|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
4-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2291.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 4 THSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGgrpDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDP 83
Cdd:PRK00405 2 VYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELGE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 84 PKFDVDECRQRDLTYSAPLKVTLRLIvfdidedtgAKSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 163
Cdd:PRK00405 79 PKYDVEECKERGLTYSAPLRVKLRLI---------NKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 164 FFDHDKGKThSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTrdgd 243
Cdd:PRK00405 150 YFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG---- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 244 nwripysaerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglKAIKATEDDLFGSYLAEDVVNYATGEIYLEA 323
Cdd:PRK00405 225 -------------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEA 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 324 GDEIDEKVlktlidtgeteinvldidhvnIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSE 403
Cdd:PRK00405 256 NDEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPK 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 404 RYDLSAVGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMER 483
Cdd:PRK00405 315 RYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMER 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 484 AIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPT 563
Cdd:PRK00405 395 AVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 564 HYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEF 643
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDEL 554
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 644 VICRHAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSG 723
Cdd:PRK00405 555 VTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSG 634
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 724 AAIAARRGGIVDQVDATRIVIRAtEELDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDL 803
Cdd:PRK00405 635 AVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGEL 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 804 ALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 883
Cdd:PRK00405 714 ALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIG 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 884 AEVHPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRhgvekderamaiereeie 963
Cdd:PRK00405 794 AEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------ 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 964 rlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqydds 1043
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1044 kkllearfmdkvekVQRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPL 1123
Cdd:PRK00405 856 --------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPL 921
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1124 GVPSRMNVGQILETHLGWACAGMGKKigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkrgvs 1203
Cdd:PRK00405 922 GVPSRMNIGQILETHLGWAAKGLGIK------------------------------------------------------ 947
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1204 IATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGG 1283
Cdd:PRK00405 948 FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1284 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDD 1363
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLD 1107
|
....*
gi 493110732 1364 TREAE 1368
Cdd:PRK00405 1108 EDGNE 1112
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1361 |
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: 1892.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 10 RKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFDVD 89
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 90 ECRQRDLTYSAPLKVTLRLIVFDIDedtgakSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 169
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEED------GTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 170 GkTHSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMdgeeilstfyktvtytrdgdnwripy 249
Cdd:TIGR02013 155 D-TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGY-------------------------- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 250 saerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvnyatgeiyleagdeide 329
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 330 kvlktlidtgetEINVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSA 409
Cdd:TIGR02013 208 ------------TIDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGR 275
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 410 VGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERM 489
Cdd:TIGR02013 276 VGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 490 SSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 569
Cdd:TIGR02013 356 STQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 570 PIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTND--VVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICR 647
Cdd:TIGR02013 436 PIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTdeIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR 515
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 648 HAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAIA 727
Cdd:TIGR02013 516 YRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIV 595
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 728 ARRGGIVDQVDATRIVIRATEELDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGR 807
Cdd:TIGR02013 596 AKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGR 675
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 808 NVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVH 887
Cdd:TIGR02013 676 NVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVK 755
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 888 PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHgvekderamaiereeierlak 967
Cdd:TIGR02013 756 AGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE--------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 968 drddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqyddskkll 1047
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1048 earfmdkvekvqRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPS 1127
Cdd:TIGR02013 815 ------------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPS 882
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1128 RMNVGQILETHLGWACAGMGKKigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkrGVSIATP 1207
Cdd:TIGR02013 883 RMNIGQILETHLGWAGKRLGRK---------------------------------------------------GVPIATP 911
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1208 VFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQF 1287
Cdd:TIGR02013 912 VFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 991
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493110732 1288 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:TIGR02013 992 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
14-1361 |
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: 1722.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 14 RKFFGKIPEVAEMPNLIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQ 93
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 94 RDLTYSAPLKVTLRLIvfdiDEDTGaksikDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKth 173
Cdd:COG0085 71 RDLTYAAPLYVKVRLV----NKETG-----EIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK-- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 174 sSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDG-EEILSTFyktvtytrdgdnwripysae 252
Cdd:COG0085 140 -SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAF-------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 253 rfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvnyatgeiyleAGDEIDEkvl 332
Cdd:COG0085 199 ----------------------------------------------------------------------GDDPIQE--- 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 333 ktlidtgeteinvldidhvnigaYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGR 412
Cdd:COG0085 206 -----------------------YILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGR 262
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 413 VKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSI 492
Cdd:COG0085 263 YKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQ 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 493 EIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIE 572
Cdd:COG0085 343 DVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIE 422
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 573 TPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEV 652
Cdd:COG0085 423 TPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEE 502
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 653 MMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFvgtgmepivardsgaaiaarrgg 732
Cdd:COG0085 503 VLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 733 ivdqvdatrivirateeldpsksgvDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVA 812
Cdd:COG0085 560 -------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVA 614
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 813 FMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDIL 892
Cdd:COG0085 615 FMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDIL 694
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 893 VGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFnrhgvekderamaiEREEierlakdrdde 972
Cdd:COG0085 695 VGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVF--------------SREE----------- 749
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 973 qaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqyddskkllearfm 1052
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1053 dkvekvqrGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVG 1132
Cdd:COG0085 750 --------GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVG 821
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1133 QILETHLGWACAgmgkkigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvKRGVSIATPVFDGA 1212
Cdd:COG0085 822 QVLETHLGWAAA------------------------------------------------------LLGRRVATPVFDGA 847
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1213 VEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRF 1292
Cdd:COG0085 848 PEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493110732 1293 GEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:COG0085 928 GEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
29-1362 |
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: 898.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 29 LIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGASM--LEFVRYEFDPPKFDVD---------ECRQRDLT 97
Cdd:cd00653 1 LVKQQIDSFNYFL----------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKVEEGgvtrkltpnECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 98 YSAPLKVTLRLIVFDIDedtgaksikDIKEQDVYMGDMPLMTD------------------------NGTFIVNGTERVI 153
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG---------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 154 VSQMHRSPGVFFDHDKGKTHSSGKLLFAARViPYRGSWLDIEFDSKDivyaridrrrklpattllmalgmdgeeilSTFY 233
Cdd:cd00653 142 INQEQRSPNVIIVEDSKGKRIYTKTSIPSYS-PYRGSWLEVKSDKKK-----------------------------DRIY 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 234 KTVTYTRdgdnwripysaerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvn 313
Cdd:cd00653 192 VRIDLKR------------------------------------------------------------------------- 198
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 314 yatgeiyleagdeidekvlktlidtgeteinvldidhvnigayirntlavdknesRQEALFDIYRVMrpgepptmdsaea 393
Cdd:cd00653 199 -------------------------------------------------------QEEALKYIGKRF------------- 210
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 394 mfhslffdserydlsavgrvkmnmrldldaedtvrvlrkEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQ 473
Cdd:cd00653 211 ---------------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNL 251
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 474 YRVGLLRMERAIKERMS--SIEIDTVMPQDLINAKPAAAAVREFFGSSQ------------LSQFMDQTNPLSEITHKRR 539
Cdd:cd00653 252 FRSGLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRR 331
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 540 LSAlgpGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkyGFIESPYRKVvdgkvtndvvylsam 619
Cdd:cd00653 332 ISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV--------------- 391
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 620 eeakhsvaqvnveldeqggfvdefvicrhagevmmapRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQA 699
Cdd:cd00653 392 -------------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQA 434
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 700 VPlvraeapfvgtgmepivardsgaaiaarrggivdqVDATRIVIRATEELdpsksgvdiYRLQKfqrsnqstciNQRPL 779
Cdd:cd00653 435 VG-----------------------------------TPALNQQYRMDTKL---------YLLLY----------PQKPL 460
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 780 VRVGDRihkgDIIAdgpstdLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEI 859
Cdd:cd00653 461 VGTGIE----EYIA------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI 530
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 860 TR-DIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMTPeekllraIFGEKASDVRDTSMRMPPGTYGTVV 938
Cdd:cd00653 531 TRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVD 603
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 939 EVRVFNRhgvekderamaiereeierlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsq 1018
Cdd:cd00653 604 DVKIFSR------------------------------------------------------------------------- 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1019 wwqfavedeklqgelealrsqyddskkllearfmdkvekvqrgdEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVV 1098
Cdd:cd00653 611 --------------------------------------------ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1099 SRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMGKKIgelldvyrktanieplrqtlehiypdnd 1178
Cdd:cd00653 647 SKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG---------------------------- 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1179 rnepvrsydddailmlanqvkrgvsiATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258
Cdd:cd00653 699 --------------------------DATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLK 752
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIV------- 1331
Cdd:cd00653 753 HMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcr 832
|
1370 1380 1390
....*....|....*....|....*....|....
gi 493110732 1332 ---RGDDTFEAGIPESFNVLVKEMRSLGLNVELD 1362
Cdd:cd00653 833 lckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
728-1286 |
1.53e-171 |
|
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: 515.54 E-value: 1.53e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 728 ARRGGIVDQVDATRIVIRATEEldpsKSGVDIYRLQKFQRSNQST---CINQRPLVRVGdRIHKGDiiadgpstdLGDLA 804
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMG----KQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGELP 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 805 LGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEvaARDTKLGP-EEITRDIPNVSEEALKNLDEAGIVYIG 883
Cdd:pfam00562 68 LGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVG 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 884 AEVHPGDILVGKITPkgespmTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFnrhgvekderamaiereeie 963
Cdd:pfam00562 146 AEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF-------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 964 rlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqydds 1043
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1044 kkllearfmdkvekvqrgdEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPL 1123
Cdd:pfam00562 200 -------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPH 260
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1124 GVPSRMNVGQILETHLGWACAGmgkkigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkRGVS 1203
Cdd:pfam00562 261 GVPSRMTIGQLLETHLGKAAAL------------------------------------------------------LGVF 286
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1204 IATPVFDGA--VEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPL 1281
Cdd:pfam00562 287 VDATPFDGAstEVEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPL 366
|
....*
gi 493110732 1282 GGKAQ 1286
Cdd:pfam00562 367 GGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
4-1368 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2291.58 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 4 THSFNGRKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGgrpDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDP 83
Cdd:PRK00405 2 VYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDVPPE---DEGLEEVFRSIFPIEDFNGNLSLEFVSYELGE 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 84 PKFDVDECRQRDLTYSAPLKVTLRLIvfdidedtgAKSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGV 163
Cdd:PRK00405 79 PKYDVEECKERGLTYSAPLRVKLRLI---------NKETGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGV 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 164 FFDHDKGKThSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTrdgd 243
Cdd:PRK00405 150 YFDHDKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG---- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 244 nwripysaerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglKAIKATEDDLFGSYLAEDVVNYATGEIYLEA 323
Cdd:PRK00405 225 -------------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEA 255
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 324 GDEIDEKVlktlidtgeteinvldidhvnIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSE 403
Cdd:PRK00405 256 NDEITEEL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPK 314
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 404 RYDLSAVGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMER 483
Cdd:PRK00405 315 RYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMER 394
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 484 AIKERMSSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPT 563
Cdd:PRK00405 395 AVRERMSLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPT 474
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 564 HYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEF 643
Cdd:PRK00405 475 HYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDEL 554
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 644 VICRHAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSG 723
Cdd:PRK00405 555 VTARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSG 634
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 724 AAIAARRGGIVDQVDATRIVIRAtEELDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDL 803
Cdd:PRK00405 635 AVVVAKRDGVVEYVDASRIVVRV-EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGEL 713
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 804 ALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 883
Cdd:PRK00405 714 ALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIG 793
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 884 AEVHPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRhgvekderamaiereeie 963
Cdd:PRK00405 794 AEVKPGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR------------------ 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 964 rlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqydds 1043
Cdd:PRK00405 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1044 kkllearfmdkvekVQRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPL 1123
Cdd:PRK00405 856 --------------IEQGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPL 921
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1124 GVPSRMNVGQILETHLGWACAGMGKKigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkrgvs 1203
Cdd:PRK00405 922 GVPSRMNIGQILETHLGWAAKGLGIK------------------------------------------------------ 947
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1204 IATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGG 1283
Cdd:PRK00405 948 FATPVFDGAKEEEIKELLEEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGG 1027
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1284 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVELDD 1363
Cdd:PRK00405 1028 KAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLD 1107
|
....*
gi 493110732 1364 TREAE 1368
Cdd:PRK00405 1108 EDGNE 1112
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
10-1361 |
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: 1892.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 10 RKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFDVD 89
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPPEKRKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 90 ECRQRDLTYSAPLKVTLRLIVFDIDedtgakSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDK 169
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEED------GTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEK 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 170 GkTHSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMdgeeilstfyktvtytrdgdnwripy 249
Cdd:TIGR02013 155 D-TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGY-------------------------- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 250 saerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvnyatgeiyleagdeide 329
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 330 kvlktlidtgetEINVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSA 409
Cdd:TIGR02013 208 ------------TIDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGR 275
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 410 VGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERM 489
Cdd:TIGR02013 276 VGRYKLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 490 SSIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 569
Cdd:TIGR02013 356 STQDTDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 570 PIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTND--VVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICR 647
Cdd:TIGR02013 436 PIETPEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVVVTdeIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVAR 515
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 648 HAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAIA 727
Cdd:TIGR02013 516 YRGEITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIV 595
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 728 ARRGGIVDQVDATRIVIRATEELDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGR 807
Cdd:TIGR02013 596 AKRGGVVEYVDAKRIVIRYDEDEEEPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGR 675
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 808 NVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVH 887
Cdd:TIGR02013 676 NVLVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVK 755
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 888 PGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHgvekderamaiereeierlak 967
Cdd:TIGR02013 756 AGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE--------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 968 drddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqyddskkll 1047
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1048 earfmdkvekvqRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPS 1127
Cdd:TIGR02013 815 ------------QGDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPS 882
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1128 RMNVGQILETHLGWACAGMGKKigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkrGVSIATP 1207
Cdd:TIGR02013 883 RMNIGQILETHLGWAGKRLGRK---------------------------------------------------GVPIATP 911
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1208 VFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQF 1287
Cdd:TIGR02013 912 VFDGASEEEIKEYLEKAGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQF 991
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 493110732 1288 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:TIGR02013 992 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
14-1361 |
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: 1722.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 14 RKFFGKIPEVAEMPNLIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQ 93
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFL----------EEGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKE 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 94 RDLTYSAPLKVTLRLIvfdiDEDTGaksikDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKth 173
Cdd:COG0085 71 RDLTYAAPLYVKVRLV----NKETG-----EIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK-- 139
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 174 sSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDG-EEILSTFyktvtytrdgdnwripysae 252
Cdd:COG0085 140 -SGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAF-------------------- 198
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 253 rfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvnyatgeiyleAGDEIDEkvl 332
Cdd:COG0085 199 ----------------------------------------------------------------------GDDPIQE--- 205
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 333 ktlidtgeteinvldidhvnigaYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGR 412
Cdd:COG0085 206 -----------------------YILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGR 262
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 413 VKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSI 492
Cdd:COG0085 263 YKINKKLGLDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQ 342
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 493 EIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIE 572
Cdd:COG0085 343 DVEAITPQSLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIE 422
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 573 TPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEV 652
Cdd:COG0085 423 TPEGPNIGLIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEE 502
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 653 MMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFvgtgmepivardsgaaiaarrgg 732
Cdd:COG0085 503 VLVPPEEVDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL----------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 733 ivdqvdatrivirateeldpsksgvDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVA 812
Cdd:COG0085 560 -------------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVA 614
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 813 FMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDIL 892
Cdd:COG0085 615 FMPWEGYNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDIL 694
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 893 VGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFnrhgvekderamaiEREEierlakdrdde 972
Cdd:COG0085 695 VGKVTPKGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVF--------------SREE----------- 749
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 973 qaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqyddskkllearfm 1052
Cdd:COG0085 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1053 dkvekvqrGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVG 1132
Cdd:COG0085 750 --------GDELPPGVNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVG 821
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1133 QILETHLGWACAgmgkkigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvKRGVSIATPVFDGA 1212
Cdd:COG0085 822 QVLETHLGWAAA------------------------------------------------------LLGRRVATPVFDGA 847
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1213 VEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRF 1292
Cdd:COG0085 848 PEEEIRELLEKAGLPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRF 927
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493110732 1293 GEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:COG0085 928 GEMEVWALEAYGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEV 996
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
28-1361 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1558.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 28 NLIEVQKASYDQFlmveePSGGRPDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFDVDECRQRDLTYSAPLKVTLR 107
Cdd:PRK14844 31 DLVKVQKESYDSF-----TPKNKGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIR 105
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 108 LIVF--------------DIDEDTGAKSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTH 173
Cdd:PRK14844 106 LVIMqdgisldeyksikeSGDHSKLATVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTY 185
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 174 SSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRIPYSAER 253
Cdd:PRK14844 186 NSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDK 265
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 254 FKGMKIISDLVDADtGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLK 333
Cdd:PRK14844 266 FKGVRLPFDLMDVE-GNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIK 344
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 334 TLIDTGETEINVLDIDHVNIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRV 413
Cdd:PRK14844 345 KLELLSIDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRL 424
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 414 KMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSIE 493
Cdd:PRK14844 425 KLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSS 504
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 494 IDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 573
Cdd:PRK14844 505 LDKVSPSDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 584
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 574 PEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEVM 653
Cdd:PRK14844 585 PEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFV 664
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 654 MAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAIAARRGGI 733
Cdd:PRK14844 665 MVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGI 744
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 734 VDQVDATRIVIRATEELDPSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAF 813
Cdd:PRK14844 745 VDSSDSNSIVIRAFDKERVNYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAF 824
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 814 MPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILV 893
Cdd:PRK14844 825 MSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILV 904
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 894 GKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDERAMAIEREEIERLAKDRDDEQ 973
Cdd:PRK14844 905 GKVTPKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYII 984
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 974 AILDRNVYGRLADMIdgkvAAAGPKGFKKGTTITRElmteyprsQWWQFAVEDEKLQGELEALRSQYDDSKKLLEARFMD 1053
Cdd:PRK14844 985 NVTSEYFYDELKKLL----INSGSQDREKFDSIERE--------QWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKR 1052
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1054 KVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQ 1133
Cdd:PRK14844 1053 KVEKLHEGYDLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQ 1132
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1134 ILETHLGWACAGMGKKIGELLDVYRK--TANIEPLR-------QTLEHIYPDNDRNEPVR-------------------- 1184
Cdd:PRK14844 1133 ILETHVGWACKKLGEKVGNILDEINKikSAFCKGIRslnddnfTKFAAAYLDNKKIENIDddeitasvlntpnknalnde 1212
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1185 --------------SYD--------------------------DDAILMLANQVKRGVSIATPVFDGAVEADINAMLTDA 1224
Cdd:PRK14844 1213 lnelvenylnscksAYSnlrnflievyscgsnvsicnnirdisDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELA 1292
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1225 GLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG 1304
Cdd:PRK14844 1293 GLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYG 1372
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|....*..
gi 493110732 1305 AAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:PRK14844 1373 AAYTLQEMLTVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDL 1429
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
10-1370 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1469.00 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 10 RKRVRKFFGKIPEVAEMPNLIEVQKASYDQFLMVEEPSggrpDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFDVD 89
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGK----ESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVR 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 90 ECRQRDLTYSAPLKVTLRLIVFDIDEDTGAK-SIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHD 168
Cdd:PRK09603 84 EAMERGITYSIPLKIKVRLILWEKDTKSGEKnGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEE 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 169 KGKThSSGKLLFAARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILSTFYKTVTYTRDGDNWRIP 248
Cdd:PRK09603 164 ESST-SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIP 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 249 YSAERFKGmKIISDLVDADtGEVVLEAGKKLTARAAKQLAEKGLKAIKATEDDLFGSYLAEDVVNyaTGEIYLEAGDEID 328
Cdd:PRK09603 243 FASLDANQ-RMEFDLKDPQ-GKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMV--GKEVLLDMLTQLD 318
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 329 EKVLKTLIDTGETEINVLDIDHVNIGAYIRNTLAVDkNES----RQEALFD---------IYRVMRPGEPPTMDSAEAMF 395
Cdd:PRK09603 319 KNKLEKIHDLGVQEFVIINDLALGHDASIIHSFSAD-SESlkllKQTEKIDdenalaairIHKVMKPGDPVTTEVAKQFV 397
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 396 HSLFFDSERYDLSAVGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYR 475
Cdd:PRK09603 398 KKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELH 477
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 476 VGLLRMERAIKERMS--SIEIDTVMPQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERA 553
Cdd:PRK09603 478 SGLVKMQKTIKDKLTtmSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRV 557
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 554 GFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVEL 633
Cdd:PRK09603 558 GFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPI 637
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 634 DEQGGFVDEFVICRHAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTG 713
Cdd:PRK09603 638 DEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTG 717
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 714 MEPIVARDSGAAIAARRGGIVDQVDATRIVIRATEEldpSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIA 793
Cdd:PRK09603 718 IEKIIARDSWGAIKANRAGVVEKIDSKNIYILGEGK---EEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIA 794
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 794 DGPSTDLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKN 873
Cdd:PRK09603 795 DGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEEALAH 874
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 874 LDEAGIVYIGAEVHPGDILVGKITPKGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRHGVEKDER 953
Cdd:PRK09603 875 LDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYEKDAR 954
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 954 AMAIEREEIERLAKDRDDEQAILDRNVYGRLADMIDGKVAAA----GPKGFKKGTTITRE------------LMTEYPRS 1017
Cdd:PRK09603 955 VLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLSQAILEEpfshNGKDYKEGDQIPKEeiasinrftlasLVKKYSKE 1034
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1018 qwwqfavedekLQGELEALRSQYDDSKKLLEARFMDKVEKVQRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGV 1097
Cdd:PRK09603 1035 -----------VQNHYEITKNNFLEQKKVLGEEHEEKLSILEKDDILPNGVIKKVKLYIATKRKLKVGDKMAGRHGNKGI 1103
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1098 VSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMGKKIGELLDVYRKTAnIEPLRQTLEHIYPDN 1177
Cdd:PRK09603 1104 VSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKDF-AKELRAKMLEIANAI 1182
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1178 DRNEP-----VRSYDDDAILMLANQVKRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYI 1252
Cdd:PRK09603 1183 NEKDPltihaLENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYM 1262
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1253 YMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVR 1332
Cdd:PRK09603 1263 YMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAK 1342
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|
gi 493110732 1333 GDDTFEAGIPESFNVLVKEMRSLGLNVEL--DDTREAEQP 1370
Cdd:PRK09603 1343 GEQVGESEIPETFYVLTKELQSLALDINIfgDDVDEDGAP 1382
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
26-1361 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1133.27 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 26 MPNLIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGASMLEFVR--YEFDPPKFDVDECRQRDLTYSAPLK 103
Cdd:CHL00207 7 LPDFLEIQRTSFCWFL----------NEGLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIY 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 104 VTLRLIVFDIDedtgaksikDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFFDHDKGKTHssgKLLFAAR 183
Cdd:CHL00207 77 LPLKFINLKTN---------KIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSAT 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 184 VIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEIL--STFYKTVTYtrdgdnwripysaerfkgmkiis 261
Cdd:CHL00207 145 LIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYsrLTKSEFLKK----------------------- 201
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 262 dlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvnyatgeiyleagdeidekvlktlidtget 341
Cdd:CHL00207 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 342 einvLDIDHVNIGAYIRNtlavdknesrqEALFDIYRVMRPGEPPTMDSAEAMFHSLFFDSERYDLSAVGRVKMNMRLDL 421
Cdd:CHL00207 202 ----LKPILLNSNSYTNE-----------EILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNL 266
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 422 DAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIKERMSSIEIDTVMPQD 501
Cdd:CHL00207 267 NIPERVRNLTYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFN 346
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 502 LINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGL 581
Cdd:CHL00207 347 LINPKPLIALIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGL 426
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 582 INSLATFARVNKYGFIESPYRKVVDGKV--TNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEVMMAPREN 659
Cdd:CHL00207 427 IGSLATNARINKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSK 506
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 660 VDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSGAAIAARRGGIVDQVDA 739
Cdd:CHL00207 507 VDFIAISPIQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSA 586
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 740 TRIVIRateeldpSKSGVDI-YRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDLALGRNVLVAFMPWNG 818
Cdd:CHL00207 587 YKIIIQ-------DDNNRYIhYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEG 659
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 819 YNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITP 898
Cdd:CHL00207 660 YNFEDAILINKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITP 739
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 899 KGESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFNRhgvekderamaiereeierlakdrddeqaildr 978
Cdd:CHL00207 740 KGESDQLPEGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSR--------------------------------- 786
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 979 nvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqyddskkllearfmdkvekv 1058
Cdd:CHL00207 --------------------------------------------------------------------------------
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1059 QRGDEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETH 1138
Cdd:CHL00207 787 SKGDELKFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECL 866
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1139 LGWACAGMGKKIgelldvyrktanieplrqtleHIYPDNDrnepvrSYDDDAILMLANQVKRGVSIATpvfDGAVEADIN 1218
Cdd:CHL00207 867 LGLAGDNLNKRF---------------------KILPFDE------MYGSEYSRILINNKLNQASIKN---NEYWLFNSY 916
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1219 AmltdaglatSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVW 1298
Cdd:CHL00207 917 H---------PGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVW 987
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 493110732 1299 ALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:CHL00207 988 ALEAFGAAYTLKELLTIKSDDMQGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
16-1360 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1097.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 16 FFGKIPEVAEMPNLIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGAsmLEFV----RYEFDPPKFDVDEC 91
Cdd:CHL00001 2 LRDGNEGMSTIPGFNQIQFEGFCRFI----------DQGLTEELSKFPKIEDTDQE--IEFQlfveTYQLVEPLIKERDA 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 92 RQRDLTYSAPLKVTLRLIvfdidedtgAKSIKDIKEQDVYMGDMPLMTDNGTFIVNGTERVIVSQMHRSPGVFF----DH 167
Cdd:CHL00001 70 VYESLTYSSELYVPAGLI---------WKKSRDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYrselDH 140
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 168 DKGKTHSsgkllfaARVIPYRGSWLDIEFDSKDIVYARIDRRRKLPATTLLMALGMDGEEILstfyktvtytrdgDNWRI 247
Cdd:CHL00001 141 NGISVYT-------GTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREIL-------------DNVCY 200
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 248 PysaerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvnyatgEIYLEAGDEI 327
Cdd:CHL00001 201 P---------------------------------------------------------------------EIFLSFLNDK 211
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 328 DEKVLktlidtgeteinvldidhvnigayirntlavdknESRQEALFDIYR--VMRPGEPPTMDSAEAMFHSLFFDSeRY 405
Cdd:CHL00001 212 EKKKI----------------------------------GSKENAILEFYQqfACVGGDPVFSESLCKELQKKFFQQ-RC 256
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 406 DLSAVGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAI 485
Cdd:CHL00001 257 ELGRIGRRNMNRKLNLDIPENNTFLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAV 336
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 486 KERMSSIEIDTVM--PQDLINAKPAAAAVREFFGSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPT 563
Cdd:CHL00001 337 RGTICGAIRRKLIptPQNLVTSTPLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPS 416
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 564 HYGRICPIETPEGPNIGLINSLATFARVNKYGFIESPYRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEF 643
Cdd:CHL00001 417 HYGRICPIDTSEGINAGLIGSLAIHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQV 496
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 644 VICRHAGEVMMAPRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPFVGTGMEPIVARDSG 723
Cdd:CHL00001 497 VPARYRQEFLTIAWEQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSG 576
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 724 AAIAARRGGIVDQVDATRIVIRateeldpSKSGVDIYRLQKFQRSNQSTCINQRPLVRVGDRIHKGDIIADGPSTDLGDL 803
Cdd:CHL00001 577 VVAIAEHEGKIIYTDTDKIILS-------GNGDTLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGEL 649
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 804 ALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEITRDIPNVSEEALKNLDEAGIVYIG 883
Cdd:CHL00001 650 ALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLG 729
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 884 AEVHPGDILVGKITPK--GESPMTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRvfnrhgvekderamaieree 961
Cdd:CHL00001 730 SWVETGDILVGKLTPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDVR-------------------- 789
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 962 ierlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwWQFAVEDeklqgelealrSQYD 1041
Cdd:CHL00001 790 ----------------------------------------------------------WIQKKGG-----------SSYN 800
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1042 dskkllearfmdkvekvqrgdemppgvMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLN 1121
Cdd:CHL00001 801 ---------------------------PETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLN 853
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1122 PLGVPSRMNVGQILETHLGWAcagmgkkiGELLDV-YRktanieplrqtlehIYPDNDRnepvrsYDDDAilmlanqvKR 1200
Cdd:CHL00001 854 PLGVPSRMNVGQIFECLLGLA--------GDLLNRhYR--------------IAPFDER------YEQEA--------SR 897
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1201 GVsiatpVFdgaveadinAMLTDAGLATS----------GQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSI 1270
Cdd:CHL00001 898 KL-----VF---------SELYEASKQTAnpwvfepeypGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSS 963
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1271 GPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIVRGDDTFEA-GIPESFNVLV 1349
Cdd:CHL00001 964 GPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLV 1043
|
1370
....*....|.
gi 493110732 1350 KEMRSLGLNVE 1360
Cdd:CHL00001 1044 RELRSLALELN 1054
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
29-1362 |
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: 898.47 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 29 LIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGASM--LEFVRYEFDPPKFDVD---------ECRQRDLT 97
Cdd:cd00653 1 LVKQQIDSFNYFL----------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKVEEGgvtrkltpnECRLRDLT 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 98 YSAPLKVTLRLIVFDIDedtgaksikDIKEQDVYMGDMPLMTD------------------------NGTFIVNGTERVI 153
Cdd:cd00653 71 YSAPLYVDIRLTVNDKG---------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVI 141
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 154 VSQMHRSPGVFFDHDKGKTHSSGKLLFAARViPYRGSWLDIEFDSKDivyaridrrrklpattllmalgmdgeeilSTFY 233
Cdd:cd00653 142 INQEQRSPNVIIVEDSKGKRIYTKTSIPSYS-PYRGSWLEVKSDKKK-----------------------------DRIY 191
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 234 KTVTYTRdgdnwripysaerfkgmkiisdlvdadtgevvleagkkltaraakqlaekglkaikateddlfgsylaedvvn 313
Cdd:cd00653 192 VRIDLKR------------------------------------------------------------------------- 198
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 314 yatgeiyleagdeidekvlktlidtgeteinvldidhvnigayirntlavdknesRQEALFDIYRVMrpgepptmdsaea 393
Cdd:cd00653 199 -------------------------------------------------------QEEALKYIGKRF------------- 210
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 394 mfhslffdserydlsavgrvkmnmrldldaedtvrvlrkEDILAVVKMLVELRDGRGEIDDIDNLGNRRVRSVGELMENQ 473
Cdd:cd00653 211 ---------------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNL 251
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 474 YRVGLLRMERAIKERMS--SIEIDTVMPQDLINAKPAAAAVREFFGSSQ------------LSQFMDQTNPLSEITHKRR 539
Cdd:cd00653 252 FRSGLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRR 331
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 540 LSAlgpGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkyGFIESPYRKVvdgkvtndvvylsam 619
Cdd:cd00653 332 ISS---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV--------------- 391
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 620 eeakhsvaqvnveldeqggfvdefvicrhagevmmapRENVDLMDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQA 699
Cdd:cd00653 392 -------------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQA 434
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 700 VPlvraeapfvgtgmepivardsgaaiaarrggivdqVDATRIVIRATEELdpsksgvdiYRLQKfqrsnqstciNQRPL 779
Cdd:cd00653 435 VG-----------------------------------TPALNQQYRMDTKL---------YLLLY----------PQKPL 460
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 780 VRVGDRihkgDIIAdgpstdLGDLALGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPEEI 859
Cdd:cd00653 461 VGTGIE----EYIA------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKNGPEEI 530
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 860 TR-DIPNVSEEALKNLDEAGIVYIGAEVHPGDILVGKITPKGESPMTPeekllraIFGEKASDVRDTSMRMPPGTYGTVV 938
Cdd:cd00653 531 TRgDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRDTSLKYPGGEKGIVD 603
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 939 EVRVFNRhgvekderamaiereeierlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsq 1018
Cdd:cd00653 604 DVKIFSR------------------------------------------------------------------------- 610
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1019 wwqfavedeklqgelealrsqyddskkllearfmdkvekvqrgdEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVV 1098
Cdd:cd00653 611 --------------------------------------------ELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVI 646
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1099 SRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMGKKIgelldvyrktanieplrqtlehiypdnd 1178
Cdd:cd00653 647 SKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGALLGKFG---------------------------- 698
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1179 rnepvrsydddailmlanqvkrgvsiATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLH 1258
Cdd:cd00653 699 --------------------------DATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLK 752
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1259 HLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVAGRTKVYEAIV------- 1331
Cdd:cd00653 753 HMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcr 832
|
1370 1380 1390
....*....|....*....|....*....|....
gi 493110732 1332 ---RGDDTFEAGIPESFNVLVKEMRSLGLNVELD 1362
Cdd:cd00653 833 lckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
728-1286 |
1.53e-171 |
|
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: 515.54 E-value: 1.53e-171
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 728 ARRGGIVDQVDATRIVIRATEEldpsKSGVDIYRLQKFQRSNQST---CINQRPLVRVGdRIHKGDiiadgpstdLGDLA 804
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMG----KQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTG-AVEAGG---------FGELP 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 805 LGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEvaARDTKLGP-EEITRDIPNVSEEALKNLDEAGIVYIG 883
Cdd:pfam00562 68 LGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKEIE--ARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVRVG 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 884 AEVHPGDILVGKITPkgespmTPEEKLLRAIFGEKASDVRDTSMRMPPGTYGTVVEVRVFnrhgvekderamaiereeie 963
Cdd:pfam00562 146 AEVKPGDILVGKVGP------TELTKLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF-------------------- 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 964 rlakdrddeqaildrnvygrladmidgkvaaagpkgfkkgttitrelmteyprsqwwqfavedeklqgelealrsqydds 1043
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1044 kkllearfmdkvekvqrgdEMPPGVMKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPL 1123
Cdd:pfam00562 200 -------------------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPH 260
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1124 GVPSRMNVGQILETHLGWACAGmgkkigelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkRGVS 1203
Cdd:pfam00562 261 GVPSRMTIGQLLETHLGKAAAL------------------------------------------------------LGVF 286
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1204 IATPVFDGA--VEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPL 1281
Cdd:pfam00562 287 VDATPFDGAstEVEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPL 366
|
....*
gi 493110732 1282 GGKAQ 1286
Cdd:pfam00562 367 GGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
28-1361 |
1.10e-87 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 310.35 E-value: 1.10e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 28 NLIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQDFSGASMLEFVRYEFDPPKFD-VD---------ECRQRDLT 97
Cdd:PRK08565 13 GLVRQHLDSYNDFI----------ERGLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKeADgserpitpmEARLRNLT 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 98 YSAPLKVTLRLIVFDIDEdtgaksikdiKEQDVYMGDMPLMTDN------------------------GTFIVNGTERVI 153
Cdd:PRK08565 83 YAAPLYLTMIPVENGIEY----------EPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVI 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 154 VSQMHRSPG-VFFDHDKgkthSSGKLLFAARVIPYRG---SWLDIEFDSKDIVYARIDR-RRKLPATTLLMALGMDGEEi 228
Cdd:PRK08565 153 VSQEDLAPNrVLVDKGE----AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETDR- 227
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 229 lstfyktvtytrdgdnwripysaerfkgmkiisdlvdadtgEVVleagkkltaraakqlaekglkaiKATEDDlfgsyla 308
Cdd:PRK08565 228 -----------------------------------------DIV-----------------------YAVSLD------- 236
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 309 edvvnyatgeiyleagDEIDEKVLKTLIDTGETEINVLD-IDHvnIGAYIRNTLAVDKNESRQEALFDIYRVMRPGEPPt 387
Cdd:PRK08565 237 ----------------PEIQQELLPSLEQASSIAATVEDaLDY--IGKRVAIGQPREYRIERAEQILDKYLLPHLGTSP- 297
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 388 mdsaeamfhslffdserydlsavgrvkmnmrldldaEDTvrvLRKEDILA-VVKMLVELRDGRGEIDDIDNLGNRRVRSV 466
Cdd:PRK08565 298 ------------------------------------EDR---IKKAYFLGqMASKLLELYLGRREPDDKDHYANKRLRLA 338
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 467 GELMENQYRVGLLRMERAIKERMSS-------IEIDTVMPQDLINAK--PAAAAVREFFGSSQLSQFMDQTNPLSEITHK 537
Cdd:PRK08565 339 GDLLAELFRVAFKQLVKDLKYQLEKsyargrkLDLRAIVRPDIITERirHALATGNWVGGRTGVSQLLDRTNYLSTLSHL 418
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 538 RRLsaLGPggLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNkYGFIESPYRKVVDGKVTNDV---- 613
Cdd:PRK08565 419 RRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQIS-VGVDEEEVEEILYELGVVPVeear 493
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 614 ---------VYL-------------------SAMEEAKHSVaQVNVELDEQGgFVDEFVICRHAGEVM-----------M 654
Cdd:PRK08565 494 eeeyiswsrVYLngrligyhpdgeelaekirELRRSGKISD-EVNVAYIETG-EINEVYVNCDSGRVRrplivvengkpK 571
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 655 APRENV-----------DL--------------------------------MDVSPKQLVSVAAALIPFLENDDANRALM 691
Cdd:PRK08565 572 LTREHVeklkkgeltfdDLvkmgvieyldaeeeenayvaldpedltpehthLEIWPPAILGITASIIPYPEHNQSPRNTY 651
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 692 GSNMQRQAVPLvraeapfvgtgmepivardsGAAIAARRggivdqVDAtriviRATEELDPsksgvdiyrlqkfqrsnqs 771
Cdd:PRK08565 652 QAAMAKQSLGL--------------------YAANFRIR------TDT-----RGHLLHYP------------------- 681
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 772 tcinQRPLVRVgdRIHkgDIIA--DGPStdlgdlalGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAA 849
Cdd:PRK08565 682 ----QRPLVQT--RAL--EIIGynDRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETEE 745
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 850 RDTKLGPE-EITRDIPNVS----EEALKNLDEAGIVYIGAEVHPGDILVGKITPkgesP-MTPEEKLLRAIFGEKasdvR 923
Cdd:PRK08565 746 RKYPGGQEdKIEIPEPNVRgyrgEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSP----PrFLEELEELSLGLQER----R 817
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 924 DTSMRMppgtygtvvevrvfnRHGvekderamaiereeierlakdrddEQAILDRNVygrladmidgkvaaagpkgfkkg 1003
Cdd:PRK08565 818 DTSVTV---------------RHG------------------------EKGIVDTVL----------------------- 835
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1004 ttITrelmteyprsqwwqfavedEKLQGElealrsqyddskkllearfmdkvekvqrgdemppgvmKMVKVFVAVKRKIQ 1083
Cdd:PRK08565 836 --IT-------------------ESPEGN-------------------------------------KLVKVRVRDLRIPE 857
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1084 PGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILETHLGWACAGMGKKIGelldvyrktani 1163
Cdd:PRK08565 858 LGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVD------------ 925
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1164 eplrqtlehiypdndrnepvrsydddailmlanqvkrgvsiATPvFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPF 1243
Cdd:PRK08565 926 -----------------------------------------ATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKI 963
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1244 DRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----- 1318
Cdd:PRK08565 964 KAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSDkttiy 1043
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|....
gi 493110732 1319 --DVAG-------RTKVYEAIVRGDDT--FEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:PRK08565 1044 vcELCGhiawydrRKNKYVCPIHGDKGniSPVEVSYAFKLLLQELMSMGISPRL 1097
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
663-1361 |
5.42e-59 |
|
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: 214.89 E-value: 5.42e-59
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 663 MDVSPKQLVSVAAALIPFLENDDANRALMGSNMQRQAVPLVRAEAPfvgtgmepivardsgaaiaarrggivdqvdatri 742
Cdd:TIGR03670 119 LEIDPSAILGIIASTIPYPEHNQSPRNTMGAAMAKQSLGLYAANYR---------------------------------- 164
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 743 vIRateeLDPsksgvDIYRLQKfqrsnqstciNQRPLVRVgdRIHKgdiiadgpSTDLGDLALGRNVLVAFMPWNGYNYE 822
Cdd:TIGR03670 165 -IR----LDT-----RGHLLHY----------PQKPLVKT--RVLE--------LIGYDDRPAGQNFVVAVMSYEGYNIE 214
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 823 DSILLSEKIVSDDVFTSIHIEEFEVAARDTKLGPE-EITRDIPNV----SEEALKNLDEAGIVYIGAEVHPGDILVGKIT 897
Cdd:TIGR03670 215 DALIMNKASIERGLARSTFFRTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTS 294
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 898 PkgesPMTPEEkllRAIFGEKASDVRDTSMRMppgtygtvvevrvfnRHGvekderamaiereeierlakdrddEQAILD 977
Cdd:TIGR03670 295 P----PRFLEE---LREFGLVTERRRDTSVTV---------------RHG------------------------EKGIVD 328
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 978 rnvygrladmidgKVaaagpkgfkkgttitreLMTEYPRSQwwqfavedeklqgelealrsqyddskkllearfmdkvek 1057
Cdd:TIGR03670 329 -------------KV-----------------IITETEEGN--------------------------------------- 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1058 vqrgdemppgvmKMVKVFVAVKRKIQPGDKMAGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILET 1137
Cdd:TIGR03670 340 ------------KLVKVRVRDLRIPELGDKFASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM 407
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1138 HLGWACAGMGKKIGelldvyrktanieplrqtlehiypdndrnepvrsydddailmlanqvkrgvsiATPvFDGAVEADI 1217
Cdd:TIGR03670 408 IAGKVAALEGRRVD-----------------------------------------------------GTP-FEGEPEEEL 433
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1218 NAMLTDAGLATSGQSTLYDGRTGEPFDRQVTMGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEV 1297
Cdd:TIGR03670 434 RKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMER 513
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1298 WALEAYGAAYTLQEMLTVKSDDV-------AGRTKVYEAI-------VRGDDT--FEAGIPESFNVLVKEMRSLGLNVEL 1361
Cdd:TIGR03670 514 DVLIGHGAAMLLKERLLDESDKYvvyvcenCGHIAWEDKRkgtaycpVCGETGdiSPVEMSYAFKLLLDELKSLGISPRL 593
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
28-507 |
8.66e-57 |
|
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: 202.61 E-value: 8.66e-57
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 28 NLIEVQKASYDQFLMVEEPSGGRPDEGLQAVFKSVFPIQDFSGASmLEFVRYEFDPPKFDVD----------ECRQRDLT 97
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGDKLS-LKFGQIRLGKPMFDETdgstreiypqECRLRNLT 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 98 YSAPLKVTLRLIVFDidedtgaksIKDIKEQDVYMGDMPLMTDN------------------------GTFIVNGTERVI 153
Cdd:pfam04563 80 YSAPLYVDLELSVYN---------GEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVI 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 154 VSQMHRS---PGVFFDHDKGKTHSSGKLLFAAR--VIPYRGSWLDI-EFDSKDIVYARIDRRRK-LPATTLLMALGMDGE 226
Cdd:pfam04563 151 VAQEHRSrnhPIVFKKADPKKRGSVASVRSSAEisVRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSD 230
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 227 EILstFYKTVTYTRDgdnwriPYSAERFKGMkiisdlvdadtgevvLEAGKKLTAraakqlaekglkaikateddlfgsY 306
Cdd:pfam04563 231 REI--FELICYDVND------QQLQEELLPS---------------LEEGFKIRI------------------------Q 263
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 307 LAEDVVNYatgeiyleagdeidekvlktlidtgeteinvldidhvnIGAYIRntlavdknesrqealfDIYRVMRPGEPP 386
Cdd:pfam04563 264 TQEQALDY--------------------------------------IGGRGR----------------AIFRMGRPREPR 289
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 387 TMDSAEAMFHSLFFDSERYDLSAVGRVKMnmrldldaedtvrvlrkedILAVVKMLVELRDGRGEIDDIDNLGNRRVRSV 466
Cdd:pfam04563 290 IKYAEEILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLA 350
|
490 500 510 520
....*....|....*....|....*....|....*....|...
gi 493110732 467 GELMENQYRVGLLRMERAIKERMSSI--EIDTVMPQDLINAKP 507
Cdd:pfam04563 351 GPLLASLFRVLFKKLVRDVRERLQKVlgSPDDLMLQLLVNAKP 393
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
776-1363 |
1.55e-55 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 204.81 E-value: 1.55e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 776 QRPLVRVgdRIHkgDIIA--DGPStdlgdlalGRNVLVAFMPWNGYNYEDSILLSEKIVSDDVFTSIHIEEFEVAARDTK 853
Cdd:PRK07225 184 QVPLVKT--QTQ--EIIGfdERPA--------GQNFVVAVMSYEGYNIEDALIMNKASIERGLGRSHFFRTYEGEERRYP 251
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 854 LGPE-EITRDIPNV----SEEALKNLDEAGIVYIGAEVHPGDILVGKITPkgesPMTPEEKllrAIFGEKASDVRDTSMR 928
Cdd:PRK07225 252 GGQEdRFEIPDKDVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSP----PRFLEEP---DDFGISPEKRRETSVT 324
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 929 MppgtygtvvevrvfnRHGvekderamaiereeierlakdrddEQAILDrnvygrladmidgKVaaagpkgfkkgttitr 1008
Cdd:PRK07225 325 M---------------RSG------------------------EEGIVD-------------TV---------------- 336
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1009 eLMTEyprsqwwqfavedeklqGElealrsqydDSKKLLearfmdkveKVQRGDEMPPGVmkmvkvfvavkrkiqpGDKM 1088
Cdd:PRK07225 337 -ILTE-----------------TE---------EGSRLV---------KVRVRDLRIPEL----------------GDKF 364
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1089 AGRHGNKGVVSRILPVEDMPFLEDGTHADIVLNPLGVPSRMNVGQILEThlgwacagMGKKIGELldvyrktanieplrq 1168
Cdd:PRK07225 365 ASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM--------IGGKVGSL--------------- 421
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1169 tlehiypdndrnepvrsydddailmlanqvkRGVSIATPVFDGAVEADINAMLTDAGLATSGQSTLYDGRTGEPFDRQVT 1248
Cdd:PRK07225 422 -------------------------------EGRRVDGTAFSGEDEEDLREALEKLGFEHTGKEVMYDGITGEKIEAEIF 470
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1249 MGYIYMLKLHHLVDDKIHARSIGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV-------A 1321
Cdd:PRK07225 471 VGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKVeiyvcakC 550
|
570 580 590 600 610
....*....|....*....|....*....|....*....|....*....|...
gi 493110732 1322 GRTKVYEAIVR-------GDDT--FEAGIPESFNVLVKEMRSLGL--NVELDD 1363
Cdd:PRK07225 551 GMIAIYDKKRNrkycpicGEETdiYPVEMSYAFKLLLDELKSLGIapRLELED 603
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
523-590 |
1.06e-37 |
|
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site.
Pssm-ID: 428011 [Multi-domain] Cd Length: 67 Bit Score: 135.35 E-value: 1.06e-37
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 493110732 523 QFMDQTNPLSEITHKRRLSAlGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFAR 590
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1288-1363 |
2.75e-33 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 123.47 E-value: 2.75e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 1288 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVAGRTKVYEA-----IVRGDDTFEAG-IPESFNVLVKEMRSLGL 1357
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*.
gi 493110732 1358 NVELDD 1363
Cdd:pfam04560 81 DPRLLL 86
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
601-666 |
2.49e-31 |
|
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: 117.08 E-value: 2.49e-31
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 493110732 601 YRKVVDGKVTNDVVYLSAMEEAKHSVAQVNVELDEQGGFVDEFVICRHAGEVMMAPRENVDLMDVS 666
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
10-593 |
4.16e-31 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 129.30 E-value: 4.16e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 10 RKRVRKFFGKIPevaempnLIEVQKASYDQFLmveepsggrpDEGLQAVFKSVFPIQ-DFSGASMLEFVRYEFDPPKF-D 87
Cdd:PRK09606 6 RVLSDAYFKEHR-------LVRHHIDSYNDFV----------DNGLQKIIDEQGPIEtEIEDGVYVELGKIRVGKPVVkE 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 88 VD---------ECRQRDLTYSAPLKVTLRLIVFDIDEDTgaksikdikeQDVYMGDMPLM-----------TDN------ 141
Cdd:PRK09606 69 ADgsereiypmEARLRNLTYSAPLYLEMSPVEGGEEEEP----------EEVYIGELPVMvgskicnlyglSEEelievg 138
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 142 -------GTFIVNGTERVIVSQMHRSPGVF---FDHDKGKTHSSGKLL-----FAARVI--PYRGSWLDIEFDSkdiVYA 204
Cdd:PRK09606 139 edpldpgGYFIVNGSERVLMTLEDLAPNKIlveKDERYGDRIEVAKVFsqrrgYRALVTveRNRDGLLEVSFPS---VPG 215
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 205 RIdrrrklPATTLLMALGMDG-EEIlstfyktvtytrdgdnwripysaerfkgMKIISDlvdadtgevvleagkkltara 283
Cdd:PRK09606 216 SI------PFVILMRALGLETdEEI----------------------------VEAVSD--------------------- 240
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 284 akqlaekglkaikateDDLFGSYLAEDvvnyatgeiyLEAGDeidekvlktlIDTGETEINvldidhvnigaYIRNTLAv 363
Cdd:PRK09606 241 ----------------DPEIVKFMLEN----------LEEAE----------VDTQEEALE-----------YIGKRVA- 272
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 364 dKNESRQealfdiYRVMRpgepptmdsAEAMFhslffdsERYDLSAVGrvkmnmrldldAEDTVRVLRKEDILAVVKMLV 443
Cdd:PRK09606 273 -PGQTKE------YRIKR---------AEYVI-------DRYLLPHLG-----------VEPEVRRAKAHYLGRMAEACF 318
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 444 ELRDGRGEIDDIDNLGNRRVRSVGELMENQYRVGLLRMERAIK---ERMSS----IEIDTVMPQDLINA--KPAAAAVRE 514
Cdd:PRK09606 319 ELALGRREEDDKDHYANKRLKLAGDLMEDLFRVAFNRLARDVKyqlERANMrnreLSIKTAVRSDVLTErlEHAMATGNW 398
|
570 580 590 600 610 620 630
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 493110732 515 FFGSSQLSQFMDQTNPLSEITHKRRLSAlgpgGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATFARVNK 593
Cdd:PRK09606 399 VGGRTGVSQLLDRTDYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEIST 473
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
368-464 |
1.53e-10 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 61.59 E-value: 1.53e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493110732 368 SRQEALFDIYRV--MRPGEPPTMDSAEAMFHSLFfdserydlsavGRVKMNMRLDLDAEDTVRVLRKEDILAVVKMLVEL 445
Cdd:pfam04561 98 TQEEALDYIGKGfaLRRGEEPRLQRAREILYSRD-----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNL 166
|
90
....*....|....*....
gi 493110732 446 RDGRGEIDDIDNLGNRRVR 464
Cdd:pfam04561 167 KLGRRKPDDIDHLGNKRVR 185
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
299-345 |
2.01e-05 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 49.30 E-value: 2.01e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*..
gi 493110732 299 EDDLFGSYLAEDVVNYATGEIYLEAGDEIDEKVLKTLIDTGETEINV 345
Cdd:PRK00566 803 EERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKI 849
|
|
| |
