|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1365 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2187.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1 MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQrkpEGLQAAFTSVFPIVSHNGFARLEFVSYALS 80
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPED---EGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 81 SPAFNIKECQQRGLTYCSALRAKVRLVILDkespnkpvVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGV 160
Cdd:PRK00405 78 EPKYDVEECKERGLTYSAPLRVKLRLINKE--------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 161 FFEHDKGKThSSGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTlmde 240
Cdd:PRK00405 150 YFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG---- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 241 gaqlefvperlrgevarfditdrdgkvivqkdkrinakhirdleaaktKFISVPEDYLLGRVLAKNVVDGDTGEVIASAN 320
Cdd:PRK00405 225 ------------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEAN 256
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 321 DEVTESVleklreagikdiqtlytndldQGPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEA 400
Cdd:PRK00405 257 DEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKR 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 401 YDLSKVGRMKFNRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERA 480
Cdd:PRK00405 316 YDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERA 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 481 VKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTH 560
Cdd:PRK00405 396 VRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 561 YGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELV 640
Cdd:PRK00405 476 YGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 641 SSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGT 720
Cdd:PRK00405 556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 721 TVQAFRGGVVDYVDAGRIVIRVndDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGEL 800
Cdd:PRK00405 636 VVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGEL 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 801 ALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIG 880
Cdd:PRK00405 714 ALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIG 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 881 AEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTRegiqrdkraqqiiddelk 960
Cdd:PRK00405 794 AEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------ 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 961 ryrldlndqlrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieek 1040
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1041 rhqfdlafeekrkkLTQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPL 1120
Cdd:PRK00405 856 --------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPL 921
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1121 GVPSRMNVGQVLEVHLGWAAKGLGWRigemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlregvpFAT 1200
Cdd:PRK00405 922 GVPSRMNIGQILETHLGWAAKGLGIK---------------------------------------------------FAT 950
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1201 PVFDGATEEEMGKMLDLAFPDDIAqqldmnpsknQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLV 1280
Cdd:PRK00405 951 PVFDGAKEEEIKELLEEAGLPEDG----------KTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLV 1020
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1281 TQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLG 1360
Cdd:PRK00405 1021 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLG 1100
|
....*
gi 500212820 1361 IDIDL 1365
Cdd:PRK00405 1101 LDVEL 1105
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1365 |
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: 1755.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 8 KKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSVFPIVSHNGFARLEFVSYALSSPAFNIK 87
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 88 ECQQRGLTYCSALRAKVRLVILDKespnkPVVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKG 167
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEE-----DGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 168 kTHSSGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTpeqilanffvfdnftlmdegaqlefv 247
Cdd:TIGR02013 156 -TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT-------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 248 perlrgevarfditdrdgkvivqkdkrinakhirdleaaktkfisvpedyllgrvlaknvvdgdtgeviasandevtesv 327
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 328 leklreagikdIQTLYTNDLDQGPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVG 407
Cdd:TIGR02013 209 -----------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVG 277
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 408 RMKFNRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQ 487
Cdd:TIGR02013 278 RYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMST 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 488 AESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPI 567
Cdd:TIGR02013 358 QDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPI 437
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 568 ETPEGPNIGLINSLALYAHLNEYGFLETPYRKVVDSKV--TDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREA 645
Cdd:TIGR02013 438 ETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYR 517
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 646 GETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGTTVQAF 725
Cdd:TIGR02013 518 GEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAK 597
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 726 RGGVVDYVDAGRIVIRvNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQN 805
Cdd:TIGR02013 598 RGGVVEYVDAKRIVIR-YDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRN 676
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 806 MLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEA 885
Cdd:TIGR02013 677 VLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKA 756
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 886 GDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREgiqrdkraqqiiddelkryrld 965
Cdd:TIGR02013 757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE---------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 966 lndqlrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfd 1045
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1046 lafeekrkkltQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSR 1125
Cdd:TIGR02013 815 -----------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1126 MNVGQVLEVHLGWAAKGLGwrigemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlREGVPFATPVFDG 1205
Cdd:TIGR02013 884 MNIGQILETHLGWAGKRLG------------------------------------------------RKGVPIATPVFDG 915
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1206 ATEEEMGKMLDLAFPddiaqqldmnPSKNQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPL 1285
Cdd:TIGR02013 916 ASEEEIKEYLEKAGL----------PRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPL 985
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1286 GGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDL 1365
Cdd:TIGR02013 986 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1365 |
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: 1569.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 12 RKSFAKRPIVHQVPFLLATQLESFSTFLQadvpatqrkpEGLQAAFTSVFPIVSHNGFARLEFVSYALSSPAFNIKECQQ 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLE----------EGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 92 RGLTYCSALRAKVRLVilDKESpnkpvvKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKths 171
Cdd:COG0085 71 RDLTYAAPLYVKVRLV--NKET------GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK--- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 172 SGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTpeqilanffvfdnftlmdegaqlefvperl 251
Cdd:COG0085 140 SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLE------------------------------ 189
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 252 rgevarfdiTDRDgkvivqkdkrinakhIRDLeaaktkFISVPEDyllgrvlaknvvdgdtgeviasandevtesvlekl 331
Cdd:COG0085 190 ---------TDEE---------------ILEA------FGDDPIQ----------------------------------- 204
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 332 reagikdiqtlytndldqgPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKF 411
Cdd:COG0085 205 -------------------EYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKI 265
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 412 NRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESE 491
Cdd:COG0085 266 NKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVE 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 492 NLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 571
Cdd:COG0085 346 AITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPE 425
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 572 GPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMV 651
Cdd:COG0085 426 GPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLV 505
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 652 TPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPvvgtgiertcavdsgttvqafrggvvd 731
Cdd:COG0085 506 PPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------------------------- 558
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 732 yvdagrivirvnddeavagevgVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQNMLIAFM 811
Cdd:COG0085 559 ----------------------LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFM 616
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 812 PWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVG 891
Cdd:COG0085 617 PWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVG 696
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 892 KVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREgiqrdkraqqiiddelkryrldlndqlr 971
Cdd:COG0085 697 KVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE---------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 972 ivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeek 1051
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1052 rkkltQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQV 1131
Cdd:COG0085 749 -----EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQV 823
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1132 LEVHLGWAAKGLGWRIgemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlregvpfATPVFDGATEEEM 1211
Cdd:COG0085 824 LETHLGWAAALLGRRV---------------------------------------------------ATPVFDGAPEEEI 852
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1212 GKMLDLAfpddiaqqldMNPSKNQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 1291
Cdd:COG0085 853 RELLEKA----------GLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQF 922
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500212820 1292 GGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDL 1365
Cdd:COG0085 923 GGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1366 |
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: 864.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 27 LLATQLESFSTFLQadvpatqrkpEGLQAAFTSVFPIVS--HNGFARLEFVSYALSSP---------AFNIKECQQRGLT 95
Cdd:cd00653 1 LVKQQIDSFNYFLN----------VGLQEIVKSIPPITDtdDDGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 96 YCSALRAKVRLVILDKEspnkpvvkEVKEQEVYMGEIPLMT------------------------PTGSFVINGTERVIV 151
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG--------KIKEQEVFIGEIPIMLrsklcnlngltpeeliklgecpldPGGYFIINGTEKVII 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 152 SQLHRSPGVFFEHDkgkthSSGKLLFSARIIP----YRGSWLDFEFDpkdilyfrvdrrrkmpvtillkaigltpeqila 227
Cdd:cd00653 143 NQEQRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSD--------------------------------- 184
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 228 nffvfdnftlmdegaqlefvperlrgevarfditdrdgkvivQKDKRINAKHirdleaaktkfisvpedyllgrvlaknv 307
Cdd:cd00653 185 ------------------------------------------KKKDRIYVRI---------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 308 vdgdtgeviasandevtesvleklreagikdiqtlytndldqgPYIsstlrvdettdrtaariaiyrmmrpgepPTEEAV 387
Cdd:cd00653 195 -------------------------------------------DLK----------------------------RQEEAL 203
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 388 EALFNRLFyseeaydlskvgrmkfnrrvgrdeivgpmtlqddDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAE 467
Cdd:cd00653 204 KYIGKRFE----------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQ 249
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 468 NQFRAGLVRVERAVKERLGQAESEN--LMPHDLINSKPISSAIREFFGSSQ------------LSQFMDQTNPLSEITHK 533
Cdd:cd00653 250 NLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHK 329
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 534 RRVSAlgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNeyGFLETPYRKvVDSKVTdqidyls 613
Cdd:cd00653 330 RRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRI-VEKEVT------- 396
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 614 aieegrymiaqanaaidengqlidelvssreagetmmvtpdriqYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQR 693
Cdd:cd00653 397 --------------------------------------------HIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK 432
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 694 QAVP----------------CLRPEKPVVGTGIErtcavdsgttvqafrggvvdyvdagrivirvnddeavagevgvdiy 757
Cdd:cd00653 433 QAVGtpalnqqyrmdtklylLLYPQKPLVGTGIE---------------------------------------------- 466
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 758 NLIKYtrsnqntninqrpivkmgdkvsrgdvladgastdlGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837
Cdd:cd00653 467 EYIAF-----------------------------------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSI 511
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 838 HIEELNVVARDTKLGPEEITR-DISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKGETQLTPeekllraIFGEKA 916
Cdd:cd00653 512 HYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKA 584
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 917 SDVKDTSLRVPSGMSGTVIDVQVFTRegiqrdkraqqiiddelkryrldlndqlrivegdafqrlarmlvgkvanggpkk 996
Cdd:cd00653 585 RDVRDTSLKYPGGEKGIVDDVKIFSR------------------------------------------------------ 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 997 lakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeekrkkltqgdELPPGVLKMVKVYLAVK 1076
Cdd:cd00653 611 ---------------------------------------------------------------ELNDGGNKLVKVYIRQK 627
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1077 RRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLGWAAKGLGWRIgemlqrqak 1156
Cdd:cd00653 628 RKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG--------- 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1157 ieelrvfltkiynesgrqedlesftdeeilelaknlregvpFATPvFDGATEEEMGKMLDLAFPDdiaqqldmNPSKnqV 1236
Cdd:cd00653 699 -----------------------------------------DATP-FDGAEEEDISELLGEAGLN--------YYGK--E 726
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1237 RLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEM 1316
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806
|
1370 1380 1390 1400 1410 1420
....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1317 LTVKSDDVTGRTKVYENLV----------KGDHVIDAGMPESFNVLVKEIRSLGIDIDLD 1366
Cdd:cd00653 807 LTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
724-1290 |
1.86e-160 |
|
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: 486.27 E-value: 1.86e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 724 AFRGGVVDYVDAGRIVIRVNDDEAVAGevgvdIYNLIKYTRSNQNT---NINQRPIVKMGdKVSRGDvladgastdLGEL 800
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMG-----IYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGEL 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 801 ALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEElnVVARDTKLGP-EEITRDISNLAEVQLGRLDESGIVYI 879
Cdd:pfam00562 67 PLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRV 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 880 GAEVEAGDVLVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTregiqrdkraqqiiddel 959
Cdd:pfam00562 145 GAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------------------ 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 960 kryrldlndqlrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsiee 1039
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1040 krhqfdlafeekrkkltqgdeLPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNP 1119
Cdd:pfam00562 201 ---------------------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1120 LGVPSRMNVGQVLEVHLGWAAKGLgwrigemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlreGVPFA 1199
Cdd:pfam00562 260 HGVPSRMTIGQLLETHLGKAAALL---------------------------------------------------GVFVD 288
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1200 TPVFDGATEEemgkmldlafPDDIAQQLD---MNPSKNQVrLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGP 1276
Cdd:pfam00562 289 ATPFDGASTE----------VEDIGELLEkagYNYYGKEV-LYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGP 357
|
570
....*....|....
gi 500212820 1277 YSLVTQQPLGGKAQ 1290
Cdd:pfam00562 358 YSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1365 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2187.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1 MQYSFTEKKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQrkpEGLQAAFTSVFPIVSHNGFARLEFVSYALS 80
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPED---EGLEEVFRSIFPIEDFNGNLSLEFVSYELG 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 81 SPAFNIKECQQRGLTYCSALRAKVRLVILDkespnkpvVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGV 160
Cdd:PRK00405 78 EPKYDVEECKERGLTYSAPLRVKLRLINKE--------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 161 FFEHDKGKThSSGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTlmde 240
Cdd:PRK00405 150 YFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG---- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 241 gaqlefvperlrgevarfditdrdgkvivqkdkrinakhirdleaaktKFISVPEDYLLGRVLAKNVVDGDTGEVIASAN 320
Cdd:PRK00405 225 ------------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEAN 256
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 321 DEVTESVleklreagikdiqtlytndldQGPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEA 400
Cdd:PRK00405 257 DEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKR 315
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 401 YDLSKVGRMKFNRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERA 480
Cdd:PRK00405 316 YDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERA 395
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 481 VKERLGQAESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTH 560
Cdd:PRK00405 396 VRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTH 475
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 561 YGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELV 640
Cdd:PRK00405 476 YGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELV 555
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 641 SSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGT 720
Cdd:PRK00405 556 TARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGA 635
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 721 TVQAFRGGVVDYVDAGRIVIRVndDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGEL 800
Cdd:PRK00405 636 VVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGEL 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 801 ALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIG 880
Cdd:PRK00405 714 ALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIG 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 881 AEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTRegiqrdkraqqiiddelk 960
Cdd:PRK00405 794 AEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------ 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 961 ryrldlndqlrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieek 1040
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1041 rhqfdlafeekrkkLTQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPL 1120
Cdd:PRK00405 856 --------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPL 921
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1121 GVPSRMNVGQVLEVHLGWAAKGLGWRigemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlregvpFAT 1200
Cdd:PRK00405 922 GVPSRMNIGQILETHLGWAAKGLGIK---------------------------------------------------FAT 950
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1201 PVFDGATEEEMGKMLDLAFPDDIAqqldmnpsknQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLV 1280
Cdd:PRK00405 951 PVFDGAKEEEIKELLEEAGLPEDG----------KTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLV 1020
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1281 TQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLG 1360
Cdd:PRK00405 1021 TQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLG 1100
|
....*
gi 500212820 1361 IDIDL 1365
Cdd:PRK00405 1101 LDVEL 1105
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1365 |
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: 1755.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 8 KKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADVPATQRKPEGLQAAFTSVFPIVSHNGFARLEFVSYALSSPAFNIK 87
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 88 ECQQRGLTYCSALRAKVRLVILDKespnkPVVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKG 167
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEE-----DGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 168 kTHSSGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTpeqilanffvfdnftlmdegaqlefv 247
Cdd:TIGR02013 156 -TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT-------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 248 perlrgevarfditdrdgkvivqkdkrinakhirdleaaktkfisvpedyllgrvlaknvvdgdtgeviasandevtesv 327
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 328 leklreagikdIQTLYTNDLDQGPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVG 407
Cdd:TIGR02013 209 -----------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVG 277
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 408 RMKFNRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQ 487
Cdd:TIGR02013 278 RYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMST 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 488 AESENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPI 567
Cdd:TIGR02013 358 QDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPI 437
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 568 ETPEGPNIGLINSLALYAHLNEYGFLETPYRKVVDSKV--TDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREA 645
Cdd:TIGR02013 438 ETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYR 517
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 646 GETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGTTVQAF 725
Cdd:TIGR02013 518 GEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAK 597
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 726 RGGVVDYVDAGRIVIRvNDDEAVAGEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQN 805
Cdd:TIGR02013 598 RGGVVEYVDAKRIVIR-YDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRN 676
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 806 MLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEA 885
Cdd:TIGR02013 677 VLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKA 756
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 886 GDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREgiqrdkraqqiiddelkryrld 965
Cdd:TIGR02013 757 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE---------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 966 lndqlrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfd 1045
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1046 lafeekrkkltQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSR 1125
Cdd:TIGR02013 815 -----------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSR 883
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1126 MNVGQVLEVHLGWAAKGLGwrigemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlREGVPFATPVFDG 1205
Cdd:TIGR02013 884 MNIGQILETHLGWAGKRLG------------------------------------------------RKGVPIATPVFDG 915
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1206 ATEEEMGKMLDLAFPddiaqqldmnPSKNQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPL 1285
Cdd:TIGR02013 916 ASEEEIKEYLEKAGL----------PRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPL 985
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1286 GGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDL 1365
Cdd:TIGR02013 986 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1365 |
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: 1569.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 12 RKSFAKRPIVHQVPFLLATQLESFSTFLQadvpatqrkpEGLQAAFTSVFPIVSHNGFARLEFVSYALSSPAFNIKECQQ 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLE----------EGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 92 RGLTYCSALRAKVRLVilDKESpnkpvvKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKths 171
Cdd:COG0085 71 RDLTYAAPLYVKVRLV--NKET------GEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK--- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 172 SGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTpeqilanffvfdnftlmdegaqlefvperl 251
Cdd:COG0085 140 SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLE------------------------------ 189
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 252 rgevarfdiTDRDgkvivqkdkrinakhIRDLeaaktkFISVPEDyllgrvlaknvvdgdtgeviasandevtesvlekl 331
Cdd:COG0085 190 ---------TDEE---------------ILEA------FGDDPIQ----------------------------------- 204
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 332 reagikdiqtlytndldqgPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKF 411
Cdd:COG0085 205 -------------------EYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKI 265
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 412 NRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESE 491
Cdd:COG0085 266 NKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVE 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 492 NLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 571
Cdd:COG0085 346 AITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPE 425
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 572 GPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMV 651
Cdd:COG0085 426 GPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLV 505
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 652 TPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPvvgtgiertcavdsgttvqafrggvvd 731
Cdd:COG0085 506 PPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAP--------------------------- 558
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 732 yvdagrivirvnddeavagevgVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQNMLIAFM 811
Cdd:COG0085 559 ----------------------LLHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFM 616
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 812 PWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVG 891
Cdd:COG0085 617 PWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVG 696
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 892 KVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREgiqrdkraqqiiddelkryrldlndqlr 971
Cdd:COG0085 697 KVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE---------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 972 ivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeek 1051
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1052 rkkltQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQV 1131
Cdd:COG0085 749 -----EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQV 823
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1132 LEVHLGWAAKGLGWRIgemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlregvpfATPVFDGATEEEM 1211
Cdd:COG0085 824 LETHLGWAAALLGRRV---------------------------------------------------ATPVFDGAPEEEI 852
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1212 GKMLDLAfpddiaqqldMNPSKNQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 1291
Cdd:COG0085 853 RELLEKA----------GLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQF 922
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500212820 1292 GGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDL 1365
Cdd:COG0085 923 GGQRFGEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
8-1365 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1416.22 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 8 KKRIRKSFAKRPIVHQVPFLLATQLESFSTFLQADvpatQRKPEGLQAAFTSVFPIVSHNGFARLEFVSYALSSPAFNIK 87
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSK----DGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 88 ECQQRGLTYCSALRAKVRLVILDKE--SPNKPVVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHD 165
Cdd:PRK09603 84 EAMERGITYSIPLKIKVRLILWEKDtkSGEKNGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 166 KGKThSSGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMDEGAQLE 245
Cdd:PRK09603 164 ESST-SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 246 FVPERLRGEVaRFDITDRDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDYLLGRVLAKNVVDGDtgEVIASANDEVTE 325
Cdd:PRK09603 243 FASLDANQRM-EFDLKDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGK--EVLLDMLTQLDK 319
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 326 SVLEKLREAGIKDIqtLYTNDLDQG----------------PYISSTLRVDETTDRTAARIaiYRMMRPGEPPTEEAVEA 389
Cdd:PRK09603 320 NKLEKIHDLGVQEF--VIINDLALGhdasiihsfsadseslKLLKQTEKIDDENALAAIRI--HKVMKPGDPVTTEVAKQ 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 390 LFNRLFYSEEAYDLSKVGRMKFNRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQ 469
Cdd:PRK09603 396 FVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANE 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 470 FRAGLVRVERAVKERLGQAES--ENLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRE 547
Cdd:PRK09603 476 LHSGLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKD 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 548 RAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANA 627
Cdd:PRK09603 556 RVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPAST 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 628 AIDENGQLIDELVSSREAGETMMVTPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVG 707
Cdd:PRK09603 636 PIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVG 715
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 708 TGIERTCAVDSGTTVQAFRGGVVDYVDAGRIVIRVNDDEavagEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGD 787
Cdd:PRK09603 716 TGIEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKE----EAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQ 791
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 788 VLADGASTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQ 867
Cdd:PRK09603 792 IIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEA 871
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 868 LGRLDESGIVYIGAEVEAGDVLVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQR 947
Cdd:PRK09603 872 LAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEK 951
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 948 DKRAQQIIDDELKRYRLDLNDQLRIVEGDAFQRLARML----VGKVANGGPKKLAKGTKIDQAYLEDLDHYHWFD-IRLA 1022
Cdd:PRK09603 952 DARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLsqaiLEEPFSHNGKDYKEGDQIPKEEIASINRFTLASlVKKY 1031
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1023 DDEAAAQLEAIKNSIEEKRHQFDLAFEEKRKKLTQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIE 1102
Cdd:PRK09603 1032 SKEVQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVA 1111
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1103 DMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLGWAAKGLGWRIGEMLQRQAK--IEELRVFLTKIYN-----ESGRQE 1175
Cdd:PRK09603 1112 DMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfAKELRAKMLEIANainekDPLTIH 1191
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1176 DLESFTDEEILELAKNLREGVPFATPVFDGATEEEMGKMLDLAfpddiaqQLDMNpskNQVRLYDGRTGEQFERRVTLGY 1255
Cdd:PRK09603 1192 ALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELA-------KIAMD---GKMDLYDGRTGEKMRERVNVGY 1261
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1256 MHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLV 1335
Cdd:PRK09603 1262 MYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIA 1341
|
1370 1380 1390
....*....|....*....|....*....|
gi 500212820 1336 KGDHVIDAGMPESFNVLVKEIRSLGIDIDL 1365
Cdd:PRK09603 1342 KGEQVGESEIPETFYVLTKELQSLALDINI 1371
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
27-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1413.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 27 LLATQLESFSTFlqadVPATQRKpEGLQAAFTSVFPIVSHNGFARLEFVSYALSSPAFNIKECQQRGLTYCSALRAKVRL 106
Cdd:PRK14844 32 LVKVQKESYDSF----TPKNKGN-ERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRL 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 107 VIL---------------DKESPNKPVVKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHS 171
Cdd:PRK14844 107 VIMqdgisldeyksikesGDHSKLATVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYN 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 172 SGKLLFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFTLMDEGAQLEFVPERL 251
Cdd:PRK14844 187 SGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKF 266
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 252 RGEVARFDITDRDGKVIVQKDKRINAKHIRDLEAAKTKFISVPEDYLLGRVLAKNVVDGDTGEVIASANDEVTESVLEKL 331
Cdd:PRK14844 267 KGVRLPFDLMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKL 346
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 332 REAGIKDIQTLYTNDLDQGPYISSTLRVDETTDRTAARIAIYRMMRPGEPPTEEAVEALFNRLFYSEEAYDLSKVGRMKF 411
Cdd:PRK14844 347 ELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKL 426
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 412 NRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESE 491
Cdd:PRK14844 427 NSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLD 506
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 492 NLMPHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 571
Cdd:PRK14844 507 KVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPE 586
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 572 GPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMV 651
Cdd:PRK14844 587 GQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMV 666
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 652 TPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVD 731
Cdd:PRK14844 667 SSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVD 746
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 732 YVDAGRIVIRVNDDEAVaGEVGVDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQNMLIAFM 811
Cdd:PRK14844 747 SSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFM 825
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 812 PWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVG 891
Cdd:PRK14844 826 SWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVG 905
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 892 KVTPKGETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREGIQRDKRAQQIIDDELKRYRLDLNDQLR 971
Cdd:PRK14844 906 KVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIIN 985
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 972 IVEGDAFQRLARMLVgkvaNGGPKklakgtkiDQAYLEDLDHYHWFDIRLADDEAAAQLEAIKNSIEEKRHQFDLAFEEK 1051
Cdd:PRK14844 986 VTSEYFYDELKKLLI----NSGSQ--------DREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRK 1053
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1052 RKKLTQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQV 1131
Cdd:PRK14844 1054 VEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQI 1133
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1132 LEVHLGWAAKGLGWRIGEMLQRQAKIEE---------------------------------------------------- 1159
Cdd:PRK14844 1134 LETHVGWACKKLGEKVGNILDEINKIKSafckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalndel 1213
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1160 -----------------LRVFLTKIYNESGRQE---DLESFTDEEILELAKNLREGVPFATPVFDGATEEEMGKMLDLAf 1219
Cdd:PRK14844 1214 nelvenylnscksaysnLRNFLIEVYSCGSNVSicnNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELA- 1292
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1220 pddiaqqlDMNPSkNQVRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEM 1299
Cdd:PRK14844 1293 --------GLDNS-GQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEM 1363
|
1370 1380 1390 1400 1410 1420
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500212820 1300 EVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDIDLDRN 1368
Cdd:PRK14844 1364 ECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQN 1432
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
25-1364 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1076.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 25 PFLLATQLESFSTFLQadvpatqrkpEGLQAAFTSVFPIVSHNGFARLEFVS--YALSSPAFNIKECQQRGLTYCSALRA 102
Cdd:CHL00001 13 PGFNQIQFEGFCRFID----------QGLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYESLTYSSELYV 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 103 KVRLVilDKESpnkpvvKEVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFF--EHDKgkthsSGKLLFSAR 180
Cdd:CHL00001 83 PAGLI--WKKS------RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYrsELDH-----NGISVYTGT 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 181 IIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANffvfdnftlmdegaqlefvperlrgevarfdi 260
Cdd:CHL00001 150 IISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDN-------------------------------- 197
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 261 tdrdgkvivqkdkrinakhirdleaaktkfISVPEDYLlgrvlaknvvdgdtgeviasandevtESVLEKLREagikdiq 340
Cdd:CHL00001 198 ------------------------------VCYPEIFL--------------------------SFLNDKEKK------- 214
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 341 tlytndldqgpYISStlrvdettdRTAARIAIYRMM--RPGEPPTEEAV-EALFNRLFysEEAYDLSKVGRMKFNRR--- 414
Cdd:CHL00001 215 -----------KIGS---------KENAILEFYQQFacVGGDPVFSESLcKELQKKFF--QQRCELGRIGRRNMNRKlnl 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 415 -VGRDEIvgpmTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESENL 493
Cdd:CHL00001 273 dIPENNT----FLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKL 348
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 494 M--PHDLINSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPE 571
Cdd:CHL00001 349 IptPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSE 428
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 572 GPNIGLINSLALYAHLNEYGFLETPYRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMV 651
Cdd:CHL00001 429 GINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTI 508
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 652 TPDRIQYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVD 731
Cdd:CHL00001 509 AWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKII 588
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 732 YVDAGRIVIRVNDDEavagevgvDIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQNMLIAFM 811
Cdd:CHL00001 589 YTDTDKIILSGNGDT--------LSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYM 660
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 812 PWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVG 891
Cdd:CHL00001 661 PWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVG 740
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 892 KVTPK--GETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQvftregiqrdkraqqiiddelkryrldlndq 969
Cdd:CHL00001 741 KLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR------------------------------- 789
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 970 lrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhWFdirladdeaaaqleaiknsieekrhqfdlafe 1049
Cdd:CHL00001 790 ----------------------------------------------WI-------------------------------- 791
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1050 ekrkkltQGDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVG 1129
Cdd:CHL00001 792 -------QKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVG 864
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1130 QVLEVHLGWAakglgwriGEMLQRQAKIEElrvfltkiYNESGRQEDLESFTDEEILELAKnlREGVPFatpVFDgatee 1209
Cdd:CHL00001 865 QIFECLLGLA--------GDLLNRHYRIAP--------FDERYEQEASRKLVFSELYEASK--QTANPW---VFE----- 918
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1210 emgkmldlafPDdiaqqldmNPSKNqvRLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKA 1289
Cdd:CHL00001 919 ----------PE--------YPGKS--RLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRS 978
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500212820 1290 QFGGQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDA-GMPESFNVLVKEIRSLGIDID 1364
Cdd:CHL00001 979 KQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 1054
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
23-1363 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1033.50 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 23 QVPFLLATQLESFSTFLQadvpatqrkpEGLQAAFTSVFPIVSHNGFARLEFVS--YALSSPAFNIKECQQRGLTYCSAL 100
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLN----------EGLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQI 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 101 RAKVRLVILDKESpnkpvvkeVKEQEVYMGEIPLMTPTGSFVINGTERVIVSQLHRSPGVFFEHDKGKTHssgKLLFSAR 180
Cdd:CHL00207 76 YLPLKFINLKTNK--------IKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSAT 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 181 IIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLTPEQILANFFVFDNFtlmdegaqlefvperlrgevarfdi 260
Cdd:CHL00207 145 LIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSEFL------------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 261 tdrdgkvivqkdkrinakhirdleaaktkfisvpedyllgrvlaknvvdgdtgeviasandevtesvleklreagikdiq 340
Cdd:CHL00207 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 341 tlytndldqgPYISSTLRVDETTDRTAARIAIYRMMRPGEPPT-EEAVEALFNRlFYSEEAYDLSKVGRMKFNRRVGRDE 419
Cdd:CHL00207 200 ----------KKLKPILLNSNSYTNEEILLEIYKNLSPIEPATvNDANQNLFSR-FFDPKNYDLGKVGRYKINNKLNLNI 268
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 420 IVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESENLMPHDLI 499
Cdd:CHL00207 269 PERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLI 348
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 500 NSKPISSAIREFFGSSQLSQFMDQTNPLSEITHKRRVSALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLIN 579
Cdd:CHL00207 349 NPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIG 428
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 580 SLALYAHLNEYGFLETPYRKVVDSKV--TDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMVTPDRIQ 657
Cdd:CHL00207 429 SLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVD 508
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 658 YMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPCLRPEKPVVGTGIERTCAVDSGTTVQAFRGGVVDYVDAGR 737
Cdd:CHL00207 509 FIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYK 588
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 738 IVIRVNDDEAVagevgvdIYNLIKYTRSNQNTNINQRPIVKMGDKVSRGDVLADGASTDLGELALGQNMLIAFMPWNGYN 817
Cdd:CHL00207 589 IIIQDDNNRYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYN 661
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 818 FEDSILISEKVVADDRYTSIHIEELNVVARDTKLGPEEITRDISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKG 897
Cdd:CHL00207 662 FEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKG 741
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 898 ETQLTPEEKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTREgiqrdkraqqiiddelkryrldlndqlrivegda 977
Cdd:CHL00207 742 ESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS---------------------------------- 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 978 fqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeekrkkltQ 1057
Cdd:CHL00207 788 -------------------------------------------------------------------------------K 788
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1058 GDELPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLG 1137
Cdd:CHL00207 789 GDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLG 868
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1138 WAAKGLGWRI-----GEMLQRQAKieelRVFLTKIYNEsgrqedLESFTDEEILelaknlregVPFATPvfdgateeemG 1212
Cdd:CHL00207 869 LAGDNLNKRFkilpfDEMYGSEYS----RILINNKLNQ------ASIKNNEYWL---------FNSYHP----------G 919
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1213 KMLdlafpddiaqqldmnpsknqvrLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 1292
Cdd:CHL00207 920 KMV----------------------LRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHG 977
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 500212820 1293 GQRFGEMEVWALEAYGASYVLQEMLTVKSDDVTGRTKVYENLVKGDHVIDAGMPESFNVLVKEIRSLGIDI 1363
Cdd:CHL00207 978 GQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDI 1048
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1366 |
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: 864.57 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 27 LLATQLESFSTFLQadvpatqrkpEGLQAAFTSVFPIVS--HNGFARLEFVSYALSSP---------AFNIKECQQRGLT 95
Cdd:cd00653 1 LVKQQIDSFNYFLN----------VGLQEIVKSIPPITDtdDDGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 96 YCSALRAKVRLVILDKEspnkpvvkEVKEQEVYMGEIPLMT------------------------PTGSFVINGTERVIV 151
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG--------KIKEQEVFIGEIPIMLrsklcnlngltpeeliklgecpldPGGYFIINGTEKVII 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 152 SQLHRSPGVFFEHDkgkthSSGKLLFSARIIP----YRGSWLDFEFDpkdilyfrvdrrrkmpvtillkaigltpeqila 227
Cdd:cd00653 143 NQEQRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSD--------------------------------- 184
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 228 nffvfdnftlmdegaqlefvperlrgevarfditdrdgkvivQKDKRINAKHirdleaaktkfisvpedyllgrvlaknv 307
Cdd:cd00653 185 ------------------------------------------KKKDRIYVRI---------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 308 vdgdtgeviasandevtesvleklreagikdiqtlytndldqgPYIsstlrvdettdrtaariaiyrmmrpgepPTEEAV 387
Cdd:cd00653 195 -------------------------------------------DLK----------------------------RQEEAL 203
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 388 EALFNRLFyseeaydlskvgrmkfnrrvgrdeivgpmtlqddDILATIKILVELRNGKGEVDDIDHLGNRRVRCVGELAE 467
Cdd:cd00653 204 KYIGKRFE----------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQ 249
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 468 NQFRAGLVRVERAVKERLGQAESEN--LMPHDLINSKPISSAIREFFGSSQ------------LSQFMDQTNPLSEITHK 533
Cdd:cd00653 250 NLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHK 329
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 534 RRVSAlgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHLNeyGFLETPYRKvVDSKVTdqidyls 613
Cdd:cd00653 330 RRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRI-VEKEVT------- 396
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 614 aieegrymiaqanaaidengqlidelvssreagetmmvtpdriqYMDVAPSQIVSVAASLIPFLEHDDANRALMGSNMQR 693
Cdd:cd00653 397 --------------------------------------------HIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQK 432
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 694 QAVP----------------CLRPEKPVVGTGIErtcavdsgttvqafrggvvdyvdagrivirvnddeavagevgvdiy 757
Cdd:cd00653 433 QAVGtpalnqqyrmdtklylLLYPQKPLVGTGIE---------------------------------------------- 466
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 758 NLIKYtrsnqntninqrpivkmgdkvsrgdvladgastdlGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSI 837
Cdd:cd00653 467 EYIAF-----------------------------------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSI 511
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 838 HIEELNVVARDTKLGPEEITR-DISNLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKGETQLTPeekllraIFGEKA 916
Cdd:cd00653 512 HYKKYEIELRKTKNGPEEITRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKA 584
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 917 SDVKDTSLRVPSGMSGTVIDVQVFTRegiqrdkraqqiiddelkryrldlndqlrivegdafqrlarmlvgkvanggpkk 996
Cdd:cd00653 585 RDVRDTSLKYPGGEKGIVDDVKIFSR------------------------------------------------------ 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 997 lakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeekrkkltqgdELPPGVLKMVKVYLAVK 1076
Cdd:cd00653 611 ---------------------------------------------------------------ELNDGGNKLVKVYIRQK 627
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1077 RRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVHLGWAAKGLGWRIgemlqrqak 1156
Cdd:cd00653 628 RKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG--------- 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1157 ieelrvfltkiynesgrqedlesftdeeilelaknlregvpFATPvFDGATEEEMGKMLDLAFPDdiaqqldmNPSKnqV 1236
Cdd:cd00653 699 -----------------------------------------DATP-FDGAEEEDISELLGEAGLN--------YYGK--E 726
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1237 RLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEM 1316
Cdd:cd00653 727 VLYDGRTGEPLEAPIFVGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQER 806
|
1370 1380 1390 1400 1410 1420
....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1317 LTVKSDDVTGRTKVYENLV----------KGDHVIDAGMPESFNVLVKEIRSLGIDIDLD 1366
Cdd:cd00653 807 LTIKSDDVVARVCVKCGIIlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
724-1290 |
1.86e-160 |
|
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: 486.27 E-value: 1.86e-160
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 724 AFRGGVVDYVDAGRIVIRVNDDEAVAGevgvdIYNLIKYTRSNQNT---NINQRPIVKMGdKVSRGDvladgastdLGEL 800
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMG-----IYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGEL 66
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 801 ALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEElnVVARDTKLGP-EEITRDISNLAEVQLGRLDESGIVYI 879
Cdd:pfam00562 67 PLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRV 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 880 GAEVEAGDVLVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDTSLRVPSGMSGTVIDVQVFTregiqrdkraqqiiddel 959
Cdd:pfam00562 145 GAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVFE------------------ 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 960 kryrldlndqlrivegdafqrlarmlvgkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsiee 1039
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1040 krhqfdlafeekrkkltqgdeLPPGVLKMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNP 1119
Cdd:pfam00562 201 ---------------------LPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNP 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1120 LGVPSRMNVGQVLEVHLGWAAKGLgwrigemlqrqakieelrvfltkiynesgrqedlesftdeeilelaknlreGVPFA 1199
Cdd:pfam00562 260 HGVPSRMTIGQLLETHLGKAAALL---------------------------------------------------GVFVD 288
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1200 TPVFDGATEEemgkmldlafPDDIAQQLD---MNPSKNQVrLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGP 1276
Cdd:pfam00562 289 ATPFDGASTE----------VEDIGELLEkagYNYYGKEV-LYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGP 357
|
570
....*....|....
gi 500212820 1277 YSLVTQQPLGGKAQ 1290
Cdd:pfam00562 358 YSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
88-1365 |
5.52e-86 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 304.96 E-value: 5.52e-86
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 88 ECQQRGLTYCSALRAKVRLVILDKEspnkpvvkeVKEQEVYMGEIPLMT------------------------PTGSFVI 143
Cdd:PRK08565 75 EARLRNLTYAAPLYLTMIPVENGIE---------YEPEEVKIGDLPIMVkskicplsglspdelieigedpkdPGGYFII 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 144 NGTERVIVSQLHRSPG---VffehDKGKTHSSGKllFSARIIPYRG---SWLDFEFDPKDILYFRVDR-RRKMPVTILLK 216
Cdd:PRK08565 146 NGSERVIVSQEDLAPNrvlV----DKGEAGSSIT--HTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMR 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 217 AIGLTpeqilanffvfdnftlmdegaqlefvperlrgevarfdiTDRDGKVIVQKDKRINAKHIRDLEAAKTKFISVPE- 295
Cdd:PRK08565 220 ALGLE---------------------------------------TDRDIVYAVSLDPEIQQELLPSLEQASSIAATVEDa 260
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 296 -DYLLGRVlaknvvdgdtgeviasandevtesVLEKLREAGIKDIQTLytndLDQG--PYIsstlrvdettdrtaariai 372
Cdd:PRK08565 261 lDYIGKRV------------------------AIGQPREYRIERAEQI----LDKYllPHL------------------- 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 373 yrmmrpGEPPTEEAVEALFnrlfyseeaydlskVGRMkfnrrvgrdeivgpmtlqdddilatIKILVELRNGKGEVDDID 452
Cdd:PRK08565 294 ------GTSPEDRIKKAYF--------------LGQM-------------------------ASKLLELYLGRREPDDKD 328
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 453 HLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESENLMPH--DLINSKPISSAIREFF-------GSSQLSQFMDQ 523
Cdd:PRK08565 329 HYANKRLRLAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDlrAIVRPDIITERIRHALatgnwvgGRTGVSQLLDR 408
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 524 TNPLSEITHKRRVsaLGPggLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAHL----NEYGFLETPYRK 599
Cdd:PRK08565 409 TNYLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIsvgvDEEEVEEILYEL 484
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 600 -VVDSKVTDQIDYLSA------------IEEGRYMIA-------------QANAAIDENGQlIDELVSSREAGETM---- 649
Cdd:PRK08565 485 gVVPVEEAREEEYISWsrvylngrligyHPDGEELAEkirelrrsgkisdEVNVAYIETGE-INEVYVNCDSGRVRrpli 563
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 650 -------MVTPDRIQ-------------------------------------------YMDVAPSQIVSVAASLIPFLEH 679
Cdd:PRK08565 564 vvengkpKLTREHVEklkkgeltfddlvkmgvieyldaeeeenayvaldpedltpehtHLEIWPPAILGITASIIPYPEH 643
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 680 DDANRALMGSNMQRQAVpclrpekpvvgtgiertcavdsGTTVQAFRggvvdyvdagrivIRVnDDEAvagevgvdiyNL 759
Cdd:PRK08565 644 NQSPRNTYQAAMAKQSL----------------------GLYAANFR-------------IRT-DTRG----------HL 677
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 760 IKYTrsnqntninQRPIVKmgdkvSRG-DVLAdgastdLGELALGQNMLIAFMPWNGYNFEDSILISEKVVadDR----- 833
Cdd:PRK08565 678 LHYP---------QRPLVQ-----TRAlEIIG------YNDRPAGQNAVVAVLSYTGYNIEDAIIMNKASI--ERglars 735
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 834 -----YTSihiEELNVV--ARDTKLGPEEITRDIsnLAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPKgetQLTPEEK 906
Cdd:PRK08565 736 tffrtYET---EERKYPggQEDKIEIPEPNVRGY--RGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELE 807
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 907 LLRAIFGEKasdvKDTSLRVPSGMSGTVIDVQVFTREgiqrdkraqqiiddelkryrldlndqlrivEGDafqrlarmlv 986
Cdd:PRK08565 808 ELSLGLQER----RDTSVTVRHGEKGIVDTVLITESP------------------------------EGN---------- 843
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 987 gkvanggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeekrkkltqgdelppgvl 1066
Cdd:PRK08565 --------------------------------------------------------------------------------
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1067 KMVKVYLAVKRRLQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVhlgwaakglgwr 1146
Cdd:PRK08565 844 KLVKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES------------ 911
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1147 IGemlqrqAKIEELRvfltkiynesGRQEDlesftdeeilelaknlregvpfATPvFDGATEEEMGKMLD-LAFPddiaq 1225
Cdd:PRK08565 912 IA------GKVAALE----------GRFVD----------------------ATP-FYGEPEEELRKELLkLGYK----- 947
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1226 qldmnPSKNQVrLYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1305
Cdd:PRK08565 948 -----PDGTEV-MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLI 1021
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 500212820 1306 AYGASYVLQEMLTVKSDDVT--------------GRTKVYENLVKGDH-----VIdagMPESFNVLVKEIRSLGIDIDL 1365
Cdd:PRK08565 1022 GHGAAMLLKERLLDSSDKTTiyvcelcghiawydRRKNKYVCPIHGDKgnispVE---VSYAFKLLLQELMSMGISPRL 1097
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
27-506 |
1.49e-68 |
|
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: 236.51 E-value: 1.49e-68
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 27 LLATQLESFSTFLQADVPATQRKPEGLQAAFTSVFPIVSHNGFArLEFVSYALSSPAFN----------IKECQQRGLTY 96
Cdd:pfam04563 2 LVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGDKLS-LKFGQIRLGKPMFDetdgstreiyPQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 97 CSALRAKVRLVILDKEspnkpvvkEVKEQEVYMGEIPLMT------------------------PTGSFVINGTERVIVS 152
Cdd:pfam04563 81 SAPLYVDLELSVYNGE--------DIKPIEVFIGRLPIMLrsnacilsgateselvklgecpldPGGYFIINGSEKVIVA 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 153 QLHRS---PGVFFEHDKGKTHSSGKLLFSARI--IPYRGSWLDF-EFDPKDILYFRVDRRRK-MPVTILLKAIGLTPEQI 225
Cdd:pfam04563 153 QEHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDRE 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 226 LANFFVFD-NFTLMDEgaqlEFVPERLrgEVARFDITDRDgkvivqkdkrinakhirdleaaktkfisVPEDYLLGRVla 304
Cdd:pfam04563 233 IFELICYDvNDQQLQE----ELLPSLE--EGFKIRIQTQE----------------------------QALDYIGGRG-- 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 305 knvvdgdtgeviasandevtesvleklreagikdiqtlytndldqgpyisstlrvdettdrtaarIAIYRMMRPGEPPTE 384
Cdd:pfam04563 277 -----------------------------------------------------------------RAIFRMGRPREPRIK 291
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 385 EAVEALFNRLFYSEEAYDLSKVGRMKFnrrvgrdeivgpmtlqdddILATIKILVELRNGKGEVDDIDHLGNRRVRCVGE 464
Cdd:pfam04563 292 YAEEILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGP 352
|
490 500 510 520
....*....|....*....|....*....|....*....|....
gi 500212820 465 LAENQFRAGLVRVERAVKERLGQA--ESENLMPHDLINSKPISS 506
Cdd:pfam04563 353 LLASLFRVLFKKLVRDVRERLQKVlgSPDDLMLQLLVNAKPITS 396
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
609-1365 |
4.51e-56 |
|
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: 206.03 E-value: 4.51e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 609 IDYLSAIEEgrymiaqANAAIdenGQLIDELvssreagetmmvTPDRiQYMDVAPSQIVSVAASLIPFLEHDDANRALMG 688
Cdd:TIGR03670 92 IEYLDAEEE-------ENAYI---ALDPEEL------------TPEH-THLEIDPSAILGIIASTIPYPEHNQSPRNTMG 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 689 SNMQRQAVpclrpekpvvgtgiertcavdsGTTVQAFRggvvdyvdagrivIRVNDDEavagevgvdiyNLIKYTrsnqn 768
Cdd:TIGR03670 149 AAMAKQSL----------------------GLYAANYR-------------IRLDTRG-----------HLLHYP----- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 769 tninQRPIVKmgdkvSRGDVLadgasTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEELNVVARD 848
Cdd:TIGR03670 178 ----QKPLVK-----TRVLEL-----IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERR 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 849 TKLG-------PEEITRDISnlAEVQLGRLDESGIVYIGAEVEAGDVLVGKVTPkgetqltP---EEkllRAIFGEKASD 918
Cdd:TIGR03670 244 YPGGqedrfeiPEPDVRGYR--GEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTER 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 919 VKDTSLRVPSGMSGtVIDvQVFTREGIQRDKraqqiiddelkryrldlndqlrivegdafqrlarmlvgkvanggpkkla 998
Cdd:TIGR03670 312 RRDTSVTVRHGEKG-IVD-KVIITETEEGNK------------------------------------------------- 340
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 999 kgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeekrkkltqgdelppgvlkMVKVYLAVKRR 1078
Cdd:TIGR03670 341 ---------------------------------------------------------------------LVKVRVRDLRI 351
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1079 LQPGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEVhlgwaakgLGWRIGEMlqrqakie 1158
Cdd:TIGR03670 352 PELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM--------IAGKVAAL-------- 415
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1159 elrvfltkiyneSGRQEDlesftdeeilelaknlregvpfATPvFDGATEEEMGKMLdlafpddiaQQLDMNPSKNQVrL 1238
Cdd:TIGR03670 416 ------------EGRRVD----------------------GTP-FEGEPEEELRKEL---------LKLGFKPDGKEV-M 450
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1239 YDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGASYVLQEMLT 1318
Cdd:TIGR03670 451 YDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLL 530
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 500212820 1319 VKSDDVT--------------GRTKVYENLVKGDHVIDAG--MPESFNVLVKEIRSLGIDIDL 1365
Cdd:TIGR03670 531 DESDKYVvyvcencghiawedKRKGTAYCPVCGETGDISPveMSYAFKLLLDELKSLGISPRL 593
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
609-1362 |
6.26e-49 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 185.16 E-value: 6.26e-49
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 609 IDYLSAIEEgrymiAQANAAIDEngqliDELvssreagetmmvTPDRiQYMDVAPSQIVSVAASLIPFLEHDDANRALMG 688
Cdd:PRK07225 98 IEYLDAEEE-----ENAYIAVYE-----EDL------------TEEH-THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 689 SNMQRQA--VPC----LRPEKpvvgtgiertcavdsgttvqafRGGVVDYVdagrivirvnddeavagevgvdiynliky 762
Cdd:PRK07225 155 AGMIKQSlgLPAanykLRPDT----------------------RGHLLHYP----------------------------- 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 763 trsnqntninQRPIVKMgdKVSRgdvladgaSTDLGELALGQNMLIAFMPWNGYNFEDSILISEKVVADDRYTSIHIEEL 842
Cdd:PRK07225 184 ----------QVPLVKT--QTQE--------IIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTY 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 843 NVVARDTKLGPE---EITRDisnlaEVQLGR-------LDESGIVYIGAEVEAGDVLVGKVTPkgetqltP---EEKllr 909
Cdd:PRK07225 244 EGEERRYPGGQEdrfEIPDK-----DVRGYRgeeayrhLDEDGLVNPETEVKEGDVLIGKTSP-------PrflEEP--- 308
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 910 AIFGEKASDVKDTSLRVPSGMSGTVidvqvftregiqrdkraqqiiddelkryrldlnDQLRIVEGDAFQRLARMLVgkv 989
Cdd:PRK07225 309 DDFGISPEKRRETSVTMRSGEEGIV---------------------------------DTVILTETEEGSRLVKVRV--- 352
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 990 anggpkklakgtkidqayledldhyhwfdirladdeaaaqleaiknsieekrhqfdlafeekRkkltqgDELPPGVlkmv 1069
Cdd:PRK07225 353 --------------------------------------------------------------R------DLRIPEL---- 360
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1070 kvylavkrrlqpGDKMAGRHGNKGVVSKIVPIEDMPYMADGRPADVVLNPLGVPSRMNVGQVLEvhlgwaakGLGWRIGE 1149
Cdd:PRK07225 361 ------------GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLE--------MIGGKVGS 420
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1150 MlqrqakieelrvfltkiyneSGRQEDLESFTDEEILELAKNLRE-GvpfatpvFDGATEEEMgkmldlafpddiaqqld 1228
Cdd:PRK07225 421 L--------------------EGRRVDGTAFSGEDEEDLREALEKlG-------FEHTGKEVM----------------- 456
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1229 mnpsknqvrlYDGRTGEQFERRVTLGYMHYLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1308
Cdd:PRK07225 457 ----------YDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHG 526
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1309 ASYVLQEMLTVKSDDVT-------GRTKVYEN-------LVKGD--HVIDAGMPESFNVLVKEIRSLGID 1362
Cdd:PRK07225 527 AAMLLKERLLDESDKVEiyvcakcGMIAIYDKkrnrkycPICGEetDIYPVEMSYAFKLLLDELKSLGIA 596
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
519-586 |
7.73e-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: 135.73 E-value: 7.73e-38
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 500212820 519 QFMDQTNPLSEITHKRRVSAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLALYAH 586
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
597-662 |
4.09e-32 |
|
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: 119.39 E-value: 4.09e-32
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 500212820 597 YRKVVDSKVTDQIDYLSAIEEGRYMIAQANAAIDENGQLIDELVSSREAGETMMVTPDRIQYMDVA 662
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1292-1366 |
8.75e-31 |
|
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: 116.53 E-value: 8.75e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 1292 GGQRFGEMEVWALEAYGASYVLQEMLTVKSD----DVTGRTKVYEN-----LVKGDHVIDAG-MPESFNVLVKEIRSLGI 1361
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*
gi 500212820 1362 DIDLD 1366
Cdd:pfam04560 81 DPRLL 85
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
438-589 |
1.29e-24 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 109.65 E-value: 1.29e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 438 LVELRNGKGEVDDIDHLGNRRVRCVGELAENQFRAGLVRVERAVKERLGQAESENLMPHdlinskpISSAIRE------- 510
Cdd:PRK09606 317 CFELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLERANMRNRELS-------IKTAVRSdvlterl 389
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 511 ---------FFGSSQLSQFMDQTNPLSEITHKRRVSAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL 581
Cdd:PRK09606 390 ehamatgnwVGGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNF 465
|
....*...
gi 500212820 582 ALYAHLNE 589
Cdd:PRK09606 466 AQMVEIST 473
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
156-460 |
1.72e-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: 64.68 E-value: 1.72e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 156 RSPGVFF--EHDKGKTHSSgkllFSARIIPYRGSWLDFEFDPKDILYFRVDRRRKMPVTILLKAIGLtpeqilanffvfd 233
Cdd:pfam04561 1 RSNGIYVekELDKNGIIAT----YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGL------------- 63
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 234 nftlmdegaqlefvperlrgevarfdITDRDgkvIVQkdkrinakHIRDLeaaktkfisvPEDYLLgrvlaknvvdgdtg 313
Cdd:pfam04561 64 --------------------------VSDRE---ILD--------RLCYD----------FNDPQM-------------- 82
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500212820 314 eviasaNDEVTESVLEKLreagikDIQTLyTNDLDqgpYISSTLRvdettdrtaariaiyrmMRPGEPPTEEavealfnr 393
Cdd:pfam04561 83 ------LELLKPELEEAE------NIYTQ-EEALD---YIGKGFA-----------------LRRGEEPRLQ-------- 121
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 500212820 394 lfYSEEAYDlSKVGRMKFNRRVGRDEIVGPMTLQDDDILATIKILVELRNGKGEVDDIDHLGNRRVR 460
Cdd:pfam04561 122 --RAREILY-SRDPKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
295-339 |
2.21e-08 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 58.93 E-value: 2.21e-08
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 500212820 295 EDYLLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKDI 339
Cdd:PRK00566 803 EERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEV 847
|
|
| rpoC2 |
PRK02597 |
DNA-directed RNA polymerase subunit beta'; Provisional |
295-339 |
1.59e-04 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 235052 [Multi-domain] Cd Length: 1331 Bit Score: 46.53 E-value: 1.59e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 500212820 295 EDYLLGRVLAKNVVDGDtGEVIASANDEVTESVLEKLREAGIKDI 339
Cdd:PRK02597 236 GDRLLGRVLAEDVVDPE-GEVIAERNTAIDPDLAKKIEKAGVEEV 279
|
|
| RpoC |
COG0086 |
DNA-directed RNA polymerase, beta' subunit/160 kD subunit [Transcription]; DNA-directed RNA ... |
295-340 |
5.13e-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: 44.77 E-value: 5.13e-04
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 500212820 295 EDYLLGRVLAKNVVDGDTGEVIASANDEVTESVLEKLREAGIKDIQ 340
Cdd:COG0086 802 KERILGRVAAEDVVDPGTGEVLVPAGTLIDEEVAEIIEEAGIDSVK 847
|
|
| |
