------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLL 612
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 811 VAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGD 890
Cdd:COG0085 613 VAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGD 692
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 891 ILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGlekddralaiekaqldayrkdlk 970
Cdd:COG0085 693 ILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREE----------------------- 749
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 971 eeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekf 1050
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1051 aekkrklatGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNV 1130
Cdd:COG0085 750 ---------GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNV 820
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1131 GQILETHLGMAAKGLGDKIekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlragvplATPVFDGAE 1210
Cdd:COG0085 821 GQVLETHLGWAAALLGRRV----------------------------------------------------ATPVFDGAP 848
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1211 ESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG 1290
Cdd:COG0085 849 EEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFG 928
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488043460 1291 EMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362
Cdd:COG0085 929 EMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSED 1000
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-1358 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1427.78 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1 MAYSYTEKKRIRKNFGKLPQVMDAPYLLSIQVDSYRTFLQdgktPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLG 80
Cdd:PRK09603 1 MSKKIPLKNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLY----SKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFG 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 81 KPEFDVRECILRGSTYAAPMRVKIRLIIKDRETKS-----IKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSP 155
Cdd:PRK09603 77 KSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSgekngIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSP 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 156 GVFFDHDKGKThSSGKVLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLD 235
Cdd:PRK09603 157 GVIFKEEESST-SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYE 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 236 MGSYQIDLVPERLRGEMaQFDIADNDGKVIVEQGKRINARHVRQMEAAGLTKLSVPDEYLYERITAENITlrDGEVIAAN 315
Cdd:PRK09603 236 NDKYLIPFASLDANQRM-EFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVM--VGKEVLLD 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 316 TL--LSHEVMVKLAEGGVKQFNIlfTNDIDRG-------SFVADT-----LRADTTAGREEAL--VEIYKVMRPGEPPTK 379
Cdd:PRK09603 313 MLtqLDKNKLEKIHDLGVQEFVI--INDLALGhdasiihSFSADSeslklLKQTEKIDDENALaaIRIHKVMKPGDPVTT 390
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 380 EAAENLFNNLFFSSERYDLSPVGRMKFNRRLGrpYEVgtdqksREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGN 459
Cdd:PRK09603 391 EVAKQFVKKLFFDPERYDLTMVGRMKMNHKLG--LHV------PDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGN 462
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 460 RRVRSVGEMTENQFRVGLVRVERAVKERLS--QAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKR 537
Cdd:PRK09603 463 RRIRAVGELLANELHSGLVKMQKTIKDKLTtmSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKR 542
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 538 RVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSA 617
Cdd:PRK09603 543 RLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTA 622
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 618 IEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQ 697
Cdd:PRK09603 623 IQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQ 702
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 698 AVPTLRADKPLVGTGMEANVARDSGVCVIANRGGAIEYVDASRIVIrVNEDEmiaGEAGVDIYNLIKYTRSNQNTCINQN 777
Cdd:PRK09603 703 AVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGK---EEAYIDAYSLQKNLRTNQNTSFNQV 778
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 778 IIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAE 857
Cdd:PRK09603 779 PIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVE 858
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 858 EITADIPNVGEAALSKLDESGIVYIGAEVTAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTV 937
Cdd:PRK09603 859 EFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTV 938
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 938 IDVQVFTRDGLEKDDRALAI---EKAQLDAyrkdlkEEYKIFEEAARERVIRL--------LKGQESNGGGSTKRGDKLV 1006
Cdd:PRK09603 939 IDVKVFTKKGYEKDARVLSAyeeEKAKLDM------EHFDRLTMLNREELLRVssllsqaiLEEPFSHNGKDYKEGDQIP 1012
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1007 EEVLSGLELVDLLE-IQPADEAIAERLTQIQVFLKEKSAEIDEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGD 1085
Cdd:PRK09603 1013 KEEIASINRFTLASlVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGD 1092
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1086 KMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAKGLGDKIEKMLKEQRT--VLELR 1163
Cdd:PRK09603 1093 KMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfAKELR 1172
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1164 ----EFLDKIYNKVGGEQEDLDSLTDAEVLALSGNLRAGVPLATPVFDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQ 1239
Cdd:PRK09603 1173 akmlEIANAINEKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEK 1252
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1240 FDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVEG 1319
Cdd:PRK09603 1253 MRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRG 1332
|
1370 1380 1390
....*....|....*....|....*....|....*....
gi 488043460 1320 RTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIEL 1358
Cdd:PRK09603 1333 RENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINI 1371
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
27-1362 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1378.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 27 LLSIQVDSYRTFlqdgkTPKNREDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDVRECILRGSTYAAPMRVKIRL 106
Cdd:PRK14844 32 LVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 107 IIKD-----RETKSIKD-------------VREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHS 168
Cdd:PRK14844 107 VIMQdgislDEYKSIKEsgdhsklatviksIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYN 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 169 SGKVLYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQILNLFYEKVPVYLDMGSYQIDLVPERL 248
Cdd:PRK14844 187 SGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKF 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 249 RGEMAQFDIADNDGKVIVEQGKRINARHVRQMEAAGLTKLSVPDEYLYERITAENI--TLRDGEVIAANTLLSHEVMVKL 326
Cdd:PRK14844 267 KGVRLPFDLMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLidSASSTKILSAGESIKLEDIKKL 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 327 AEGGVKQFNILFTNDIDRGSFVADTLRADTTAGREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKF 406
Cdd:PRK14844 347 ELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKL 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 407 NRRLGRPYEvgtdqksrEVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKE 486
Cdd:PRK14844 427 NSYLGLNYD--------EDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVD 498
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 487 RLSQAETDNLSPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGR 566
Cdd:PRK14844 499 SMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGR 578
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 567 VCPIETPEGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVR 646
Cdd:PRK14844 579 ICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCR 658
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 647 HQGEFVRMPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCVI 726
Cdd:PRK14844 659 YAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVL 738
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 727 ANRGGAIEYVDASRIVIRVNEDEMIaGEAGVDIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALG 806
Cdd:PRK14844 739 AKRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALG 817
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 807 QNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEV 886
Cdd:PRK14844 818 QNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRV 897
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 887 TAGDILVGKVTPKGETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDDRALAIEKAQLDayr 966
Cdd:PRK14844 898 GPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEIN--- 974
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 967 kDLKEEYKIFEEAARERVIRLLKGQESNGGGSTKrgdklveEVLSGLELVDLLEIQPADEAIAERLTQIQVFLKEKSAEI 1046
Cdd:PRK14844 975 -DFEKERDYIINVTSEYFYDELKKLLINSGSQDR-------EKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHA 1046
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1047 DEKFAEKKRKLATGDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPS 1126
Cdd:PRK14844 1047 IAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPS 1126
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1127 RMNVGQILETHLGMAAKGLGDKIEKML----------------------------------------------------- 1153
Cdd:PRK14844 1127 RMNVGQILETHVGWACKKLGEKVGNILdeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnk 1206
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1154 ----KEQRTVLE------------LREFLDKIYNkVGGEQE---DLDSLTDAEVLALSGNLRAGVPLATPVFDGAEESQI 1214
Cdd:PRK14844 1207 nalnDELNELVEnylnscksaysnLRNFLIEVYS-CGSNVSicnNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQI 1285
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1215 KDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1294
Cdd:PRK14844 1286 AKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMEC 1365
|
1370 1380 1390 1400 1410 1420
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488043460 1295 WALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKNGD 1362
Cdd:PRK14844 1366 WALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQND 1433
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
25-1360 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1065.09 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 25 PYLLSIQVDSYRTFLQDGktpknredigLQAAFRSVFPIESYSGNAALEFV--EYSLGKPEFDVRECILRGSTYAAPMRV 102
Cdd:CHL00207 8 PDFLEIQRTSFCWFLNEG----------LNEELNIFSKIFDYTGNLELLLFgkNYKLKYPKYNLLSAKSYDSNYSIQIYL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 103 KIRLIIKDretksIKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDHDKGKTHssgKVLYSARIIPYR 182
Cdd:CHL00207 78 PLKFINLK-----TNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLIPNR 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 183 GSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQIL-NLFYEKVPVYLDMGSYQIDLVPerlrgemaqfdiadnd 261
Cdd:CHL00207 150 GSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYsRLTKSEFLKKLKPILLNSNSYT---------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 262 gkviveqgkrinarhvrqmeaagltklsvpdeylyeritaenitlrdgeviaantllshevmvklaeggvkqfnilftnd 341
Cdd:CHL00207 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 342 idrgsfvadtlradttagREEALVEIYKVMRPGEPPTKEAAENLFNNLFFSSERYDLSPVGRMKFNRRLgrpyevgtDQK 421
Cdd:CHL00207 214 ------------------NEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKL--------NLN 267
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 422 SREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQAETDNLSPQDL 501
Cdd:CHL00207 268 IPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNL 347
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 502 INAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLI 581
Cdd:CHL00207 348 INPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLI 427
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 582 NSLSVYAKANDFGFLETPYRKVVDGRV--TDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFVRMPPEKV 659
Cdd:CHL00207 428 GSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKV 507
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 660 THMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCVIANRGGAIEYVDAS 739
Cdd:CHL00207 508 DFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAY 587
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 740 RIVIRVNEDEMIageagvdIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAFMTWNGY 819
Cdd:CHL00207 588 KIIIQDDNNRYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGY 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 820 NYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDILVGKVTPK 899
Cdd:CHL00207 661 NFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPK 740
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 900 GETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDglekddralaiekaqldayrkdlkeeykifeea 979
Cdd:CHL00207 741 GESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS--------------------------------- 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 980 arervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfaekkrklaT 1059
Cdd:CHL00207 788 -------------------------------------------------------------------------------K 788
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1060 GDELTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLG 1139
Cdd:CHL00207 789 GDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLG 868
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1140 MAakglGDKIEKMLKeqrtVLELREFLDKIYNKVggeqedldsltdaevlaLSGN-LRagvplatpvfdgaEESQIKDLL 1218
Cdd:CHL00207 869 LA----GDNLNKRFK----ILPFDEMYGSEYSRI-----------------LINNkLN-------------QASIKNNEY 910
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1219 ELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1298
Cdd:CHL00207 911 WLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALE 990
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 488043460 1299 AYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDPGMPESFNVLTKEIRSLGINIELKN 1360
Cdd:CHL00207 991 AFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEAYK 1052
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
25-1357 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1053.73 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 25 PYLLSIQVDSYRTFLqdgktpknreDIGLQAAFRSVFPIESYSGNAALEFV--EYSLGKPEFDVRECILRGSTYAAPMRV 102
Cdd:CHL00001 13 PGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTDQEIEFQLFveTYQLVEPLIKERDAVYESLTYSSELYV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 103 KIRLIIKDRetksiKDVREQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFF----DHdkgkthsSGKVLYSARI 178
Cdd:CHL00001 83 PAGLIWKKS-----RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYrselDH-------NGISVYTGTI 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 179 IPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALGYNNEQIL-NLFYekvpvyldmgsyqidlvPERLrgemaqfdi 257
Cdd:CHL00001 151 ISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILdNVCY-----------------PEIF--------- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 258 adndgkviveqgkrinarhvrqmeaagltkLSVPDEYLYERITaenitlrdgeviaantllshevmvklaeggvkqfnil 337
Cdd:CHL00001 205 ------------------------------LSFLNDKEKKKIG------------------------------------- 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 338 ftndidrgsfvadtlradttaGREEALVEIYK--VMRPGEPPTKEAAENLFNNLFFSSeRYDLSPVGRMKFNRRLGRPye 415
Cdd:CHL00001 218 ---------------------SKENAILEFYQqfACVGGDPVFSESLCKELQKKFFQQ-RCELGRIGRRNMNRKLNLD-- 273
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 416 vgtdqkSREVEGILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQAETDN 495
Cdd:CHL00001 274 ------IPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRK 347
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 496 L--SPQDLINAKPVAAAIKEFFGSSQLSQFMDQNNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHQTHYGRVCPIETP 573
Cdd:CHL00001 348 LipTPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTS 427
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 574 EGPNIGLINSLSVYAKANDFGFLETPYRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFVR 653
Cdd:CHL00001 428 EGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLT 507
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 654 MPPEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRADKPLVGTGMEANVARDSGVCVIANRGGAI 733
Cdd:CHL00001 508 IAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKI 587
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 734 EYVDASRIVIRVNEDEMiageagvdIYNLIKYTRSNQNTCINQNIIVNLGDKVARGDILADGPSTDMGELALGQNMRVAF 813
Cdd:CHL00001 588 IYTDTDKIILSGNGDTL--------SIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAY 659
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 814 MTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVARDTKLGAEEITADIPNVGEAALSKLDESGIVYIGAEVTAGDILV 893
Cdd:CHL00001 660 MPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILV 739
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 894 GKVTPK--GETQLTPEEKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTRDGLEKDDRalaiekaqldayrkdlke 971
Cdd:CHL00001 740 GKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVRWIQKKGGSSYNP------------------ 801
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 972 eykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfa 1051
Cdd:CHL00001 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1052 ekkrklatgdelttgvlKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVG 1131
Cdd:CHL00001 802 -----------------ETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVG 864
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1132 QILETHLGMAAkglgdkieKMLKEQRTVLElrefLDKIYnkvggEQEdldsltDAEVLALSGNLRAGVPLATP-VFDgae 1210
Cdd:CHL00001 865 QIFECLLGLAG--------DLLNRHYRIAP----FDERY-----EQE------ASRKLVFSELYEASKQTANPwVFE--- 918
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1211 esqikdlLELAGISRtgqtvLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG 1290
Cdd:CHL00001 919 -------PEYPGKSR-----LFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVG 986
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488043460 1291 EMEVWALEAYGAAYTLQEMLTVKSDDVEGRTRIYKNIVDGNHYMDP-GMPESFNVLTKEIRSLGINIE 1357
Cdd:CHL00001 987 EMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 1054
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1359 |
0e+00 |
|
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Each RNA polymerase complex contains two related members of this family, in each case they are the two largest subunits.The clamp is a mobile structure that grips DNA during elongation.
Pssm-ID: 238353 [Multi-domain] Cd Length: 866 Bit Score: 876.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 27 LLSIQVDSYRTFLQDGktpknredigLQAAFRSVFPIESYS--GNAALEFVEYSLGKP---------EFDVRECILRGST 95
Cdd:cd00653 1 LVKQQIDSFNYFLNVG----------LQEIVKSIPPITDTDddGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 96 YAAPMRVKIRLIIKDREtksikDVREQEVYMGEIPLMTE------------------------NGTFVINGTERVIVSQL 151
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG-----KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 152 HRSPGVFFDHDkgkthSSGKVLYSARIIP----YRGSWLDFEFDAKDlvyvridrrrkllatvvlralgynneqilnlfy 227
Cdd:cd00653 146 QRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKK--------------------------------- 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 228 ekvpvyldmgsyqidlvperlrgemaqfdiadndgkviveqgKRINARHvrqmeaagltklsvpdeylyeritaenitlr 307
Cdd:cd00653 188 ------------------------------------------DRIYVRI------------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 308 dgeviaantllshevmvklaeggvkqfnilftnDIDRgsfvadtlradttagREEALVEIYKvmrpgepptkeaaenlfn 387
Cdd:cd00653 195 ---------------------------------DLKR---------------QEEALKYIGK------------------ 208
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 388 nlffsserydlspvgrmKFnrrlgrpyevgtdqksrevegilshEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGE 467
Cdd:cd00653 209 -----------------RF-------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGE 246
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 468 MTENQFRVGLVRVERAVKERLSQA--ETDNLSPQDLINAKPVAAAIKEFFGSSQ------------LSQFMDQNNPLSEI 533
Cdd:cd00653 247 LLQNLFRSGLKRLEREVKEKLQKQlsKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSEL 326
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 534 THKRRVSAlgpGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAKANdfGFLETPYRKVVdgrvtdave 613
Cdd:cd00653 327 SHKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE--------- 392
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 614 ylsaieevgtviaqadsavdkdgnlteefvsvrhqgefvrmppEKVTHMDVSAQQVVSVAASLIPFLEHDDANRALMGSN 693
Cdd:cd00653 393 -------------------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSN 429
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 694 MQRQAVPT----------------LRADKPLVGTGMEANVARDsgvcvianrggaieyvdasrivirvnedemiageagv 757
Cdd:cd00653 430 MQKQAVGTpalnqqyrmdtklyllLYPQKPLVGTGIEEYIAFG------------------------------------- 472
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 758 diynlikytrsnqntcinqniivnlgdkvargdiladgpstdmgELALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRL 837
Cdd:cd00653 473 --------------------------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFF 508
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 838 TSIHIQELSCVARDTKLGAEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTAGDILVGKVTPKGETQLTPeekllraIFG 916
Cdd:cd00653 509 RSIHYKKYEIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFG 581
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 917 EKAADVKDSSLRVPSGTKGTVIDVQVFTRdglekddralaiekaqldayrkdlkeeykifeeaarervirllkgqesngg 996
Cdd:cd00653 582 EKARDVRDTSLKYPGGEKGIVDDVKIFSR--------------------------------------------------- 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 997 gstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfaekkrklatgdELTTGVLKVVKVYLA 1076
Cdd:cd00653 611 -----------------------------------------------------------------ELNDGGNKLVKVYIR 625
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1077 VKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILETHLGMAAkglgdkiekmlkeq 1156
Cdd:cd00653 626 QKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAG-------------- 691
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1157 rtvlelrefldkiynkvggeqedldsltdaevlALSGNLRAGvplatPVFDGAEESQIKDLLELAGISRTGQTVLFDGRT 1236
Cdd:cd00653 692 ---------------------------------ALLGKFGDA-----TPFDGAEEEDISELLGEAGLNYYGKEVLYDGRT 733
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1237 GEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDD 1316
Cdd:cd00653 734 GEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDD 813
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|...
gi 488043460 1317 VEGRTRIYKNIV----------DGNHYMDPGMPESFNVLTKEIRSLGINIELK 1359
Cdd:cd00653 814 VVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
726-1283 |
1.35e-161 |
|
RNA polymerase Rpb2, domain 6; 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 represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 488.96 E-value: 1.35e-161
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 726 IANRGGAIEYVDASRIVIRVNEdemiaGEAGVDIYNLIKYTRSNQNT---CINQNIIVNLGdKVARGDiladgpstdMGE 802
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 803 LALGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQElsCVARDTKLGA-EEITADIPNVGEAALSKLDESGIVY 881
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 882 IGAEVTAGDILVGKVtpkGETQLTpeeKLLRAIFGEKAADVKDSSLRVPSGTKGTVIDVQVFTrdglekddralaiekaq 961
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE----------------- 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 962 ldayrkdlkeeykifeeaarervirllkgqesngggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflke 1041
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1042 ksaeidekfaekkrklatgdeLTTGVLKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNP 1121
Cdd:pfam00562 201 ---------------------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1122 LGVPSRMNVGQILETHLGMAAKGLgdkiekmlkeqrtvlelrefldkiynkvggeqedldsltdaevlalsgnlraGVPL 1201
Cdd:pfam00562 260 HGVPSRMTIGQLLETHLGKAAALL----------------------------------------------------GVFV 287
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1202 ATPVFDGA--EESQIKDLLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG 1279
Cdd:pfam00562 288 DATPFDGAstEVEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLG 367
|
....
gi 488043460 1280 GKAQ 1283
Cdd:pfam00562 368 GRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1362 |
1.71e-86 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 306.50 E-value: 1.71e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 31 QVDSYRTFLqdgktpknreDIGLQAAFRSVFPIESYSGNAALEFVEYSLGKPEFDV----------RECILRGSTYAAPM 100
Cdd:PRK08565 18 HLDSYNDFI----------ERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEadgserpitpMEARLRNLTYAAPL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 101 RVKIRLIIKDRETKsikdvrEQEVYMGEIPLMTEN------------------------GTFVINGTERVIVSQLHRSPG 156
Cdd:PRK08565 88 YLTMIPVENGIEYE------PEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPN 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 157 -VFFDHDKgkthSSGKVLYSARIIPYRGSWLdfefdakdlVYVRIDRRRKLLATVVLRALGYnneqilnlfyeKVPVyld 235
Cdd:PRK08565 162 rVLVDKGE----AGSSITHTAKVISSRAGYR---------AQVTVERRKDGTIYVSFPAVPG-----------KIPF--- 214
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 236 mgsyqidlvperlrgemaqfdiadndgkVIVeqgkrinarhvrqMEAAGLtklsvpdeylyeritaenitLRDGEVIAAn 315
Cdd:PRK08565 215 ----------------------------VIL-------------MRALGL--------------------ETDRDIVYA- 232
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 316 TLLSHEVMvklaeggvkqfNILFTNdIDRGSFVADTlradttagREEALVEIYKVMRPGEPPTK--EAAENLFNNLFFss 393
Cdd:PRK08565 233 VSLDPEIQ-----------QELLPS-LEQASSIAAT--------VEDALDYIGKRVAIGQPREYriERAEQILDKYLL-- 290
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 394 erydlspvgrmkfnrrlgrPYeVGTDQKSREVEGILshedIIDVLRTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQF 473
Cdd:PRK08565 291 -------------------PH-LGTSPEDRIKKAYF----LGQMASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELF 346
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 474 RVGLVRVERAVKERL--SQAETDNLSPQDLINAKPVAAAIKEFF-------GSSQLSQFMDQNNPLSEITHKRRVsaLGP 544
Cdd:PRK08565 347 RVAFKQLVKDLKYQLekSYARGRKLDLRAIVRPDIITERIRHALatgnwvgGRTGVSQLLDRTNYLSTLSHLRRV--VSP 424
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 545 ggLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSL-------------SVYAKANDFGF------LETPY----R 601
Cdd:PRK08565 425 --LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLalmaqisvgvdeeEVEEILYELGVvpveeaREEEYiswsR 502
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 602 KVVDGR----VTDAVEYLSAI--------------------EEVGTVIAQADSA-------VDKDGN--LTEEFVSVRHQ 648
Cdd:PRK08565 503 VYLNGRligyHPDGEELAEKIrelrrsgkisdevnvayietGEINEVYVNCDSGrvrrpliVVENGKpkLTREHVEKLKK 582
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 649 GEF-----VRM------------------PPEKV----THMDVSAQQVVSVAASLIPFLEHDDANRALMGSNMQRQA--V 699
Cdd:PRK08565 583 GELtfddlVKMgvieyldaeeeenayvalDPEDLtpehTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSlgL 662
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 700 PT----LRAD----------KPLVGT-GMEanvardsgvcvianrggaieyvdasrivirvnedemiageagvdiynLIK 764
Cdd:PRK08565 663 YAanfrIRTDtrghllhypqRPLVQTrALE-----------------------------------------------IIG 695
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 765 YTrsnqntcinqniivnlgdkvargdilaDGPStdmgelalGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQE 844
Cdd:PRK08565 696 YN---------------------------DRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRT 740
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 845 LSCVARDTKLGAE-EITADIPNV----GEAALSKLDESGIVYIGAEVTAGDILVGKVTPKgetQLTPEEKLLRAIFGEKa 919
Cdd:PRK08565 741 YETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER- 816
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 920 advKDSSLRVPSGTKGtVIDVQVFTrdglekddralaiekaqldayrkdlkeeykifeeaarervirllkgqESNGGGst 999
Cdd:PRK08565 817 ---RDTSVTVRHGEKG-IVDTVLIT-----------------------------------------------ESPEGN-- 843
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1000 krgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfaekkrklatgdelttgvlKVVKVYLAVKR 1079
Cdd:PRK08565 844 ---------------------------------------------------------------------KLVKVRVRDLR 854
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1080 RIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILEThlgMAAKglgdkiekmlkeqrtv 1159
Cdd:PRK08565 855 IPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES---IAGK---------------- 915
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1160 lelrefldkiynkvggeqedldsltdaeVLALSGNLRAGVPlatpvFDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQ 1239
Cdd:PRK08565 916 ----------------------------VAALEGRFVDATP-----FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEK 962
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1240 FDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdveg 1319
Cdd:PRK08565 963 IKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD---- 1038
|
1450 1460 1470 1480 1490 1500
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 488043460 1320 RTRIY--------------KNIVDGNHYMDPG------MPESFNVLTKEIRSLGINIELKNGD 1362
Cdd:PRK08565 1039 KTTIYvcelcghiawydrrKNKYVCPIHGDKGnispveVSYAFKLLLQELMSMGISPRLKLGD 1101
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
26-509 |
3.61e-73 |
|
RNA polymerase beta subunit; 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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 249.60 E-value: 3.61e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 26 YLLSIQVDSYRTFLQDgkTPKnrEDIGLQAAFRSVFPIESYSGNAA---LEFVEYSLGKPEFDVR----------ECILR 92
Cdd:pfam04563 1 GLVRQQLDSFNEFVDN--DLQ--KIIDENALIESEFEIQHPGENGDklsLKFGQIRLGKPMFDETdgstreiypqECRLR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 93 GSTYAAPMRVKIRLIIKDREtksikDVREQEVYMGEIPLMTEN------------------------GTFVINGTERVIV 148
Cdd:pfam04563 77 NLTYSAPLYVDLELSVYNGE-----DIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIV 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 149 SQLHRS---PGVFFDHDKGKTHSSGKVLYSARI--IPYRGSWLDF-EFDAKDLVYVRIDRRRKLL-ATVVLRALGYNNEQ 221
Cdd:pfam04563 152 AQEHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKEIpIVIILRALGFTSDR 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 222 ILnlfYEKVPVYLDMGSYQIDLVPErlrgemaqfdiadndgkviVEQGKRINArhvrqmeaaglTKLSVPDEYLYERITA 301
Cdd:pfam04563 232 EI---FELICYDVNDQQLQEELLPS-------------------LEEGFKIRI-----------QTQEQALDYIGGRGRA 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 302 enitlrdgeviaantllshevmvklaeggvkqfnilftndidrgsfvadtlradttagreealveIYKVMRPGEPPTKEA 381
Cdd:pfam04563 279 -----------------------------------------------------------------IFRMGRPREPRIKYA 293
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 382 AENLFNNLFFSSERYDLSPVGRMKFnrrlgrpyevgtdqksrevegilshedIIDVLRTLVEIRNGKGEVDDIDHLGNRR 461
Cdd:pfam04563 294 EEILQKEVLPHLGTYELDETKKAYF---------------------------IGYMIRRLLLLALGRREVDDRDHLGNKR 346
|
490 500 510 520 530
....*....|....*....|....*....|....*....|....*....|
gi 488043460 462 VRSVGEMTENQFRVGLVRVERAVKERL--SQAETDNLSPQDLINAKPVAA 509
Cdd:pfam04563 347 LRLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
611-1362 |
3.73e-57 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 209.50 E-value: 3.73e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 611 AVEYLSAIEEVGTVIAQADSavdkdgNLTEEFvsvrhqgefvrmppekvTHMDVSAQQVVSVAASLIPFLEHDDANRALM 690
Cdd:TIGR03670 91 VIEYLDAEEEENAYIALDPE------ELTPEH-----------------THLEIDPSAILGIIASTIPYPEHNQSPRNTM 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 691 GSNMQRQAVPTLRADKPLvgtgmeanvaR-DSgvcvianRGGAIEYVDASRIVIRVNEdemiageagvdiynLIKYTrsn 769
Cdd:TIGR03670 148 GAAMAKQSLGLYAANYRI----------RlDT-------RGHLLHYPQKPLVKTRVLE--------------LIGYD--- 193
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 770 qntcinqniivnlgdkvargdilaDGPStdmgelalGQNMRVAFMTWNGYNYEDSILLSERVLQEDRLTSIHIQELSCVA 849
Cdd:TIGR03670 194 ------------------------DRPA--------GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEE 241
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 850 RDTKLGAE-EITADIPNV----GEAALSKLDESGIVYIGAEVTAGDILVGKVTPkgetqltP---EEkllRAIFGEKAAD 921
Cdd:TIGR03670 242 RRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTER 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 922 VKDSSLRVPSGTKGTVidvqvftrdglekddralaiekaqldayrkdlkeeykifeeaarERVIrLLKGQESNgggstkr 1001
Cdd:TIGR03670 312 RRDTSVTVRHGEKGIV--------------------------------------------DKVI-ITETEEGN------- 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1002 gdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfaekkrklatgdelttgvlKVVKVYLAVKRRI 1081
Cdd:TIGR03670 340 -------------------------------------------------------------------KLVKVRVRDLRIP 352
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1082 QPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILEThlgmaakglgdkiekmlkeqrtvle 1161
Cdd:TIGR03670 353 ELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM------------------------- 407
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1162 lrefldkIYNKVGgeqedldsltdaevlALSGNLRAGVPlatpvFDGAEESQIKDLLELAGISRTGQTVLFDGRTGEQFD 1241
Cdd:TIGR03670 408 -------IAGKVA---------------ALEGRRVDGTP-----FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLE 460
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1242 RPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVE--- 1318
Cdd:TIGR03670 461 AEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVvyv 540
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*....
gi 488043460 1319 -----------GRTRIYKNIVDGN----HYMDpgMPESFNVLTKEIRSLGINIELKNGD 1362
Cdd:TIGR03670 541 cencghiawedKRKGTAYCPVCGEtgdiSPVE--MSYAFKLLLDELKSLGISPRLELGD 597
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
612-1362 |
7.07e-51 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 190.94 E-value: 7.07e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 612 VEYLSAIEEVGTVIAqadsaVDKDgNLTEEfvsvrHqgefvrmppekvTHMDVSAQQVVSVAASLIPFLEHDDANRALMG 691
Cdd:PRK07225 98 IEYLDAEEEENAYIA-----VYEE-DLTEE-----H------------THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 692 SNMQRQA--VPT----LRADkplvgtgmeanvardsgvcviaNRGGAIEYVDASRIVIRVNEdemiageagvdiynLIKY 765
Cdd:PRK07225 155 AGMIKQSlgLPAanykLRPD----------------------TRGHLLHYPQVPLVKTQTQE--------------IIGF 198
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 766 TrsnqntcinqniivnlgdkvargdilaDGPStdmgelalGQNMRVAFMTWNGYNYEDSILLS----ERVL--------- 832
Cdd:PRK07225 199 D---------------------------ERPA--------GQNFVVAVMSYEGYNIEDALIMNkasiERGLgrshffrty 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 833 ----------QEDRLTsIHIQELScvardtklGAEeitadipnvGEAALSKLDESGIVYIGAEVTAGDILVGKVTP---- 898
Cdd:PRK07225 244 egeerrypggQEDRFE-IPDKDVR--------GYR---------GEEAYRHLDEDGLVNPETEVKEGDVLIGKTSPprfl 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 899 --KGETQLTPEEKllraifgekaadvKDSSLRVPSGTKGTVidvqvftrdglekddralaiekaqlDAyrkdlkeeykif 976
Cdd:PRK07225 306 eePDDFGISPEKR-------------RETSVTMRSGEEGIV-------------------------DT------------ 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 977 eeaarerVIrLLKGQESNgggstkrgdklveevlsglelvdlleiqpadeaiaerltqiqvflkeksaeidekfaekkrk 1056
Cdd:PRK07225 336 -------VI-LTETEEGS-------------------------------------------------------------- 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1057 latgdelttgvlKVVKVYLAVKRRIQPGDKMAGRHGNKGVVSNILPVEDMPHDANGVPVDIVLNPLGVPSRMNVGQILET 1136
Cdd:PRK07225 346 ------------RLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM 413
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1137 hlgmaakglgdkiekmlkeqrtvlelrefldkIYNKVGgeqedldsltdaevlALSGNLRAGVPlatpvFDGAEESQIKD 1216
Cdd:PRK07225 414 --------------------------------IGGKVG---------------SLEGRRVDGTA-----FSGEDEEDLRE 441
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1217 LLELAGISRTGQTVLFDGRTGEQFDRPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWA 1296
Cdd:PRK07225 442 ALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDV 521
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1297 LEAYGAAYTLQEMLTVKSDDVE-------GRTRIY---KNIV------DGNHYMDPGMPESFNVLTKEIRSLGINIELKN 1360
Cdd:PRK07225 522 LIGHGAAMLLKERLLDESDKVEiyvcakcGMIAIYdkkRNRKycpicgEETDIYPVEMSYAFKLLLDELKSLGIAPRLEL 601
|
..
gi 488043460 1361 GD 1362
Cdd:PRK07225 602 ED 603
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
522-589 |
5.26e-35 |
|
RNA polymerase Rpb2, 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). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 127.64 E-value: 5.26e-35
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 488043460 522 QFMDQNNPLSEITHKRRVSAlGPGGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAK 589
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1285-1359 |
8.80e-32 |
|
RNA polymerase Rpb2, domain 7; 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 119.23 E-value: 8.80e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 1285 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVEGRTRIYKN-----IVDGNHYMDPG-MPESFNVLTKEIRSLGI 1354
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*
gi 488043460 1355 NIELK 1359
Cdd:pfam04560 81 DPRLL 85
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
600-665 |
3.93e-29 |
|
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pssm-ID: 463067 [Multi-domain] Cd Length: 66 Bit Score: 110.92 E-value: 3.93e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488043460 600 YRKVVDGRVTDAVEYLSAIEEVGTVIAQADSAVDKDGNLTEEFVSVRHQGEFVRMPPEKVTHMDVS 665
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
439-589 |
1.77e-22 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 102.72 E-value: 1.77e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 439 RTLVEIRNGKGEVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSQAETDN--LSPQDLINAKPVAAAIKEFF- 515
Cdd:PRK09606 315 EACFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNreLSIKTAVRSDVLTERLEHAMa 394
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 516 ------GSSQLSQFMDQNNPLSEITHKRRVSAlgpgGLTRERAGFEVRDVHQTHYGRVCPIETPEGPNIGLINSLSVYAK 589
Cdd:PRK09606 395 tgnwvgGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
153-463 |
3.89e-10 |
|
RNA polymerase Rpb2, 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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 60.44 E-value: 3.89e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 153 RSPGVFF--DHDKGKTHSSgkvlYSARIIPYRGSWLDFEFDAKDLVYVRIDRRRKLLATVVLRALG-YNNEQILNLFyek 229
Cdd:pfam04561 1 RSNGIYVekELDKNGIIAT----YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGlVSDREILDRL--- 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 230 vpVYLDMGSYQIDLVPERLrgemaqfdiadndgkvivEQgkrinarhvrqmeaagltklsvpdeylyeritAENITlrdg 309
Cdd:pfam04561 74 --CYDFNDPQMLELLKPEL------------------EE--------------------------------AENIY---- 97
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488043460 310 eviaantllshevmvklaeggvkqfnilftndidrgsfvadtlradttaGREEALVEIYKV--MRPGEPPTKEAAENLFN 387
Cdd:pfam04561 98 -------------------------------------------------TQEEALDYIGKGfaLRRGEEPRLQRAREILY 128
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 488043460 388 NLFfsserydlspvGRMKFNRRLGRpyEVGTDQKsrevegILSHEDIIDVLRTLVEIRNGKGEVDDIDHLGNRRVR 463
Cdd:pfam04561 129 SRD-----------PKYNLNKHLGL--NEPFENE------RLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
