|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
1-1024 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 2240.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 1 NQEIDFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRRryIQEQTILIGKIPLMTSLGAFIVNGIYRIV 80
Cdd:CHL00001 45 DQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGLIWKKSRD--MQEQTVFIGNIPLMNSLGTFIINGIYRVV 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 81 INQILQSPGFYYQSELNDNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160
Cdd:CHL00001 123 INQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPE 202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 161 LFLSFLNDK--KKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLL 238
Cdd:CHL00001 203 IFLSFLNDKekKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTFLL 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 239 PRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLT 318
Cdd:CHL00001 283 PQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLT 362
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 319 DTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHA 398
Cdd:CHL00001 363 TTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHA 442
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 399 RVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQ 478
Cdd:CHL00001 443 RIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQ 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 479 YFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKILLSGNGD 558
Cdd:CHL00001 523 YFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGD 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 559 TLRIPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDI 638
Cdd:CHL00001 603 TLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDI 682
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 639 YTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKESSYAPEDRLLRTI 715
Cdd:CHL00001 683 YTSFHIRKYEIQThvtSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAI 762
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 716 LGMRVYTSKETCLKLPIGGRGRVIDVRWVQsSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPY 795
Cdd:CHL00001 763 FGIQVSTSKETCLKLPIGGRGRVIDVRWIQ-KKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPY 841
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 796 LQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPES 875
Cdd:CHL00001 842 LQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEY 921
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 876 PGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYI 955
Cdd:CHL00001 922 PGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYI 1001
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 186885957 956 LQEMLTYKSDHIRARQEVLGTIIFGGRIPTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKEA 1024
Cdd:CHL00001 1002 LQEMLTYKSDHIRARQEVLGAIITGGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKEV 1070
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
5-1008 |
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: 1068.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 5 DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLI-WKNDRRRYIQEQTILIGKIPLMTSLGAFIVNGIYRIVINQ 83
Cdd:TIGR02013 62 NIELEYLSYRLGEPKYSVEECKERGLTYSAPLKVKLRLInKEEDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQ 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 84 ILQSPGFYYQSELN--DNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVC--YP 159
Cdd:TIGR02013 142 LHRSPGVFFSSEKDttKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLgsGE 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 160 ELFLSFLNDKKKigSKENAILEFYQQFAcvEGDPVFSESLSKDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLL 238
Cdd:TIGR02013 222 YIRNTLRKDPTN--SEEEALVEIYRKLR--PGEPPTVEAARSLLENLFFdPKRYDLGRVGRYKLNKKLGLDVPESIGVLT 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 239 PRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIyaALKHNWTPTPQNLVNSTPLT 318
Cdd:TIGR02013 298 KEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM--STQDTDTLTPQDLINAKPIS 375
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 319 DTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHA 398
Cdd:TIGR02013 376 AAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYA 455
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 399 RVGRWGSLESPFYKIS--ERSKGARMLYLSPGRDEYYMVAAGNS-LALNQGIQEEqVVPARYRQEFLTIAWEQVHLRSIF 475
Cdd:TIGR02013 456 RVNEYGFIETPYRKVKdgKVVVTDEIDYLTADEEDNYVIAQANApLDENGRFVED-LVVARYRGEITLVSPDQVDYMDVS 534
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 476 SFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKILLSG 555
Cdd:TIGR02013 535 PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY 614
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 556 NGDTL-------RIPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 628
Cdd:TIGR02013 615 DEDEEepdggidIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAIL 694
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 629 ISERLVYEDIYTSFHIRKYEIQINQ---GPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvKESSY 705
Cdd:TIGR02013 695 ISERLVKDDVFTSIHIEEYEVEARDtklGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPK--GETEL 772
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 706 APEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEK--TESIRVYILQKREIKVGDKVAGRHGNKGI 783
Cdd:TIGR02013 773 TPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGV 852
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 784 ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHyriapfderyEQEASRKLVFSELYEASK 863
Cdd:TIGR02013 853 VSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRK----------GVPIATPVFDGASEEEIK 922
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 864 QTANPWIFEPEspGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEME 943
Cdd:TIGR02013 923 EYLEKAGLPRD--GKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 1000
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 186885957 944 VWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPeDAPESFRLFVRELRSLALELN 1008
Cdd:TIGR02013 1001 VWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEP-GIPESFNVLIKELQSLGLDIE 1064
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
5-1005 |
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: 1023.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 5 DFELFLERYQLVEPLI-----KERDavyesLTYSSELYVSARLIwkNDRRRYIQEQTILIGKIPLMTSLGAFIVNGIYRI 79
Cdd:COG0085 48 NLSLEFGDYRLGEPKYtpeecKERD-----LTYAAPLYVKVRLV--NKETGEIKEQEVFMGDFPLMTDSGTFIINGTERV 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 80 VINQILQSPGFYYQSELNDNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLN----IREILEN 155
Cdd:COG0085 121 IVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLEtdeeILEAFGD 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 156 VCYPELFLSFLnDKKKIGSKENAILEFYQQFAcvEGDPVFSESLSKDLQKKFFQ-QRCELGGIGRRNMNRRLNLDIPQNN 234
Cdd:COG0085 201 DPIQEYILATL-EKDNTKTQEEALLEIYRKLR--PGEPPTIERAEQLLDNLFFDpKRYDLAHVGRYKINKKLGLDVPPED 277
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 235 TFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIyaALKHNWTPTPQNLVNS 314
Cdd:COG0085 278 RVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERM--TTQDVEAITPQSLINI 355
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 315 TPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSL 394
Cdd:COG0085 356 RPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSL 435
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 395 AIHARVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSI 474
Cdd:COG0085 436 ALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDV 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 475 FSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEkcivgtglegqAALDsgalaiaehegkiIYtntdkills 554
Cdd:COG0085 516 SPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE-----------APLL-------------HY--------- 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 555 gngdtlriPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLV 634
Cdd:COG0085 563 --------PLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLV 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 635 YEDIYTSFHIRKYEIQINQ---GPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKESSyaPEDRL 711
Cdd:COG0085 635 KDDVLTSIHIEEYEIEARDtklGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELT--PEERL 712
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 712 LRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEK--TESIRVYILQKREIKVGDKVAGRHGNKGIISKILP 789
Cdd:COG0085 713 LRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILP 792
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 790 RQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEasrklVFSELYEASkqtanpw 869
Cdd:COG0085 793 QEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEE-----IRELLEKAG------- 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 870 ifePESPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEG 949
Cdd:COG0085 861 ---LPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 937
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*.
gi 186885957 950 FGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPEdAPESFRLFVRELRSLAL 1005
Cdd:COG0085 938 YGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPG-IPESFKVLLKELQSLGL 992
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-1010 |
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: 800.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 1 NQEIDFELFLERYQLVEPLIKE---------RDAVYESLTYSSELYVSARLIWKNDRRryIQEQTILIGKIPLMTSL--- 68
Cdd:cd00653 31 DDDGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIRLTVNDKGK--IKEQEVFIGEIPIMLRSklc 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 69 ---------------------GAFIVNGIYRIVINQILQSPGFYYQSElnDNGISVYTGTIISDWGGRlelgidRKSRIW 127
Cdd:cd00653 109 nlngltpeeliklgecpldpgGYFIINGTEKVIINQEQRSPNVIIVED--SKGKRIYTKTSIPSYSPY------RGSWLE 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 128 VRVSRQQKLsilvllsamglnireilenvcypelfLSFLNDKKKigsKENAILEFYQQFacvegdpvfseslskdlqkkf 207
Cdd:cd00653 181 VKSDKKKDR--------------------------IYVRIDLKR---QEEALKYIGKRF--------------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 208 fqqrcelggigrrnmnrrlnldipqnntfllpRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVR 287
Cdd:cd00653 211 --------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKR 258
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 288 LENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHP------------LSQVLDRTNPLTQIVHGRKLSylgPG 355
Cdd:cd00653 259 LEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRIS---SL 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 356 GLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGrwGSLESPFYKISErskgarmlylspgrdeyymv 435
Cdd:cd00653 336 GLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEK-------------------- 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 436 aagnslalnqgiqeeqvvparyrqefltiaweQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVP----- 510
Cdd:cd00653 394 --------------------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpaln 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 511 -----------LSQSEKCIVGTGLEGQAALDsgalaiaehegkiiytntdkillsgngdtlriplvmyersnkntcihqk 579
Cdd:cd00653 442 qqyrmdtklylLLYPQKPLVGTGIEEYIAFG------------------------------------------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 580 phvqrgkcikkgqilaygaatvggELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGP---- 655
Cdd:cd00653 473 ------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKngpe 528
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 656 ERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKESSYapedrllrtILGMRVYTSKETCLKLPIGGR 735
Cdd:cd00653 529 EITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP---------IFGEKARDVRDTSLKYPGGEK 599
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 736 GRVIDVRWvqSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRM 815
Cdd:cd00653 600 GIVDDVKI--FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRM 677
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 816 NVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELyeaskqtanpwifepESPGKSRIFDGRTGDPFEQPVI 895
Cdd:cd00653 678 TIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGL---------------NYYGKEVLYDGRTGEPLEAPIF 742
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 896 IGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLG 975
Cdd:cd00653 743 VGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKC 822
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|....*
gi 186885957 976 TIIF----------GGRIPTPEdAPESFRLFVRELRSLALELNHF 1010
Cdd:cd00653 823 GIILsanlcrlckkGTNISKVG-IPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
484-933 |
9.61e-130 |
|
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: 397.67 E-value: 9.61e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 484 ASLIPFIEHNDANRALMSSNMQRQAVPLsqsekcivgtglegqaaldsgalaiaehegkiiytntdkillsgngdtlrIP 563
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGI--------------------------------------------------YT 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 564 LVMYERSNKNT---CIHQKPHVQRGKcIKKGQIlaygaatvgGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYT 640
Cdd:pfam00562 32 LNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFT 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 641 SFHIRKYEIQINQG--PERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvkessyaPEDRLLRTILGM 718
Cdd:pfam00562 102 SIHIKEIEARKTKLgpIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGPT--------ELTKLLRAIFGE 173
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 719 RVYTSKETCLKLPIGGRGRVIDVRWVQSSKtdetEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQD 798
Cdd:pfam00562 174 KARDVKDTSLKVPPGEEGVVDDVIVFELPP----GGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTED 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 799 GRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDeryEQEASRKLVFSELYEASKqtaNPWifepespGK 878
Cdd:pfam00562 250 GIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAGY---NYY-------GK 316
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 186885957 879 SRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAK 933
Cdd:pfam00562 317 EVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
1-1024 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 2240.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 1 NQEIDFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRRryIQEQTILIGKIPLMTSLGAFIVNGIYRIV 80
Cdd:CHL00001 45 DQEIEFQLFVETYQLVEPLIKERDAVYESLTYSSELYVPAGLIWKKSRD--MQEQTVFIGNIPLMNSLGTFIINGIYRVV 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 81 INQILQSPGFYYQSELNDNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPE 160
Cdd:CHL00001 123 INQILRSPGIYYRSELDHNGISVYTGTIISDWGGRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPE 202
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 161 LFLSFLNDK--KKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFFQQRCELGGIGRRNMNRRLNLDIPQNNTFLL 238
Cdd:CHL00001 203 IFLSFLNDKekKKIGSKENAILEFYQQFACVGGDPVFSESLCKELQKKFFQQRCELGRIGRRNMNRKLNLDIPENNTFLL 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 239 PRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLT 318
Cdd:CHL00001 283 PQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIPTPQNLVTSTPLT 362
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 319 DTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHA 398
Cdd:CHL00001 363 TTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIHA 442
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 399 RVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQ 478
Cdd:CHL00001 443 RIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPFQ 522
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 479 YFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKILLSGNGD 558
Cdd:CHL00001 523 YFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNGD 602
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 559 TLRIPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDI 638
Cdd:CHL00001 603 TLSIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDI 682
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 639 YTSFHIRKYEIQI---NQGPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKESSYAPEDRLLRTI 715
Cdd:CHL00001 683 YTSFHIRKYEIQThvtSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQEAEESSYAPEGRLLRAI 762
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 716 LGMRVYTSKETCLKLPIGGRGRVIDVRWVQsSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPY 795
Cdd:CHL00001 763 FGIQVSTSKETCLKLPIGGRGRVIDVRWIQ-KKGGSSYNPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPY 841
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 796 LQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPES 875
Cdd:CHL00001 842 LQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGDLLNRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWVFEPEY 921
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 876 PGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYI 955
Cdd:CHL00001 922 PGKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYI 1001
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 186885957 956 LQEMLTYKSDHIRARQEVLGTIIFGGRIPTPEDAPESFRLFVRELRSLALELNHFLVSEKTFQLNRKEA 1024
Cdd:CHL00001 1002 LQEMLTYKSDHIRARQEVLGAIITGGTIPKPEDAPESFRLLVRELRSLALELNHFLVSEKNFQINRKEV 1070
|
|
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
5-1007 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 1088.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 5 DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIWKNDRrrYIQEQTILIGKIPLMTSLGAFIVNGIYRIVINQI 84
Cdd:PRK00405 66 NLSLEFVSYELGEPKYDVEECKERGLTYSAPLRVKLRLINKETG--EIKEQEVYMGDIPLMTENGTFIINGTERVIVSQL 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 85 LQSPGFYYQSELND--NGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILE-------- 154
Cdd:PRK00405 144 HRSPGVYFDHDKDKtsSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDlfyekeef 223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 155 ---------------------------------NVCYPELFLSFLND---KKKIGSKENAILEFYQQFAcvEGDPVFSES 198
Cdd:PRK00405 224 gkeievpveyllgkvlaedivdeetgevlaeanDEITEELDGPYIRNtleKDPTSSREEALVEIYRRLR--PGEPPTVEA 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 199 LSKDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLL 277
Cdd:PRK00405 302 ARSLLENLFFdPKRYDLSKVGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELL 381
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 278 QEQFGLALVRLENMARGNIyaALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGL 357
Cdd:PRK00405 382 QNQFRIGLSRMERAVRERM--SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGL 459
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 358 TARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAA 437
Cdd:PRK00405 460 TRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQ 539
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 438 GNSlALNQ--GIQEEQVVpARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSE 515
Cdd:PRK00405 540 ANA-PLDEdgRFVDELVT-ARYKGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPE 617
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 516 KCIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKI------LLSGNGDTLRIPLVMYERSNKNTCIHQKPHVQRGKCIK 589
Cdd:PRK00405 618 APLVGTGMERRVARDSGAVVVAKRDGVVEYVDASRIvvrveeLDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVE 697
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 590 KGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQ---GPERVTNEIPHLE 666
Cdd:PRK00405 698 KGDVLADGPSTDNGELALGQNVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDtklGPEEITRDIPNVS 777
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 667 VHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRwVQS 746
Cdd:PRK00405 778 EEALRNLDESGIVRIGAEVKPGDILVGKVTPK--GETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVK-VFT 854
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 747 SKTDETEKT----ESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFE 822
Cdd:PRK00405 855 RIEQGDELPpgvnKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILE 934
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 823 SSLGLAGGLLDRHYRIAPFDERYEQEasrklVFSELYEASkqtanpwifePESPGKSRIFDGRTGDPFEQPVIIGNPYIL 902
Cdd:PRK00405 935 THLGWAAKGLGIKFATPVFDGAKEEE-----IKELLEEAG----------LPEDGKTTLYDGRTGEPFDRPVTVGYMYML 999
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 903 KLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGR 982
Cdd:PRK00405 1000 KLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGEN 1079
|
1050 1060
....*....|....*....|....*
gi 186885957 983 IPTPeDAPESFRLFVRELRSLALEL 1007
Cdd:PRK00405 1080 IPEP-GIPESFNVLVKELQSLGLDV 1103
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
5-1008 |
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: 1068.90 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 5 DFELFLERYQLVEPLIKERDAVYESLTYSSELYVSARLI-WKNDRRRYIQEQTILIGKIPLMTSLGAFIVNGIYRIVINQ 83
Cdd:TIGR02013 62 NIELEYLSYRLGEPKYSVEECKERGLTYSAPLKVKLRLInKEEDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQ 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 84 ILQSPGFYYQSELN--DNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVC--YP 159
Cdd:TIGR02013 142 LHRSPGVFFSSEKDttKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYTIDTLILNRLgsGE 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 160 ELFLSFLNDKKKigSKENAILEFYQQFAcvEGDPVFSESLSKDLQKKFF-QQRCELGGIGRRNMNRRLNLDIPQNNTFLL 238
Cdd:TIGR02013 222 YIRNTLRKDPTN--SEEEALVEIYRKLR--PGEPPTVEAARSLLENLFFdPKRYDLGRVGRYKLNKKLGLDVPESIGVLT 297
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 239 PRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIyaALKHNWTPTPQNLVNSTPLT 318
Cdd:TIGR02013 298 KEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERM--STQDTDTLTPQDLINAKPIS 375
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 319 DTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHA 398
Cdd:TIGR02013 376 AAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGPNIGLINSLSTYA 455
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 399 RVGRWGSLESPFYKIS--ERSKGARMLYLSPGRDEYYMVAAGNS-LALNQGIQEEqVVPARYRQEFLTIAWEQVHLRSIF 475
Cdd:TIGR02013 456 RVNEYGFIETPYRKVKdgKVVVTDEIDYLTADEEDNYVIAQANApLDENGRFVED-LVVARYRGEITLVSPDQVDYMDVS 534
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 476 SFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKILLSG 555
Cdd:TIGR02013 535 PKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRGGVVEYVDAKRIVIRY 614
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 556 NGDTL-------RIPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVL 628
Cdd:TIGR02013 615 DEDEEepdggidIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVLVAFMPWNGYNYEDAIL 694
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 629 ISERLVYEDIYTSFHIRKYEIQINQ---GPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvKESSY 705
Cdd:TIGR02013 695 ISERLVKDDVFTSIHIEEYEVEARDtklGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGDILVGKVTPK--GETEL 772
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 706 APEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEK--TESIRVYILQKREIKVGDKVAGRHGNKGI 783
Cdd:TIGR02013 773 TPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSREQGDELPPgvNKLVKVYIAQKRKIQVGDKMAGRHGNKGV 852
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 784 ISKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHyriapfderyEQEASRKLVFSELYEASK 863
Cdd:TIGR02013 853 VSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAGKRLGRK----------GVPIATPVFDGASEEEIK 922
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 864 QTANPWIFEPEspGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEME 943
Cdd:TIGR02013 923 EYLEKAGLPRD--GKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEME 1000
|
970 980 990 1000 1010 1020
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 186885957 944 VWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPeDAPESFRLFVRELRSLALELN 1008
Cdd:TIGR02013 1001 VWALEAYGAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEP-GIPESFNVLIKELQSLGLDIE 1064
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
5-1005 |
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: 1023.51 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 5 DFELFLERYQLVEPLI-----KERDavyesLTYSSELYVSARLIwkNDRRRYIQEQTILIGKIPLMTSLGAFIVNGIYRI 79
Cdd:COG0085 48 NLSLEFGDYRLGEPKYtpeecKERD-----LTYAAPLYVKVRLV--NKETGEIKEQEVFMGDFPLMTDSGTFIINGTERV 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 80 VINQILQSPGFYYQSELNDNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLN----IREILEN 155
Cdd:COG0085 121 IVSQLVRSPGVYFVEEEDKSGKDLYSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLEtdeeILEAFGD 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 156 VCYPELFLSFLnDKKKIGSKENAILEFYQQFAcvEGDPVFSESLSKDLQKKFFQ-QRCELGGIGRRNMNRRLNLDIPQNN 234
Cdd:COG0085 201 DPIQEYILATL-EKDNTKTQEEALLEIYRKLR--PGEPPTIERAEQLLDNLFFDpKRYDLAHVGRYKINKKLGLDVPPED 277
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 235 TFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIyaALKHNWTPTPQNLVNS 314
Cdd:COG0085 278 RVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERM--TTQDVEAITPQSLINI 355
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 315 TPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSL 394
Cdd:COG0085 356 RPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIGLIGSL 435
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 395 AIHARVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSI 474
Cdd:COG0085 436 ALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEVDYMDV 515
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 475 FSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEkcivgtglegqAALDsgalaiaehegkiIYtntdkills 554
Cdd:COG0085 516 SPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPE-----------APLL-------------HY--------- 562
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 555 gngdtlriPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLV 634
Cdd:COG0085 563 --------PLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGYNYEDAIIISERLV 634
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 635 YEDIYTSFHIRKYEIQINQ---GPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKESSyaPEDRL 711
Cdd:COG0085 635 KDDVLTSIHIEEYEIEARDtklGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPKGETELT--PEERL 712
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 712 LRTILGMRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDETEK--TESIRVYILQKREIKVGDKVAGRHGNKGIISKILP 789
Cdd:COG0085 713 LRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSREEGDELPPgvNKLVRVYVAQKRKIEVGDKLAGRHGNKGVISRILP 792
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 790 RQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEasrklVFSELYEASkqtanpw 869
Cdd:COG0085 793 QEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAALLGRRVATPVFDGAPEEE-----IRELLEKAG------- 860
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 870 ifePESPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEG 949
Cdd:COG0085 861 ---LPPDGKEVLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEA 937
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*.
gi 186885957 950 FGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPEdAPESFRLFVRELRSLAL 1005
Cdd:COG0085 938 YGAAYTLQERLTIKSDDVCGRVKVYEAIVKGENIPEPG-IPESFKVLLKELQSLGL 992
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
8-1011 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1009.62 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 8 LFLERYQLVEPLIKERDAVYESLTYSSELYVSARLIwkNDRRRYIQEQTILIGKIPLMTSLGAFIVNGIYRIVINQILQS 87
Cdd:CHL00207 47 LFGKNYKLKYPKYNLLSAKSYDSNYSIQIYLPLKFI--NLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRS 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 88 PGFYYQSELNDNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILENVCYPELFLSFLN 167
Cdd:CHL00207 125 PGIYFKKEIKKNSNKIYSATLIPNRGSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSEFLKKLKP 204
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 168 DKKKIGS--KENAILEFYQQFAcvEGDPVFSESLSKDLQKKFFQ-QRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILA 244
Cdd:CHL00207 205 ILLNSNSytNEEILLEIYKNLS--PIEPATVNDANQNLFSRFFDpKNYDLGKVGRYKINNKLNLNIPERVRNLTYEDILS 282
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 245 AADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVRLENMARGNIyaaLKHNWTP-TPQNLVNSTPLTDTYKV 323
Cdd:CHL00207 283 IIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRM---TICDIDSlSKFNLINPKPLIALIRE 359
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 324 FFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGRW 403
Cdd:CHL00207 360 FFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARINKF 439
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 404 GSLESPFYKISERS--KGARMLYLSPGRDEYYMVAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFS 481
Cdd:CHL00207 440 GFIETPFYKVINGKvkKFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQVFS 519
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 482 IGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKI-LLSGNGDTL 560
Cdd:CHL00207 520 IAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIiIQDDNNRYI 599
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 561 RIPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYT 640
Cdd:CHL00207 600 HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILINKRLVYEDLFT 679
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 641 SFHIRKYEIQINQ---GPERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvKESSYAPEDRLLRTILG 717
Cdd:CHL00207 680 SIHIEKYEIELRQtklGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPK--GESDQLPEGKLLRAIFG 757
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 718 MRVYTSKETCLKLPIGGRGRVIDVRWVQSSKTDE--TEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPY 795
Cdd:CHL00207 758 EKAKDVKDTSLRMPNGGYGRVIKVEIFSRSKGDElkFGYYLKIRVFIAQIRKIQVGDKLAGRHGNKGIISRILPRQDMPY 837
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 796 LQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELYEASKQTANPWIFEPES 875
Cdd:CHL00207 838 LPDGTPPDIILNPLGVPSRMNVGQLFECLLGLAGDNLNKRFKILPFDEMYGSEYSRILINNKLNQASIKNNEYWLFNSYH 917
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 876 PGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYI 955
Cdd:CHL00207 918 PGKMVLRDGRTGYKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYT 997
|
970 980 990 1000 1010
....*....|....*....|....*....|....*....|....*....|....*.
gi 186885957 956 LQEMLTYKSDHIRARQEVLGTIIFGGRIPTPeDAPESFRLFVRELRSLALELNHFL 1011
Cdd:CHL00207 998 LKELLTIKSDDMQGRNETLNAIVKGQPIPKP-GTPESFKVLMRELQSLGLDIEAYK 1052
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
1-1010 |
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: 800.63 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 1 NQEIDFELFLERYQLVEPLIKE---------RDAVYESLTYSSELYVSARLIWKNDRRryIQEQTILIGKIPLMTSL--- 68
Cdd:cd00653 31 DDDGRLKLKFGDIYLGKPKVEEggvtrkltpNECRLRDLTYSAPLYVDIRLTVNDKGK--IKEQEVFIGEIPIMLRSklc 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 69 ---------------------GAFIVNGIYRIVINQILQSPGFYYQSElnDNGISVYTGTIISDWGGRlelgidRKSRIW 127
Cdd:cd00653 109 nlngltpeeliklgecpldpgGYFIINGTEKVIINQEQRSPNVIIVED--SKGKRIYTKTSIPSYSPY------RGSWLE 180
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 128 VRVSRQQKLsilvllsamglnireilenvcypelfLSFLNDKKKigsKENAILEFYQQFacvegdpvfseslskdlqkkf 207
Cdd:cd00653 181 VKSDKKKDR--------------------------IYVRIDLKR---QEEALKYIGKRF--------------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 208 fqqrcelggigrrnmnrrlnldipqnntfllpRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALVR 287
Cdd:cd00653 211 --------------------------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSGLKR 258
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 288 LENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHP------------LSQVLDRTNPLTQIVHGRKLSylgPG 355
Cdd:cd00653 259 LEREVKEKLQKQLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRIS---SL 335
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 356 GLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGrwGSLESPFYKISErskgarmlylspgrdeyymv 435
Cdd:cd00653 336 GLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEK-------------------- 393
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 436 aagnslalnqgiqeeqvvparyrqefltiaweQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVP----- 510
Cdd:cd00653 394 --------------------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGtpaln 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 511 -----------LSQSEKCIVGTGLEGQAALDsgalaiaehegkiiytntdkillsgngdtlriplvmyersnkntcihqk 579
Cdd:cd00653 442 qqyrmdtklylLLYPQKPLVGTGIEEYIAFG------------------------------------------------- 472
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 580 phvqrgkcikkgqilaygaatvggELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGP---- 655
Cdd:cd00653 473 ------------------------ELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKYEIELRKTKngpe 528
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 656 ERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKESSYapedrllrtILGMRVYTSKETCLKLPIGGR 735
Cdd:cd00653 529 EITRGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP---------IFGEKARDVRDTSLKYPGGEK 599
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 736 GRVIDVRWvqSSKTDETEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPVDMVFNPLGVPSRM 815
Cdd:cd00653 600 GIVDDVKI--FSRELNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGVISKILPQEDMPFTEDGIPPDIILNPHGFPSRM 677
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 816 NVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEASRKLVFSELyeaskqtanpwifepESPGKSRIFDGRTGDPFEQPVI 895
Cdd:cd00653 678 TIGQLLESLLGKAGALLGKFGDATPFDGAEEEDISELLGEAGL---------------NYYGKEVLYDGRTGEPLEAPIF 742
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 896 IGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLG 975
Cdd:cd00653 743 VGPVYYQRLKHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKC 822
|
1050 1060 1070 1080
....*....|....*....|....*....|....*....|....*
gi 186885957 976 TIIF----------GGRIPTPEdAPESFRLFVRELRSLALELNHF 1010
Cdd:cd00653 823 GIILsanlcrlckkGTNISKVG-IPYAFKLLFQELQSMNIDPRLK 866
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
23-1010 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 669.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 23 RDAVYESLTYSSELYVSARLI-WKNDRR-------RYIQEQTILIGKIPLMTSLGAFIVNGIYRIVINQILQSPGFYYQS 94
Cdd:PRK09603 83 REAMERGITYSIPLKIKVRLIlWEKDTKsgekngiKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKE 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 95 ELNDNGIS--VYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREILEnVCYPELFLSFLNDK--- 169
Cdd:PRK09603 163 EESSTSLNklIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIK-MFYPLVKVRYENDKyli 241
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 170 ---------------------------KKIGSK----------------------------------------------- 175
Cdd:PRK09603 242 pfasldanqrmefdlkdpqgkiillagKKLTSRkikelkenhlewveypmdillnrhlaepvmvgkevlldmltqldknk 321
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 176 -----ENAILEFY------------------------------------QQFACVE-------GDPVFSESLSKDLQKKF 207
Cdd:PRK09603 322 lekihDLGVQEFViindlalghdasiihsfsadseslkllkqtekiddeNALAAIRihkvmkpGDPVTTEVAKQFVKKLF 401
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 208 FQ-QRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFGLALV 286
Cdd:PRK09603 402 FDpERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANELHSGLV 481
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 287 RLENMARGNIYAALKHNWTPTPQNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGGLTARTATFPI 366
Cdd:PRK09603 482 KMQKTIKDKLTTMSGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKDRVGFEA 561
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 367 RDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVAAGNSLALNQG 446
Cdd:PRK09603 562 RDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPASTPIDEEG 641
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 447 IQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEKCIVGTGLEGQ 526
Cdd:PRK09603 642 NILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIVGTGIEKI 721
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 527 AALDSGALAIAEHEGKIIYTNTDKILLSGNGDTL----RIPLVMYERSNKNTCIHQKPHVQRGKCIKKGQILAYGAATVG 602
Cdd:PRK09603 722 IARDSWGAIKANRAGVVEKIDSKNIYILGEGKEEayidAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAGQIIADGPSMDR 801
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 603 GELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEI---QINQGPERVTNEIPHLEVHLLRNLDKNGIV 679
Cdd:PRK09603 802 GELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVdarELKHGVEEFTADIPDVKEEALAHLDESGIV 881
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 680 MLGSWVETGDILIGKLTPQmvKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVR----------------- 742
Cdd:PRK09603 882 KVGTYVSAGMILVGKTSPK--GEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKvftkkgyekdarvlsay 959
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 --------------------------------------------------------------------------------
Cdd:PRK09603 960 eeekakldmehfdrltmlnreellrvssllsqaileepfshngkdykegdqipkeeiasinrftlaslvkkyskevqnhy 1039
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 743 ------WVQSSKT--DETEKTESI---------------RVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDG 799
Cdd:PRK09603 1040 eitknnFLEQKKVlgEEHEEKLSIlekddilpngvikkvKLYIATKRKLKVGDKMAGRHGNKGIVSNIVPVADMPYTADG 1119
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 800 RPVDMVFNPLGVPSRMNVGQIFESSLGLAG------------------------------------GLLDRHYRIAPFDE 843
Cdd:PRK09603 1120 EPVDIVLNPLGVPSRMNIGQILEMHLGLVGkefgkqiasmledktkdfakelrakmleianainekDPLTIHALENCSDE 1199
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 844 R---YEQEASRKLVFS-ELYEASKQTANPWIFE---PESPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRS 916
Cdd:PRK09603 1200 ElleYAKDWSKGVKMAiPVFEGISQEKFYKLFElakIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHHLVDEKVHARS 1279
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 917 SGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRIPTPEdAPESFRLF 996
Cdd:PRK09603 1280 TGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGESE-IPETFYVL 1358
|
1290
....*....|....
gi 186885957 997 VRELRSLALELNHF 1010
Cdd:PRK09603 1359 TKELQSLALDINIF 1372
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
17-1008 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 621.26 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 17 EPLIKERDAVYESLTYSSELYVSARLIWKNDRR---------------------RYIQEQTILIGKIPLMTSLGAFIVNG 75
Cdd:PRK14844 81 DPKYDESECIKRGITFSAQVIASIRLVIMQDGIsldeyksikesgdhsklatviKSIEEQEVHFCELPMMTDKGTFIING 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 76 IYRIVINQILQSPGFYYQSELN---DNGISVYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGLNIREI 152
Cdd:PRK14844 161 VEKVIVSQMHRSPGVFFDSDKGktyNSGKLIYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDI 240
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 153 L----ENVCY------------PELF----LSF----------LNDKKKIGSK------ENAILEFYQQFACVEG----- 191
Cdd:PRK14844 241 LdrfyEKIKYikhkdgwkvpfvPDKFkgvrLPFdlmdvegnvlLKANVRITSRlakklyDNELKEYLVPFDSICGlflae 320
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 192 DPVFSESLSK-----------DLQK------------------------------------------------------- 205
Cdd:PRK14844 321 DLIDSASSTKilsagesikleDIKKlellsideisvlnidnlsvgpyilntlfldenmsyqdalyeiykvlrpgevpvle 400
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 206 ---KFFQ------QRCELGGIGRRNMNRRLNLDIPQNNTFLLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIRSVADL 276
Cdd:PRK14844 401 iveEFFRnlffspEYYDLSNIGRLKLNSYLGLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEF 480
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 277 LQEQFGLALVRLENMARGNIYAALKHNWTPTpqNLVNSTPLTDTYKVFFRLHPLSQVLDRTNPLTQIVHGRKLSYLGPGG 356
Cdd:PRK14844 481 IENQFRTGLLKLERAVVDSMSTSSLDKVSPS--DFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGG 558
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 357 LTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGRWGSLESPFYKISERSKGARMLYLSPGRDEYYMVA 436
Cdd:PRK14844 559 LTRERAGFEVRDVHPTHYGRICPIETPEGQNIGLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIA 638
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 437 AGNSLALNQGIQEEQVVPARYRQEFLTIAWEQVHLRSIFSFQYFSIGASLIPFIEHNDANRALMSSNMQRQAVPLSQSEK 516
Cdd:PRK14844 639 DTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTA 718
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 517 CIVGTGLEGQAALDSGALAIAEHEGKIIYTNTDKILLSGNgDTLRIP--------LVMYERSNKNTCIHQKPHVQRGKCI 588
Cdd:PRK14844 719 PLVATGMESFVASGSGAVVLAKRDGIVDSSDSNSIVIRAF-DKERVNyldvdiyhLRKFQRSNHNTCINQKPLVCVGDYV 797
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 589 KKGQILAYGAATVGGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYEIQINQGP---ERVTNEIPHL 665
Cdd:PRK14844 798 KEGDVIADGPAINSGELALGQNLLVAFMSWQGYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPlgsEKITRAIPGV 877
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 666 EVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvKESSYAPEDRLLRTILGMRVYTSKETCLKLPIGGRGRVIDVR--- 742
Cdd:PRK14844 878 NEENLYHLDDSGIVKIGTRVGPGYILVGKVTPK--PSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQvft 955
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 743 --------------------------------------------------------------W-------------VQSS 747
Cdd:PRK14844 956 rrgveenerallikqkeindfekerdyiinvtseyfydelkkllinsgsqdrekfdsiereqWwgiglknqsiseqVKSL 1035
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 748 KTDETEKTE-------------------------SIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQDGRPV 802
Cdd:PRK14844 1036 KKDFDEKVShaiaqfkrkveklhegydlpqgvsmSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPV 1115
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 803 DMVFNPLGVPSRMNVGQIFESSLGLA--------GGLLDRHYRI-APF--------DERYEQ------------------ 847
Cdd:PRK14844 1116 DIILNPLGVPSRMNVGQILETHVGWAckklgekvGNILDEINKIkSAFckgirslnDDNFTKfaaayldnkkieniddde 1195
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 848 -----------------------------------------------------------------EASRKL-----VFSE 857
Cdd:PRK14844 1196 itasvlntpnknalndelnelvenylnscksaysnlrnflievyscgsnvsicnnirdisdnnliEFARKLrdgipVAAP 1275
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 858 LYEASKQTANPWIFE---PESPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKK 934
Cdd:PRK14844 1276 VFEGPKDEQIAKLFElagLDNSGQAVLYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHF 1355
|
1290 1300 1310 1320 1330 1340 1350
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 186885957 935 GGQRVGEMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGTIIFGGRiPTPEDAPESFRLFVRELRSLALELN 1008
Cdd:PRK14844 1356 GGQRFGEMECWALQAYGAAYTLQEMLTVKSDDINGRVKIYESIIKGDS-NFECGIPESFNVMIKELRSLCLNVD 1428
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
484-933 |
9.61e-130 |
|
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: 397.67 E-value: 9.61e-130
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 484 ASLIPFIEHNDANRALMSSNMQRQAVPLsqsekcivgtglegqaaldsgalaiaehegkiiytntdkillsgngdtlrIP 563
Cdd:pfam00562 2 ASLIPFVDHNQSPRNTYQCAMGKQAMGI--------------------------------------------------YT 31
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 564 LVMYERSNKNT---CIHQKPHVQRGKcIKKGQIlaygaatvgGELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYT 640
Cdd:pfam00562 32 LNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGGF---------GELPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFT 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 641 SFHIRKYEIQINQG--PERVTNEIPHLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPQmvkessyaPEDRLLRTILGM 718
Cdd:pfam00562 102 SIHIKEIEARKTKLgpIEEITRDIPNVSEEALKKLDEDGIVRVGAEVKPGDILVGKVGPT--------ELTKLLRAIFGE 173
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 719 RVYTSKETCLKLPIGGRGRVIDVRWVQSSKtdetEKTESIRVYILQKREIKVGDKVAGRHGNKGIISKILPRQDMPYLQD 798
Cdd:pfam00562 174 KARDVKDTSLKVPPGEEGVVDDVIVFELPP----GGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTED 249
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 799 GRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDeryEQEASRKLVFSELYEASKqtaNPWifepespGK 878
Cdd:pfam00562 250 GIPPDIILNPHGVPSRMTIGQLLETHLGKAAALLGVFVDATPFD---GASTEVEDIGELLEKAGY---NYY-------GK 316
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*
gi 186885957 879 SRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAK 933
Cdd:pfam00562 317 EVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
5-1003 |
1.39e-81 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 288.01 E-value: 1.39e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 5 DFELFLERYQLVEPLIKERD----------AVYESLTYSSELYVSARLIWKNDRRRyiqEQTILIGKIPLM--------T 66
Cdd:PRK08565 46 GLKIVLGKIRVGEPEIKEADgserpitpmeARLRNLTYAAPLYLTMIPVENGIEYE---PEEVKIGDLPIMvkskicplS 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 67 SL----------------GAFIVNGIYRIVINQILQSPG--FYYQSELNDNgiSVYTGTIISDWGG-RLELGIDRKSR-- 125
Cdd:PRK08565 123 GLspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrvLVDKGEAGSS--ITHTAKVISSRAGyRAQVTVERRKDgt 200
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 126 IWVRVSR-QQKLSILVLLSAMGLNI-REILENVCY-----PELFLSFLNDKKKIGSKENAILEFYQQFAcvEGDPvfses 198
Cdd:PRK08565 201 IYVSFPAvPGKIPFVILMRALGLETdRDIVYAVSLdpeiqQELLPSLEQASSIAATVEDALDYIGKRVA--IGQP----- 273
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 199 lskdlqKKFFQQRCE-------LGGIGRRNMNRRlnldipqNNTFLLPRdilaAADRLIRIKFGMGTLDDMNHLQNKRIR 271
Cdd:PRK08565 274 ------REYRIERAEqildkylLPHLGTSPEDRI-------KKAYFLGQ----MASKLLELYLGRREPDDKDHYANKRLR 336
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 272 SVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLTDtykvffRL-HPL------------SQVLDRTN 338
Cdd:PRK08565 337 LAGDLLAELFRVAFKQLVKDLKYQLEKSYARGRKLDLRAIVRPDIITE------RIrHALatgnwvggrtgvSQLLDRTN 410
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 339 PLTQIVHGRKLsyLGPggLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARVGRwGSLESPFYKI----- 413
Cdd:PRK08565 411 YLSTLSHLRRV--VSP--LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQISV-GVDEEEVEEIlyelg 485
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 414 ---------SERSKGARmLYLSpGR-------------------------DE----YYMVAAGNSLALN----------- 444
Cdd:PRK08565 486 vvpveeareEEYISWSR-VYLN-GRligyhpdgeelaekirelrrsgkisDEvnvaYIETGEINEVYVNcdsgrvrrpli 563
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 445 -----------------------------QGI-------QEEQVVPARYRQEFLTiawEQVHLrSIFSFQYFSIGASLIP 488
Cdd:PRK08565 564 vvengkpkltrehveklkkgeltfddlvkMGVieyldaeEEENAYVALDPEDLTP---EHTHL-EIWPPAILGITASIIP 639
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 489 FIEHNDANRALMSSNMQRQAVPLSQSEKcivgtglegQAALDSgalaiaehegkiiytntdkillsgngdtlRIPLVMYE 568
Cdd:PRK08565 640 YPEHNQSPRNTYQAAMAKQSLGLYAANF---------RIRTDT-----------------------------RGHLLHYP 681
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 569 rsnkntcihQKPHVQrgkcIKKGQILAYGaatvggELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIYTSFHIRKYE 648
Cdd:PRK08565 682 ---------QRPLVQ----TRALEIIGYN------DRPAGQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYE 742
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 649 IQINQ--GPERVTNEIP------HLEVHLLRNLDKNGIVMLGSWVETGDILIGKLTPqmvkeSSYAPEDRLLRTILGMRv 720
Cdd:PRK08565 743 TEERKypGGQEDKIEIPepnvrgYRGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSP-----PRFLEELEELSLGLQER- 816
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 721 ytsKETCLKLPIGGRGRVIDVRWVQSSktdETEKTESIRVYILQKREIkvGDKVAGRHGNKGIISKILPRQDMPYLQDGR 800
Cdd:PRK08565 817 ---RDTSVTVRHGEKGIVDTVLITESP---EGNKLVKVRVRDLRIPEL--GDKFASRHGQKGVIGMLVPQEDMPFTEDGI 888
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 801 PVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEAsRKLVFSELYEASkqtanpwifepespGKSR 880
Cdd:PRK08565 889 VPDLIINPHAIPSRMTVGQLLESIAGKVAALEGRFVDATPFYGEPEEEL-RKELLKLGYKPD--------------GTEV 953
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 881 IFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFGVAYILQEML 960
Cdd:PRK08565 954 MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERL 1033
|
1130 1140 1150 1160 1170
....*....|....*....|....*....|....*....|....*....|....*....
gi 186885957 961 TYKSD-----------HI---RARQEVLGTIIFG--GRIpTPEDAPESFRLFVRELRSL 1003
Cdd:PRK08565 1034 LDSSDkttiyvcelcgHIawyDRRKNKYVCPIHGdkGNI-SPVEVSYAFKLLLQELMSM 1091
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
480-1003 |
5.54e-62 |
|
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: 222.21 E-value: 5.54e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 480 FSIGASLIPFIEHNDANRALMSSNMQRQAVPLsqsekcivgtglegqaaldsgalaiaehegkiiYTNTDKILLSGNGDT 559
Cdd:TIGR03670 127 LGIIASTIPYPEHNQSPRNTMGAAMAKQSLGL---------------------------------YAANYRIRLDTRGHL 173
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 560 LRIPlvmyersnkntcihQKPHVQrgkcIKKGQILAYGaatvggELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIY 639
Cdd:TIGR03670 174 LHYP--------------QKPLVK----TRVLELIGYD------DRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLA 229
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 640 TSFHIRKYEIQINQGP--ERVTNEIPHLEVH------LLRNLDKNGIVMLGSWVETGDILIGKLTPQMVKEssyapEDRL 711
Cdd:TIGR03670 230 RSTFFRTYEAEERRYPggQEDRFEIPEPDVRgyrgeeAYKHLDEDGIVYPEVEVKGGDVLIGKTSPPRFLE-----ELRE 304
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 712 LRTILGMRvytsKETCLKLPIGGRGrVIDVrwVQSSKTDETEKTESIRVYILQKREIkvGDKVAGRHGNKGIISKILPRQ 791
Cdd:TIGR03670 305 FGLVTERR----RDTSVTVRHGEKG-IVDK--VIITETEEGNKLVKVRVRDLRIPEL--GDKFASRHGQKGVIGMIVPQE 375
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 792 DMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPFDERYEQEAsRKLVFSELYEASkqtanpwif 871
Cdd:TIGR03670 376 DMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVDGTPFEGEPEEEL-RKELLKLGFKPD--------- 445
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 872 epespGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGEMEVWALEGFG 951
Cdd:TIGR03670 446 -----GKEVMYDGITGEKLEAEIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHG 520
|
490 500 510 520 530 540
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 186885957 952 VAYILQEMLTYKSD-----------HI---RARQEVLGTIIFG--GRIpTPEDAPESFRLFVRELRSL 1003
Cdd:TIGR03670 521 AAMLLKERLLDESDkyvvyvcencgHIaweDKRKGTAYCPVCGetGDI-SPVEMSYAFKLLLDELKSL 587
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
480-965 |
2.13e-56 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 206.35 E-value: 2.13e-56
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 480 FSIGASLIPFIEHNDANRALMSSNMQRQAVPLsqsekcivgtglegqaaldsgalaiaehegkiiYTNTDKILLSGNGDT 559
Cdd:PRK07225 133 LGIGAGMIPYPEHNASPRITMGAGMIKQSLGL---------------------------------PAANYKLRPDTRGHL 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 560 LRIPlvmyersnkntcihQKPHVQrgkcIKKGQILAYGaatvggELALGKNVLVAYMPWEGYNFEDAVLISERLVYEDIY 639
Cdd:PRK07225 180 LHYP--------------QVPLVK----TQTQEIIGFD------ERPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLG 235
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 640 TSFHIRKYEiqinqGPERVTN-------EIPHLEVH------LLRNLDKNGIVMLGSWVETGDILIGKLTPqmvkessya 706
Cdd:PRK07225 236 RSHFFRTYE-----GEERRYPggqedrfEIPDKDVRgyrgeeAYRHLDEDGLVNPETEVKEGDVLIGKTSP--------- 301
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 707 PedRLLR--TILGMRVYTSKETCLKLPIGGRGrVIDVrwVQSSKTDETEKTESIRVYILQKREIkvGDKVAGRHGNKGII 784
Cdd:PRK07225 302 P--RFLEepDDFGISPEKRRETSVTMRSGEEG-IVDT--VILTETEEGSRLVKVRVRDLRIPEL--GDKFASRHGQKGVI 374
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 785 SKILPRQDMPYLQDGRPVDMVFNPLGVPSRMNVGQIFESSLGLAGGLLDRHYRIAPF-DERYE--QEASRKLVFselyea 861
Cdd:PRK07225 375 GLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEMIGGKVGSLEGRRVDGTAFsGEDEEdlREALEKLGF------ 448
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 862 skqtanpwifepESPGKSRIFDGRTGDPFEQPVIIGNPYILKLIHQVDDKIHGRSSGRYSRLTQQPLKGRAKKGGQRVGE 941
Cdd:PRK07225 449 ------------EHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGE 516
|
490 500
....*....|....*....|....
gi 186885957 942 MEVWALEGFGVAYILQEMLTYKSD 965
Cdd:PRK07225 517 MERDVLIGHGAAMLLKERLLDESD 540
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
86-271 |
3.68e-47 |
|
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: 166.75 E-value: 3.68e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 86 QSPGFYYQSELNDNGIS-VYTGTIISDWGGRLELGIDRKSRIWVRVSRQQKLSILVLLSAMGL-NIREILENVCYP---- 159
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIaTYTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLvSDREILDRLCYDfndp 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 160 ---ELFLSFLNDKKKIGSKENAILEFYQQFACVEGDPVFSESLSKDLQKKFfqqrcelggiGRRNMNRRLNLDIPQNNTF 236
Cdd:pfam04561 81 qmlELLKPELEEAENIYTQEEALDYIGKGFALRRGEEPRLQRAREILYSRD----------PKYNLNKHLGLNEPFENER 150
|
170 180 190
....*....|....*....|....*....|....*
gi 186885957 237 LLPRDILAAADRLIRIKFGMGTLDDMNHLQNKRIR 271
Cdd:pfam04561 151 LKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
332-399 |
3.33e-28 |
|
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: 108.00 E-value: 3.33e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 186885957 332 QVLDRTNPLTQIVHGRKLSYlGPGGLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHAR 399
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
935-1012 |
1.05e-26 |
|
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: 104.59 E-value: 1.05e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 935 GGQRVGEMEVWALEGFGVAYILQEMLTYKSD----HIRARQEVLG-----TIIFGGRIPTPEDAPESFRLFVRELRSLAL 1005
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAaynkcPICKGETDISPGYIPESFKLLFQELQSLGI 80
|
....*..
gi 186885957 1006 ELNHFLV 1012
Cdd:pfam04560 81 DPRLLLE 87
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
10-400 |
1.51e-19 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 93.09 E-value: 1.51e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 10 LERYQLVEPLIKERD----------AVYESLTYSSELYVSARLIWKNDRRryiQEQTILIGKIPLMTS------------ 67
Cdd:PRK09606 56 LGKIRVGKPVVKEADgsereiypmeARLRNLTYSAPLYLEMSPVEGGEEE---EPEEVYIGELPVMVGskicnlyglsee 132
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 68 ------------LGAFIVNGIYRIVINQILQSPGFYYQSELNDNGISVYTGTIISDWGG---RLELGIDRKSRIWV---R 129
Cdd:PRK09606 133 elievgedpldpGGYFIVNGSERVLMTLEDLAPNKILVEKDERYGDRIEVAKVFSQRRGyraLVTVERNRDGLLEVsfpS 212
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 130 VSRqqKLSILVLLSAMGL-NIREILENVC-YPELFLSFLND--KKKIGSKENAIlEFYqqfacveGDPVFSESlSKDLQK 205
Cdd:PRK09606 213 VPG--SIPFVILMRALGLeTDEEIVEAVSdDPEIVKFMLENleEAEVDTQEEAL-EYI-------GKRVAPGQ-TKEYRI 281
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 206 KFFQQ---RCELGGIGRRNMNRRlnldipqNNTFLLPRdilaAADRLIRIKFGMGTLDDMNHLQNKRIRSVADLLQEQFG 282
Cdd:PRK09606 282 KRAEYvidRYLLPHLGVEPEVRR-------AKAHYLGR----MAEACFELALGRREEDDKDHYANKRLKLAGDLMEDLFR 350
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 283 LALVRLenmARGNIYA---ALKHNWTPTPQNLVNSTPLTDtykvffRL-HPL------------SQVLDRTNPLTQIVHG 346
Cdd:PRK09606 351 VAFNRL---ARDVKYQlerANMRNRELSIKTAVRSDVLTE------RLeHAMatgnwvggrtgvSQLLDRTDYMATLSHL 421
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....
gi 186885957 347 RKLsyLGPggLTARTATFPIRDIHPSHYGRICPIDTSEGINVGLIGSLAIHARV 400
Cdd:PRK09606 422 RRV--VSP--LSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVEI 471
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
6-318 |
7.76e-16 |
|
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: 80.89 E-value: 7.76e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 6 FELFLERYQLVEPLIKERDAVYES----------LTYSSELYVsaRLIWKNDRRRYIQEQTILIGKIPLMT--------- 66
Cdd:pfam04563 44 LSLKFGQIRLGKPMFDETDGSTREiypqecrlrnLTYSAPLYV--DLELSVYNGEDIKPIEVFIGRLPIMLrsnacilsg 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 67 ---------------SLGAFIVNGIYRIVINQILQS---PGFYYQSELNDNGI--SVYTGTIIS---DWGGRLE-LGIDR 122
Cdd:pfam04563 122 ateselvklgecpldPGGYFIINGSEKVIVAQEHRSrnhPIVFKKADPKKRGSvaSVRSSAEISvrpDSTSWVNvLEYLS 201
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 123 KSRIWVRVS-RQQKLSILVLLSAMGLNI-REILENVCYpELFLSFLNDKKKIGSKENAILEFYQQFACVE-----GDPVF 195
Cdd:pfam04563 202 NGTIYFKFPyIKKEIPIVIILRALGFTSdREIFELICY-DVNDQQLQEELLPSLEEGFKIRIQTQEQALDyiggrGRAIF 280
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 186885957 196 SESLSKD---------LQKKFFQQRCELGGIGRRNMnrrlnldipqnntfllpRDILAAADRLIRIKFGMGTLDDMNHLQ 266
Cdd:pfam04563 281 RMGRPREprikyaeeiLQKEVLPHLGTYELDETKKA-----------------YFIGYMIRRLLLLALGRREVDDRDHLG 343
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|..
gi 186885957 267 NKRIRSVADLLQEQFGLALVRLENMARGNIYAALKHNWTPTPQNLVNSTPLT 318
Cdd:pfam04563 344 NKRLRLAGPLLASLFRVLFKKLVRDVRERLQKVLGSPDDLMLQLLVNAKPIT 395
|
|
| |
