|
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: 2281.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 80 FDVQECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEirdnklqm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 240 elvperlrgetasfdieangkvyvekgrritarhirqlekddvKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSL 319
Cdd:PRK00405 225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 320 DLlaklsqsghkrietlftndldHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 400 VGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSK 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 720 RGGVVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405 641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405 719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405 799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 960 lseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405 856 ----------------------------------------------------------------------------IEQG 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405 860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405 940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1200 KLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
5NWT_C 1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 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: 1943.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQ 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 84 ECQIRGVTYSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffekvifeirdnklqmelvp 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 244 erlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakdyidestgelicaanmelsldlla 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 324 klsqsghkrIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 404 KFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 564 PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGE 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013 520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 722 GVVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013 600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013 679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdls 961
Cdd:TIGR02013 759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 962 eelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDD 1041
Cdd:TIGR02013 815 ----------------------------------------------------------------------------QGDE 818
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1042 LAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013 819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1122 KGIGdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKL 1201
Cdd:TIGR02013 899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1202 GDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
5NWT_C 1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL 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: 1652.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 12 RKDFGKRPQVLDVPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 92 YSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFEKVIFEIrdnklqmelvperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 251 asfdIEANgkvyvekgrritarhirqLEKDDVKlievpveyiagkvvakdyidestgelicaanmelsldllaklsqsgh 330
Cdd:COG0085 207 ----ILAT------------------LEKDNTK----------------------------------------------- 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 331 krietlftndldhgpyisetlrvdptnDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085 218 ---------------------------TQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 411 REEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 571 LINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggvvqyvdas 730
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085 560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileag 970
Cdd:COG0085 702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 971 lfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085 749 -------------------------------------------------------------------EGDELPPGVNKLV 761
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1051 KVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkina 1130
Cdd:COG0085 762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1131 mlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1211 RLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
5NWT_C 1291 LTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 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: 893.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVQECQIRGVTYSAP 95
Cdd:cd00653 1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffe 226
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 227 kvifeirdnklqmelvperlrgetasfdieangkvyvekgrritarhIRQLEkddvklievpveyiagkvvAKDYIDest 306
Cdd:cd00653 197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 307 gelicaanmelsldllaklsqsghKRIEtlftndldhgpyisetlrvdptndrlsalveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653 208 ------------------------KRFE---------------------------------------------------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 387 nlffsedrydlsavgrmkfnrsllreeiegsgilskdDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653 212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653 255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieeg 612
Cdd:cd00653 335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV------------------ 391
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 613 nyviaqansnldeeghfvedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653 392 ----------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggvvqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 757 trsnqntcinqmpcvslgepvergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653 471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriravlvaggveaekldklprd 995
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 996 rwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1076 ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinamlkqqqevaklrefiqraydlgadv 1155
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1156 rqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKL 1235
Cdd:cd00653 693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653 752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831
|
1370 1380 1390
....*....|....*....|....*....|....*
5NWT_C 1310 ----DGNHQMEPGMPESFNVLLKEIRSLGINIELE 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 |
9.20e-167 |
|
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: 502.06 E-value: 9.20e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 717 VAKRGGVVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpVERGDvladgpstdLGE 793
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 953 lkqakkdlseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1033 rrkitqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1113 LETHLGMAAKGigdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrKGMPIATPVFDGAKE 1192
Cdd:pfam00562 272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
5NWT_C 1193 --AEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562 298 evEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| HMG-box_IXR1-like_rpt1 |
cd22011 |
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ... |
972-1029 |
2.44e-04 |
|
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.
Pssm-ID: 438827 [Multi-domain] Cd Length: 75 Bit Score: 40.98 E-value: 2.44e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
5NWT_C 972 FSRIRAVLVAGGVEAEK---LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011 12 SQEIRKNLKSQGSPEEKvpeLSKRAAEQWR--SLTLAEKQpyyDEVEVLKKQYDVEKEEYEKEL 73
|
|
| |
|
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: 2281.56 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 80 FDVQECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEirdnklqm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 240 elvperlrgetasfdieangkvyvekgrritarhirqlekddvKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSL 319
Cdd:PRK00405 225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 320 DLlaklsqsghkrietlftndldHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 400 VGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSK 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 720 RGGVVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405 641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405 719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405 799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 960 lseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405 856 ----------------------------------------------------------------------------IEQG 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405 860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405 940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1200 KLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
5NWT_C 1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 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: 1943.69 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQ 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 84 ECQIRGVTYSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffekvifeirdnklqmelvp 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 244 erlrgetasfdieangkvyvekgrritarhirqlekddvklievpveyiagkvvakdyidestgelicaanmelsldlla 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 324 klsqsghkrIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 404 KFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 564 PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGE 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013 520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 722 GVVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013 600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013 679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdls 961
Cdd:TIGR02013 759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 962 eelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDD 1041
Cdd:TIGR02013 815 ----------------------------------------------------------------------------QGDE 818
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1042 LAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013 819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1122 KGIGdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKL 1201
Cdd:TIGR02013 899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1202 GDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
5NWT_C 1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL 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: 1652.15 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 12 RKDFGKRPQVLDVPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 92 YSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFEKVIFEIrdnklqmelvperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 251 asfdIEANgkvyvekgrritarhirqLEKDDVKlievpveyiagkvvakdyidestgelicaanmelsldllaklsqsgh 330
Cdd:COG0085 207 ----ILAT------------------LEKDNTK----------------------------------------------- 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 331 krietlftndldhgpyisetlrvdptnDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085 218 ---------------------------TQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 411 REEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 571 LINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggvvqyvdas 730
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085 560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileag 970
Cdd:COG0085 702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 971 lfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085 749 -------------------------------------------------------------------EGDELPPGVNKLV 761
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1051 KVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkina 1130
Cdd:COG0085 762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1131 mlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1211 RLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
5NWT_C 1291 LTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE 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: 1434.80 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 27 LLSIQLDSFQKFIEQDpEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVI-- 104
Cdd:PRK14844 32 LVKVQKESYDSFTPKN-KGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLVImq 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 105 -------YEREAPEG-------TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKV 170
Cdd:PRK14844 111 dgisldeYKSIKESGdhsklatVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 171 LYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGET 250
Cdd:PRK14844 191 IYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVR 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 251 ASFDI-EANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSG 329
Cdd:PRK14844 271 LPFDLmDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLS 350
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 330 HKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSL 409
Cdd:PRK14844 351 IDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYL 430
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 410 LREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMP 489
Cdd:PRK14844 431 GLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSP 510
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 490 QDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 569
Cdd:PRK14844 511 SDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 570 GLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQ 649
Cdd:PRK14844 591 GLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQ 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 650 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDA 729
Cdd:PRK14844 671 VSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDS 750
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 730 SRIVIKVNEDEMYpGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNG 809
Cdd:PRK14844 751 NSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQG 829
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 810 YNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK14844 830 YNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 890 KGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEA 969
Cdd:PRK14844 910 KPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSE 989
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 970 GLFSRIRAVLV-AGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLK 1048
Cdd:PRK14844 990 YFYDELKKLLInSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSM 1069
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKI 1128
Cdd:PRK14844 1070 SVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKV 1149
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1129 NAML--------------------------------KQQQEV-------------------------------------A 1139
Cdd:PRK14844 1150 GNILdeinkiksafckgirslnddnftkfaaayldnKKIENIdddeitasvlntpnknalndelnelvenylnscksayS 1229
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1140 KLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGE 1219
Cdd:PRK14844 1230 NLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGE 1309
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1220 QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:PRK14844 1310 KFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN 1389
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|.
5NWT_C 1300 GRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELE 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: 1415.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQI 87
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 88 RGVTYSAPLRVKLRLVIYEREAPEG---TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKT 164
Cdd:PRK09603 88 RGITYSIPLKIKVRLILWEKDTKSGeknGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 165 hSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPE 244
Cdd:PRK09603 168 -SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 245 RLRGEtASFDI-EANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDEStgelicaanmELSLDLLA 323
Cdd:PRK09603 247 DANQR-MEFDLkDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGK----------EVLLDMLT 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 324 KLSQSGHKRI------ETLFTNDLDHG----------------PYISETLRVDPTNDRlsALVEIYRMMRPGEPPTREAA 381
Cdd:PRK09603 316 QLDKNKLEKIhdlgvqEFVIINDLALGhdasiihsfsadseslKLLKQTEKIDDENAL--AAIRIHKVMKPGDPVTTEVA 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 382 ESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:PRK09603 394 KQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLA 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 462 NQFRVGLVRVERAVKERLSL--GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLT 539
Cdd:PRK09603 474 NELHSGLVKMQKTIKDKLTTmsGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLV 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 540 RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQA 619
Cdd:PRK09603 554 KDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPA 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 620 NSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPL 699
Cdd:PRK09603 634 STPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 700 VGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIkVNEDEmypGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVER 779
Cdd:PRK09603 714 VGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGK---EEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEA 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 780 GDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGE 859
Cdd:PRK09603 790 GQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 860 AALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGV 939
Cdd:PRK09603 870 EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGY 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 940 EKDKRALEIEEMQlkQAKKDLS--EELQILEAGLFSRIRAVL---------VAGGVEAEKLDKLPR------DRWLELGL 1002
Cdd:PRK09603 950 EKDARVLSAYEEE--KAKLDMEhfDRLTMLNREELLRVSSLLsqaileepfSHNGKDYKEGDQIPKeeiasiNRFTLASL 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1003 TD---EEKQNQLEQLA----EQYDELKHEFEKKLEakrrkITQGDDLAP-GVLKIVKVYLAVKRRIQPGDKMAGRHGNKG 1074
Cdd:PRK09603 1028 VKkysKEVQNHYEITKnnflEQKKVLGEEHEEKLS-----ILEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKG 1102
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1075 VISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQE------VAKLREFIQRA 1148
Cdd:PRK09603 1103 IVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfakelRAKMLEIANAI 1182
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1149 YDLGADVRQKvdLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVG 1228
Cdd:PRK09603 1183 NEKDPLTIHA--LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVG 1260
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNI 1308
Cdd:PRK09603 1261 YMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAI 1340
|
1370 1380 1390
....*....|....*....|....*....|.
5NWT_C 1309 VDGNHQMEPGMPESFNVLLKEIRSLGINIEL 1339
Cdd:PRK09603 1341 AKGEQVGESEIPETFYVLTKELQSLALDINI 1371
|
|
| rpoB |
CHL00001 |
RNA polymerase beta subunit |
25-1338 |
0e+00 |
|
RNA polymerase beta subunit
Pssm-ID: 214330 [Multi-domain] Cd Length: 1070 Bit Score: 1067.98 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 25 PYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVQECQIRGVTYSAPLRVKLRL 102
Cdd:CHL00001 13 PGFNQIQFEGFCRFIDQ------GLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYESLTYSSELYVPAGL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 103 vIYEREapegtvKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVLYNARIIPYRGS 182
Cdd:CHL00001 87 -IWKKS------RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDH---NGISVYTGTIISDWGG 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 183 WLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKlqmelvperlrgetasfdieangkvy 262
Cdd:CHL00001 157 RLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILDNVCYPEIFLSFLND-------------------------- 210
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 263 vekgrritarhirqleKDDVKLievpveyiagkvvakdyidESTGElicaanmelsldllaklsqsghkrietlftndld 342
Cdd:CHL00001 211 ----------------KEKKKI-------------------GSKEN---------------------------------- 221
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 343 hgpyisetlrvdptndrlsALVEIYRMM--RPGEPPTREAAESLFENLFFSEdRYDLSAVGRMKFNRSLLREEIEGSGIL 420
Cdd:CHL00001 222 -------------------AILEFYQQFacVGGDPVFSESLCKELQKKFFQQ-RCELGRIGRRNMNRKLNLDIPENNTFL 281
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 421 SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLM--PQDMINAKPI 498
Cdd:CHL00001 282 LPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIptPQNLVTSTPL 361
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 499 SAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVY 578
Cdd:CHL00001 362 TTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIH 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 579 AQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQ 658
Cdd:CHL00001 442 ARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPF 521
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 659 QVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNE 738
Cdd:CHL00001 522 QYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNG 601
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 739 DEMYpgeagidiYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILV 818
Cdd:CHL00001 602 DTLS--------IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 819 SERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK--GETQLT 896
Cdd:CHL00001 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYA 753
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 897 PEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVqvftrdgvekdkraleieemqlkqakkdlseelqileaglfsrir 976
Cdd:CHL00001 754 PEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV--------------------------------------------- 788
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 977 avlvaggveaekldklprdRWLelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIVKVYLAV 1056
Cdd:CHL00001 789 -------------------RWI---------------------------------------QKKGGSSYNPETIHVYILQ 810
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1057 KRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinaMLKQQQ 1136
Cdd:CHL00001 811 KREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGD--------LLNRHY 882
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1137 EVAKLrefiqraydlgadvrqkvdlstfsDEevMRLAENLRKgmpiatPVFdgakeaeiKELLK---------LGDLPTS 1207
Cdd:CHL00001 883 RIAPF------------------------DE--RYEQEASRK------LVF--------SELYEaskqtanpwVFEPEYP 922
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1208 GQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTL 1287
Cdd:CHL00001 923 GKSRLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYIL 1002
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
5NWT_C 1288 QEMLTVKSDDVNGRTKMYKNIVDGNHQMEP-GMPESFNVLLKEIRSLGINIE 1338
Cdd:CHL00001 1003 QEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 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: 1063.55 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 24 VPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVQECQIRGVTYSAPLRVKLR 101
Cdd:CHL00207 7 LPDFLEIQRTSFCWFLNE------GLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIYLPLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 102 LViyereapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHssgKVLYNARIIPYRG 181
Cdd:CHL00207 81 FI-------NLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLIPNRG 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 182 SWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQmelvperlrgetasfdieangkv 261
Cdd:CHL00207 151 SWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYSRLTKSEFLKKLKPILL----------------------- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 262 yvekgrritarhirqlekddvklievpveyiagkvvakdyidestgelicaanmelsldllaklsqsghkrietlftndl 341
Cdd:CHL00207 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 342 DHGPYISETlrvdptndrlsALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILS 421
Cdd:CHL00207 208 NSNSYTNEE-----------ILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLT 276
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 422 KDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA 501
Cdd:CHL00207 277 YEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIAL 356
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 502 VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQT 581
Cdd:CHL00207 357 IREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARI 436
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 582 NEYGFLETPYRKVTDGVV--TDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQ 659
Cdd:CHL00207 437 NKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQ 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 660 VVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNED 739
Cdd:CHL00207 517 VFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNN 596
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 740 EMYpgeagidIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVS 819
Cdd:CHL00207 597 RYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILIN 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 820 ERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEE 899
Cdd:CHL00207 670 KRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEG 749
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 900 KLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriravl 979
Cdd:CHL00207 750 KLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS------------------------------------------ 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 980 vaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIVKVYLAVKRR 1059
Cdd:CHL00207 788 ----------------------------------------------------------KGDELKFGYYLKIRVFIAQIRK 809
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1060 IQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAakgiGDKINAMLKQqqeva 1139
Cdd:CHL00207 810 IQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLA----GDNLNKRFKI----- 880
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1140 klrefiqraydlgadvrqkVDLSTFSDEEVMRLAENlRKGMPIATpvfdgakeaeIKELLKLGDLPTSGQIRLYDGRTGE 1219
Cdd:CHL00207 881 -------------------LPFDEMYGSEYSRILIN-NKLNQASI----------KNNEYWLFNSYHPGKMVLRDGRTGY 930
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1220 QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:CHL00207 931 KFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQ 1010
|
1290 1300 1310 1320
....*....|....*....|....*....|....*....|
5NWT_C 1300 GRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIEL 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: 893.08 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVQECQIRGVTYSAP 95
Cdd:cd00653 1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffe 226
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 227 kvifeirdnklqmelvperlrgetasfdieangkvyvekgrritarhIRQLEkddvklievpveyiagkvvAKDYIDest 306
Cdd:cd00653 197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 307 gelicaanmelsldllaklsqsghKRIEtlftndldhgpyisetlrvdptndrlsalveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653 208 ------------------------KRFE---------------------------------------------------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 387 nlffsedrydlsavgrmkfnrsllreeiegsgilskdDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653 212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653 255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtdgvvtdeihylsaieeg 612
Cdd:cd00653 335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV------------------ 391
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 613 nyviaqansnldeeghfvedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653 392 ----------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggvvqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 757 trsnqntcinqmpcvslgepvergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653 471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriravlvaggveaekldklprd 995
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 996 rwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1076 ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinamlkqqqevaklrefiqraydlgadv 1155
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1156 rqkvdlstfsdeevmrlaenlRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKL 1235
Cdd:cd00653 693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653 752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831
|
1370 1380 1390
....*....|....*....|....*....|....*
5NWT_C 1310 ----DGNHQMEPGMPESFNVLLKEIRSLGINIELE 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 |
9.20e-167 |
|
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: 502.06 E-value: 9.20e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 717 VAKRGGVVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpVERGDvladgpstdLGE 793
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 953 lkqakkdlseelqileaglfsriravlvaggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1033 rrkitqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1113 LETHLGMAAKGigdkinamlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrKGMPIATPVFDGAKE 1192
Cdd:pfam00562 272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
5NWT_C 1193 --AEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 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 |
2.23e-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: 353.22 E-value: 2.23e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 26 YLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGN---SELQYVSYRLGEPVFDV----------QECQIRGVTY 92
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENgdkLSLKFGQIRLGKPMFDEtdgstreiypQECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 93 SAPLRVKLRLVIYereapegTVKDIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQ 148
Cdd:pfam04563 81 SAPLYVDLELSVY-------NGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 149 LHRS---PGVFFDSDKGKTHSSGKVLYNARI--IPYRGSWLDF-EFDPKDNLFVRIDRRRK-LPATIILRALNYTTEQIL 221
Cdd:pfam04563 154 EHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 222 dlfFEKVIFEIRDNKLQMELVPErlrgetasfdieangkvyVEKGRRITarhirqlekddVKLIEVPVEYIAGKVVAkdy 301
Cdd:pfam04563 234 ---FELICYDVNDQQLQEELLPS------------------LEEGFKIR-----------IQTQEQALDYIGGRGRA--- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 302 idestgelicaanmelsldllaklsqsghkrietlftndldhgpyisetlrvdptndrlsalveIYRMMRPGEPPTREAA 381
Cdd:pfam04563 279 ----------------------------------------------------------------IFRMGRPREPRIKYAE 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 382 ESLFENLFFSEDRYDLSAVGRMKFnrsllreeiegsgilskddIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:pfam04563 295 EILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLA 355
|
490 500 510 520
....*....|....*....|....*....|....*....|.
5NWT_C 462 NQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISA 500
Cdd:pfam04563 356 SLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1340 |
1.65e-88 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 312.28 E-value: 1.65e-88
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 31 QLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDV----------QECQIRGVTYSAPLRVKL 100
Cdd:PRK08565 18 HLDSYNDFIER------GLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEadgserpitpMEARLRNLTYAAPLYLTM 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 101 RLVIYEREapegtvkdIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQLHRSPG-V 155
Cdd:PRK08565 92 IPVENGIE--------YEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrV 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 156 FFDSDKgkthSSGKVLYNARIIPYRG---SWLDFEFDPKDNLFVRIDR-RRKLPATIILRALNYTTEQ-ILDLFFEkvif 230
Cdd:PRK08565 164 LVDKGE----AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETDRdIVYAVSL---- 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 231 eirDNKLQMELVPerlrgetaSFdieangkvyvEKGRRItarhirqlekddvklievpveyiagkvvakdyidestgeli 310
Cdd:PRK08565 236 ---DPEIQQELLP--------SL----------EQASSI----------------------------------------- 253
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 311 cAANMELSLDLLAKLSQSGHKRietlftndldhgpyisetlrvdptNDRLsalveiyrmmrpgepptREAAESLfenlff 390
Cdd:PRK08565 254 -AATVEDALDYIGKRVAIGQPR------------------------EYRI-----------------ERAEQIL------ 285
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 391 seDRYDLSAVGRMKFNRsllreeiegsgiLSKDDIIDVM-KKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLV 469
Cdd:PRK08565 286 --DKYLLPHLGTSPEDR------------IKKAYFLGQMaSKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAFK 351
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 470 RVERAVKERL----SLG---DLDTLMPQDMINAKPISA-AVKEFFGS-SQLSQFMDQNNPLSEITHKRRIsaLGPggLTR 540
Cdd:PRK08565 352 QLVKDLKYQLeksyARGrklDLRAIVRPDIITERIRHAlATGNWVGGrTGVSQLLDRTNYLSTLSHLRRV--VSP--LSR 427
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 541 ERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ----TNEYGFLETPYRKvtdGVVtdeiHYLSAIEEGNYVI 616
Cdd:PRK08565 428 GQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQisvgVDEEEVEEILYEL---GVV----PVEEAREEEYISW 500
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 617 AQA--NSNL---DEEGH-FVEDLVTCRSKGESSlfsrdqvdymdvstqQVVSVGaslipFLEHDDANRALMGANMQRQAV 690
Cdd:PRK08565 501 SRVylNGRLigyHPDGEeLAEKIRELRRSGKIS---------------DEVNVA-----YIETGEINEVYVNCDSGRVRR 560
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 691 PTL--RADKPLVGtgMERAVAVDSGVTAVAK--RGGVVQYVDASR---IVIKVNEDEMYPGEAGIDIY---------NLT 754
Cdd:PRK08565 561 PLIvvENGKPKLT--REHVEKLKKGELTFDDlvKMGVIEYLDAEEeenAYVALDPEDLTPEHTHLEIWppailgitaSII 638
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 755 KYTRSNQ---NTCINQMPCVSLGEPV--------ERGDVL------------------ADGPStdlgelalGQNMRVAFM 805
Cdd:PRK08565 639 PYPEHNQsprNTYQAAMAKQSLGLYAanfrirtdTRGHLLhypqrplvqtraleiigyNDRPA--------GQNAVVAVL 710
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 806 PWNGYNFEDSILVSERVVqeDR-------FTTIHIQELacvsrdTKLGPEEITADIP--NV----GEAALSKLDESGIVY 872
Cdd:PRK08565 711 SYTGYNIEDAIIMNKASI--ERglarstfFRTYETEER------KYPGGQEDKIEIPepNVrgyrGEEYYRKLDEDGIVS 782
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 873 IGAEVTGGDILVGKVTPKgetQLTPEEKLLRAIFGEKasdvKDSSLRVPNGVSGTVidvqvftrdgvekDKraleieemq 952
Cdd:PRK08565 783 PEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----RDTSVTVRHGEKGIV-------------DT--------- 833
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 953 lkqakkdlseelqileaglfsriraVLVAGGVEAEKLdklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:PRK08565 834 -------------------------VLITESPEGNKL------------------------------------------- 845
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1033 rrkitqgddlapgvlkiVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:PRK08565 846 -----------------VKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQL 908
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1113 LEThlgmaakgIGDKINAMlkqqqevaklrefiqraydlgadvrqkvdlstfsdeevmrlaenlrKGMPI-ATPvFDGAK 1191
Cdd:PRK08565 909 LES--------IAGKVAAL----------------------------------------------EGRFVdATP-FYGEP 933
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1192 EAEI-KELLKLGDLPTSGQIrLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRF 1270
Cdd:PRK08565 934 EEELrKELLKLGYKPDGTEV-MYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRF 1012
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1271 GEMEVWALEAYGAAYTLQEMLTVKSDdvngRTKMY--------------KNI----VDGN----HQMEpgMPESFNVLLK 1328
Cdd:PRK08565 1013 GEMERDCLIGHGAAMLLKERLLDSSD----KTTIYvcelcghiawydrrKNKyvcpIHGDkgniSPVE--VSYAFKLLLQ 1086
|
1450
....*....|..
5NWT_C 1329 EIRSLGINIELE 1340
Cdd:PRK08565 1087 ELMSMGISPRLK 1098
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
603-1341 |
7.31e-61 |
|
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: 220.28 E-value: 7.31e-61
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 603 IHYLSAIEEGNYVIAQansnldeeghFVEDLvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 682
Cdd:TIGR03670 92 IEYLDAEEEENAYIAL----------DPEEL-------------TPEHTHLEIDPSAILGIIASTIPYPEHNQSPRNTMG 148
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 683 ANMQRQAVPTLRADKPLvgtgmeravAVDSgvtavakRGGVVQYvdasrivikvnedemyPgeagidiynltkytrsnqn 762
Cdd:TIGR03670 149 AAMAKQSLGLYAANYRI---------RLDT-------RGHLLHY----------------P------------------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 763 tcinQMPCVSlgepvERGDVLadgpsTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRD 842
Cdd:TIGR03670 178 ----QKPLVK-----TRVLEL-----IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEERR 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 843 TKLGPE-EITADIPNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTPkgetqltP---EEkllRAIFGEKASDVK 914
Cdd:TIGR03670 244 YPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTERRR 313
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 915 DSSLRVPNGVSGTVidvqvftrdgvekDKraleieemqlkqakkdlseelqileaglfsriraVLVAGGVEAEKLdklpr 994
Cdd:TIGR03670 314 DTSVTVRHGEKGIV-------------DK----------------------------------VIITETEEGNKL----- 341
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 995 drwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddlapgvlkiVKVYLAVKRRIQPGDKMAGRHGNKG 1074
Cdd:TIGR03670 342 -------------------------------------------------------VKVRVRDLRIPELGDKFASRHGQKG 366
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1075 VISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILEThlgmaakgIGDKINAMlkqqqevaklrefiqraydlgad 1154
Cdd:TIGR03670 367 VIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM--------IAGKVAAL----------------------- 415
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1155 vrqkvdlstfsdeevmrlaenlrKGMPI-ATPvFDGAKEAEI-KELLKLGDLPTSGQIrLYDGRTGEQFERPVTVGYMYM 1232
Cdd:TIGR03670 416 -----------------------EGRRVdGTP-FEGEPEEELrKELLKLGFKPDGKEV-MYDGITGEKLEAEIFIGVIYY 470
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1233 LKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV-------------- 1298
Cdd:TIGR03670 471 QKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYvvyvcencghiawe 550
|
730 740 750 760
....*....|....*....|....*....|....*....|....*....
5NWT_C 1299 NGRTKMYKNIVDGN----HQMEpgMPESFNVLLKEIRSLGI--NIELED 1341
Cdd:TIGR03670 551 DKRKGTAYCPVCGEtgdiSPVE--MSYAFKLLLDELKSLGIspRLELGD 597
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
603-1341 |
2.51e-50 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 189.02 E-value: 2.51e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 603 IHYLSAIEEGNYVIAQANSNLDEEgHfvedlvtcrskgesslfsrdqvDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 682
Cdd:PRK07225 98 IEYLDAEEEENAYIAVYEEDLTEE-H----------------------THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 683 ANMQRQA--VPT----LRADKplvgtgmeravavdsgvtavakRGGVVQYVDASRIVIKVNEdemypgEAGIDiynltky 756
Cdd:PRK07225 155 AGMIKQSlgLPAanykLRPDT----------------------RGHLLHYPQVPLVKTQTQE------IIGFD------- 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 757 trsnqntcinqmpcvslgepvERgdvladgPStdlgelalGQNMRVAFMPWNGYNFEDSILVSERVV------------- 823
Cdd:PRK07225 200 ---------------------ER-------PA--------GQNFVVAVMSYEGYNIEDALIMNKASIerglgrshffrty 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 824 ----------QEDRFTTihiqelacvsrdtklgPEEitadipNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK07225 244 egeerrypggQEDRFEI----------------PDK------DVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSP 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 890 kgetqltP---EEKllrAIFGEKASDVKDSSLRVPNGVSGTVidvqvftrdgvekdkraleieemqlkqakkdlseelqi 966
Cdd:PRK07225 302 -------PrflEEP---DDFGISPEKRRETSVTMRSGEEGIV-------------------------------------- 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 967 leaglfsriRAVLVAGGVEAEKLDKLpRDRwlelgltdeekqnqleqlaeqyDELKHEFekkleakrrkitqgddlapgv 1046
Cdd:PRK07225 334 ---------DTVILTETEEGSRLVKV-RVR----------------------DLRIPEL--------------------- 360
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1047 lkivkvylavkrriqpGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILEThlgmaakgIGD 1126
Cdd:PRK07225 361 ----------------GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM--------IGG 416
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1127 KINAMLKQqqevaklrefiqraydlgadvrqKVDlstfsdeevmrlaenlrkgmpiATPvFDGAKEAEIKELLKLGDLPT 1206
Cdd:PRK07225 417 KVGSLEGR-----------------------RVD----------------------GTA-FSGEDEEDLREALEKLGFEH 450
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1207 SGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Cdd:PRK07225 451 TGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAML 530
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
5NWT_C 1287 LQEMLTVKSDDVN-------GRTKMY---KNIV--------DGNHQMEpgMPESFNVLLKEIRSLGI--NIELED 1341
Cdd:PRK07225 531 LKERLLDESDKVEiyvcakcGMIAIYdkkRNRKycpicgeeTDIYPVE--MSYAFKLLLDELKSLGIapRLELED 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
....*....|....*....|....*....|....*....|....*....|....*....|....*...
5NWT_C 513 QFMDQNNPLSEITHKRRISAlGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
591-656 |
9.90e-35 |
|
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: 126.71 E-value: 9.90e-35
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
5NWT_C 591 YRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVS 656
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSARYRGEFPLVPPEEVDYMDVS 66
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1266-1342 |
2.65e-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: 126.55 E-value: 2.65e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 1266 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVNGRTKMYKN-----IVDGNHQMEPG-MPESFNVLLKEIRSLGI 1335
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*..
5NWT_C 1336 NIELEDE 1342
Cdd:pfam04560 81 DPRLLLE 87
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
31-580 |
1.41e-26 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 115.43 E-value: 1.41e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 31 QLDSFQKFIEqdpegqYGLEAAFRSVFPIQSYSGNSE-LQYVSYRLGEPV----------FDVQECQIRGVTYSAPLRvk 99
Cdd:PRK09606 22 HIDSYNDFVD------NGLQKIIDEQGPIETEIEDGVyVELGKIRVGKPVvkeadgsereIYPMEARLRNLTYSAPLY-- 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 100 LRLVIYEREAPEGTVkdikeqEVYMGEIPLM-----------TDN-------------GTFVINGTERVIVSQLHRSPGV 155
Cdd:PRK09606 94 LEMSPVEGGEEEEPE------EVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERVLMTLEDLAPNK 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 156 F---FDSDKGKTHSSGKVL-----YNARIIPYRGswldfefdpKDNL----FVRIDRRrkLPATIILRALNYTTEQildl 223
Cdd:PRK09606 168 IlveKDERYGDRIEVAKVFsqrrgYRALVTVERN---------RDGLlevsFPSVPGS--IPFVILMRALGLETDE---- 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 224 ffekvifEIrdnklqMELVperlrgetaSFDIEangkvyvekgrrITARHIRQLEKDDVKLIEVPVEYIAGKVV---AKD 300
Cdd:PRK09606 233 -------EI------VEAV---------SDDPE------------IVKFMLENLEEAEVDTQEEALEYIGKRVApgqTKE 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 301 YidestgelicaanmelsldllaKLsqsghKRIETLFTNdldhgpYISETLRVDPtNDRLSALVEIYRMmrpgepptrea 380
Cdd:PRK09606 279 Y----------------------RI-----KRAEYVIDR------YLLPHLGVEP-EVRRAKAHYLGRM----------- 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 381 AESLFEnlffsedrydlsavgrmkfnrsllreeiegsgilskddiidvmkklidIRNGKGEVDDIDHLGNRRIRSVGEMA 460
Cdd:PRK09606 314 AEACFE------------------------------------------------LALGRREEDDKDHYANKRLKLAGDLM 345
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 461 ENQFRVGLVRVERAVK---ERlslgdldtlmpQDMINAKP-ISAAVKE----------------FFGSSQLSQFMDQNNP 520
Cdd:PRK09606 346 EDLFRVAFNRLARDVKyqlER-----------ANMRNRELsIKTAVRSdvlterlehamatgnwVGGRTGVSQLLDRTDY 414
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 521 LSEITHKRRISAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:PRK09606 415 MATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
151-454 |
8.30e-09 |
|
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: 56.59 E-value: 8.30e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 151 RSPGVFFDSDKGKTHSSGKvlYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQ-ILDlffekvi 229
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIAT--YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDReILD------- 71
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 230 feirdnklqmelvperlrgetasfdieangkvyvekgrRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIdestgel 309
Cdd:pfam04561 72 --------------------------------------RLCYDFNDPQMLELLKPELEEAENIYTQEEALDYI------- 106
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5NWT_C 310 icaanmelsldllaklsqsgHKRIetlftndldhgpyisetlrvdptndrlsalveiyrMMRPGEPPTREAAESLFENLF 389
Cdd:pfam04561 107 --------------------GKGF-----------------------------------ALRRGEEPRLQRAREILYSRD 131
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*
5NWT_C 390 fsedrydlsavGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Cdd:pfam04561 132 -----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| HMG-box_IXR1-like_rpt1 |
cd22011 |
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ... |
972-1029 |
2.44e-04 |
|
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link recognition protein (Ixr1) and similar proteins; Ixr1, also called structure-specific recognition protein (SSRP), is a homolog of the yeast mitochondrial regulator ABF2. It binds to platinated DNA and confers sensitivity to the anticancer drug cisplatin. Ixr1 contains two HMG-box domains. This model corresponds to the first one.
Pssm-ID: 438827 [Multi-domain] Cd Length: 75 Bit Score: 40.98 E-value: 2.44e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
5NWT_C 972 FSRIRAVLVAGGVEAEK---LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011 12 SQEIRKNLKSQGSPEEKvpeLSKRAAEQWR--SLTLAEKQpyyDEVEVLKKQYDVEKEEYEKEL 73
|
|
| |
