|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
9-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2230.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 9 QYSHAEKKRFRKSFGKQADKMAIPNLLEIQLKSYRDFLQADSKANEHfntGLHAAFSSVFPIDSFSGNARLEYVGYKLGE 88
Cdd:PRK00405 2 VYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDE---GLEEVFRSIFPIEDFNGNLSLEFVSYELGE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 89 PAFDVRECKLRGLTYSAPLRVKIRLVILDkdasedpkpIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGV 168
Cdd:PRK00405 79 PKYDVEECKERGLTYSAPLRVKLRLINKE---------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 169 IFEHDKGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILGEFFEMTSCHlkng 248
Cdd:PRK00405 150 YFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG---- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 249 eyhidlipqrlrgeiasfdilvpgtgeliveqgrritarhikqmekaqmKDLIVPRDYLIGKTLAKNIIDTLTGELVAQA 328
Cdd:PRK00405 225 -------------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEA 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 329 NDEVTEDLldamitsgihefdmiytndldHGSYISDTVKIDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEE 408
Cdd:PRK00405 256 NDEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPK 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 409 RYDLSAVGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVER 488
Cdd:PRK00405 315 RYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMER 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 489 AVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTT 568
Cdd:PRK00405 395 AVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 569 HYGRVCPIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGNILADL 648
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDEL 554
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 649 VPCRHQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDSG 728
Cdd:PRK00405 555 VTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSG 634
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 729 VSVVAKRGGVIDLVDASRIVVRVndDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGE 808
Cdd:PRK00405 635 AVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGE 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 809 LALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYI 888
Cdd:PRK00405 713 LALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRI 792
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 889 GAEVNAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRdglekdaraksieeehl 968
Cdd:PRK00405 793 GAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 969 arvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlem 1048
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1049 ltkemekrfndsrkkIIQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNP 1128
Cdd:PRK00405 856 ---------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNP 920
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1129 LGVPSRMNIGQVLETHLGLAAKGLGNKisqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlragvpM 1208
Cdd:PRK00405 921 LGVPSRMNIGQILETHLGWAAKGLGIK----------------------------------------------------F 948
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1209 ATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGK 1288
Cdd:PRK00405 949 ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1028
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1289 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368
Cdd:PRK00405 1029 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
15-1365 |
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: 1837.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 15 KKRFRKSFGKQADKMAIPNLLEIQLKSYRDFLQADSKANEHFNTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDVR 94
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 95 ECKLRGLTYSAPLRVKIRLVILDKDAsedpkpIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDK 174
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEEDG------TKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 175 GkTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILgeffemtschlkngeyhidl 254
Cdd:TIGR02013 155 D-TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI-------------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 255 ipqrlrgeiasfdilvpgtgeliveqgrritarhikqmekaqmkdlivprdyligktlakniidtltgelvaqandevte 334
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 335 dlldamitsgihefdmiyTNDLDHGSYISDTVKIDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSA 414
Cdd:TIGR02013 214 ------------------LNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGR 275
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 415 VGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERL 494
Cdd:TIGR02013 276 VGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 495 SLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVC 574
Cdd:TIGR02013 356 STQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 575 PIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRV--TDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCR 652
Cdd:TIGR02013 436 PIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR 515
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 653 HQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDSGVSVV 732
Cdd:TIGR02013 516 YRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIV 595
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 733 AKRGGVIDLVDASRIVVRVNDDETTAgETGVDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGELALG 812
Cdd:TIGR02013 596 AKRGGVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALG 674
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 813 QNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYIGAEV 892
Cdd:TIGR02013 675 RNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEV 754
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 893 NAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDglekdaraksieeehlarvr 972
Cdd:TIGR02013 755 KAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE-------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 973 kdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltke 1052
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1053 mekrfndsrkkiiQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVP 1132
Cdd:TIGR02013 815 -------------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVP 881
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1133 SRMNIGQVLETHLGLAAKGLGNKisqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlraGVPMATPV 1212
Cdd:TIGR02013 882 SRMNIGQILETHLGWAGKRLGRK-------------------------------------------------GVPIATPV 912
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1213 FDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFG 1292
Cdd:TIGR02013 913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 269987148 1293 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIEL 1365
Cdd:TIGR02013 993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
19-1366 |
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: 1650.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 19 RKSFGKQADKMAIPNLLEIQLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDVRECKL 98
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 99 RGLTYSAPLRVKIRLVilDKDASEdpkpikdIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDKGKth 178
Cdd:COG0085 71 RDLTYAAPLYVKVRLV--NKETGE-------IKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK-- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 179 sSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYET-EDILGEFfemtschlkngeyhidlipq 257
Cdd:COG0085 140 -SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAF-------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 258 rlrGEIASFDILVPgtgeliveqgrritarhikqmekaqmkdlivprdyligkTLAKniidtltgelvaqandevtedll 337
Cdd:COG0085 199 ---GDDPIQEYILA---------------------------------------TLEK----------------------- 213
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 338 damitsgihefdmiytndldhgsyisdtvkiDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGR 417
Cdd:COG0085 214 -------------------------------DNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGR 262
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 418 MKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSLV 497
Cdd:COG0085 263 YKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQ 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 498 ESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIE 577
Cdd:COG0085 343 DVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIE 422
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 578 TPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCRHQNEF 657
Cdd:COG0085 423 TPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEE 502
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 658 SLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLvgtgmerivasdsgvsvvakrgg 737
Cdd:COG0085 503 VLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 738 vidlvdasrivvrvnddettagetgvDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGELALGQNLLV 817
Cdd:COG0085 560 --------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLV 613
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 818 AFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYIGAEVNAGDI 897
Cdd:COG0085 614 AFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDI 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 898 LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDglekdaraksieeehlarvrkdlvd 977
Cdd:COG0085 694 LVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 978 errireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltkemekrf 1057
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1058 ndsrkkiiQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNI 1137
Cdd:COG0085 749 --------EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNV 820
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1138 GQVLETHLGLAAKGLGNKIsqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlragvpmATPVFDGAS 1217
Cdd:COG0085 821 GQVLETHLGWAAALLGRRV----------------------------------------------------ATPVFDGAP 848
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1218 EAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG 1297
Cdd:COG0085 849 EEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFG 928
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 269987148 1298 EMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELE 1366
Cdd:COG0085 929 EMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVL 997
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
34-1366 |
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: 876.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 34 LLEIQLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFS--GNARLEYVGYKLGEP---------AFDVRECKLRGLT 102
Cdd:cd00653 1 LVKQQIDSFNYFL----------NVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 103 YSAPLRVKIRLVILDKDasedpkpikDIREQDVFMGEIPLMTDV------------------------GTFVINGTERVV 158
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG---------KIKEQEVFIGEIPIMLRSklcnlngltpeeliklgecpldpgGYFIINGTEKVI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 159 VSQLHRSPGVIFEHDkgkthSSGKLLYSARIIP----YRGSWLDFEFDPKDcvyvridrrrklpvsillralgyetedil 234
Cdd:cd00653 142 INQEQRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKK----------------------------- 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 235 geffemtschlkngeyhidlipqrlrgeiasfdilvpgtgeliveqgRRITARHikqmekaqmkdlivprdyligktlak 314
Cdd:cd00653 188 -----------------------------------------------DRIYVRI-------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 315 niidtltgelvaqandevtedlldamitsgihefdmiytndldhgsYISDtvkidptssQLEALVEIYRmmrpgepptke 394
Cdd:cd00653 195 ----------------------------------------------DLKR---------QEEALKYIGK----------- 208
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 395 aaealfknlffveerydlsavgrmKFnrrvgrknddgpgtltkEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEM 474
Cdd:cd00653 209 ------------------------RF-----------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGEL 247
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 475 TENQFRVGLVRVERAVKERLSLVESEN--LMPQDLINAKPVSAAIKEFFGSSQ------------LSQFMDQVNPLSGVT 540
Cdd:cd00653 248 LQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELS 327
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 541 HKRRVSAlgpGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNdyGFIETPCRKVIEgrvtdeiey 620
Cdd:cd00653 328 HKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEK--------- 393
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 621 lsaieevdqyiaqssvaldedgniladlvpcrhqnefslttpdKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNM 700
Cdd:cd00653 394 -------------------------------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNM 430
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 701 QRQAVPTlrsekplvgtgmerivasdsgvsvvakrggvidlvdasrivvrvnddettagetgvdiYNLTKYFRsnQDTCI 780
Cdd:cd00653 431 QKQAVGT----------------------------------------------------------PALNQQYR--MDTKL 450
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 781 N-----QRPIVKTGDMIQrgdvladgpcTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIA 855
Cdd:cd00653 451 YlllypQKPLVGTGIEEY----------IAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIEL 520
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 856 RDTKLGAEEIT-ADIPNVGESALSSLDESGVVYIGAEVNAGDILVGKVTPKGETQLTPeekllraIFGEKASDVKDSSLR 934
Cdd:cd00653 521 RKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLK 593
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 935 VPSGMNGTVIDVQVFTRDglekdaraksieeehlarvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtq 1014
Cdd:cd00653 594 YPGGEKGIVDDVKIFSRE-------------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1015 eylqsitrdkwfdirlendttsqqleqlskqlemltkemekrfndsrkkiiqgddLAPGVLKIVKVYLAVKRRIQPGDKM 1094
Cdd:cd00653 612 -------------------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKF 636
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1095 AGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGLAAKGLGNKIsqmldlkqnateirtfln 1174
Cdd:cd00653 637 ASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG------------------ 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1175 kiynhdgiqrvnldclndeelyrladnlragvpmATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVG 1254
Cdd:cd00653 699 ----------------------------------DATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVG 744
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1255 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNI 1334
Cdd:cd00653 745 PVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGI 824
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|..
gi 269987148 1335 V----------DGDHRMDPGMPESFNVLLKEIRALGIDIELE 1366
Cdd:cd00653 825 IlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
732-1290 |
3.14e-170 |
|
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: 511.69 E-value: 3.14e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 732 VAKRGGVIDLVDASRIVVRVNDDETTAGetgvdIYNLTKYFRSNQDT---CINQRPIVKTGDMiqrgdvladgPCTDMGE 808
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMG-----IYTLNKFYRSDQNTyvlCYPQKPLVKTGAV----------EAGGFGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 809 LALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEEltCIARDTKLGA-EEITADIPNVGESALSSLDESGVVY 887
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 888 IGAEVNAGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFtrdglekdaraksieeeh 967
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 968 larvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqle 1047
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1048 mltkemekrfndsrkkiiqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLN 1127
Cdd:pfam00562 200 ---------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILN 258
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1128 PLGVPSRMNIGQVLETHLGLAAKGLgnkisqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlraGVP 1207
Cdd:pfam00562 259 PHGVPSRMTIGQLLETHLGKAAALL----------------------------------------------------GVF 286
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1208 MATPVFDGASE--AEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 1285
Cdd:pfam00562 287 VDATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPL 366
|
....*
gi 269987148 1286 GGKAQ 1290
Cdd:pfam00562 367 GGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
9-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2230.33 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 9 QYSHAEKKRFRKSFGKQADKMAIPNLLEIQLKSYRDFLQADSKANEHfntGLHAAFSSVFPIDSFSGNARLEYVGYKLGE 88
Cdd:PRK00405 2 VYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPEDE---GLEEVFRSIFPIEDFNGNLSLEFVSYELGE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 89 PAFDVRECKLRGLTYSAPLRVKIRLVILDkdasedpkpIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGV 168
Cdd:PRK00405 79 PKYDVEECKERGLTYSAPLRVKLRLINKE---------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 169 IFEHDKGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILGEFFEMTSCHlkng 248
Cdd:PRK00405 150 YFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG---- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 249 eyhidlipqrlrgeiasfdilvpgtgeliveqgrritarhikqmekaqmKDLIVPRDYLIGKTLAKNIIDTLTGELVAQA 328
Cdd:PRK00405 225 -------------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEA 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 329 NDEVTEDLldamitsgihefdmiytndldHGSYISDTVKIDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEE 408
Cdd:PRK00405 256 NDEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPK 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 409 RYDLSAVGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVER 488
Cdd:PRK00405 315 RYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMER 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 489 AVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTT 568
Cdd:PRK00405 395 AVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 569 HYGRVCPIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGNILADL 648
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDEL 554
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 649 VPCRHQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDSG 728
Cdd:PRK00405 555 VTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSG 634
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 729 VSVVAKRGGVIDLVDASRIVVRVndDETTAGETGVDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGE 808
Cdd:PRK00405 635 AVVVAKRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGE 712
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 809 LALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYI 888
Cdd:PRK00405 713 LALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRI 792
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 889 GAEVNAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRdglekdaraksieeehl 968
Cdd:PRK00405 793 GAEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 969 arvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlem 1048
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1049 ltkemekrfndsrkkIIQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNP 1128
Cdd:PRK00405 856 ---------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNP 920
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1129 LGVPSRMNIGQVLETHLGLAAKGLGNKisqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlragvpM 1208
Cdd:PRK00405 921 LGVPSRMNIGQILETHLGWAAKGLGIK----------------------------------------------------F 948
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1209 ATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGK 1288
Cdd:PRK00405 949 ATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGK 1028
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1289 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368
Cdd:PRK00405 1029 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
15-1365 |
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: 1837.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 15 KKRFRKSFGKQADKMAIPNLLEIQLKSYRDFLQADSKANEHFNTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDVR 94
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 95 ECKLRGLTYSAPLRVKIRLVILDKDAsedpkpIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDK 174
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEEDG------TKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 175 GkTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILgeffemtschlkngeyhidl 254
Cdd:TIGR02013 155 D-TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLI-------------------- 213
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 255 ipqrlrgeiasfdilvpgtgeliveqgrritarhikqmekaqmkdlivprdyligktlakniidtltgelvaqandevte 334
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 335 dlldamitsgihefdmiyTNDLDHGSYISDTVKIDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSA 414
Cdd:TIGR02013 214 ------------------LNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGR 275
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 415 VGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERL 494
Cdd:TIGR02013 276 VGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 495 SLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVC 574
Cdd:TIGR02013 356 STQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 575 PIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRV--TDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCR 652
Cdd:TIGR02013 436 PIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR 515
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 653 HQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDSGVSVV 732
Cdd:TIGR02013 516 YRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIV 595
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 733 AKRGGVIDLVDASRIVVRVNDDETTAgETGVDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGELALG 812
Cdd:TIGR02013 596 AKRGGVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALG 674
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 813 QNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYIGAEV 892
Cdd:TIGR02013 675 RNVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEV 754
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 893 NAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDglekdaraksieeehlarvr 972
Cdd:TIGR02013 755 KAGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE-------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 973 kdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltke 1052
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1053 mekrfndsrkkiiQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVP 1132
Cdd:TIGR02013 815 -------------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVP 881
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1133 SRMNIGQVLETHLGLAAKGLGNKisqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlraGVPMATPV 1212
Cdd:TIGR02013 882 SRMNIGQILETHLGWAGKRLGRK-------------------------------------------------GVPIATPV 912
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1213 FDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFG 1292
Cdd:TIGR02013 913 FDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFG 992
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 269987148 1293 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIEL 1365
Cdd:TIGR02013 993 GQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
19-1366 |
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: 1650.61 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 19 RKSFGKQADKMAIPNLLEIQLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDVRECKL 98
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 99 RGLTYSAPLRVKIRLVilDKDASEdpkpikdIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDKGKth 178
Cdd:COG0085 71 RDLTYAAPLYVKVRLV--NKETGE-------IKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK-- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 179 sSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYET-EDILGEFfemtschlkngeyhidlipq 257
Cdd:COG0085 140 -SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAF-------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 258 rlrGEIASFDILVPgtgeliveqgrritarhikqmekaqmkdlivprdyligkTLAKniidtltgelvaqandevtedll 337
Cdd:COG0085 199 ---GDDPIQEYILA---------------------------------------TLEK----------------------- 213
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 338 damitsgihefdmiytndldhgsyisdtvkiDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGR 417
Cdd:COG0085 214 -------------------------------DNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGR 262
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 418 MKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSLV 497
Cdd:COG0085 263 YKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQ 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 498 ESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIE 577
Cdd:COG0085 343 DVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIE 422
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 578 TPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCRHQNEF 657
Cdd:COG0085 423 TPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEE 502
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 658 SLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLvgtgmerivasdsgvsvvakrgg 737
Cdd:COG0085 503 VLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 738 vidlvdasrivvrvnddettagetgvDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGELALGQNLLV 817
Cdd:COG0085 560 --------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLV 613
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 818 AFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYIGAEVNAGDI 897
Cdd:COG0085 614 AFMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDI 693
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 898 LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDglekdaraksieeehlarvrkdlvd 977
Cdd:COG0085 694 LVGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 978 errireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltkemekrf 1057
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1058 ndsrkkiiQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNI 1137
Cdd:COG0085 749 --------EGDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNV 820
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1138 GQVLETHLGLAAKGLGNKIsqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlragvpmATPVFDGAS 1217
Cdd:COG0085 821 GQVLETHLGWAAALLGRRV----------------------------------------------------ATPVFDGAP 848
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1218 EAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG 1297
Cdd:COG0085 849 EEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFG 928
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 269987148 1298 EMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELE 1366
Cdd:COG0085 929 EMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVL 997
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
15-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1434.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 15 KKRFRKSFGKQADKMAIPNLLEIQLKSYRDFLQADSKANehfnTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDVR 94
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKE----SGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 95 ECKLRGLTYSAPLRVKIRLVILDKDASEDPK-PIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHD 173
Cdd:PRK09603 84 EAMERGITYSIPLKIKVRLILWEKDTKSGEKnGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 174 KGKThSSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILGEFFEMTSCHLKNGEYHID 253
Cdd:PRK09603 164 ESST-SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 254 LIPQRLRGEIaSFDILVPgTGELIVEQGRRITARHIKQMEKAQMKDLIVPRDYLIGKTLAKNIIDTltGELVAQANDEVT 333
Cdd:PRK09603 243 FASLDANQRM-EFDLKDP-QGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVG--KEVLLDMLTQLD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 334 EDLLDAMITSGIHEFDMIYTNDLDHGSYI-------SDTVKIDPTSSQLE-----ALVEIYRMMRPGEPPTKEAAEALFK 401
Cdd:PRK09603 319 KNKLEKIHDLGVQEFVIINDLALGHDASIihsfsadSESLKLLKQTEKIDdenalAAIRIHKVMKPGDPVTTEVAKQFVK 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 402 NLFFVEERYDLSAVGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRV 481
Cdd:PRK09603 399 KLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHS 478
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 482 GLVRVERAVKERLSLVES--ENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAG 559
Cdd:PRK09603 479 GLVKMQKTIKDKLTTMSGafDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVG 558
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 560 FEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALD 639
Cdd:PRK09603 559 FEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPID 638
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 640 EDGNILADLVPCRHQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGM 719
Cdd:PRK09603 639 EEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGI 718
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 720 ERIVASDSGVSVVAKRGGVIDLVDASRIVVRVNDDEttagETGVDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLA 799
Cdd:PRK09603 719 EKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGKE----EAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIA 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 800 DGPCTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSS 879
Cdd:PRK09603 795 DGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAH 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 880 LDESGVVYIGAEVNAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDAR 959
Cdd:PRK09603 875 LDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDAR 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 960 AKSIEEEHLARVRKDLVDERRIREEDIYHRVSNiILDKVATGGPGNL-----RPGSKVTQEYLQSITRdkwFDIRLENDT 1034
Cdd:PRK09603 955 VLSAYEEEKAKLDMEHFDRLTMLNREELLRVSS-LLSQAILEEPFSHngkdyKEGDQIPKEEIASINR---FTLASLVKK 1030
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1035 TSQQLEQLSKQLEMLTKEMEKRFNDSRKK---IIQGDDLAP-GVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPV 1110
Cdd:PRK09603 1031 YSKEVQNHYEITKNNFLEQKKVLGEEHEEklsILEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPV 1110
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1111 EDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGLAAKGLGNKISQMLD--LKQNATEIRTFLNKIYN----HDGIQR 1184
Cdd:PRK09603 1111 ADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEdkTKDFAKELRAKMLEIANaineKDPLTI 1190
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1185 VNLDCLNDEELYRLADNLRAGVPMATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHL 1264
Cdd:PRK09603 1191 HALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHL 1270
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1265 VDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPG 1344
Cdd:PRK09603 1271 VDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESE 1350
|
1370 1380
....*....|....*....|....
gi 269987148 1345 MPESFNVLLKEIRALGIDIELEHD 1368
Cdd:PRK09603 1351 IPETFYVLTKELQSLALDINIFGD 1374
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
19-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1410.92 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 19 RKSFGKQAD-KMAIPNLLEIQLKSYRDFlqadsKANEHFNTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDVRECK 97
Cdd:PRK14844 16 RVSYSRSIDlKDSLLDLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECI 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 98 LRGLTYSAPLRVKIRLVIL--------------DKDASEDPKPIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLH 163
Cdd:PRK14844 91 KRGITFSAQVIASIRLVIMqdgisldeyksikeSGDHSKLATVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMH 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 164 RSPGVIFEHDKGKTHSSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILGEFFEMTSC 243
Cdd:PRK14844 171 RSPGVFFDSDKGKTYNSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKY 250
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 244 HLKNGEYHIDLIPQRLRGEIASFDiLVPGTGELIVEQGRRITARHIKQMEKAQMKDLIVPRDYLIGKTLAKNIIDTLTGE 323
Cdd:PRK14844 251 IKHKDGWKVPFVPDKFKGVRLPFD-LMDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASST 329
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 324 LVAQANDEVTEDLLDAMITSGIHEFDMIYTNDLDHGSYISDTVKIDPTSSQLEALVEIYRMMRPGEPPTKEAAEALFKNL 403
Cdd:PRK14844 330 KILSAGESIKLEDIKKLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNL 409
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 404 FFVEERYDLSAVGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGL 483
Cdd:PRK14844 410 FFSPEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGL 489
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 484 VRVERAVKERLSLVESENLMPQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVR 563
Cdd:PRK14844 490 LKLERAVVDSMSTSSLDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVR 569
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 564 DVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGN 643
Cdd:PRK14844 570 DVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNC 649
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 644 ILADLVPCRHQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIV 723
Cdd:PRK14844 650 FVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFV 729
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 724 ASDSGVSVVAKRGGVIDLVDASRIVVRVNDDETTaGETGVDIYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPC 803
Cdd:PRK14844 730 ASGSGAVVLAKRDGIVDSSDSNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPA 808
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 804 TDMGELALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDES 883
Cdd:PRK14844 809 INSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDS 888
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 884 GVVYIGAEVNAGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDGLEKDARAKSI 963
Cdd:PRK14844 889 GIVKIGTRVGPGYILVGKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLI 968
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 964 EEEHLarvrKDLVDER----RIREEDIYHRVSNIILDKvatggpgnlrpGSKvTQEYLQSITRDKWFDIRLENDTTSQQL 1039
Cdd:PRK14844 969 KQKEI----NDFEKERdyiiNVTSEYFYDELKKLLINS-----------GSQ-DREKFDSIEREQWWGIGLKNQSISEQV 1032
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1040 EQLSKQLEMLTKEMEKRFNDSRKKIIQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDG 1119
Cdd:PRK14844 1033 KSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDG 1112
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1120 TAVDIVLNPLGVPSRMNIGQVLETHLGLAAKGLGNKISQMLD-------------------------------------- 1161
Cdd:PRK14844 1113 TPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKVGNILDeinkiksafckgirslnddnftkfaaayldnkkienid 1192
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1162 -------------------------------LKQNATEIRTFLNKIYNHDGIQRV--NLDCLNDEELYRLADNLRAGVPM 1208
Cdd:PRK14844 1193 ddeitasvlntpnknalndelnelvenylnsCKSAYSNLRNFLIEVYSCGSNVSIcnNIRDISDNNLIEFARKLRDGIPV 1272
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1209 ATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGK 1288
Cdd:PRK14844 1273 AAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGK 1352
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1289 AQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIELEHD 1368
Cdd:PRK14844 1353 SHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQN 1432
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
22-1364 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1092.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 22 FGKQADKMAIPNLLEIQLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFSGNARLEYVG--YKLGEPAFDVRECKLR 99
Cdd:CHL00001 3 RDGNEGMSTIPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYE 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 100 GLTYSAPLRVKIRLVIldkdasedpKPIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIF--EHDKgkt 177
Cdd:CHL00001 73 SLTYSSELYVPAGLIW---------KKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYrsELDH--- 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 178 hsSGKLLYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILgeffeMTSCHLKngeyhidlipq 257
Cdd:CHL00001 141 --NGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREIL-----DNVCYPE----------- 202
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 258 rlrgeiasfdILVpgtgeliveqgrritarhikqmekaqmkdlivprdyligktlakniidtltgelvaqandevtedll 337
Cdd:CHL00001 203 ----------IFL------------------------------------------------------------------- 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 338 damitsgihefdmiytndldhgSYISDTVKIDPTSSQlEALVEIYRMM--RPGEPptkEAAEALFKNLF--FVEERYDLS 413
Cdd:CHL00001 206 ----------------------SFLNDKEKKKIGSKE-NAILEFYQQFacVGGDP---VFSESLCKELQkkFFQQRCELG 259
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 414 AVGRMKFNRRVgrkNDDGPG---TLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAV 490
Cdd:CHL00001 260 RIGRRNMNRKL---NLDIPEnntFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAV 336
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 491 KERLS-LVESENLM-PQDLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTT 568
Cdd:CHL00001 337 RGTICgAIRRKLIPtPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPS 416
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 569 HYGRVCPIETPEGPNIGLINSLSVYARTNDYGFIETPCRKVIEGRVTDEIEYLSAIEEvDQYI--AQSSVALDEdGNILA 646
Cdd:CHL00001 417 HYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSED-EYYMiaAGNSLALNQ-GIQEE 494
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 647 DLVPCRHQNEFSLTTPDKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASD 726
Cdd:CHL00001 495 QVVPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALD 574
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 727 SGVSVVAKRGGVIDLVDASRIVVRVNDDETTagetgvdiYNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDM 806
Cdd:CHL00001 575 SGVVAIAEHEGKIIYTDTDKIILSGNGDTLS--------IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVG 646
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 807 GELALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVV 886
Cdd:CHL00001 647 GELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIV 726
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 887 YIGAEVNAGDILVGKVTPK--GETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVqvftrdglekdaraksie 964
Cdd:CHL00001 727 MLGSWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV------------------ 788
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 965 eehlarvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdKWfdirlendttsqqleqlsk 1044
Cdd:CHL00001 789 -----------------------------------------------------------RW------------------- 790
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1045 qlemltkemekrfndsrkkiIQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDI 1124
Cdd:CHL00001 791 --------------------IQKKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDM 850
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1125 VLNPLGVPSRMNIGQVLETHLGLAAkglgnkisqmldlkqnateirTFLNKiynHdgiqrvnldclndeelYRLadnlra 1204
Cdd:CHL00001 851 VLNPLGVPSRMNVGQIFECLLGLAG---------------------DLLNR---H----------------YRI------ 884
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1205 gvpmaTPvFDGASEAEIKSMLQLADL-------------SPD--GKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKM 1269
Cdd:CHL00001 885 -----AP-FDERYEQEASRKLVFSELyeaskqtanpwvfEPEypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKI 958
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1270 HARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGdHRMD--PGMPE 1347
Cdd:CHL00001 959 HARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITG-GTIPkpEDAPE 1037
|
1370
....*....|....*..
gi 269987148 1348 SFNVLLKEIRALGIDIE 1364
Cdd:CHL00001 1038 SFRLLVRELRSLALELN 1054
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
28-1365 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1070.10 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 28 KMAIPNLLEIQLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFSGNARLEYVG--YKLGEPAFDVRECKLRGLTYSA 105
Cdd:CHL00207 4 NFALPDFLEIQRTSFCWFL----------NEGLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSI 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 106 PLRVKIRLVILDkdasedpkpIKDIREQDVFMGEIPLMTDVGTFVINGTERVVVSQLHRSPGVIFEHDKGKTHssgKLLY 185
Cdd:CHL00207 74 QIYLPLKFINLK---------TNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIY 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 186 SARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGYETEDILgeffeMTSCHLKNGEYhidlipqrlrgeias 265
Cdd:CHL00207 142 SATLIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIY-----SRLTKSEFLKK--------------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 266 fdilvpgtgeliveqgrritarhikqmekaqmkdlivprdyligKTLAKNIIDTLTGElvaqandevtedlldamitsgi 345
Cdd:CHL00207 202 --------------------------------------------LKPILLNSNSYTNE---------------------- 215
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 346 hefdmiytndldhgsyisdtvkidptssqlEALVEIYRMMRPGEPPTKEAAEALFKNLFFVEERYDLSAVGRMKFNRRVG 425
Cdd:CHL00207 216 ------------------------------EILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLN 265
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 426 RKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMTENQFRVGLVRVERAVKERLSLVESENLMPQ 505
Cdd:CHL00207 266 LNIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKF 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 506 DLINAKPVSAAIKEFFGSSQLSQFMDQVNPLSGVTHKRRVSALGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIG 585
Cdd:CHL00207 346 NLINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCG 425
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 586 LINSLSVYARTNDYGFIETPCRKVIEGRV--TDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCRHQNEFSLTTPD 663
Cdd:CHL00207 426 LIGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPS 505
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 664 KINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQAVPTLRSEKPLVGTGMERIVASDSGVSVVAKRGGVIDLVD 743
Cdd:CHL00207 506 KVDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVS 585
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 744 ASRIVVRvnDDEttagetGVDI-YNLTKYFRSNQDTCINQRPIVKTGDMIQRGDVLADGPCTDMGELALGQNLLVAFMPW 822
Cdd:CHL00207 586 AYKIIIQ--DDN------NRYIhYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPW 657
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 823 NGYNFEDSILISERIVQDDRFTTIHIEELTCIARDTKLGAEEITADIPNVGESALSSLDESGVVYIGAEVNAGDILVGKV 902
Cdd:CHL00207 658 EGYNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKI 737
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 903 TPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFTRDglekdaraksieeehlarvrkdlvderrir 982
Cdd:CHL00207 738 TPKGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS------------------------------ 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 983 eediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltkemekrfndsrk 1062
Cdd:CHL00207 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1063 kiiQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLE 1142
Cdd:CHL00207 788 ---KGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFE 864
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1143 THLGLAAKGLGNKISQM-LDLKQNATEIRTFLNKIYNhdgiqrvNLDCLNDEelyrladnlragvpmatpvfdgaseaei 1221
Cdd:CHL00207 865 CLLGLAGDNLNKRFKILpFDEMYGSEYSRILINNKLN-------QASIKNNE---------------------------- 909
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1222 ksmLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV 1301
Cdd:CHL00207 910 ---YWLFNSYHPGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEV 986
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 269987148 1302 WALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNIVDGDHRMDPGMPESFNVLLKEIRALGIDIEL 1365
Cdd:CHL00207 987 WALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
34-1366 |
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: 876.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 34 LLEIQLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFS--GNARLEYVGYKLGEP---------AFDVRECKLRGLT 102
Cdd:cd00653 1 LVKQQIDSFNYFL----------NVGLQEIVKSIPPITDTDddGRLKLKFGDIYLGKPkveeggvtrKLTPNECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 103 YSAPLRVKIRLVILDKDasedpkpikDIREQDVFMGEIPLMTDV------------------------GTFVINGTERVV 158
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG---------KIKEQEVFIGEIPIMLRSklcnlngltpeeliklgecpldpgGYFIINGTEKVI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 159 VSQLHRSPGVIFEHDkgkthSSGKLLYSARIIP----YRGSWLDFEFDPKDcvyvridrrrklpvsillralgyetedil 234
Cdd:cd00653 142 INQEQRSPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKK----------------------------- 187
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 235 geffemtschlkngeyhidlipqrlrgeiasfdilvpgtgeliveqgRRITARHikqmekaqmkdlivprdyligktlak 314
Cdd:cd00653 188 -----------------------------------------------DRIYVRI-------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 315 niidtltgelvaqandevtedlldamitsgihefdmiytndldhgsYISDtvkidptssQLEALVEIYRmmrpgepptke 394
Cdd:cd00653 195 ----------------------------------------------DLKR---------QEEALKYIGK----------- 208
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 395 aaealfknlffveerydlsavgrmKFnrrvgrknddgpgtltkEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEM 474
Cdd:cd00653 209 ------------------------RF-----------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGEL 247
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 475 TENQFRVGLVRVERAVKERLSLVESEN--LMPQDLINAKPVSAAIKEFFGSSQ------------LSQFMDQVNPLSGVT 540
Cdd:cd00653 248 LQNLFRSGLKRLEREVKEKLQKQLSKKkdLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELS 327
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 541 HKRRVSAlgpGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYARTNdyGFIETPCRKVIEgrvtdeiey 620
Cdd:cd00653 328 HKRRISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEK--------- 393
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 621 lsaieevdqyiaqssvaldedgniladlvpcrhqnefslttpdKINYMDISPKQIVSVAASLIPFLEHDDANRALMGSNM 700
Cdd:cd00653 394 -------------------------------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNM 430
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 701 QRQAVPTlrsekplvgtgmerivasdsgvsvvakrggvidlvdasrivvrvnddettagetgvdiYNLTKYFRsnQDTCI 780
Cdd:cd00653 431 QKQAVGT----------------------------------------------------------PALNQQYR--MDTKL 450
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 781 N-----QRPIVKTGDMIQrgdvladgpcTDMGELALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIA 855
Cdd:cd00653 451 YlllypQKPLVGTGIEEY----------IAFGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIEL 520
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 856 RDTKLGAEEIT-ADIPNVGESALSSLDESGVVYIGAEVNAGDILVGKVTPKGETQLTPeekllraIFGEKASDVKDSSLR 934
Cdd:cd00653 521 RKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLK 593
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 935 VPSGMNGTVIDVQVFTRDglekdaraksieeehlarvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtq 1014
Cdd:cd00653 594 YPGGEKGIVDDVKIFSRE-------------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1015 eylqsitrdkwfdirlendttsqqleqlskqlemltkemekrfndsrkkiiqgddLAPGVLKIVKVYLAVKRRIQPGDKM 1094
Cdd:cd00653 612 -------------------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKF 636
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1095 AGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGLAAKGLGNKIsqmldlkqnateirtfln 1174
Cdd:cd00653 637 ASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG------------------ 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1175 kiynhdgiqrvnldclndeelyrladnlragvpmATPVFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVG 1254
Cdd:cd00653 699 ----------------------------------DATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVG 744
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1255 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVGGRTKIYKNI 1334
Cdd:cd00653 745 PVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGI 824
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|..
gi 269987148 1335 V----------DGDHRMDPGMPESFNVLLKEIRALGIDIELE 1366
Cdd:cd00653 825 IlsanlcrlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
732-1290 |
3.14e-170 |
|
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: 511.69 E-value: 3.14e-170
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 732 VAKRGGVIDLVDASRIVVRVNDDETTAGetgvdIYNLTKYFRSNQDT---CINQRPIVKTGDMiqrgdvladgPCTDMGE 808
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAMGKQAMG-----IYTLNKFYRSDQNTyvlCYPQKPLVKTGAV----------EAGGFGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 809 LALGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEEltCIARDTKLGA-EEITADIPNVGESALSSLDESGVVY 887
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 888 IGAEVNAGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPSGMNGTVIDVQVFtrdglekdaraksieeeh 967
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 968 larvrkdlvderrireediyhrvsniildkvatggpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqle 1047
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1048 mltkemekrfndsrkkiiqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLN 1127
Cdd:pfam00562 200 ---------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILN 258
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1128 PLGVPSRMNIGQVLETHLGLAAKGLgnkisqmldlkqnateirtflnkiynhdgiqrvnldclndeelyrladnlraGVP 1207
Cdd:pfam00562 259 PHGVPSRMTIGQLLETHLGKAAALL----------------------------------------------------GVF 286
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1208 MATPVFDGASE--AEIKSMLQLADLSPDGKTVLYDGRTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 1285
Cdd:pfam00562 287 VDATPFDGASTevEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPL 366
|
....*
gi 269987148 1286 GGKAQ 1290
Cdd:pfam00562 367 GGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
38-1366 |
1.51e-90 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 318.44 E-value: 1.51e-90
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 38 QLKSYRDFLqadskanehfNTGLHAAFSSVFPIDSFSGNARLEYVGYKLGEPAFDV----------RECKLRGLTYSAPL 107
Cdd:PRK08565 18 HLDSYNDFI----------ERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEadgserpitpMEARLRNLTYAAPL 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 108 RVKIRLVildkdasEDPKPIKdirEQDVFMGEIPLMTDV------------------------GTFVINGTERVVVSQLH 163
Cdd:PRK08565 88 YLTMIPV-------ENGIEYE---PEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQED 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 164 RSPGVIFeHDKGKTHSSGKllYSARIIPYRG---SWLDFEFDPKDCVYVRIDR-RRKLPVSILLRALGYET-EDILgeff 238
Cdd:PRK08565 158 LAPNRVL-VDKGEAGSSIT--HTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETdRDIV---- 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 239 emtschlkngeYHIDLIPQRLRGEIASFdilvpgtgelivEQGRRItarhIKQMEKAqmkdlivpRDYlIGKTLAkniid 318
Cdd:PRK08565 231 -----------YAVSLDPEIQQELLPSL------------EQASSI----AATVEDA--------LDY-IGKRVA----- 269
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 319 tltgelVAQAND---EVTEDLLDamitsgihefdmiyTNDLDHgsyisdtvkidptssqlealveiyrmmrPGEPPTKEA 395
Cdd:PRK08565 270 ------IGQPREyriERAEQILD--------------KYLLPH----------------------------LGTSPEDRI 301
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 396 AEALFknlffveerydlsaVGRMkfnrrvgrknddgpgtltkedimavIKTLIDIRNGIGMVDDIDHLGNRRVRSVGEMT 475
Cdd:PRK08565 302 KKAYF--------------LGQM-------------------------ASKLLELYLGRREPDDKDHYANKRLRLAGDLL 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 476 ENQFRVGLVRVERAVKERL--SLVESENLMPQDLINAKPVSAAIKEFF-------GSSQLSQFMDQVNPLSGVTHKRRVs 546
Cdd:PRK08565 343 AELFRVAFKQLVKDLKYQLekSYARGRKLDLRAIVRPDIITERIRHALatgnwvgGRTGVSQLLDRTNYLSTLSHLRRV- 421
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 547 aLGPggLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLS--------------------------VYARTNDY- 599
Cdd:PRK08565 422 -VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLAlmaqisvgvdeeeveeilyelgvvpvEEAREEEYi 498
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 600 ------------GFIETP---CRKVIE----GRVTDEIE--YLSAIEEVDQYIAQSS------VALDEDGNIL------- 645
Cdd:PRK08565 499 swsrvylngrliGYHPDGeelAEKIRElrrsGKISDEVNvaYIETGEINEVYVNCDSgrvrrpLIVVENGKPKltrehve 578
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 646 ---------ADLV---------PCRHQNEFSLTTPDKI----NYMDISPKQIVSVAASLIPFLEHDDANRALMGSNMQRQ 703
Cdd:PRK08565 579 klkkgeltfDDLVkmgvieyldAEEEENAYVALDPEDLtpehTHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQ 658
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 704 AVptlrsekplvgtgmerivasdsgvsvvakrggvidlvdasrivvrvnddettagetGVDIYNltkyFRSNQDTCIN-- 781
Cdd:PRK08565 659 SL--------------------------------------------------------GLYAAN----FRIRTDTRGHll 678
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 782 ---QRPIVKTGDMIQRGdvLADGPCtdmgelalGQNLLVAFMPWNGYNFEDSILISERIVqdDR-------FTTIHIEEL 851
Cdd:PRK08565 679 hypQRPLVQTRALEIIG--YNDRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASI--ERglarstfFRTYETEER 746
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 852 TciardtKLGAEEITADIP--NV----GESALSSLDESGVVYIGAEVNAGDILVGKVTPKgetQLTPEEKLLRAIFGEKa 925
Cdd:PRK08565 747 K------YPGGQEDKIEIPepNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER- 816
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 926 sdvKDSSLRVPSGMNGTVIDVQVftrdglekdarAKSIEEEHLARVRkdlVDERRIREediyhrvsniildkvatggpgn 1005
Cdd:PRK08565 817 ---RDTSVTVRHGEKGIVDTVLI-----------TESPEGNKLVKVR---VRDLRIPE---------------------- 857
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1006 lrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltkemekrfndsrkkiiqgddlapgvlkivkvylavk 1085
Cdd:PRK08565 --------------------------------------------------------------------------------
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1086 rriqPGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLETHLGLAAKGLGnkisqmldlkqn 1165
Cdd:PRK08565 858 ----LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEG------------ 921
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1166 ateirtflnkiynhdgiqrvnldclndeelyRLADnlragvpmATPvFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGN 1245
Cdd:PRK08565 922 -------------------------------RFVD--------ATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGE 961
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1246 RFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvg 1325
Cdd:PRK08565 962 KIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD--- 1038
|
1450 1460 1470 1480 1490 1500
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 269987148 1326 gRTKIY--------------KNI----VDGDH-RMDP-GMPESFNVLLKEIRALGIDIELE 1366
Cdd:PRK08565 1039 -KTTIYvcelcghiawydrrKNKyvcpIHGDKgNISPvEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
33-515 |
9.15e-73 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 248.83 E-value: 9.15e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 33 NLLEIQLKSYRDFLQADSKANehfnTGLHAAFSSVFPIDSFSGNAR---LEYVGYKLGEPAFDVR----------ECKLR 99
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKI----IDENALIESEFEIQHPGENGDklsLKFGQIRLGKPMFDETdgstreiypqECRLR 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 100 GLTYSAPLRVKIRLVILDKdasedpkpiKDIREQDVFMGEIPLMTD------------------------VGTFVINGTE 155
Cdd:pfam04563 77 NLTYSAPLYVDLELSVYNG---------EDIKPIEVFIGRLPIMLRsnacilsgateselvklgecpldpGGYFIINGSE 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 156 RVVVSQLHRS---PGVIFEHDKGKTHSSGKLLYSARI--IPYRGSWLDF-EFDPKDCVYVRIDRRRK-LPVSILLRALGY 228
Cdd:pfam04563 148 KVIVAQEHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGF 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 229 ETEdilGEFFEMTSCHLKNGEYHidlipqrlrgeiasfDILVPgtgelIVEQGRRITarhikqmekAQMKDliVPRDYLI 308
Cdd:pfam04563 228 TSD---REIFELICYDVNDQQLQ---------------EELLP-----SLEEGFKIR---------IQTQE--QALDYIG 273
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 309 GKtlakniidtltgelvaqandevtedlldamitsgihefdmiytndldhgsyisdtvkidptssqleaLVEIYRMMRPG 388
Cdd:pfam04563 274 GR-------------------------------------------------------------------GRAIFRMGRPR 286
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 389 EPPTKEAAEALFKNLFFVEERYDLSAVGRMKFnrrvgrknddgpgtltkedIMAVIKTLIDIRNGIGMVDDIDHLGNRRV 468
Cdd:pfam04563 287 EPRIKYAEEILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRL 347
|
490 500 510 520
....*....|....*....|....*....|....*....|....*....
gi 269987148 469 RSVGEMTENQFRVGLVRVERAVKERL--SLVESENLMPQDLINAKPVSA 515
Cdd:pfam04563 348 RLAGPLLASLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
618-1366 |
7.15e-63 |
|
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Pssm-ID: 274713 [Multi-domain] Cd Length: 599 Bit Score: 226.45 E-value: 7.15e-63
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 618 IEYLSAIEEVDQYIAQssvaldedgniladlvpcrhqNEFSLTtpDKINYMDISPKQIVSVAASLIPFLEHDDANRALMG 697
Cdd:TIGR03670 92 IEYLDAEEEENAYIAL---------------------DPEELT--PEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMG 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 698 SNMQRQAVptlrsekplvgtgmerivasdsGVSVVAKRggvidlvdasrivVRVnddETTAgetgvdiyNLTKYfrsnqd 777
Cdd:TIGR03670 149 AAMAKQSL----------------------GLYAANYR-------------IRL---DTRG--------HLLHY------ 176
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 778 tciNQRPIVKTGDMIQRGdvLADGPCtdmgelalGQNLLVAFMPWNGYNFEDSILISERIVQDDRFTTIHIEELTCIARD 857
Cdd:TIGR03670 177 ---PQKPLVKTRVLELIG--YDDRPA--------GQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERR 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 858 TKLGAE-EITADIPNV----GESALSSLDESGVVYIGAEVNAGDILVGKVTPkgetqltP---EEkllRAIFGEKASDVK 929
Cdd:TIGR03670 244 YPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTERRR 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 930 DSSLRVPSGMNGtvidvqvftrdglekdaraksieeehlarvrkdlvderrireediyhrvsniILDKVatggpgnlrpg 1009
Cdd:TIGR03670 314 DTSVTVRHGEKG----------------------------------------------------IVDKV----------- 330
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1010 skvtqeylqsitrdkwfdirlendttsqqleqlskqleMLTKEMEKRfndsrkkiiqgddlapgvlKIVKVYLAVKRRIQ 1089
Cdd:TIGR03670 331 --------------------------------------IITETEEGN-------------------KLVKVRVRDLRIPE 353
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1090 PGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLEThlglaakgLGNKISQMldlkqnatei 1169
Cdd:TIGR03670 354 LGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM--------IAGKVAAL---------- 415
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1170 rtflnkiynhDGiQRVNldclndeelyrladnlragvpmATPvFDGASEAEIKSMLQLADLSPDGKTVLYDGRTGNRFDN 1249
Cdd:TIGR03670 416 ----------EG-RRVD----------------------GTP-FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEA 461
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1250 PVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVG---- 1325
Cdd:TIGR03670 462 EIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYVvyvc 541
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|...
gi 269987148 1326 ---GRTKIY---KNI----VDGDHRMDPG--MPESFNVLLKEIRALGIDIELE 1366
Cdd:TIGR03670 542 encGHIAWEdkrKGTaycpVCGETGDISPveMSYAFKLLLDELKSLGISPRLE 594
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
618-1367 |
6.11e-57 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 209.05 E-value: 6.11e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 618 IEYLSAIEEVDQYIAqssvaLDEDgnilaDLvpcrhqnefsltTPDKiNYMDISPKQIVSVAASLIPFLEHDDANRALMG 697
Cdd:PRK07225 98 IEYLDAEEEENAYIA-----VYEE-----DL------------TEEH-THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 698 SNMQRQAVptlrsekplvgtgmerivasdsGVSvvakrggvidlvdASRIVVRVnddETTAgetgvdiyNLTKYfrsnqd 777
Cdd:PRK07225 155 AGMIKQSL----------------------GLP-------------AANYKLRP---DTRG--------HLLHY------ 182
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 778 tciNQRPIVKTgdmiQRGDVLadgpctDMGELALGQNLLVAFMPWNGYNFEDSILISERIVqdDR-------FTTIHIEE 850
Cdd:PRK07225 183 ---PQVPLVKT----QTQEII------GFDERPAGQNFVVAVMSYEGYNIEDALIMNKASI--ERglgrshfFRTYEGEE 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 851 LTciardtKLGAEEITADIPNV------GESALSSLDESGVVYIGAEVNAGDILVGKVTPkgetqltP---EEKllrAIF 921
Cdd:PRK07225 248 RR------YPGGQEDRFEIPDKdvrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSP-------PrflEEP---DDF 311
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 922 GEKASDVKDSSLRVPSGMNGTViDVQVFTrdglekdaraKSIEEEHLARVRkdlvderrIREEdiyhRVSNIildkvatg 1001
Cdd:PRK07225 312 GISPEKRRETSVTMRSGEEGIV-DTVILT----------ETEEGSRLVKVR--------VRDL----RIPEL-------- 360
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1002 gpgnlrpgskvtqeylqsitrdkwfdirlendttsqqleqlskqlemltkemekrfndsrkkiiqgddlapgvlkivkvy 1081
Cdd:PRK07225 --------------------------------------------------------------------------------
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1082 lavkrriqpGDKMAGRHGNKGVISIVVPVEDMPHMEDGTAVDIVLNPLGVPSRMNIGQVLEThlglaakgLGNKISQMld 1161
Cdd:PRK07225 361 ---------GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM--------IGGKVGSL-- 421
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1162 lkqnateirtflnkiynhDGiQRVNldclndeelyrladnlragvpmATPvFDGASEAEIKSMLQLADLSPDGKTVLYDG 1241
Cdd:PRK07225 422 ------------------EG-RRVD----------------------GTA-FSGEDEEDLREALEKLGFEHTGKEVMYDG 459
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1242 RTGNRFDNPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1321
Cdd:PRK07225 460 ITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDES 539
|
730 740 750 760 770 780
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 269987148 1322 DDVG-------GRTKIY---KNI----VDGDHRMDPG--MPESFNVLLKEIRALGID--IELEH 1367
Cdd:PRK07225 540 DKVEiyvcakcGMIAIYdkkRNRkycpICGEETDIYPveMSYAFKLLLDELKSLGIAprLELED 603
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
528-595 |
3.25e-34 |
|
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: 125.33 E-value: 3.25e-34
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 269987148 528 QFMDQVNPLSGVTHKRRVSAlGPGGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYAR 595
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1292-1366 |
3.48e-32 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 120.39 E-value: 3.48e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 1292 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVGGRTKIYKN-----IVDGDHRMDPG-MPESFNVLLKEIRALGI 1361
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*
gi 269987148 1362 DIELE 1366
Cdd:pfam04560 81 DPRLL 85
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
607-671 |
2.50e-29 |
|
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pssm-ID: 463067 [Multi-domain] Cd Length: 66 Bit Score: 111.69 E-value: 2.50e-29
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 269987148 607 RKVIEGRVTDEIEYLSAIEEVDQYIAQSSVALDEDGNILADLVPCRHQNEFSLTTPDKINYMDIS 671
Cdd:pfam10385 2 RKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
95-594 |
1.83e-22 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 102.72 E-value: 1.83e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 95 ECKLRGLTYSAPLRVKIRLVILDKDasEDPkpikdireQDVFMGEIPLM----------------TDVGT--------FV 150
Cdd:PRK09606 80 EARLRNLTYSAPLYLEMSPVEGGEE--EEP--------EEVYIGELPVMvgskicnlyglseeelIEVGEdpldpggyFI 149
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 151 INGTERVVVSQLHRSPGVIFEHdkgKTHSSGKLLYSARIIPYRGSW---LDFEFDPKDCVYVRIDR-RRKLPVSILLRAL 226
Cdd:PRK09606 150 VNGSERVLMTLEDLAPNKILVE---KDERYGDRIEVAKVFSQRRGYralVTVERNRDGLLEVSFPSvPGSIPFVILMRAL 226
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 227 GYETEdilgeffemtschlkngeyhidlipqrlrgeiasfdilvpgtgELIVEqgrritarhikqmekaqmkdlIVPRDY 306
Cdd:PRK09606 227 GLETD-------------------------------------------EEIVE---------------------AVSDDP 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 307 LIGKTLAKNIIDtltgelvaqandevtedlldamitsgiHEFDmiytndldhgsyisdtvkidptsSQLEALVEIYRMMR 386
Cdd:PRK09606 243 EIVKFMLENLEE---------------------------AEVD-----------------------TQEEALEYIGKRVA 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 387 PGEpptkeAAEALFKNLFFVEERYDLSAVGRMKFNRR-----VGRknddgpgtltkediMAviKTLIDIRNGIGMVDDID 461
Cdd:PRK09606 273 PGQ-----TKEYRIKRAEYVIDRYLLPHLGVEPEVRRakahyLGR--------------MA--EACFELALGRREEDDKD 331
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 462 HLGNRRVRSVGEMTENQFRVGLVRVERAVKERL--SLVESENLMPQDLINAKPVSAAIKEFF-------GSSQLSQFMDQ 532
Cdd:PRK09606 332 HYANKRLKLAGDLMEDLFRVAFNRLARDVKYQLerANMRNRELSIKTAVRSDVLTERLEHAMatgnwvgGRTGVSQLLDR 411
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 269987148 533 VNPLSGVTHKRRVSAlgpgGLTRERAGFEVRDVHTTHYGRVCPIETPEGPNIGLINSLSVYA 594
Cdd:PRK09606 412 TDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMV 469
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
164-469 |
2.08e-13 |
|
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: 70.07 E-value: 2.08e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 164 RSPGVIF--EHDKGKTHSSgkllYSARIIPYRGSWLDFEFDPKDCVYVRIDRRRKLPVSILLRALGyetedilgeffemt 241
Cdd:pfam04561 1 RSNGIYVekELDKNGIIAT----YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALG-------------- 62
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 242 schlkngeyhidLIPQRlrgeiasfDILvpgtgeliveqgrritarhikqmekaqmkdlivprDYLIGKTLAKNIIDTLT 321
Cdd:pfam04561 63 ------------LVSDR--------EIL-----------------------------------DRLCYDFNDPQMLELLK 87
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 322 GELVAQANdevtedlldamitsgihefdmIYTndldhgsyisdtvkidptssQLEALVEIYRM--MRPGEPPTKEAAEAL 399
Cdd:pfam04561 88 PELEEAEN---------------------IYT--------------------QEEALDYIGKGfaLRRGEEPRLQRAREI 126
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 269987148 400 FKNLFfveerydlsavGRMKFNRRVGRKNDDGPGTLTKEDIMAVIKTLIDIRNGIGMVDDIDHLGNRRVR 469
Cdd:pfam04561 127 LYSRD-----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
285-347 |
4.00e-05 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 48.14 E-value: 4.00e-05
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 269987148 285 TARHIKQMEKAQMKDLIVP-RDYLIGKTLAKNIIDTLTGELVAQANDEVTEDLLDAMITSGIHE 347
Cdd:PRK00566 783 TDRGIEVTAIIEGGEVIEPlEERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEE 846
|
|
| |
