|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1342 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2268.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1 MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 80 FDVKECQIRGVTFSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKIVFEirdnklqm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 240 elvperlrgetasfdieangkiyvekgrritarhirqlekddiQSIEVPVEYIAGKVVAKDYIDTNTGELICAANMELSL 319
Cdd:PRK00405 225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 320 DLlaklsqsghkrietlftndldHGAYISETLRVDPTNDRLSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 400 VGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSK 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 720 RGGVIQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405 641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405 719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405 799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 960 lteelqileaglfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkITQG 1039
Cdd:PRK00405 856 ----------------------------------------------------------------------------IEQG 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1040 DDLAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405 860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1120 AAKGIGEKinqmlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlkkgmpIATPVFDGAKETEIKKLL 1199
Cdd:PRK00405 940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1200 EMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491068271 1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:PRK00405 1046 AYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1339 |
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: 1927.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 8 KKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVK 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 84 ECQIRGVTFSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffdkivfeirdnklqmelvp 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 244 erlrgetasfdieangkiyvekgrritarhirqlekddiqsievpveyiagkvvakdyidtntgelicaanmelsldlla 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 324 klsqsghkrIETLFTNDLDHGAYISETLRVDPTNDRLSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 404 KFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 564 PEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVV--TDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGE 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013 520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 722 GVIQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013 600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013 679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlt 961
Cdd:TIGR02013 759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 962 eelqileaglfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitQGDD 1041
Cdd:TIGR02013 815 ----------------------------------------------------------------------------QGDE 818
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1042 LAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013 819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1122 KGIGekinqmlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlKKGMPIATPVFDGAKETEIKKLLEM 1201
Cdd:TIGR02013 899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1202 GGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
gi 491068271 1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:TIGR02013 1008 GAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1342 |
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: 1646.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 12 RKDFGKRPQVLDIPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 92 FSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFDKIVFEIrdnklqmelvperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 251 asfdIEANgkiyvekgrritarhirqLEKDDIQSIEvpveyiagkvvakdyidtntgelicaanmelsldllaklsqsgh 330
Cdd:COG0085 207 ----ILAT------------------LEKDNTKTQE-------------------------------------------- 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 331 krietlftndldhgayisetlrvdptndrlSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085 221 ------------------------------EALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 411 RDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 571 LINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggviqyvdas 730
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085 560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlteelqileag 970
Cdd:COG0085 702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 971 lfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085 749 -------------------------------------------------------------------EGDELPPGVNKLV 761
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1051 KVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigekinq 1130
Cdd:COG0085 762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1131 mlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlKKGMPIATPVFDGAKETEIKKLLEMGGIPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1211 TLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
gi 491068271 1291 LTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:COG0085 948 LTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1340 |
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: 879.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVKECQIRGVTFSAP 95
Cdd:cd00653 1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTE------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffd 226
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 227 kivfeirdnklqmelvperlrgetasfdieangkiyvekgrritarhIRQLEkddiqsievpveyiagkvvAKDYIDtnt 306
Cdd:cd00653 197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 307 gelicaanmelsldllaklsqsghKRIEtlftndldhgayisetlrvdptndrlsslveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653 208 ------------------------KRFE---------------------------------------------------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 387 nlffsedrydlsavgrmkfnrsllrdeiegsgilskdDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653 212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653 255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRRVRDgvvtdeinylsaieeg 612
Cdd:cd00653 335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEK---------------- 393
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 613 nfviaqansnldeegrfvedlvtcrskgesslfsrdQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653 394 ------------------------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggviqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 757 trsnqntcinqmpcvnlgepiergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653 471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlteelqileaglfarihavlvaggieadklsklprd 995
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 996 rwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitqgddLAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGV 1075
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1076 ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigekinqmlkqqqevaklrefiqkaydlgddv 1155
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1156 cqkvdlntfsddevlrlaenlKKGMPIATPVFDGAKETEIKKLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKL 1235
Cdd:cd00653 693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653 752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831
|
1370 1380 1390
....*....|....*....|....*....|....*
gi 491068271 1310 ----DGDHRMEPGMPESFNVLLKEIRSLGINIELE 1340
Cdd:cd00653 832 rlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
717-1264 |
1.62e-164 |
|
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: 496.28 E-value: 1.62e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 717 VAKRGGVIQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVNLGEpIERGDvladgpstdLGE 793
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 953 lkqakkdlteelqileaglfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleak 1032
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1033 rrkitqgdDLAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1113 LETHLGMAAKGigekinqmlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlkKGMPIATPVFDGAKE 1192
Cdd:pfam00562 272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491068271 1193 T--EIKKLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562 298 EveDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1342 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2268.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1 MVYSYTEKKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 80 FDVKECQIRGVTFSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKIVFEirdnklqm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 240 elvperlrgetasfdieangkiyvekgrritarhirqlekddiQSIEVPVEYIAGKVVAKDYIDTNTGELICAANMELSL 319
Cdd:PRK00405 225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 320 DLlaklsqsghkrietlftndldHGAYISETLRVDPTNDRLSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 400 VGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSK 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 720 RGGVIQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405 641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405 719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405 799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 960 lteelqileaglfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkITQG 1039
Cdd:PRK00405 856 ----------------------------------------------------------------------------IEQG 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1040 DDLAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405 860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1120 AAKGIGEKinqmlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlkkgmpIATPVFDGAKETEIKKLL 1199
Cdd:PRK00405 940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1200 EMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 491068271 1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:PRK00405 1046 AYGAAYTLQEMLTVKSDDVVGRTKVYEAIVKGENIPEPGIPESFNVLVKELQSLGLDVELLDE 1108
|
|
| rpoB |
TIGR02013 |
DNA-directed RNA polymerase, beta subunit; This model describes orthologs of the beta subunit ... |
8-1339 |
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: 1927.12 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 8 KKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVK 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 84 ECQIRGVTFSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffdkivfeirdnklqmelvp 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 244 erlrgetasfdieangkiyvekgrritarhirqlekddiqsievpveyiagkvvakdyidtntgelicaanmelsldlla 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 324 klsqsghkrIETLFTNDLDHGAYISETLRVDPTNDRLSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 404 KFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 564 PEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVV--TDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGE 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013 520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 722 GVIQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013 600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013 679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlt 961
Cdd:TIGR02013 759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 962 eelqileaglfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitQGDD 1041
Cdd:TIGR02013 815 ----------------------------------------------------------------------------QGDE 818
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1042 LAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013 819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1122 KGIGekinqmlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlKKGMPIATPVFDGAKETEIKKLLEM 1201
Cdd:TIGR02013 899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1202 GGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
gi 491068271 1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:TIGR02013 1008 GAAYTLQEMLTVKSDDVVGRTKAYEAIVKGENVPEPGIPESFNVLIKELQSLGLDIEL 1065
|
|
| RpoB |
COG0085 |
DNA-directed RNA polymerase, beta subunit/140 kD subunit [Transcription]; DNA-directed RNA ... |
12-1342 |
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: 1646.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 12 RKDFGKRPQVLDIPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 92 FSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFDKIVFEIrdnklqmelvperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 251 asfdIEANgkiyvekgrritarhirqLEKDDIQSIEvpveyiagkvvakdyidtntgelicaanmelsldllaklsqsgh 330
Cdd:COG0085 207 ----ILAT------------------LEKDNTKTQE-------------------------------------------- 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 331 krietlftndldhgayisetlrvdptndrlSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085 221 ------------------------------EALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 411 RDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 571 LINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggviqyvdas 730
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085 560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlteelqileag 970
Cdd:COG0085 702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 971 lfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085 749 -------------------------------------------------------------------EGDELPPGVNKLV 761
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1051 KVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigekinq 1130
Cdd:COG0085 762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1131 mlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlKKGMPIATPVFDGAKETEIKKLLEMGGIPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1211 TLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
gi 491068271 1291 LTVKSDDVNGRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELEDE 1342
Cdd:COG0085 948 LTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEVLSE 999
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
27-1340 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1430.18 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 27 LLSIQLDSFQKFIEQDpEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTFSAPLRVKLRLVI-- 104
Cdd:PRK14844 32 LVKVQKESYDSFTPKN-KGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLVImq 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 105 -------YEREAPEG-------TVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKV 170
Cdd:PRK14844 111 dgisldeYKSIKESGdhsklatVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 171 LYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKIVFEIRDNKLQMELVPERLRGET 250
Cdd:PRK14844 191 IYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVR 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 251 ASFDI-EANGKIYVEKGRRITARHIRQLEKDDIQSIEVPVEYIAGKVVAKDYIDTNTGELICAANMELSLDLLAKLSQSG 329
Cdd:PRK14844 271 LPFDLmDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLS 350
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 330 HKRIETLFTNDLDHGAYISETLRVDPTNDRLSSLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSL 409
Cdd:PRK14844 351 IDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYL 430
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 410 LRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMP 489
Cdd:PRK14844 431 GLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSP 510
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 490 QDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 569
Cdd:PRK14844 511 SDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 570 GLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQ 649
Cdd:PRK14844 591 GLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQ 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 650 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVIQYVDA 729
Cdd:PRK14844 671 VSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDS 750
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 730 SRIVIKVNEDEMYpGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNG 809
Cdd:PRK14844 751 NSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQG 829
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 810 YNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK14844 830 YNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 890 KGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLTEELQILEA 969
Cdd:PRK14844 910 KPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSE 989
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 970 GLFARIHAVLV-AGGIEADKLSKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKSDFEKKLEAKRRKITQGDDLAPGVLK 1048
Cdd:PRK14844 990 YFYDELKKLLInSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSM 1069
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1049 IVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGEKI 1128
Cdd:PRK14844 1070 SVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKV 1149
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1129 NQML--------------------------------KQQQEV-------------------------------------A 1139
Cdd:PRK14844 1150 GNILdeinkiksafckgirslnddnftkfaaayldnKKIENIdddeitasvlntpnknalndelnelvenylnscksayS 1229
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1140 KLREFIQKAYDLGDDVCQKVDLNTFSDDEVLRLAENLKKGMPIATPVFDGAKETEIKKLLEMGGIPTSGQITLFDGRTGE 1219
Cdd:PRK14844 1230 NLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGE 1309
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1220 QFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:PRK14844 1310 KFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN 1389
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|.
gi 491068271 1300 GRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIELE 1340
Cdd:PRK14844 1390 GRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLK 1430
|
|
| PRK09603 |
PRK09603 |
DNA-directed RNA polymerase subunit beta/beta'; |
8-1339 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 181983 [Multi-domain] Cd Length: 2890 Bit Score: 1410.06 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 8 KKRIRKDFGKRPQVLDIPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQI 87
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 88 RGVTFSAPLRVKLRLVIYEREAPEG---TVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKT 164
Cdd:PRK09603 88 RGITYSIPLKIKVRLILWEKDTKSGeknGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 165 hSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFDKIVFEIRDNKLQMELVPE 244
Cdd:PRK09603 168 -SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 245 RLRGEtASFDI-EANGKIYVEKGRRITARHIRQLEKDDIQSIEVPVEYIAGKVVAKDYIDTNtgelicaanmELSLDLLA 323
Cdd:PRK09603 247 DANQR-MEFDLkDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGK----------EVLLDMLT 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 324 KLSQSGHKRI------ETLFTNDLDHGA----------------YISETLRVDPTNDRLSslVEIYRMMRPGEPPTREAA 381
Cdd:PRK09603 316 QLDKNKLEKIhdlgvqEFVIINDLALGHdasiihsfsadseslkLLKQTEKIDDENALAA--IRIHKVMKPGDPVTTEVA 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 382 ESLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:PRK09603 394 KQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLA 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 462 NQFRVGLVRVERAVKERLSL--GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLT 539
Cdd:PRK09603 474 NELHSGLVKMQKTIKDKLTTmsGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLV 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 540 RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQA 619
Cdd:PRK09603 554 KDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPA 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 620 NSNLDEEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPL 699
Cdd:PRK09603 634 STPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 700 VGTGMERAVAVDSGVTAVAKRGGVIQYVDASRIVIkVNEDEmypGEAGIDIYNLTKYTRSNQNTCINQMPCVNLGEPIER 779
Cdd:PRK09603 714 VGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGK---EEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEA 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 780 GDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGE 859
Cdd:PRK09603 790 GQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 860 AALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGV 939
Cdd:PRK09603 870 EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGY 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 940 EKDKRALEIEEMQlkQAKKDLT--EELQILEAGLFARIHAVLVAGGIEAD---------KLSKLPRDrwlELGLTDEEKQ 1008
Cdd:PRK09603 950 EKDARVLSAYEEE--KAKLDMEhfDRLTMLNREELLRVSSLLSQAILEEPfshngkdykEGDQIPKE---EIASINRFTL 1024
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1009 NQL-----EQLAEQYDELKSDF--EKKL----EAKRRKITQGDDLAP-GVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVI 1076
Cdd:PRK09603 1025 ASLvkkysKEVQNHYEITKNNFleQKKVlgeeHEEKLSILEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIV 1104
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1077 SKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGEKINQMLKQQQE------VAKLREFIQKAYD 1150
Cdd:PRK09603 1105 SNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfakelRAKMLEIANAINE 1184
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1151 lgDDVCQKVDLNTFSDDEVLRLAENLKKGMPIATPVFDGAKETEIKKLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYM 1230
Cdd:PRK09603 1185 --KDPLTIHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYM 1262
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1231 YMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVD 1310
Cdd:PRK09603 1263 YMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAK 1342
|
1370 1380
....*....|....*....|....*....
gi 491068271 1311 GDHRMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:PRK09603 1343 GEQVGESEIPETFYVLTKELQSLALDINI 1371
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
24-1338 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1060.28 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 24 IPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVKECQIRGVTFSAPLRVKLR 101
Cdd:CHL00001 12 IPGFNQIQFEGFCRFIDQ------GLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYESLTYSSELYVPAG 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 102 LvIYEREapegtvKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVLYNARIIPYRG 181
Cdd:CHL00001 86 L-IWKKS------RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDH---NGISVYTGTIISDWG 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 182 SWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILD-LFFDKIVFEIRDNKlqmelvperlrgetasfdieangk 260
Cdd:CHL00001 156 GRLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDnVCYPEIFLSFLNDK------------------------ 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 261 iyvekgrritarhirqlEKDDIQSIEvpveyiagkvvakdyidtntgelicaanmelsldllaklsqsghkrietlftnd 340
Cdd:CHL00001 212 -----------------EKKKIGSKE------------------------------------------------------ 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 341 ldhgayisetlrvdptndrlSSLVEIYRMM--RPGEPPTREAAESLFENLFFSEdRYDLSAVGRMKFNRSLLRDEIEGSG 418
Cdd:CHL00001 221 --------------------NAILEFYQQFacVGGDPVFSESLCKELQKKFFQQ-RCELGRIGRRNMNRKLNLDIPENNT 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 419 ILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLM--PQDMINAK 496
Cdd:CHL00001 280 FLLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIptPQNLVTST 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 497 PISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLS 576
Cdd:CHL00001 360 PLTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLA 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 577 VYAQTNEYGFLETPYRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVDYMDVS 656
Cdd:CHL00001 440 IHARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIF 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 657 TQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVIQYVDASRIVIKV 736
Cdd:CHL00001 520 PFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 737 NEDEMYpgeagidiYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSI 816
Cdd:CHL00001 600 NGDTLS--------IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAV 671
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 817 LVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK--GETQ 894
Cdd:CHL00001 672 LISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESS 751
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 895 LTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVqvftrdgvekdkraleieemqlkqakkdlteelqileaglfar 974
Cdd:CHL00001 752 YAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV------------------------------------------- 788
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 975 ihavlvaggieadklsklprdRWLelgltdeekqnqleqlaeqydelksdfekkleakrrkitQGDDLAPGVLKIVKVYL 1054
Cdd:CHL00001 789 ---------------------RWI---------------------------------------QKKGGSSYNPETIHVYI 808
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1055 AVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAkgigekinQMLKQ 1134
Cdd:CHL00001 809 LQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAG--------DLLNR 880
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1135 QQEVAKLREfiqkAYdlGDDVCQKVdlnTFSDdevlrlaenlkkgmpiatpVFDGAKETEIKKLLEmggiPTS-GQITLF 1213
Cdd:CHL00001 881 HYRIAPFDE----RY--EQEASRKL---VFSE-------------------LYEASKQTANPWVFE----PEYpGKSRLF 928
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1214 DGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTV 1293
Cdd:CHL00001 929 DGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEMLTY 1008
|
1290 1300 1310 1320
....*....|....*....|....*....|....*....|....*.
gi 491068271 1294 KSDDVNGRTKMYKNIVDGDHRMEP-GMPESFNVLLKEIRSLGINIE 1338
Cdd:CHL00001 1009 KSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 1054
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
24-1339 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1041.59 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 24 IPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVKECQIRGVTFSAPLRVKLR 101
Cdd:CHL00207 7 LPDFLEIQRTSFCWFLNE------GLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIYLPLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 102 LViyereapEGTVKDIKEQEVYMGEIPLMTENGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHssgKVLYNARIIPYRG 181
Cdd:CHL00207 81 FI-------NLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLIPNRG 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 182 SWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQIldlffdkivfeirdnklqmelvperlrgetasfdieangki 261
Cdd:CHL00207 151 SWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDI----------------------------------------- 189
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 262 yvekgrRITARHIRQLEKDDIqsievpveyiagkvvAKDYIDTNTGELIcaanmelsldllaklsqsghkrietlftndl 341
Cdd:CHL00207 190 ------YSRLTKSEFLKKLKP---------------ILLNSNSYTNEEI------------------------------- 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 342 dhgayisetlrvdptndrlssLVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILS 421
Cdd:CHL00207 218 ---------------------LLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLT 276
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 422 KDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA 501
Cdd:CHL00207 277 YEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIAL 356
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 502 VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQT 581
Cdd:CHL00207 357 IREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARI 436
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 582 NEYGFLETPYRRVRDGVV--TDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQ 659
Cdd:CHL00207 437 NKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQ 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 660 VVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVIQYVDASRIVIKVNED 739
Cdd:CHL00207 517 VFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNN 596
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 740 EMYpgeagidIYNLTKYTRSNQNTCINQMPCVNLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVS 819
Cdd:CHL00207 597 RYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILIN 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 820 ERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEE 899
Cdd:CHL00207 670 KRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEG 749
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 900 KLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlteelqileaglfarihavl 979
Cdd:CHL00207 750 KLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS------------------------------------------ 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 980 vaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitQGDDLAPGVLKIVKVYLAVKRQ 1059
Cdd:CHL00207 788 ----------------------------------------------------------KGDELKFGYYLKIRVFIAQIRK 809
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1060 IQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAakgiGEKINQMLKQqqeva 1139
Cdd:CHL00207 810 IQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLA----GDNLNKRFKI----- 880
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1140 klrefiqkaydlgddvcqkVDLNTFSDDEVLRLAENlKKGMPIatpvfdgakeTEIKKLLEMGGIPTSGQITLFDGRTGE 1219
Cdd:CHL00207 881 -------------------LPFDEMYGSEYSRILIN-NKLNQA----------SIKNNEYWLFNSYHPGKMVLRDGRTGY 930
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1220 QFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:CHL00207 931 KFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQ 1010
|
1290 1300 1310 1320
....*....|....*....|....*....|....*....|
gi 491068271 1300 GRTKMYKNIVDGDHRMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:CHL00207 1011 GRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDIEA 1050
|
|
| RNA_pol_B_RPB2 |
cd00653 |
RNA polymerase beta subunit. RNA polymerases catalyse the DNA dependent polymerization of RNA. ... |
27-1340 |
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: 879.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVKECQIRGVTFSAP 95
Cdd:cd00653 1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTE------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffd 226
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 227 kivfeirdnklqmelvperlrgetasfdieangkiyvekgrritarhIRQLEkddiqsievpveyiagkvvAKDYIDtnt 306
Cdd:cd00653 197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 307 gelicaanmelsldllaklsqsghKRIEtlftndldhgayisetlrvdptndrlsslveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653 208 ------------------------KRFE---------------------------------------------------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 387 nlffsedrydlsavgrmkfnrsllrdeiegsgilskdDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653 212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653 255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRRVRDgvvtdeinylsaieeg 612
Cdd:cd00653 335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVEK---------------- 393
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 613 nfviaqansnldeegrfvedlvtcrskgesslfsrdQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653 394 ------------------------------------EVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggviqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 757 trsnqntcinqmpcvnlgepiergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653 471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlteelqileaglfarihavlvaggieadklsklprd 995
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 996 rwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitqgddLAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGV 1075
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1076 ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigekinqmlkqqqevaklrefiqkaydlgddv 1155
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1156 cqkvdlntfsddevlrlaenlKKGMPIATPVFDGAKETEIKKLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKL 1235
Cdd:cd00653 693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653 752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831
|
1370 1380 1390
....*....|....*....|....*....|....*
gi 491068271 1310 ----DGDHRMEPGMPESFNVLLKEIRSLGINIELE 1340
Cdd:cd00653 832 rlckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
717-1264 |
1.62e-164 |
|
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: 496.28 E-value: 1.62e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 717 VAKRGGVIQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVNLGEpIERGDvladgpstdLGE 793
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 953 lkqakkdlteelqileaglfarihavlvaggieadklsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleak 1032
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1033 rrkitqgdDLAPGVLKIVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1113 LETHLGMAAKGigekinqmlkqqqevaklrefiqkaydlgddvcqkvdlntfsddevlrlaenlkKGMPIATPVFDGAKE 1192
Cdd:pfam00562 272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 491068271 1193 T--EIKKLLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562 298 EveDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
26-500 |
8.32e-110 |
|
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: 351.68 E-value: 8.32e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 26 YLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGN---SELQYVSYRLGEPVFDVK----------ECQIRGVTF 92
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENgdkLSLKFGQIRLGKPMFDETdgstreiypqECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 93 SAPLRVKLRLVIYereapegTVKDIKEQEVYMGEIPLMTEN------------------------GTFVINGTERVIVSQ 148
Cdd:pfam04563 81 SAPLYVDLELSVY-------NGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 149 LHRS---PGVFFDSDKGKTHSSGKVLYNARI--IPYRGSWLDF-EFDPKDNLFVRIDRRRK-LPATIILRALNYTTEQIL 221
Cdd:pfam04563 154 EHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 222 dlfFDKIVFEIRDNKLQMELVPErlrgetasfdieangkiyVEKGRRITarhirqlekddIQSIEVPVEYIAGKVVAkdy 301
Cdd:pfam04563 234 ---FELICYDVNDQQLQEELLPS------------------LEEGFKIR-----------IQTQEQALDYIGGRGRA--- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 302 idtntgelicaanmelsldllaklsqsghkrietlftndldhgayisetlrvdptndrlsslveIYRMMRPGEPPTREAA 381
Cdd:pfam04563 279 ----------------------------------------------------------------IFRMGRPREPRIKYAE 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 382 ESLFENLFFSEDRYDLSAVGRMKFnrsllrdeiegsgilskddIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:pfam04563 295 EILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLA 355
|
490 500 510 520
....*....|....*....|....*....|....*....|.
gi 491068271 462 NQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISA 500
Cdd:pfam04563 356 SLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1340 |
1.59e-89 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 315.36 E-value: 1.59e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 31 QLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVK----------ECQIRGVTFSAPLRVKL 100
Cdd:PRK08565 18 HLDSYNDFIER------GLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEAdgserpitpmEARLRNLTYAAPLYLTM 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 101 RLVIYEREapegtvkdIKEQEVYMGEIPLMTEN------------------------GTFVINGTERVIVSQLHRSPG-V 155
Cdd:PRK08565 92 IPVENGIE--------YEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrV 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 156 FFDSDKgkthSSGKVLYNARIIPYRG---SWLDFEFDPKDNLFVRIDR-RRKLPATIILRALNYTTEQ-ILDLFFDkivf 230
Cdd:PRK08565 164 LVDKGE----AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETDRdIVYAVSL---- 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 231 eirDNKLQMELVPerlrgetaSFDIEANGKIYVEK-----GRRITARHIRqlekddiqsiEVPVEYiagkvvAKDYIDTN 305
Cdd:PRK08565 236 ---DPEIQQELLP--------SLEQASSIAATVEDaldyiGKRVAIGQPR----------EYRIER------AEQILDKY 288
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 306 tgelicaanmelsldLLAKLSQSGHKRIETlftndldhgAYIsetlrvdptndrlsslveiyrmmrpgepptreaaeslf 385
Cdd:PRK08565 289 ---------------LLPHLGTSPEDRIKK---------AYF-------------------------------------- 306
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 386 enlffsedrydlsaVGRMkfnrsllrdeiegsgilskddiievMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFR 465
Cdd:PRK08565 307 --------------LGQM-------------------------ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFR 347
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 466 VGLVRVERAVKERL----SLG---DLDTLMPQDMINAKPISA-AVKEFFGS-SQLSQFMDQNNPLSEITHKRRIsaLGPg 536
Cdd:PRK08565 348 VAFKQLVKDLKYQLeksyARGrklDLRAIVRPDIITERIRHAlATGNWVGGrTGVSQLLDRTNYLSTLSHLRRV--VSP- 424
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 537 gLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ----TNEYGFLETPYR------------------RV 594
Cdd:PRK08565 425 -LSRGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQisvgVDEEEVEEILYElgvvpveeareeeyiswsRV 503
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 595 ------------------------RDGVVTDEIN--YLSAIEEGNFVIaqaNSNldeEGRF------VE--------DLV 634
Cdd:PRK08565 504 ylngrligyhpdgeelaekirelrRSGKISDEVNvaYIETGEINEVYV---NCD---SGRVrrplivVEngkpkltrEHV 577
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 635 TCRSKGE---SSLFSRDQVDYMDVSTQQ------------------------VVSVGASLIPFLEHDDANRALMGANMQR 687
Cdd:PRK08565 578 EKLKKGEltfDDLVKMGVIEYLDAEEEEnayvaldpedltpehthleiwppaILGITASIIPYPEHNQSPRNTYQAAMAK 657
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 688 QAVptlradkplvgtGMERA---VAVDSgvtavakRGGVIQYvdasrivikvnedemyPgeagidiynltkytrsnqntc 764
Cdd:PRK08565 658 QSL------------GLYAAnfrIRTDT-------RGHLLHY----------------P--------------------- 681
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 765 inQMPCVNlgepiERG-DVLA--DGPStdlgelalGQNMRVAFMPWNGYNFEDSILVSERVVqeDR-------FTTIHIQ 834
Cdd:PRK08565 682 --QRPLVQ-----TRAlEIIGynDRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASI--ERglarstfFRTYETE 744
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 835 ELacvsrdTKLGPEEITADIP--NV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTPKgetQLTPEEKLLRAIFGE 908
Cdd:PRK08565 745 ER------KYPGGQEDKIEIPepNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQE 815
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 909 KasdvKDSSLRVPNGVSGTVidvqvftrdgvekDKraleieemqlkqakkdlteelqileaglfarihaVLVAGGIEADK 988
Cdd:PRK08565 816 R----RDTSVTVRHGEKGIV-------------DT----------------------------------VLITESPEGNK 844
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 989 LsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitqgddlapgvlkiVKVYLAVKRQIQPGDKMAG 1068
Cdd:PRK08565 845 L------------------------------------------------------------VKVRVRDLRIPELGDKFAS 864
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1069 RHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILEThlgMAAKgigekinqmlkqqqeVAKLREfiqka 1148
Cdd:PRK08565 865 RHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES---IAGK---------------VAALEG----- 921
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1149 ydlgddvcQKVDlntfsddevlrlaenlkkgmpiATPvFDGAKETEIKKLLEMGGIPTSGQITLFDGRTGEQFERQVTVG 1228
Cdd:PRK08565 922 --------RFVD----------------------ATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIG 970
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvngRTKMY--- 1305
Cdd:PRK08565 971 VVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD----KTTIYvce 1046
|
1450 1460 1470 1480 1490
....*....|....*....|....*....|....*....|....*....|..
gi 491068271 1306 -----------KNI----VDGDH-RMEP-GMPESFNVLLKEIRSLGINIELE 1340
Cdd:PRK08565 1047 lcghiawydrrKNKyvcpIHGDKgNISPvEVSYAFKLLLQELMSMGISPRLK 1098
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
594-1341 |
2.83e-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: 224.52 E-value: 2.83e-62
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 594 VRDGVvtdeINYLSAIEEGNFVIAQansnldeegrFVEDLvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEH 673
Cdd:TIGR03670 87 VKQGV----IEYLDAEEEENAYIAL----------DPEEL-------------TPEHTHLEIDPSAILGIIASTIPYPEH 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 674 DDANRALMGANMQRQAVPTLRADKPLvgtgmeravAVDSgvtavakRGGVIQYvdasrivikvnedemyPgeagidiynl 753
Cdd:TIGR03670 140 NQSPRNTMGAAMAKQSLGLYAANYRI---------RLDT-------RGHLLHY----------------P---------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 754 tkytrsnqntcinQMPCVNlgepiERGDVLadgpsTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHI 833
Cdd:TIGR03670 178 -------------QKPLVK-----TRVLEL-----IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFF 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 834 QELACVSRDTKLGPE-EITADIPNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTPkgetqltP---EEkllRAI 905
Cdd:TIGR03670 235 RTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LRE 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 906 FGEKASDVKDSSLRVPNGVSGTVidvqvftrdgvekDKraleieemqlkqakkdlteelqileaglfarihaVLVAGGIE 985
Cdd:TIGR03670 305 FGLVTERRRDTSVTVRHGEKGIV-------------DK----------------------------------VIITETEE 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 986 ADKLsklprdrwlelgltdeekqnqleqlaeqydelksdfekkleakrrkitqgddlapgvlkiVKVYLAVKRQIQPGDK 1065
Cdd:TIGR03670 338 GNKL------------------------------------------------------------VKVRVRDLRIPELGDK 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1066 MAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGEKINqmlkqqqevaklrefi 1145
Cdd:TIGR03670 358 FASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEMIAGKVAALEGRRVD---------------- 421
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1146 qkaydlgddvcqkvdlntfsddevlrlaenlkkgmpiATPvFDGAKETEIKKLLEMGGIPTSGQITLFDGRTGEQFERQV 1225
Cdd:TIGR03670 422 -------------------------------------GTP-FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEI 463
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1226 TVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV------- 1298
Cdd:TIGR03670 464 FIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYvvyvcen 543
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*.
gi 491068271 1299 -------NGRTKMYKNIVDGD----HRMEpgMPESFNVLLKEIRSLGI--NIELED 1341
Cdd:TIGR03670 544 cghiaweDKRKGTAYCPVCGEtgdiSPVE--MSYAFKLLLDELKSLGIspRLELGD 597
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
594-1341 |
8.41e-55 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 202.50 E-value: 8.41e-55
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 594 VRDGVvtdeINYLSAIEEGNFVIAQANSNLDEEGRFVEdlvtcrskgesslfsrdqvdymdVSTQQVVSVGASLIPFLEH 673
Cdd:PRK07225 93 VKQGV----IEYLDAEEEENAYIAVYEEDLTEEHTHLE-----------------------IDPSLILGIGAGMIPYPEH 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 674 DDANRALMGANMQRQA--VPT----LRADKplvgtgmeravavdsgvtavakRGGVIQYVDASRIVIKVNEdemypgEAG 747
Cdd:PRK07225 146 NASPRITMGAGMIKQSlgLPAanykLRPDT----------------------RGHLLHYPQVPLVKTQTQE------IIG 197
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 748 IDiynltkytrsnqntcinqmpcvnlgepiERgdvladgPStdlgelalGQNMRVAFMPWNGYNFEDSILVSERVV---- 823
Cdd:PRK07225 198 FD----------------------------ER-------PA--------GQNFVVAVMSYEGYNIEDALIMNKASIergl 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 824 -------------------QEDRFTTihiqelacvsrdtklgPEEitadipNV----GEAALSKLDESGIVYIGAEVTGG 880
Cdd:PRK07225 235 grshffrtyegeerrypggQEDRFEI----------------PDK------DVrgyrGEEAYRHLDEDGLVNPETEVKEG 292
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 881 DILVGKVTPkgetqltP---EEKllrAIFGEKASDVKDSSLRVPNGVSGTVidvqvftrdgvekdkraleieemqlkqak 957
Cdd:PRK07225 293 DVLIGKTSP-------PrflEEP---DDFGISPEKRRETSVTMRSGEEGIV----------------------------- 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 958 kdlteelqileaglfariHAVLVAGGIEADKLSKLpRDRwlelgltdeekqnqleqlaeqyDElksdfekkleakrrkit 1037
Cdd:PRK07225 334 ------------------DTVILTETEEGSRLVKV-RVR----------------------DL----------------- 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1038 qgddlapgvlkivkvylavkRQIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILEThl 1117
Cdd:PRK07225 356 --------------------RIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM-- 413
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1118 gmaakgIGEKinqmlkqqqeVAKLRefiqkaydlgddvCQKVDlntfsddevlrlaenlkkgmpiATPvFDGAKETEIKK 1197
Cdd:PRK07225 414 ------IGGK----------VGSLE-------------GRRVD----------------------GTA-FSGEDEEDLRE 441
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1198 LLEMGGIPTSGQITLFDGRTGEQFERQVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWA 1277
Cdd:PRK07225 442 ALEKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDV 521
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1278 LEAYGAAYTLQEMLTVKSDDVN-------GRTKMY---KNIV--------DGDHRMEpgMPESFNVLLKEIRSLGI--NI 1337
Cdd:PRK07225 522 LIGHGAAMLLKERLLDESDKVEiyvcakcGMIAIYdkkRNRKycpicgeeTDIYPVE--MSYAFKLLLDELKSLGIapRL 599
|
....
gi 491068271 1338 ELED 1341
Cdd:PRK07225 600 ELED 603
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
513-580 |
2.63e-36 |
|
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: 131.49 E-value: 2.63e-36
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 491068271 513 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1266-1342 |
1.68e-34 |
|
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: 126.93 E-value: 1.68e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 1266 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVNGRTKMYKN-----IVDGDHRMEPG-MPESFNVLLKEIRSLGI 1335
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*..
gi 491068271 1336 NIELEDE 1342
Cdd:pfam04560 81 DPRLLLE 87
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
591-656 |
2.09e-33 |
|
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: 123.24 E-value: 2.09e-33
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 491068271 591 YRRVRDGVVTDEINYLSAIEEGNFVIAQANSNLDEEGRFVEDLVTCRSKGESSLFSRDQVDYMDVS 656
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
31-580 |
4.47e-28 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 120.05 E-value: 4.47e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 31 QLDSFQKFIEqdpegqYGLEAAFRSVFPIQSYSGNSE-LQYVSYRLGEPVfdVKECQ------------IRGVTFSAPLR 97
Cdd:PRK09606 22 HIDSYNDFVD------NGLQKIIDEQGPIETEIEDGVyVELGKIRVGKPV--VKEADgsereiypmearLRNLTYSAPLY 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 98 vkLRLVIYEREAPEGTVkdikeqEVYMGEIPLMTEN------------------------GTFVINGTERVIVSQLHRSP 153
Cdd:PRK09606 94 --LEMSPVEGGEEEEPE------EVYIGELPVMVGSkicnlyglseeelievgedpldpgGYFIVNGSERVLMTLEDLAP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 154 GVF---FDSDKGKTHSSGKVL-----YNARIIPYRGswldfefdpKDNL----FVRIDRRrkLPATIILRALNYTTEQil 221
Cdd:PRK09606 166 NKIlveKDERYGDRIEVAKVFsqrrgYRALVTVERN---------RDGLlevsFPSVPGS--IPFVILMRALGLETDE-- 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 222 dlffdKIVFEIRDNKlqmelvperlrgETASFDIEangkiyvekgrritarhirQLEKDDIQSIEVPVEYIAGKVV---A 298
Cdd:PRK09606 233 -----EIVEAVSDDP------------EIVKFMLE-------------------NLEEAEVDTQEEALEYIGKRVApgqT 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 299 KDYidtntgelicaanmelsldllaKLsqsghKRIETLFTNdldhgaYISETLRVDPtNDRLSSLVEIYRMmrpgepptr 378
Cdd:PRK09606 277 KEY----------------------RI-----KRAEYVIDR------YLLPHLGVEP-EVRRAKAHYLGRM--------- 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 379 eaAESLFEnlffsedrydlsavgrmkfnrsllrdeiegsgilskddiievmkklidIRNGKGEVDDIDHLGNRRIRSVGE 458
Cdd:PRK09606 314 --AEACFE------------------------------------------------LALGRREEDDKDHYANKRLKLAGD 343
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 459 MAENQFRVGLVRVERAVK---ERlslgdldtlmpQDMINAKP-ISAAVKE----------------FFGSSQLSQFMDQN 518
Cdd:PRK09606 344 LMEDLFRVAFNRLARDVKyqlER-----------ANMRNRELsIKTAVRSdvlterlehamatgnwVGGRTGVSQLLDRT 412
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 491068271 519 NPLSEITHKRRISAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:PRK09606 413 DYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
151-454 |
9.18e-11 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 62.36 E-value: 9.18e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 151 RSPGVFFDSDKGKTHSSGKvlYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQ-ILDLffdkIV 229
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIAT--YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDReILDR----LC 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 230 FEIRDNKLQMELVPERLRGEtasfdieangkiyvekgrritarhirqlekdDIQSIEVPVEYIaGKVVAkdyidtntgel 309
Cdd:pfam04561 75 YDFNDPQMLELLKPELEEAE-------------------------------NIYTQEEALDYI-GKGFA----------- 111
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 491068271 310 icaanmelsldllaklsqsghkrietlftndldhgayisetlrvdptndrlsslveiyrmMRPGEPPTREAAESLFENLF 389
Cdd:pfam04561 112 ------------------------------------------------------------LRRGEEPRLQRAREILYSRD 131
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 491068271 390 fsedrydlsavGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Cdd:pfam04561 132 -----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| |
