|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1392 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2278.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1 MAKSFTGRKRVRKSFGRIPEVTQMPNLIEVQRSSYDHFLQMDVPPEkraNLGLQEVFRSVFPIKDFSDRAVLDFVKYELE 80
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 81 QPKYDVEECQQRGMTFAAPLKVTLRLsvfdVEEDTGlrsirDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPG 160
Cdd:PRK00405 78 EPKYDVEECKERGLTYSAPLRVKLRL----INKETG-----EIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 161 VFFDHDKGKThSSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdgaetealraerkaqkkdllp 240
Cdd:PRK00405 149 VYFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRAL--------------------- 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 241 yeaqGMAKEEILNFFYDTITYTRasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglaEQLV 320
Cdd:PRK00405 207 ----GYSDEEILDLFYEKEEFGK-----------------------------------------------------EIEV 229
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 321 STEELTGRYLAVDIINERTGEVLFEAGDElsasdldklekagvdelpvlaIDHLNVGAYIRNTMAADRNASREDALIDIY 400
Cdd:PRK00405 230 PVEYLLGKVLAEDIVDEETGEVLAEANDE---------------------ITEELDGPYIRNTLEKDPTSSREEALVEIY 288
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 401 RVMRPGEPPTLESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDH 480
Cdd:PRK00405 289 RRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDH 368
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 481 LGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 560
Cdd:PRK00405 369 LGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHK 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 561 RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIVTDEVVYLS 640
Cdd:PRK00405 449 RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLT 528
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 641 AMEEGRYVVAQANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQR 720
Cdd:PRK00405 529 ADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 608
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 721 QAVPLVKADAPLVGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRAtDSSDATAPGVDIYNLLKFQRSNQNTCITQR 800
Cdd:PRK00405 609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNTCINQR 687
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 801 PLVKVGDRVAAGDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQE 880
Cdd:PRK00405 688 PIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPE 767
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 881 EITRDIPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTI 960
Cdd:PRK00405 768 EITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTV 847
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 961 VEVRVFSRrgvdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkg 1040
Cdd:PRK00405 848 IDVKVFTR------------------------------------------------------------------------ 855
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1041 qwrqisiadeqvmetveslgkvfddsiqalqnrfenkvekLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGV 1120
Cdd:PRK00405 856 ----------------------------------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGV 895
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1121 VSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQigraidqyrlamkgrgdaaqtmdglrit 1200
Cdd:PRK00405 896 VSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK---------------------------- 947
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1201 lkeaygqkvyddqiadmtegellelggnlrkgvpFATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTV 1280
Cdd:PRK00405 948 ----------------------------------FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1281 GYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEA 1360
Cdd:PRK00405 994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEA 1073
|
1370 1380 1390
....*....|....*....|....*....|..
gi 1719379330 1361 IVRGDDNFEAGIPESFNVLVKELRSLGLNVEL 1392
Cdd:PRK00405 1074 IVKGENIPEPGIPESFNVLVKELQSLGLDVEL 1105
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1392 |
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: 1888.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 8 RKRVRKSFGRIPEVTQMPNLIEVQRSSYDHFLQMDVPPEKRANLGLQEVFRSVFPIKDFSDRAVLDFVKYELEQPKYDVE 87
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 88 ECQQRGMTFAAPLKVTLRLSVFDvEEDTGlrsirDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDK 167
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE-EDGTK-----EIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 168 GkTHSSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALDgaetealraerkaqkkdllpyeaqgma 247
Cdd:TIGR02013 155 D-TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALG--------------------------- 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 248 keeilnFFYDTitytrasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglaeqlvsteeltg 327
Cdd:TIGR02013 207 ------YTIDT--------------------------------------------------------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 328 rylavdiinertgevlfeagdelsasdldklekagvdelpvLAIDHLNVGAYIRNTMAADRNASREDALIDIYRVMRPGE 407
Cdd:TIGR02013 212 -----------------------------------------LILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGE 250
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 408 PPTLESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVR 487
Cdd:TIGR02013 251 PPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIR 330
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 488 SVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 567
Cdd:TIGR02013 331 SVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 410
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 568 PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIV--TDEVVYLSAMEEG 645
Cdd:TIGR02013 411 PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEED 490
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 646 RYVVAQANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPL 725
Cdd:TIGR02013 491 NYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPL 570
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 726 VKADAPLVGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRATDSSDATAPGVDIYNLLKFQRSNQNTCITQRPLVKV 805
Cdd:TIGR02013 571 LRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSV 650
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 806 GDRVAAGDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRD 885
Cdd:TIGR02013 651 GDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRD 730
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 886 IPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRV 965
Cdd:TIGR02013 731 IPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKV 810
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 966 FSRrgvdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqi 1045
Cdd:TIGR02013 811 FSR----------------------------------------------------------------------------- 813
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1046 siadeqvmetveslgkvfddsiqalqnrfenkveklQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRIL 1125
Cdd:TIGR02013 814 ------------------------------------EQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKIL 857
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1126 PQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKqigraidqyrlamkgrgdaaqtmdglritlkeay 1205
Cdd:TIGR02013 858 PIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGR---------------------------------- 903
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1206 gqkvyddqiadmtegellelggnlrKGVPFATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYM 1285
Cdd:TIGR02013 904 -------------------------KGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYM 958
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1286 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGD 1365
Cdd:TIGR02013 959 LKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGE 1038
|
1370 1380
....*....|....*....|....*..
gi 1719379330 1366 DNFEAGIPESFNVLVKELRSLGLNVEL 1392
Cdd:TIGR02013 1039 NVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1392 |
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: 1705.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 12 RKSFGRIPEVTQMPNLIEVQRSSYDHFLqmdvppekraNLGLQEVFRSVFPIKDFSDRAVLDFVKYELEQPKYDVEECQQ 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 92 RGMTFAAPLKVTLRLsvfdVEEDTGlrsirDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDKGKth 171
Cdd:COG0085 71 RDLTYAAPLYVKVRL----VNKETG-----EIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK-- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 172 sSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdGAETEalraerkaqkkdllpyeaqgmakEEI 251
Cdd:COG0085 140 -SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRAL-GLETD-----------------------EEI 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 252 LNFFYDtitytrasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglaeqlvsteeltgryla 331
Cdd:COG0085 195 LEAFGD-------------------------------------------------------------------------- 200
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 332 vDIINErtgevlfeagdelsasdldklekagvdelpvlaidhlnvgaYIRNTMAADRNASREDALIDIYRVMRPGEPPTL 411
Cdd:COG0085 201 -DPIQE-----------------------------------------YILATLEKDNTKTQEEALLEIYRKLRPGEPPTI 238
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 412 ESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGE 491
Cdd:COG0085 239 ERAEQLLDNLFFDPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGE 318
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 492 LMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGL 571
Cdd:COG0085 319 LLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGL 398
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 572 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIVTDEVVYLSAMEEGRYVVAQ 651
Cdd:COG0085 399 SRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQ 478
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 652 ANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAP 731
Cdd:COG0085 479 ANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP 558
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 732 LvgtgmeatvardsgvtivakrkgivdqidatrivvratdssdatapgvDIYNLLKFQRSNQNTCITQRPLVKVGDRVAA 811
Cdd:COG0085 559 L------------------------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEK 590
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 812 GDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGE 891
Cdd:COG0085 591 GDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSE 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 892 EALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFSRrgv 971
Cdd:COG0085 671 EALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSR--- 747
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 972 dkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqisiadeq 1051
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1052 vmetveslgkvfddsiqalqnrfENkveklqrGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMP 1131
Cdd:COG0085 748 -----------------------EE-------GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMP 797
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1132 YLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIgraidqyrlamkgrgdaaqtmdglritlkeaygqkvyd 1211
Cdd:COG0085 798 FLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV-------------------------------------- 839
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1212 dqiadmtegellelggnlrkgvpfATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHL 1291
Cdd:COG0085 840 ------------------------ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHM 895
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1292 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAG 1371
Cdd:COG0085 896 VDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPG 975
|
1370 1380
....*....|....*....|.
gi 1719379330 1372 IPESFNVLVKELRSLGLNVEL 1392
Cdd:COG0085 976 IPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1393 |
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: 863.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 27 LIEVQRSSYDHFLQMdvppekranlGLQEVFRSVFPIKDFSD--RAVLDFVKYELEQP---------KYDVEECQQRGMT 95
Cdd:cd00653 1 LVKQQIDSFNYFLNV----------GLQEIVKSIPPITDTDDdgRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 96 FAAPLKVTLRLSVFDveedtglrsIRDIKEQDVYMGDMPLMTANGTFIING---TERVIVSQMHRSPGVFFdhdkgkths 172
Cdd:cd00653 71 YSAPLYVDIRLTVND---------KGKIKEQEVFIGEIPIMLRSKLCNLNGltpEELIKLGECPLDPGGYF--------- 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 173 sgkylfaarVIpyRGSwldfEfdaKDLVYVrIDRRRklpattllfaldgaetealraerkaqkkdllpyeaqgmakeeil 252
Cdd:cd00653 133 ---------II--NGT----E---KVIINQ-EQRSP-------------------------------------------- 149
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 253 NFFYdtitytrasggwktpfnADRMKGVKVASdlvdaasgqvvaeagtkmtprlikklvegglaeqlvsteeltgrylaV 332
Cdd:cd00653 150 NVII-----------------VEDSKGKRIYT-----------------------------------------------K 165
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 333 DIINERTGEvlfeAGDELSASDLDKlekagvdelpvlaIDHLNVGAYIRNtmaadrnasREDALIDIYRVMRpgepptle 412
Cdd:cd00653 166 TSIPSYSPY----RGSWLEVKSDKK-------------KDRIYVRIDLKR---------QEEALKYIGKRFE-------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 413 saealfaglffdserydlsavgrvkmnarlnfqtedsvrvlrkqDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGEL 492
Cdd:cd00653 212 --------------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGEL 247
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 493 MENQYRVGLLRMERAIRERMSSVEI--DTVMPHDLINAKPAAAAVREFFGSSQ------------LSQFMDQTNPLSEIT 558
Cdd:cd00653 248 LQNLFRSGLKRLEREVKEKLQKQLSkkKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELS 327
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 559 HKRRLSAlgpGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNqyGFIESPYRKVRDSIvtdevvy 638
Cdd:cd00653 328 HKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEKEV------- 395
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 639 lsameegryvvaqanaeldadnrfaadlvscrqggeylmfrpeaiDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNM 718
Cdd:cd00653 396 ---------------------------------------------THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNM 430
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 719 QRQAVPlvkadaplvgtgmeatvardsgvtivakrkgivdqIDATRIVVRaTDSSdatapgvdIYNLLKfqrsnqntciT 798
Cdd:cd00653 431 QKQAVG-----------------------------------TPALNQQYR-MDTK--------LYLLLY----------P 456
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 799 QRPLVKVGDRvaagDIIAdgpsteLGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLG 878
Cdd:cd00653 457 QKPLVGTGIE----EYIA------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNG 526
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 879 QEEITR-DIPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPeekllraIFGEKASDVRDTSLRLPPGVA 957
Cdd:cd00653 527 PEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEK 599
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 958 GTIVEVRVFSRrgvdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanl 1037
Cdd:cd00653 600 GIVDDVKIFSR--------------------------------------------------------------------- 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1038 tkgqwrqisiadeqvmetveslgkvfddsiqalqnrfenkveklqrgdELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGN 1117
Cdd:cd00653 611 ------------------------------------------------ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1118 KGVVSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIgraidqyrlamkgrgdaaqtmdgl 1197
Cdd:cd00653 643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG------------------------ 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1198 ritlkeaygqkvyddqiadmtegellelggnlrkgvpFATPvFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRK 1277
Cdd:cd00653 699 -------------------------------------DATP-FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAP 740
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1278 VTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKV 1357
Cdd:cd00653 741 IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCV 820
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|....*.
gi 1719379330 1358 YEAIV----------RGDDNFEAGIPESFNVLVKELRSLGLNVELN 1393
Cdd:cd00653 821 KCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
750-1317 |
3.84e-177 |
|
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: 530.56 E-value: 3.84e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 750 VAKRKGIVDQIDATRIVVRATDSSDAtapgVDIYNLLKFQRSNQNT---CITQRPLVKVGdRVAAGDiiadgpsteLGEL 826
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQA----MGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGEL 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 827 ALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEvmARDTKLGQ-EEITRDIPNVGEEALKNLDEAGIVYI 905
Cdd:pfam00562 67 PLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRV 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 906 GAEVRPGDILVGKVTPkgespmTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFsrrgvdkderalaieraei 985
Cdd:pfam00562 145 GAEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 986 eklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqisiadeqvmetveslgkvfdd 1065
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1066 siqalqnrfenkveklqrgdELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQPVDLVLNP 1145
Cdd:pfam00562 200 --------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1146 LGVPSRMNIGQILETHLGWASAGlgkqigraidqyrlamkgrgdaaqtmdglritlkeaygqkvyddqiadmtegellel 1225
Cdd:pfam00562 260 HGVPSRMTIGQLLETHLGKAAAL--------------------------------------------------------- 282
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1226 ggnlrKGVPFATPVFDGARE--EDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGP 1303
Cdd:pfam00562 283 -----LGVFVDATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGP 357
|
570
....*....|....
gi 1719379330 1304 YSLVTQQPLGGKAQ 1317
Cdd:pfam00562 358 YSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1392 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2278.48 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1 MAKSFTGRKRVRKSFGRIPEVTQMPNLIEVQRSSYDHFLQMDVPPEkraNLGLQEVFRSVFPIKDFSDRAVLDFVKYELE 80
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 81 QPKYDVEECQQRGMTFAAPLKVTLRLsvfdVEEDTGlrsirDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPG 160
Cdd:PRK00405 78 EPKYDVEECKERGLTYSAPLRVKLRL----INKETG-----EIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPG 148
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 161 VFFDHDKGKThSSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdgaetealraerkaqkkdllp 240
Cdd:PRK00405 149 VYFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRAL--------------------- 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 241 yeaqGMAKEEILNFFYDTITYTRasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglaEQLV 320
Cdd:PRK00405 207 ----GYSDEEILDLFYEKEEFGK-----------------------------------------------------EIEV 229
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 321 STEELTGRYLAVDIINERTGEVLFEAGDElsasdldklekagvdelpvlaIDHLNVGAYIRNTMAADRNASREDALIDIY 400
Cdd:PRK00405 230 PVEYLLGKVLAEDIVDEETGEVLAEANDE---------------------ITEELDGPYIRNTLEKDPTSSREEALVEIY 288
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 401 RVMRPGEPPTLESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDH 480
Cdd:PRK00405 289 RRLRPGEPPTVEAARSLLENLFFDPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDH 368
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 481 LGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHK 560
Cdd:PRK00405 369 LGNRRVRSVGELLQNQFRIGLSRMERAVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHK 448
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 561 RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIVTDEVVYLS 640
Cdd:PRK00405 449 RRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLT 528
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 641 AMEEGRYVVAQANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQR 720
Cdd:PRK00405 529 ADEEDNYVIAQANAPLDEDGRFVDELVTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQR 608
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 721 QAVPLVKADAPLVGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRAtDSSDATAPGVDIYNLLKFQRSNQNTCITQR 800
Cdd:PRK00405 609 QAVPLLRPEAPLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNTCINQR 687
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 801 PLVKVGDRVAAGDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQE 880
Cdd:PRK00405 688 PIVKVGDRVEKGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPE 767
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 881 EITRDIPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTI 960
Cdd:PRK00405 768 EITRDIPNVSEEALRNLDESGIVRIGAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTV 847
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 961 VEVRVFSRrgvdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkg 1040
Cdd:PRK00405 848 IDVKVFTR------------------------------------------------------------------------ 855
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1041 qwrqisiadeqvmetveslgkvfddsiqalqnrfenkvekLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGV 1120
Cdd:PRK00405 856 ----------------------------------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGV 895
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1121 VSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQigraidqyrlamkgrgdaaqtmdglrit 1200
Cdd:PRK00405 896 VSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAAKGLGIK---------------------------- 947
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1201 lkeaygqkvyddqiadmtegellelggnlrkgvpFATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTV 1280
Cdd:PRK00405 948 ----------------------------------FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTV 993
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1281 GYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEA 1360
Cdd:PRK00405 994 GYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEA 1073
|
1370 1380 1390
....*....|....*....|....*....|..
gi 1719379330 1361 IVRGDDNFEAGIPESFNVLVKELRSLGLNVEL 1392
Cdd:PRK00405 1074 IVKGENIPEPGIPESFNVLVKELQSLGLDVEL 1105
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1392 |
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: 1888.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 8 RKRVRKSFGRIPEVTQMPNLIEVQRSSYDHFLQMDVPPEKRANLGLQEVFRSVFPIKDFSDRAVLDFVKYELEQPKYDVE 87
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 88 ECQQRGMTFAAPLKVTLRLSVFDvEEDTGlrsirDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDK 167
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE-EDGTK-----EIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 168 GkTHSSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALDgaetealraerkaqkkdllpyeaqgma 247
Cdd:TIGR02013 155 D-TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALG--------------------------- 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 248 keeilnFFYDTitytrasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglaeqlvsteeltg 327
Cdd:TIGR02013 207 ------YTIDT--------------------------------------------------------------------- 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 328 rylavdiinertgevlfeagdelsasdldklekagvdelpvLAIDHLNVGAYIRNTMAADRNASREDALIDIYRVMRPGE 407
Cdd:TIGR02013 212 -----------------------------------------LILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGE 250
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 408 PPTLESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVR 487
Cdd:TIGR02013 251 PPTVEAARSLLENLFFDPKRYDLGRVGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIR 330
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 488 SVGELMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALG 567
Cdd:TIGR02013 331 SVGELLQNQFRVGLARMERIVRERMSTQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALG 410
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 568 PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIV--TDEVVYLSAMEEG 645
Cdd:TIGR02013 411 PGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEED 490
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 646 RYVVAQANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPL 725
Cdd:TIGR02013 491 NYVIAQANAPLDENGRFVEDLVVARYRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPL 570
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 726 VKADAPLVGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRATDSSDATAPGVDIYNLLKFQRSNQNTCITQRPLVKV 805
Cdd:TIGR02013 571 LRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSV 650
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 806 GDRVAAGDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRD 885
Cdd:TIGR02013 651 GDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRD 730
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 886 IPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRV 965
Cdd:TIGR02013 731 IPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKV 810
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 966 FSRrgvdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqi 1045
Cdd:TIGR02013 811 FSR----------------------------------------------------------------------------- 813
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1046 siadeqvmetveslgkvfddsiqalqnrfenkveklQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRIL 1125
Cdd:TIGR02013 814 ------------------------------------EQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKIL 857
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1126 PQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKqigraidqyrlamkgrgdaaqtmdglritlkeay 1205
Cdd:TIGR02013 858 PIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGR---------------------------------- 903
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1206 gqkvyddqiadmtegellelggnlrKGVPFATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYM 1285
Cdd:TIGR02013 904 -------------------------KGVPIATPVFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYM 958
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1286 LKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGD 1365
Cdd:TIGR02013 959 LKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGE 1038
|
1370 1380
....*....|....*....|....*..
gi 1719379330 1366 DNFEAGIPESFNVLVKELRSLGLNVEL 1392
Cdd:TIGR02013 1039 NVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1392 |
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: 1705.31 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 12 RKSFGRIPEVTQMPNLIEVQRSSYDHFLqmdvppekraNLGLQEVFRSVFPIKDFSDRAVLDFVKYELEQPKYDVEECQQ 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 92 RGMTFAAPLKVTLRLsvfdVEEDTGlrsirDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDKGKth 171
Cdd:COG0085 71 RDLTYAAPLYVKVRL----VNKETG-----EIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK-- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 172 sSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdGAETEalraerkaqkkdllpyeaqgmakEEI 251
Cdd:COG0085 140 -SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRAL-GLETD-----------------------EEI 194
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 252 LNFFYDtitytrasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglaeqlvsteeltgryla 331
Cdd:COG0085 195 LEAFGD-------------------------------------------------------------------------- 200
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 332 vDIINErtgevlfeagdelsasdldklekagvdelpvlaidhlnvgaYIRNTMAADRNASREDALIDIYRVMRPGEPPTL 411
Cdd:COG0085 201 -DPIQE-----------------------------------------YILATLEKDNTKTQEEALLEIYRKLRPGEPPTI 238
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 412 ESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGE 491
Cdd:COG0085 239 ERAEQLLDNLFFDPKRYDLAHVGRYKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGE 318
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 492 LMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGL 571
Cdd:COG0085 319 LLQNQFRVGLSRMERVVRERMTTQDVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGL 398
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 572 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIVTDEVVYLSAMEEGRYVVAQ 651
Cdd:COG0085 399 SRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQ 478
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 652 ANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAP 731
Cdd:COG0085 479 ANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP 558
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 732 LvgtgmeatvardsgvtivakrkgivdqidatrivvratdssdatapgvDIYNLLKFQRSNQNTCITQRPLVKVGDRVAA 811
Cdd:COG0085 559 L------------------------------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEK 590
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 812 GDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGE 891
Cdd:COG0085 591 GDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSE 670
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 892 EALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFSRrgv 971
Cdd:COG0085 671 EALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSR--- 747
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 972 dkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqisiadeq 1051
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1052 vmetveslgkvfddsiqalqnrfENkveklqrGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMP 1131
Cdd:COG0085 748 -----------------------EE-------GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMP 797
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1132 YLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIgraidqyrlamkgrgdaaqtmdglritlkeaygqkvyd 1211
Cdd:COG0085 798 FLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRV-------------------------------------- 839
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1212 dqiadmtegellelggnlrkgvpfATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHL 1291
Cdd:COG0085 840 ------------------------ATPVFDGAPEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHM 895
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1292 VDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAG 1371
Cdd:COG0085 896 VDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPG 975
|
1370 1380
....*....|....*....|.
gi 1719379330 1372 IPESFNVLVKELRSLGLNVEL 1392
Cdd:COG0085 976 IPESFKVLLKELQSLGLDVEV 996
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
26-1394 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1595.81 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 26 NLIEVQRSSYDHFlqmdvPPEKRANLGLQEVFRSVFPIKDFSDRAVLDFVKYELEQPKYDVEECQQRGMTFAAPLKVTLR 105
Cdd:PRK14844 31 DLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIR 105
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 106 LSVF----DVEEDTGLRS----------IRDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDKGKTH 171
Cdd:PRK14844 106 LVIMqdgiSLDEYKSIKEsgdhsklatvIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTY 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 172 SSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdgaetealraerkaqkkdllpyeaqGMAKEEI 251
Cdd:PRK14844 186 NSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKAL-------------------------GLSNNDI 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 252 LNFFYDTITYTRASGGWKTPFNADRMKGVKVASDLVDAaSGQVVAEAGTKMTPRLIKKLVEGGLAEQLVSTEELTGRYLA 331
Cdd:PRK14844 241 LDRFYEKIKYIKHKDGWKVPFVPDKFKGVRLPFDLMDV-EGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLA 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 332 VDIINERTGEVLFEAGDELSASDLDKLEKAGVDELPVLAIDHLNVGAYIRNTMAADRNASREDALIDIYRVMRPGEPPTL 411
Cdd:PRK14844 320 EDLIDSASSTKILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVL 399
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 412 ESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGE 491
Cdd:PRK14844 400 EIVEEFFRNLFFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGE 479
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 492 LMENQYRVGLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGL 571
Cdd:PRK14844 480 FIENQFRTGLLKLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGL 559
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 572 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIVTDEVVYLSAMEEGRYVVAQ 651
Cdd:PRK14844 560 TRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIAD 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 652 ANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAP 731
Cdd:PRK14844 640 TSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAP 719
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 732 LVGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRATDSSDATAPGVDIYNLLKFQRSNQNTCITQRPLVKVGDRVAA 811
Cdd:PRK14844 720 LVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKE 799
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 812 GDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGE 891
Cdd:PRK14844 800 GDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNE 879
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 892 EALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFSRRGV 971
Cdd:PRK14844 880 ENLYHLDDSGIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGV 959
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 972 DKDERALAIERAEIEKLAKDRDDERAILERSFYTRLKEVILGQTAQSGPKgmkagtvltdaeLANLTKGQWRQISIADEQ 1051
Cdd:PRK14844 960 EENERALLIKQKEINDFEKERDYIINVTSEYFYDELKKLLINSGSQDREK------------FDSIEREQWWGIGLKNQS 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1052 VMETVESLGKVFDDSIQALQNRFENKVEKLQRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMP 1131
Cdd:PRK14844 1028 ISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMP 1107
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1132 YLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIGRAIDQ-------YRLAMKGRGD------AAQTMDGLR 1198
Cdd:PRK14844 1108 YLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDEinkiksaFCKGIRSLNDdnftkfAAAYLDNKK 1187
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1199 I----------------------------------TLKEAYGQ------KVYD--------DQIADMTEGELLELGGNLR 1230
Cdd:PRK14844 1188 IenidddeitasvlntpnknalndelnelvenylnSCKSAYSNlrnfliEVYScgsnvsicNNIRDISDNNLIEFARKLR 1267
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1231 KGVPFATPVFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQ 1310
Cdd:PRK14844 1268 DGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQ 1347
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1311 PLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIPESFNVLVKELRSLGLNV 1390
Cdd:PRK14844 1348 PLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNV 1427
|
....
gi 1719379330 1391 ELNQ 1394
Cdd:PRK14844 1428 DLKQ 1431
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
1-1392 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1455.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1 MAKSFTGRKRVRKSFGRIPEVTQMPNLIEVQRSSYDHFLQMDVPPEKranlGLQEVFRSVFPIKDFSDRAVLDFVKYELE 80
Cdd:PRK09603 1 MSKKIPLKNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKES----GIEKVFKSIFPIQDEHNRITLEYAGCEFG 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 81 QPKYDVEECQQRGMTFAAPLKVTLRLSVFDVEEDTGLR-SIRDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSP 159
Cdd:PRK09603 77 KSKYTVREAMERGITYSIPLKIKVRLILWEKDTKSGEKnGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSP 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 160 GVFFDHDKGKThSSGKYLFAARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdgaetealraerkaqkkdll 239
Cdd:PRK09603 157 GVIFKEEESST-SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAM-------------------- 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 240 pyeaqGMAKEEILNFFYDTITYTRASGGWKTPFNADRMKGvKVASDLVDAaSGQVVAEAGTKMTPRLIKKLVEGGLAEQL 319
Cdd:PRK09603 216 -----DYQKQDIIKMFYPLVKVRYENDKYLIPFASLDANQ-RMEFDLKDP-QGKIILLAGKKLTSRKIKELKENHLEWVE 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 320 VSTEELTGRYLAVDIINERtgEVLFEAGDELSASDLDKLEKAGVDELPVLAIDHLNVGAYIRNTMAADRNASR------- 392
Cdd:PRK09603 289 YPMDILLNRHLAEPVMVGK--EVLLDMLTQLDKNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSADSESLKllkqtek 366
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 393 -----EDALIDIYRVMRPGEPPTLESAEALFAGLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVN 467
Cdd:PRK09603 367 iddenALAAIRIHKVMKPGDPVTTEVAKQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMK 446
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 468 LKDGRGEIDDIDHLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSVEI--DTVMPHDLINAKPAAAAVREFFGSSQLS 545
Cdd:PRK09603 447 IKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLS 526
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 546 QFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYR 625
Cdd:PRK09603 527 QFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYK 606
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 626 KVRDSIVTDEVVYLSAMEEGRYVVAQANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLE 705
Cdd:PRK09603 607 KVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLE 686
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 706 NDDANRALMGSNMQRQAVPLVKADAPLVGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRATDSSDATapgVDIYNL 785
Cdd:PRK09603 687 HDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEAY---IDAYSL 763
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 786 LKFQRSNQNTCITQRPLVKVGDRVAAGDIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHI 865
Cdd:PRK09603 764 QKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHI 843
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 866 EEFEVMARDTKLGQEEITRDIPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDV 945
Cdd:PRK09603 844 YEKEVDARELKHGVEEFTADIPDVKEEALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHV 923
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 946 RDTSLRLPPGVAGTIVEVRVFSRRGVDKDERALAIERAEIEKLAKDRDDERAILERSFYTR----LKEVILGQTAQSGPK 1021
Cdd:PRK09603 924 VNKSLYCPPSLEGTVIDVKVFTKKGYEKDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRvsslLSQAILEEPFSHNGK 1003
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1022 GMKAGTVLTDAELANLTKGQWRQ-ISIADEQVMETVESLGKVFDDSIQALQNRFENKVEKLQRGDELPPGVMKMVKVFVA 1100
Cdd:PRK09603 1004 DYKEGDQIPKEEIASINRFTLASlVKKYSKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIA 1083
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1101 VKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIGRAIDQy 1180
Cdd:PRK09603 1084 TKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLED- 1162
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1181 rlamkgrgDAAQTMDGLRITLKEAY-----GQKVYDDQIADMTEGELLELGGNLRKGVPFATPVFDGAREEDICQQLEKA 1255
Cdd:PRK09603 1163 --------KTKDFAKELRAKMLEIAnaineKDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELA 1234
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1256 GLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1335
Cdd:PRK09603 1235 KIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYG 1314
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|....*..
gi 1719379330 1336 AAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIPESFNVLVKELRSLGLNVEL 1392
Cdd:PRK09603 1315 AAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESEIPETFYVLTKELQSLALDINI 1371
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
22-1397 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1109.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 22 TQMPNLIEVQRSSYDHFLqmdvppekraNLGLQEVFRSVFPIKDFSDRA--VLDFVKYELEQPKYDVEECQQRGMTFAAP 99
Cdd:CHL00207 5 FALPDFLEIQRTSFCWFL----------NEGLNEELNIFSKIFDYTGNLelLLFGKNYKLKYPKYNLLSAKSYDSNYSIQ 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 100 LKVTLRLSVFDveedtglrsIRDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFFDHDKGKTHssgKYLFA 179
Cdd:CHL00207 75 IYLPLKFINLK---------TNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYS 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 180 ARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdgaetealraerkaqkkdllpyeaqGMAKEEILNFfydtI 259
Cdd:CHL00207 143 ATLIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKAL-------------------------GLTDQDIYSR----L 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 260 TYTRasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmTPRLIKKLvegglaeqLVSTEELTgrylavdiinert 339
Cdd:CHL00207 194 TKSE---------------------------------------FLKKLKPI--------LLNSNSYT------------- 213
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 340 gevlfeagdelsasdldklekagvdelpvlaidhlnvgayirntmaadrnasREDALIDIYRVMRPGEPPTLESAEALFA 419
Cdd:CHL00207 214 ----------------------------------------------------NEEILLEIYKNLSPIEPATVNDANQNLF 241
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 420 GLFFDSERYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGELMENQYRV 499
Cdd:CHL00207 242 SRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRI 321
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 500 GLLRMERAIRERMSSVEIDTVMPHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFE 579
Cdd:CHL00207 322 GLKRLERILRNRMTICDIDSLSKFNLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFA 401
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 580 VRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDS--IVTDEVVYLSAMEEGRYVVAQANAELD 657
Cdd:CHL00207 402 VRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKFGFIETPFYKVINGkvKKFGNPIYLTADSEDLYRIAPNDINLN 481
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 658 ADNRFAADLVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPLVGTGM 737
Cdd:CHL00207 482 KNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGY 561
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 738 EATVARDSGVTIVAKRKGIVDQIDATRIVVRatdssDATAPGVdIYNLLKFQRSNQNTCITQRPLVKVGDRVAAGDIIAD 817
Cdd:CHL00207 562 EKQIALDSGMTIISLTEGIVVSVSAYKIIIQ-----DDNNRYI-HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILAD 635
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 818 GPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEEALKNL 897
Cdd:CHL00207 636 GSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNL 715
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 898 DEAGIVYIGAEVRPGDILVGKVTPKGESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFSRRgvdkdera 977
Cdd:CHL00207 716 DENGIISIGSKVLAGDILVGKITPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS-------- 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 978 laieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqisiadeqvmetve 1057
Cdd:CHL00207 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1058 slgkvfddsiqalqnrfenkveklqRGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQ 1137
Cdd:CHL00207 788 -------------------------KGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGT 842
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1138 PVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIGRA-IDqyrlamkgrgdaaqTMDGL---RITLKEAYGQkvyddq 1213
Cdd:CHL00207 843 PPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILpFD--------------EMYGSeysRILINNKLNQ------ 902
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1214 iADMTEGELLELGGNLrkgvpfatpvfdgareedicqqlekagldrSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVD 1293
Cdd:CHL00207 903 -ASIKNNEYWLFNSYH------------------------------PGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVD 951
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1294 DKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEAIVRGDDNFEAGIP 1373
Cdd:CHL00207 952 DKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTP 1031
|
1370 1380
....*....|....*....|....
gi 1719379330 1374 ESFNVLVKELRSLGLNVELNQRSY 1397
Cdd:CHL00207 1032 ESFKVLMRELQSLGLDIEAYKIEN 1055
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
25-1396 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1108.43 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 25 PNLIEVQRSSYDHFLqmdvppekraNLGLQEVFRSVFPIKDfSDRAV--LDFVK-YELEQPKYDVEECQQRGMTFAAPLK 101
Cdd:CHL00001 13 PGFNQIQFEGFCRFI----------DQGLTEELSKFPKIED-TDQEIefQLFVEtYQLVEPLIKERDAVYESLTYSSELY 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 102 VTLRLSvfdveedtgLRSIRDIKEQDVYMGDMPLMTANGTFIINGTERVIVSQMHRSPGVFF----DHDKGKTHSsgkyl 177
Cdd:CHL00001 82 VPAGLI---------WKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYrselDHNGISVYT----- 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 178 faARVIPYRGSWLDFEFDAKDLVYVRIDRRRKLPATTLLFALdgaetealraerkaqkkdllpyeaqGMAKEEILnffyD 257
Cdd:CHL00001 148 --GTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAM-------------------------GLNLREIL----D 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 258 TITYtrasggwktpfnadrmkgvkvasdlvdaasgqvvaeagtkmtprlikklvegglAEQLVSTEeltgrylavdiine 337
Cdd:CHL00001 197 NVCY------------------------------------------------------PEIFLSFL-------------- 208
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 338 rtgevlfeagdelsasdLDKLEKagvdelpvlaidhlNVGayirntmaadrnaSREDALIDIYR--VMRPGEPPTLESAE 415
Cdd:CHL00001 209 -----------------NDKEKK--------------KIG-------------SKENAILEFYQqfACVGGDPVFSESLC 244
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 416 ALFAGLFFDSeRYDLSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGELMEN 495
Cdd:CHL00001 245 KELQKKFFQQ-RCELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQD 323
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 496 QYRVGLLRMERAIRERMSSVEIDTVM--PHDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTR 573
Cdd:CHL00001 324 QFGLALNRLENAVRGTICGAIRRKLIptPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTG 403
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 574 ERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQYGFIESPYRKVRDSIVTDEVVYLSAMEEGRYVVAQAN 653
Cdd:CHL00001 404 RTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGN 483
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 654 AeLDADNRFAAD-LVSCRQGGEYLMFRPEAIDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPL 732
Cdd:CHL00001 484 S-LALNQGIQEEqVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCI 562
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 733 VGTGMEATVARDSGVTIVAKRKGIVDQIDATRIVVRATDSsdatapgVDIYNLLKFQRSNQNTCITQRPLVKVGDRVAAG 812
Cdd:CHL00001 563 VGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGD-------TLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKG 635
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 813 DIIADGPSTELGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQEEITRDIPNVGEE 892
Cdd:CHL00001 636 QILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAH 715
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 893 ALKNLDEAGIVYIGAEVRPGDILVGKVTPK--GESPMTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRvfsrrg 970
Cdd:CHL00001 716 LLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR------ 789
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 971 vdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqWRQisiade 1050
Cdd:CHL00001 790 -----------------------------------------------------------------------WIQ------ 792
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1051 qvmetveslgkvfddsiqalqnrfenkveklqrGDELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDM 1130
Cdd:CHL00001 793 ---------------------------------KKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDM 839
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1131 PYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKqigraidQYRLAmkgrgdaaqtmdglriTLKEAYGQKVY 1210
Cdd:CHL00001 840 PYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNR-------HYRIA----------------PFDERYEQEAS 896
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1211 ddqiadmtegellelggnlRKgvpfatPVFdgareedicQQLEKAG----------LDRSGQVTLIDGRTGEAFDRKVTV 1280
Cdd:CHL00001 897 -------------------RK------LVF---------SELYEASkqtanpwvfePEYPGKSRLFDGRTGDPFEQPVTI 942
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1281 GYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKVYEA 1360
Cdd:CHL00001 943 GKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGA 1022
|
1370 1380 1390
....*....|....*....|....*....|....*...
gi 1719379330 1361 IVRGD--DNFEaGIPESFNVLVKELRSLGLNVELNQRS 1396
Cdd:CHL00001 1023 IITGGtiPKPE-DAPESFRLLVRELRSLALELNHFLVS 1059
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1393 |
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: 863.42 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 27 LIEVQRSSYDHFLQMdvppekranlGLQEVFRSVFPIKDFSD--RAVLDFVKYELEQP---------KYDVEECQQRGMT 95
Cdd:cd00653 1 LVKQQIDSFNYFLNV----------GLQEIVKSIPPITDTDDdgRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 96 FAAPLKVTLRLSVFDveedtglrsIRDIKEQDVYMGDMPLMTANGTFIING---TERVIVSQMHRSPGVFFdhdkgkths 172
Cdd:cd00653 71 YSAPLYVDIRLTVND---------KGKIKEQEVFIGEIPIMLRSKLCNLNGltpEELIKLGECPLDPGGYF--------- 132
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 173 sgkylfaarVIpyRGSwldfEfdaKDLVYVrIDRRRklpattllfaldgaetealraerkaqkkdllpyeaqgmakeeil 252
Cdd:cd00653 133 ---------II--NGT----E---KVIINQ-EQRSP-------------------------------------------- 149
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 253 NFFYdtitytrasggwktpfnADRMKGVKVASdlvdaasgqvvaeagtkmtprlikklvegglaeqlvsteeltgrylaV 332
Cdd:cd00653 150 NVII-----------------VEDSKGKRIYT-----------------------------------------------K 165
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 333 DIINERTGEvlfeAGDELSASDLDKlekagvdelpvlaIDHLNVGAYIRNtmaadrnasREDALIDIYRVMRpgepptle 412
Cdd:cd00653 166 TSIPSYSPY----RGSWLEVKSDKK-------------KDRIYVRIDLKR---------QEEALKYIGKRFE-------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 413 saealfaglffdserydlsavgrvkmnarlnfqtedsvrvlrkqDIMSILKVLVNLKDGRGEIDDIDHLGNRRVRSVGEL 492
Cdd:cd00653 212 --------------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGEL 247
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 493 MENQYRVGLLRMERAIRERMSSVEI--DTVMPHDLINAKPAAAAVREFFGSSQ------------LSQFMDQTNPLSEIT 558
Cdd:cd00653 248 LQNLFRSGLKRLEREVKEKLQKQLSkkKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELS 327
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 559 HKRRLSAlgpGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNqyGFIESPYRKVRDSIvtdevvy 638
Cdd:cd00653 328 HKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEKEV------- 395
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 639 lsameegryvvaqanaeldadnrfaadlvscrqggeylmfrpeaiDLIDVSPKQLVSVAAALIPFLENDDANRALMGSNM 718
Cdd:cd00653 396 ---------------------------------------------THIEISPSQILSVAASLIPFPEHNQSPRNLYQSNM 430
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 719 QRQAVPlvkadaplvgtgmeatvardsgvtivakrkgivdqIDATRIVVRaTDSSdatapgvdIYNLLKfqrsnqntciT 798
Cdd:cd00653 431 QKQAVG-----------------------------------TPALNQQYR-MDTK--------LYLLLY----------P 456
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 799 QRPLVKVGDRvaagDIIAdgpsteLGELALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEVMARDTKLG 878
Cdd:cd00653 457 QKPLVGTGIE----EYIA------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNG 526
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 879 QEEITR-DIPNVGEEALKNLDEAGIVYIGAEVRPGDILVGKVTPKGESPMTPeekllraIFGEKASDVRDTSLRLPPGVA 957
Cdd:cd00653 527 PEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEK 599
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 958 GTIVEVRVFSRrgvdkderalaieraeieklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanl 1037
Cdd:cd00653 600 GIVDDVKIFSR--------------------------------------------------------------------- 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1038 tkgqwrqisiadeqvmetveslgkvfddsiqalqnrfenkveklqrgdELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGN 1117
Cdd:cd00653 611 ------------------------------------------------ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQ 642
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1118 KGVVSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILETHLGWASAGLGKQIgraidqyrlamkgrgdaaqtmdgl 1197
Cdd:cd00653 643 KGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG------------------------ 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1198 ritlkeaygqkvyddqiadmtegellelggnlrkgvpFATPvFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRK 1277
Cdd:cd00653 699 -------------------------------------DATP-FDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAP 740
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1278 VTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVSGRTKV 1357
Cdd:cd00653 741 IFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCV 820
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|....*.
gi 1719379330 1358 YEAIV----------RGDDNFEAGIPESFNVLVKELRSLGLNVELN 1393
Cdd:cd00653 821 KCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
750-1317 |
3.84e-177 |
|
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: 530.56 E-value: 3.84e-177
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 750 VAKRKGIVDQIDATRIVVRATDSSDAtapgVDIYNLLKFQRSNQNT---CITQRPLVKVGdRVAAGDiiadgpsteLGEL 826
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQA----MGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGEL 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 827 ALGRNVLVAFMPWNGYNFEDSILINERIVKDDVFTSIHIEEFEvmARDTKLGQ-EEITRDIPNVGEEALKNLDEAGIVYI 905
Cdd:pfam00562 67 PLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRV 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 906 GAEVRPGDILVGKVTPkgespmTPEEKLLRAIFGEKASDVRDTSLRLPPGVAGTIVEVRVFsrrgvdkderalaieraei 985
Cdd:pfam00562 145 GAEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 986 eklakdrdderailersfytrlkevilgqtaqsgpkgmkagtvltdaelanltkgqwrqisiadeqvmetveslgkvfdd 1065
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1066 siqalqnrfenkveklqrgdELPPGVMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQPVDLVLNP 1145
Cdd:pfam00562 200 --------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1146 LGVPSRMNIGQILETHLGWASAGlgkqigraidqyrlamkgrgdaaqtmdglritlkeaygqkvyddqiadmtegellel 1225
Cdd:pfam00562 260 HGVPSRMTIGQLLETHLGKAAAL--------------------------------------------------------- 282
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1226 ggnlrKGVPFATPVFDGARE--EDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGP 1303
Cdd:pfam00562 283 -----LGVFVDATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGP 357
|
570
....*....|....
gi 1719379330 1304 YSLVTQQPLGGKAQ 1317
Cdd:pfam00562 358 YSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
26-1393 |
1.29e-86 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 307.27 E-value: 1.29e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 26 NLIEVQRSSYDHFLqmdvppekraNLGLQEVFRSVFPIKDFSDRAVLDFVKYELEQPKYDvE-----------ECQQRGM 94
Cdd:PRK08565 13 GLVRQHLDSYNDFI----------ERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIK-EadgserpitpmEARLRNL 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 95 TFAAPLKVTLRLSVFDVEEdtglrsirdiKEQDVYMGDMPLMTAN------------------------GTFIINGTERV 150
Cdd:PRK08565 82 TYAAPLYLTMIPVENGIEY----------EPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERV 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 151 IVSQMHRSPG---VffdhDKGKTHSSGKYLfaARVIPYRG---SWLDFEFDAKDLVYVRIDR-RRKLPATTLLFALdgae 223
Cdd:PRK08565 152 IVSQEDLAPNrvlV----DKGEAGSSITHT--AKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRAL---- 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 224 tealraerkaqkkdllpyeaqGMAKEEilnffydtitytrasggwktpfnadrmkgvkvasDLVDAASgqvvaeagtkMT 303
Cdd:PRK08565 222 ---------------------GLETDR----------------------------------DIVYAVS----------LD 236
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 304 PRLIKKLvegglaeqlvsteeltgrylavdiinertgevlfeagdelsasdLDKLEKAGvdelpvlaidhlnvgayirnt 383
Cdd:PRK08565 237 PEIQQEL--------------------------------------------LPSLEQAS--------------------- 251
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 384 maaDRNASREDALIDIYRVMRPGEPPT--LESAEALFaglffdsERYDLSAVGrvkmnarlnfqTEDSVRVLRKQDIMSI 461
Cdd:PRK08565 252 ---SIAATVEDALDYIGKRVAIGQPREyrIERAEQIL-------DKYLLPHLG-----------TSPEDRIKKAYFLGQM 310
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 462 LKVLVNLKDGRGEIDDIDHLGNRRVRSVGELMENQYRVGLLRMERAIRERMSS-------VEIDTVMPHDLINAK--PAA 532
Cdd:PRK08565 311 ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKsyargrkLDLRAIVRPDIITERirHAL 390
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 533 AAVREFFGSSQLSQFMDQTNPLSEITHKRRLsaLGPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYA 612
Cdd:PRK08565 391 ATGNWVGGRTGVSQLLDRTNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMA 466
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 613 RVNQ-----------YGF--------IESPY-----------------------RKVRD----SIVTDEV---------- 636
Cdd:PRK08565 467 QISVgvdeeeveeilYELgvvpveeaREEEYiswsrvylngrligyhpdgeelaEKIRElrrsGKISDEVnvayietgei 546
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 637 --VYLSAmEEGR-----YVVAQANAELDADNRFA--------ADLVscRQGG-EYLMFRPE-----AIDLIDVSPKQ--- 692
Cdd:PRK08565 547 neVYVNC-DSGRvrrplIVVENGKPKLTREHVEKlkkgeltfDDLV--KMGViEYLDAEEEenayvALDPEDLTPEHthl 623
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 693 ------LVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPLvgtgmeatvardsgvtivakrkgivdqidatRIV 766
Cdd:PRK08565 624 eiwppaILGITASIIPYPEHNQSPRNTYQAAMAKQSLGLYAANFRI-------------------------------RTD 672
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 767 VRAtdssdatapgvdiyNLLKFqrsnqntciTQRPLVKVgdRVAagDIIA--DGPStelgelalGRNVLVAFMPWNGYNF 844
Cdd:PRK08565 673 TRG--------------HLLHY---------PQRPLVQT--RAL--EIIGynDRPA--------GQNAVVAVLSYTGYNI 717
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 845 EDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQE-EITRDIPNV----GEEALKNLDEAGIVYIGAEVRPGDILVGKV 919
Cdd:PRK08565 718 EDAIIMNKASIERGLARSTFFRTYETEERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKT 797
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 920 TPkgesP-MTPEEKLLRAIFGEKasdvRDTSLRLPPGVAGTivevrvfsrrgVDKderalaieraeieklakdrdderai 998
Cdd:PRK08565 798 SP----PrFLEELEELSLGLQER----RDTSVTVRHGEKGI-----------VDT------------------------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 999 lersfytrlkeVILGQTAQSGpkgmkagtvltdaelanltkgqwrqisiadeqvmetveslgkvfddsiqalqnrfenkv 1078
Cdd:PRK08565 834 -----------VLITESPEGN----------------------------------------------------------- 843
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1079 eklqrgdelppgvmKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQIL 1158
Cdd:PRK08565 844 --------------KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLL 909
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1159 ETHLGWASAGLGkqigRAIDqyrlamkgrgdaaqtmdglritlkeaygqkvyddqiadmtegellelggnlrkgvpfATP 1238
Cdd:PRK08565 910 ESIAGKVAALEG----RFVD---------------------------------------------------------ATP 928
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1239 vFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQF 1318
Cdd:PRK08565 929 -FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRARE 1007
|
1450 1460 1470 1480 1490 1500 1510 1520
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1319 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD-------DVSG-------RTKVYEAIVRGDDN--FEAGIPESFNVLVKE 1382
Cdd:PRK08565 1008 GGLRFGEMERDCLIGHGAAMLLKERLLDSSDkttiyvcELCGhiawydrRKNKYVCPIHGDKGniSPVEVSYAFKLLLQE 1087
|
1530
....*....|.
gi 1719379330 1383 LRSLGLNVELN 1393
Cdd:PRK08565 1088 LMSMGISPRLK 1098
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
686-1393 |
1.61e-63 |
|
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: 228.37 E-value: 1.61e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 686 IDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPLvgtgmeatvardsgvtivakrkgivdqidatRI 765
Cdd:TIGR03670 119 LEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYRI-------------------------------RL 167
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 766 VVRAtdssdatapgvdiyNLLKFqrsnqntciTQRPLVKVgdRVAagDIIadgpstELGELALGRNVLVAFMPWNGYNFE 845
Cdd:TIGR03670 168 DTRG--------------HLLHY---------PQKPLVKT--RVL--ELI------GYDDRPAGQNFVVAVMSYEGYNIE 214
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 846 DSILINERIVKDDVFTSIHIEEFEVMARDTKLGQE-EITRDIPNV----GEEALKNLDEAGIVYIGAEVRPGDILVGKVT 920
Cdd:TIGR03670 215 DALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTS 294
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 921 PkgesPMTPEEkllRAIFGEKASDVRDTSLRLPPGVAGTivevrvfsrrgVDKderalaieraeieklakdrdderaile 1000
Cdd:TIGR03670 295 P----PRFLEE---LREFGLVTERRRDTSVTVRHGEKGI-----------VDK--------------------------- 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1001 rsfytrlkeVILgqtaqsgpkgmkagtvltdaelanltkgqwrqisiadeqvMETVESlgkvfddsiqalqnrfenkvek 1080
Cdd:TIGR03670 330 ---------VII----------------------------------------TETEEG---------------------- 338
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1081 lqrgdelppgvMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQILET 1160
Cdd:TIGR03670 339 -----------NKLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1161 HLGWASAglgkQIGRAIDqyrlamkgrgdaaqtmdglritlkeaygqkvyddqiadmtegellelggnlrkgvpfATPvF 1240
Cdd:TIGR03670 408 IAGKVAA----LEGRRVD---------------------------------------------------------GTP-F 425
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1241 DGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGG 1320
Cdd:TIGR03670 426 EGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGG 505
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1321 QRFGEMEVWALEAYGAAYTLQEMLTVKSDDVS-------GRTKVYEAI-------VRGD--DNFEAGIPESFNVLVKELR 1384
Cdd:TIGR03670 506 LRFGEMERDVLIGHGAAMLLKERLLDESDKYVvyvcencGHIAWEDKRkgtaycpVCGEtgDISPVEMSYAFKLLLDELK 585
|
....*....
gi 1719379330 1385 SLGLNVELN 1393
Cdd:TIGR03670 586 SLGISPRLE 594
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
686-1388 |
6.78e-59 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 214.82 E-value: 6.78e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 686 IDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVKADAPLvgtgmeatvardsgvtivakrkgivdqidatRI 765
Cdd:PRK07225 125 LEIDPSLILGIGAGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKL-------------------------------RP 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 766 VVRAtdssdatapgvdiyNLLKFqrsnqntciTQRPLVKVgdrvAAGDIIA--DGPStelgelalGRNVLVAFMPWNGYN 843
Cdd:PRK07225 174 DTRG--------------HLLHY---------PQVPLVKT----QTQEIIGfdERPA--------GQNFVVAVMSYEGYN 218
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 844 FEDSILINERIVKDDVFTSIHIEEFEVMARDTKLGQE-EITRDIPNV----GEEALKNLDEAGIVYIGAEVRPGDILVGK 918
Cdd:PRK07225 219 IEDALIMNKASIERGLGRSHFFRTYEGEERRYPGGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGK 298
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 919 VTPkgesPMTPEEKllrAIFGEKASDVRDTSLrlppgvagtivevrvfsrrgvdkderalaieraeieklakdrdderai 998
Cdd:PRK07225 299 TSP----PRFLEEP---DDFGISPEKRRETSV------------------------------------------------ 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 999 lersfytrlkevilgqTAQSGPKGMkAGTVLtdaelanltkgqwrqisiadeqVMETVESlgkvfddsiqalqnrfenkv 1078
Cdd:PRK07225 324 ----------------TMRSGEEGI-VDTVI----------------------LTETEEG-------------------- 344
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1079 eklqrgdelppgvMKMVKVFVAVKRKLQPGDKMAGRHGNKGVVSRILPQEDMPYLEDGQPVDLVLNPLGVPSRMNIGQIL 1158
Cdd:PRK07225 345 -------------SRLVKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVL 411
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1159 EThlgwasagLGKQIGraidqyrlAMKGRgdaaqTMDGlritlkeaygqkvyddqiadmtegellelggnlrkgvpfaTP 1238
Cdd:PRK07225 412 EM--------IGGKVG--------SLEGR-----RVDG----------------------------------------TA 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1239 vFDGAREEDICQQLEKAGLDRSGQVTLIDGRTGEAFDRKVTVGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQF 1318
Cdd:PRK07225 431 -FSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRARE 509
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1319 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVS-------GRTKVYEAIVR-------GD--DNFEAGIPESFNVLVKE 1382
Cdd:PRK07225 510 GGLRFGEMERDVLIGHGAAMLLKERLLDESDKVEiyvcakcGMIAIYDKKRNrkycpicGEetDIYPVEMSYAFKLLLDE 589
|
....*.
gi 1719379330 1383 LRSLGL 1388
Cdd:PRK07225 590 LKSLGI 595
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
26-530 |
2.54e-55 |
|
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: 198.37 E-value: 2.54e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 26 NLIEVQRSSYDHFLQMDVPPEKRANLGLQEVFRSVFPIKDfSDRAVLDFVKYELEQPKYDV----------EECQQRGMT 95
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGEN-GDKLSLKFGQIRLGKPMFDEtdgstreiypQECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 96 FAAPLKVTLRLSVFDVEedtglrsirDIKEQDVYMGDMPLMTAN------------------------GTFIINGTERVI 151
Cdd:pfam04563 80 YSAPLYVDLELSVYNGE---------DIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVI 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 152 VSQMHRS---PGVFFDHDKGKTHSSGKYLFAAR--VIPYRGSWLDF-EFDAKDLVYVRIDRRRK-LPATTLLFALdGAET 224
Cdd:pfam04563 151 VAQEHRSrnhPIVFKKADPKKRGSVASVRSSAEisVRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRAL-GFTS 229
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 225 EalraerkaqkkdllpyeaqgmakEEILNffydtitytrasggwktpfnadrmkgvKVASDLVDAasgqvvaeagtkmtp 304
Cdd:pfam04563 230 D-----------------------REIFE---------------------------LICYDVNDQ--------------- 244
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 305 rlikklvegglaeQLVsteeltgrylavdiinertgevlfeagDELSASdldkLEKAGVDELPvlaiDHLNVGAYIRNTM 384
Cdd:pfam04563 245 -------------QLQ---------------------------EELLPS----LEEGFKIRIQ----TQEQALDYIGGRG 276
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 385 AAdrnasredalidIYRVMRPGEPPTLESAEALFAGLFFDSERYDLSAVGRVKMnarlnfqtedsvrvlrkqdIMSILKV 464
Cdd:pfam04563 277 RA------------IFRMGRPREPRIKYAEEILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRR 325
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1719379330 465 LVNLKDGRGEIDDIDHLGNRRVRSVGELMENQYRVGLLRMERAIRERMSSV--EIDTVMPHDLINAKP 530
Cdd:pfam04563 326 LLLLALGRREVDDRDHLGNKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVlgSPDDLMLQLLVNAKP 393
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
546-613 |
5.73e-38 |
|
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: 136.12 E-value: 5.73e-38
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1719379330 546 QFMDQTNPLSEITHKRRLSAlGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYAR 613
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1319-1392 |
1.36e-33 |
|
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: 124.62 E-value: 1.36e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 1319 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVSGRTKVYEA-----IVRGDDNFEAG-IPESFNVLVKELRSLGL 1388
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....
gi 1719379330 1389 NVEL 1392
Cdd:pfam04560 81 DPRL 84
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
624-689 |
1.41e-30 |
|
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: 115.16 E-value: 1.41e-30
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1719379330 624 YRKVRDSIVTDEVVYLSAMEEGRYVVAQANAELDADNRFAADLVSCRQGGEYLMFRPEAIDLIDVS 689
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
468-616 |
4.70e-26 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 113.89 E-value: 4.70e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 468 LKDGRGEIDDIDHLGNRRVRSVGELMENQYRVGLLRM--------ERA-IRERMSSVEidTVMPHDLINA--KPAAAAVR 536
Cdd:PRK09606 320 LALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLardvkyqlERAnMRNRELSIK--TAVRSDVLTErlEHAMATGN 397
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 537 EFFGSSQLSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNQ 616
Cdd:PRK09606 398 WVGGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
389-487 |
1.20e-11 |
|
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: 65.06 E-value: 1.20e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 389 NASREDALIDIYRV--MRPGEPPTLESAEALFAglffdserydlSAVGRVKMNARLNFQTEDSVRVLRKQDIMSILKVLV 466
Cdd:pfam04561 96 IYTQEEALDYIGKGfaLRRGEEPRLQRAREILY-----------SRDPKYNLNKHLGLNEPFENERLKAQDILYMIDRLL 164
|
90 100
....*....|....*....|.
gi 1719379330 467 NLKDGRGEIDDIDHLGNRRVR 487
Cdd:pfam04561 165 NLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
286-368 |
8.07e-09 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 60.47 E-value: 8.07e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 286 LVDAASGQVVAE------AGTKMTPrlikkLVEGGlaEQLVSTEE-LTGRYLAVDIINERTGEVLFEAGDELSASDLDKL 358
Cdd:PRK00566 767 LVDVAQDVIVREddcgtdRGIEVTA-----IIEGG--EVIEPLEErILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKI 839
|
90
....*....|
gi 1719379330 359 EKAGVDELPV 368
Cdd:PRK00566 840 EEAGIEEVKI 849
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
286-365 |
2.91e-04 |
|
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA polymerase, beta' subunit/160 kD subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 439856 [Multi-domain] Cd Length: 1165 Bit Score: 45.54 E-value: 2.91e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1719379330 286 LVDAASGQVVAEAGTKMTPRL-IKKLVEGG-LAEQLvsTEELTGRYLAVDIINERTGEVLFEAGDELSASDLDKLEKAGV 363
Cdd:COG0086 766 LVDVAQDVIVTEEDCGTDRGItVTAIKEGGeVIEPL--KERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGI 843
|
..
gi 1719379330 364 DE 365
Cdd:COG0086 844 DS 845
|
|
| |
