|
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: 2277.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 80 FDVKECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEirdnklqm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 240 eliperlrgetasfdieangkvyvekgrritarhirqlekddiKHIEVPVEYIAGKVAAKDYIDEATGELICPANMELSL 319
Cdd:PRK00405 225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 320 DLlaklsqsghkrietlftndldHGPYISETVRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 400 VGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSK 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 720 RGGTVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405 641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405 719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405 799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 960 lseelqileaglfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405 856 ----------------------------------------------------------------------------IEQG 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405 860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405 940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1200 QLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490254324 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: 1938.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVK 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 84 ECQIRGVTYSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffekvvfeirdnklqmelip 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 244 erlrgetasfdieangkvyvekgrritarhirqlekddikhievpveyiagkvaakdyideatgelicpanmelsldlla 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 324 klsqsghkrIETLFTNDLDHGPYISETVRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 404 KFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 564 PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVV--TDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGE 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013 520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 722 GTVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013 600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013 679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdls 961
Cdd:TIGR02013 759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 962 eelqileaglfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDD 1041
Cdd:TIGR02013 815 ----------------------------------------------------------------------------QGDE 818
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1042 LAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013 819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1122 KGIGdkinamlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlRKGMPIATPVFDGAKEAEIKELLQL 1201
Cdd:TIGR02013 899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1202 GDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
gi 490254324 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: 1651.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 12 RKDFGKRPQVLDVPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 92 YSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFEKVVFEIrdnklqmeliperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 251 asfdIEANgkvyvekgrritarhirqLEKDDIKhievpveyiagkvaakdyideatgelicpanmelsldllaklsqsgh 330
Cdd:COG0085 207 ----ILAT------------------LEKDNTK----------------------------------------------- 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 331 krietlftndldhgpyisetvrvdptnDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085 218 ---------------------------TQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 411 RDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 571 LINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggtvqyvdas 730
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085 560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileag 970
Cdd:COG0085 702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 971 lfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085 749 -------------------------------------------------------------------EGDELPPGVNKLV 761
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1051 KVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkina 1130
Cdd:COG0085 762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1131 mlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlRKGMPIATPVFDGAKEAEIKELLQLGDLPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1211 TLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
gi 490254324 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: 885.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVKECQIRGVTYSAP 95
Cdd:cd00653 1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffe 226
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 227 kvvfeirdnklqmeliperlrgetasfdieangkvyvekgrritarhIRQLEkddikhievpveyiagkvaAKDYIDeat 306
Cdd:cd00653 197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 307 gelicpanmelsldllaklsqsghKRIEtlftndldhgpyisetvrvdptndrlsalveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653 208 ------------------------KRFE---------------------------------------------------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 387 nlffsedrydlsavgrmkfnrsllrdeiegsgilskdDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653 212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653 255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtngvvtdeihylsaieeg 612
Cdd:cd00653 335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV------------------ 391
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 613 nyviaqansnldenghfvedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653 392 ----------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggtvqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 757 trsnqntcinqmpcvslgepiergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653 471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriyavlvsggveaekldklprd 995
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 996 rwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1076 ISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinamlkqqqevaklrefiqraydlgadv 1155
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1156 rqkvdlntfsdeevlrlaenlRKGMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKL 1235
Cdd:cd00653 693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653 752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831
|
1370 1380 1390
....*....|....*....|....*....|....*
gi 490254324 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 |
1.30e-163 |
|
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: 493.97 E-value: 1.30e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 717 VAKRGGTVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpIERGDvladgpstdLGE 793
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 953 lkqakkdlseelqileaglfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1033 rrkitqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1113 LETHLGMAAKGigdkinamlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlrKGMPIATPVFDGAKE 1192
Cdd:pfam00562 272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490254324 1193 --AEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 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 ... |
989-1029 |
6.15e-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: 39.83 E-value: 6.15e-04
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 490254324 989 LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011 32 LSKRAAEQWR--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: 2277.71 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1 MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD-PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 80 FDVKECQIRGVTYSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEirdnklqm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFG-------- 224
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 240 eliperlrgetasfdieangkvyvekgrritarhirqlekddiKHIEVPVEYIAGKVAAKDYIDEATGELICPANMELSL 319
Cdd:PRK00405 225 -------------------------------------------KEIEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 320 DLlaklsqsghkrietlftndldHGPYISETVRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 400 VGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 480 SLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 560 PIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSK 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTARYK 560
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 640 GESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAK 719
Cdd:PRK00405 561 GEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVAK 640
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 720 RGGTVQYVDASRIVIKVneDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQN 799
Cdd:PRK00405 641 RDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQN 718
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 800 MRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTG 879
Cdd:PRK00405 719 VLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVKP 798
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 880 GDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRdgvekdkraleieemqlkqakkd 959
Cdd:PRK00405 799 GDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR----------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 960 lseelqileaglfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkITQG 1039
Cdd:PRK00405 856 ----------------------------------------------------------------------------IEQG 859
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1040 DDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGM 1119
Cdd:PRK00405 860 DELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLGW 939
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1120 AAKGIGDKinamlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlrkgmpIATPVFDGAKEAEIKELL 1199
Cdd:PRK00405 940 AAKGLGIK------------------------------------------------------FATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1200 QLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 490254324 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: 1938.68 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPE----GQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVK 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 84 ECQIRGVTYSAPLRVKLRLVIYEreapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKE----EDGTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTteqildlffekvvfeirdnklqmelip 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 244 erlrgetasfdieangkvyvekgrritarhirqlekddikhievpveyiagkvaakdyideatgelicpanmelsldlla 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 324 klsqsghkrIETLFTNDLDHGPYISETVRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 404 KFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 484 LDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 564 PEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVV--TDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGE 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYRGE 519
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 642 SSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRG 721
Cdd:TIGR02013 520 ITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKRG 599
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 722 GTVQYVDASRIVIKVNEDEMYPgEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMR 801
Cdd:TIGR02013 600 GVVEYVDAKRIVIRYDEDEEEP-DGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNVL 678
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 802 VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGD 881
Cdd:TIGR02013 679 VAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAGD 758
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 882 ILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdls 961
Cdd:TIGR02013 759 ILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE------------------------ 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 962 eelqileaglfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDD 1041
Cdd:TIGR02013 815 ----------------------------------------------------------------------------QGDE 818
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1042 LAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Cdd:TIGR02013 819 LPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWAG 898
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1122 KGIGdkinamlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlRKGMPIATPVFDGAKEAEIKELLQL 1201
Cdd:TIGR02013 899 KRLG---------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1202 GDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
gi 490254324 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: 1651.38 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 12 RKDFGKRPQVLDVPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLEE------GLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 92 YSAPLRVKLRLVIYEreapegtVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTT-EQILDLFFEKVVFEIrdnklqmeliperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQEY------------------ 206
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 251 asfdIEANgkvyvekgrritarhirqLEKDDIKhievpveyiagkvaakdyideatgelicpanmelsldllaklsqsgh 330
Cdd:COG0085 207 ----ILAT------------------LEKDNTK----------------------------------------------- 217
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 331 krietlftndldhgpyisetvrvdptnDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLL 410
Cdd:COG0085 218 ---------------------------TQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 411 RDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 491 DMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 571 LINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQV 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVRYRGEEVLVPPEEV 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 651 DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeravavdsgvtavakrggtvqyvdas 730
Cdd:COG0085 511 DYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------- 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 731 rivikvnedemypgeagiDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGY 810
Cdd:COG0085 560 ------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEGY 621
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 811 NFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK 890
Cdd:COG0085 622 NYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTPK 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 891 GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileag 970
Cdd:COG0085 702 GETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE--------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 971 lfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIV 1050
Cdd:COG0085 749 -------------------------------------------------------------------EGDELPPGVNKLV 761
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1051 KVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkina 1130
Cdd:COG0085 762 RVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA-------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1131 mlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlRKGMPIATPVFDGAKEAEIKELLQLGDLPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1211 TLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|..
gi 490254324 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: 1433.64 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 27 LLSIQLDSFQKFIEQDpEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQIRGVTYSAPLRVKLRLVI-- 104
Cdd:PRK14844 32 LVKVQKESYDSFTPKN-KGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLVImq 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 105 -------YEREAPEG-------TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKV 170
Cdd:PRK14844 111 dgisldeYKSIKESGdhsklatVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 171 LYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRDNKLQMELIPERLRGET 250
Cdd:PRK14844 191 IYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVR 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 251 ASFDI-EANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEYIAGKVAAKDYIDEATGELICPANMELSLDLLAKLSQSG 329
Cdd:PRK14844 271 LPFDLmDVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLS 350
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 330 HKRIETLFTNDLDHGPYISETVRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSL 409
Cdd:PRK14844 351 IDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYL 430
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 410 LRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMP 489
Cdd:PRK14844 431 GLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSP 510
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 490 QDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNI 569
Cdd:PRK14844 511 SDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 570 GLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQ 649
Cdd:PRK14844 591 GLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCRYAGSFVMVSSDQ 670
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 650 VDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDA 729
Cdd:PRK14844 671 VSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSDS 750
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 730 SRIVIKVNEDEMYpGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNG 809
Cdd:PRK14844 751 NSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQG 829
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 810 YNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK14844 830 YNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVTP 909
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 890 KGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEA 969
Cdd:PRK14844 910 KPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTSE 989
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 970 GLFSRIYAVLV-SGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLK 1048
Cdd:PRK14844 990 YFYDELKKLLInSGSQDREKFDSIEREQWWGIGLKNQSISEQVKSLKKDFDEKVSHAIAQFKRKVEKLHEGYDLPQGVSM 1069
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKI 1128
Cdd:PRK14844 1070 SVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWACKKLGEKV 1149
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1129 NAML--------------------------------KQQQEV-------------------------------------A 1139
Cdd:PRK14844 1150 GNILdeinkiksafckgirslnddnftkfaaayldnKKIENIdddeitasvlntpnknalndelnelvenylnscksayS 1229
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1140 KLREFIQRAYDLGADVRQKVDLNTFSDEEVLRLAENLRKGMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGE 1219
Cdd:PRK14844 1230 NLRNFLIEVYSCGSNVSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAVLYDGCSGE 1309
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1220 QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:PRK14844 1310 KFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEMLTVKSDDIN 1389
|
1370 1380 1390 1400
....*....|....*....|....*....|....*....|.
gi 490254324 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: 1410.45 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 8 KKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVKECQI 87
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 88 RGVTYSAPLRVKLRLVIYEREAPEG---TVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKT 164
Cdd:PRK09603 88 RGITYSIPLKIKVRLILWEKDTKSGeknGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 165 hSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVVFEIRDNKLQMELIPE 244
Cdd:PRK09603 168 -SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 245 RLRGEtASFDI-EANGKVYVEKGRRITARHIRQLEKDDIKHIEVPVEYIAGKVAAKDYIDEAtgelicpanmELSLDLLA 323
Cdd:PRK09603 247 DANQR-MEFDLkDPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGK----------EVLLDMLT 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 324 KLSQSGHKRI------ETLFTNDLDHG----------------PYISETVRVDPTNDRlsALVEIYRMMRPGEPPTREAA 381
Cdd:PRK09603 316 QLDKNKLEKIhdlgvqEFVIINDLALGhdasiihsfsadseslKLLKQTEKIDDENAL--AAIRIHKVMKPGDPVTTEVA 393
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 382 ESLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:PRK09603 394 KQFVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLA 473
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 462 NQFRVGLVRVERAVKERLSL--GDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLT 539
Cdd:PRK09603 474 NELHSGLVKMQKTIKDKLTTmsGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLV 553
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 540 RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQA 619
Cdd:PRK09603 554 KDRVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPA 633
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 620 NSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPL 699
Cdd:PRK09603 634 STPIDEEGNILGDLIETRVEGEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPI 713
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 700 VGTGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIkVNEDEmypGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPIER 779
Cdd:PRK09603 714 VGTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGK---EEAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEA 789
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 780 GDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGE 859
Cdd:PRK09603 790 GQIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKE 869
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 860 AALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGV 939
Cdd:PRK09603 870 EALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGY 949
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 940 EKDKRALEIEEMQlkQAKKDLS--EELQILEAGLFSRIYAVLVSGGVEAE---------KLDKLPR------DRWLELGL 1002
Cdd:PRK09603 950 EKDARVLSAYEEE--KAKLDMEhfDRLTMLNREELLRVSSLLSQAILEEPfshngkdykEGDQIPKeeiasiNRFTLASL 1027
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1003 TD---EEKQNQLEQLA----EQYDELKHEFEKKLEakrrkITQGDDLAP-GVLKIVKVYLAVKRRIQPGDKMAGRHGNKG 1074
Cdd:PRK09603 1028 VKkysKEVQNHYEITKnnflEQKKVLGEEHEEKLS-----ILEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKG 1102
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1075 VISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQE------VAKLREFIQRA 1148
Cdd:PRK09603 1103 IVSNIVPVADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDKTKdfakelRAKMLEIANAI 1182
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1149 YDLGADVRQKvdLNTFSDEEVLRLAENLRKGMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVG 1228
Cdd:PRK09603 1183 NEKDPLTIHA--LENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVG 1260
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNI 1308
Cdd:PRK09603 1261 YMYMIKLHHLVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAI 1340
|
1370 1380 1390
....*....|....*....|....*....|.
gi 490254324 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: 1065.29 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 25 PYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVKECQIRGVTYSAPLRVKLRL 102
Cdd:CHL00001 13 PGFNQIQFEGFCRFIDQ------GLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYESLTYSSELYVPAGL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 103 vIYEREapegtvKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVLYNARIIPYRGS 182
Cdd:CHL00001 87 -IWKKS------RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDH---NGISVYTGTIISDWGG 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 183 WLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDlffekvvfeirdnklqmeliperlrgetasfdieangkvy 262
Cdd:CHL00001 157 RLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILD---------------------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 263 vekgrritarhirqlekdDIKHIEVPVEYIAGKVAAKDYIDEAtgelicpanmelsldllaklsqsghkrietlftndld 342
Cdd:CHL00001 197 ------------------NVCYPEIFLSFLNDKEKKKIGSKEN------------------------------------- 221
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 343 hgpyisetvrvdptndrlsALVEIYRMM--RPGEPPTREAAESLFENLFFSEdRYDLSAVGRMKFNRSLLRDEIEGSGIL 420
Cdd:CHL00001 222 -------------------AILEFYQQFacVGGDPVFSESLCKELQKKFFQQ-RCELGRIGRRNMNRKLNLDIPENNTFL 281
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 421 SKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLM--PQDMINAKPI 498
Cdd:CHL00001 282 LPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICGAIRRKLIptPQNLVTSTPL 361
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 499 SAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVY 578
Cdd:CHL00001 362 TTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAIH 441
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 579 AQTNEYGFLETPYRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQ 658
Cdd:CHL00001 442 ARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQGIQEEQVVPARYRQEFLTIAWEQIHLRSIFPF 521
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 659 QVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNE 738
Cdd:CHL00001 522 QYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYTDTDKIILSGNG 601
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 739 DEMYpgeagidiYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILV 818
Cdd:CHL00001 602 DTLS--------IPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPWEGYNFEDAVLI 673
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 819 SERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPK--GETQLT 896
Cdd:CHL00001 674 SERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKLTPQeaEESSYA 753
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 897 PEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVqvftrdgvekdkraleieemqlkqakkdlseelqileaglfsriy 976
Cdd:CHL00001 754 PEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV--------------------------------------------- 788
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 977 avlvsggveaekldklprdRWLelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIVKVYLAV 1056
Cdd:CHL00001 789 -------------------RWI---------------------------------------QKKGGSSYNPETIHVYILQ 810
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1057 KRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinaMLKQQQ 1136
Cdd:CHL00001 811 KREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAGD--------LLNRHY 882
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1137 EVAKLREFIQRaydlgadvrqkvdlntfsdeevlrlaENLRKgmpiatPVFDGAKEAEikelLQLG-----DLPTSGQIT 1211
Cdd:CHL00001 883 RIAPFDERYEQ--------------------------EASRK------LVFSELYEAS----KQTAnpwvfEPEYPGKSR 926
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1212 LFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1291
Cdd:CHL00001 927 LFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVGEMEVWALEGFGVAYILQEML 1006
|
1290 1300 1310 1320
....*....|....*....|....*....|....*....|....*...
gi 490254324 1292 TVKSDDVNGRTKMYKNIVDGNHQMEP-GMPESFNVLLKEIRSLGINIE 1338
Cdd:CHL00001 1007 TYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 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: 1061.24 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 24 VPYLLSIQLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVS--YRLGEPVFDVKECQIRGVTYSAPLRVKLR 101
Cdd:CHL00207 7 LPDFLEIQRTSFCWFLNE------GLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIYLPLK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 102 LViyereapEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHssgKVLYNARIIPYRG 181
Cdd:CHL00207 81 FI-------NLKTNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLIPNRG 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 182 SWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQIldlffekvvfeirdnklqmeliperlrgetasfdieangkv 261
Cdd:CHL00207 151 SWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDI----------------------------------------- 189
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 262 yvekgrRITARHIRQLEKDDIkhievpveyiagkvaakdyideatgelicpanmelsldllaklsqsghkrietlftNDL 341
Cdd:CHL00207 190 ------YSRLTKSEFLKKLKP--------------------------------------------------------ILL 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 342 DHGPYISETvrvdptndrlsALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLRDEIEGSGILS 421
Cdd:CHL00207 208 NSNSYTNEE-----------ILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNLT 276
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 422 KDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA 501
Cdd:CHL00207 277 YEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIAL 356
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 502 VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQT 581
Cdd:CHL00207 357 IREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNARI 436
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 582 NEYGFLETPYRKVTNGVV--TDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQ 659
Cdd:CHL00207 437 NKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVRYKQEFKTVNPSKVDFIAISPIQ 516
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 660 VVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGTVQYVDASRIVIKVNED 739
Cdd:CHL00207 517 VFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDDNN 596
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 740 EMYpgeagidIYNLTKYTRSNQNTCINQMPCVSLGEPIERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVS 819
Cdd:CHL00207 597 RYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAILIN 669
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 820 ERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEE 899
Cdd:CHL00207 670 KRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLPEG 749
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 900 KLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriyavl 979
Cdd:CHL00207 750 KLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS------------------------------------------ 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 980 vsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitQGDDLAPGVLKIVKVYLAVKRR 1059
Cdd:CHL00207 788 ----------------------------------------------------------KGDELKFGYYLKIRVFIAQIRK 809
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1060 IQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAakgiGDKINAMLKQqqeva 1139
Cdd:CHL00207 810 IQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLA----GDNLNKRFKI----- 880
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1140 klrefiqraydlgadvrqkVDLNTFSDEEVLRLAENlRKGMPIATpvfdgakeaeIKELLQLGDLPTSGQITLFDGRTGE 1219
Cdd:CHL00207 881 -------------------LPFDEMYGSEYSRILIN-NKLNQASI----------KNNEYWLFNSYHPGKMVLRDGRTGY 930
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1220 QFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVN 1299
Cdd:CHL00207 931 KFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDMQ 1010
|
1290 1300 1310 1320
....*....|....*....|....*....|....*....|
gi 490254324 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: 885.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 27 LLSIQLDSFQKFIeqdpegQYGLEAAFRSVFPIQSYSGNSE--LQYVSYRLGEPV---------FDVKECQIRGVTYSAP 95
Cdd:cd00653 1 LVKQQIDSFNYFL------NVGLQEIVKSIPPITDTDDDGRlkLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 96 LRVKLRLVIYEREapegtvkDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDN-LFVRIDRrrklpatiilralnytteqildlffe 226
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKDrIYVRIDL-------------------------- 196
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 227 kvvfeirdnklqmeliperlrgetasfdieangkvyvekgrritarhIRQLEkddikhievpveyiagkvaAKDYIDeat 306
Cdd:cd00653 197 -----------------------------------------------KRQEE-------------------ALKYIG--- 207
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 307 gelicpanmelsldllaklsqsghKRIEtlftndldhgpyisetvrvdptndrlsalveiyrmmrpgepptreaaeslfe 386
Cdd:cd00653 208 ------------------------KRFE---------------------------------------------------- 211
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 387 nlffsedrydlsavgrmkfnrsllrdeiegsgilskdDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRV 466
Cdd:cd00653 212 -------------------------------------DLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRS 254
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 467 GLVRVERAVKERLS--LGDLDTLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISA 532
Cdd:cd00653 255 GLKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 533 lgpGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNeyGFLETPYRKVtngvvtdeihylsaieeg 612
Cdd:cd00653 335 ---LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIV------------------ 391
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 613 nyviaqansnldenghfvedlvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPT 692
Cdd:cd00653 392 ----------------------------------EKEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 693 ----------------LRADKPLVGTGMERAVAvdsgvtavakrggtvqyvdasrivikvnedemypgeagidiynltky 756
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIA----------------------------------------------- 470
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 757 trsnqntcinqmpcvslgepiergdvladgpstdLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQEL 836
Cdd:cd00653 471 ----------------------------------FGELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 837 ACVSRDTKLGPEEIT-ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 915
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 916 SSLRVPNGVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlseelqileaglfsriyavlvsggveaekldklprd 995
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 996 rwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV 1075
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1076 ISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKgigdkinamlkqqqevaklrefiqraydlgadv 1155
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1156 rqkvdlntfsdeevlrlaenlRKGMPIATPVFDGAKEAEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKL 1235
Cdd:cd00653 693 ---------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRL 751
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------ 1309
Cdd:cd00653 752 KHMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlc 831
|
1370 1380 1390
....*....|....*....|....*....|....*
gi 490254324 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 |
1.30e-163 |
|
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: 493.97 E-value: 1.30e-163
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 717 VAKRGGTVQYVDASRIVIKVNEdemypGEAGIDIYNLTKYTRSNQNT---CINQMPCVSLGEpIERGDvladgpstdLGE 793
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAGG---------FGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 794 LALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQElaCVSRDTKLGP-EEITADIPNVGEAALSKLDESGIVY 872
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGPiEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 873 IGAEVTGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFtrdgvekdkraleieemq 952
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 953 lkqakkdlseelqileaglfsriyavlvsggveaekldklprdrwlelgltdeekqnqleqlaeqydelkhefekkleak 1032
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1033 rrkitqgdDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQI 1112
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1113 LETHLGMAAKGigdkinamlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlrKGMPIATPVFDGAKE 1192
Cdd:pfam00562 272 LETHLGKAAAL------------------------------------------------------LGVFVDATPFDGAST 297
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490254324 1193 --AEIKELLQLGDLPTSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562 298 evEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
26-500 |
8.15e-110 |
|
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the protrusion domain. The other lobe (pfam04561) is nested within this domain.
Pssm-ID: 367994 [Multi-domain] Cd Length: 396 Bit Score: 351.68 E-value: 8.15e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 26 YLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGN---SELQYVSYRLGEPVFDVK----------ECQIRGVTY 92
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENgdkLSLKFGQIRLGKPMFDETdgstreiypqECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 93 SAPLRVKLRLVIYereapegTVKDIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQ 148
Cdd:pfam04563 81 SAPLYVDLELSVY-------NGEDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 149 LHRS---PGVFFDSDKGKTHSSGKVLYNARI--IPYRGSWLDF-EFDPKDNLFVRIDRRRK-LPATIILRALNYTTEQIL 221
Cdd:pfam04563 154 EHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 222 dlfFEKVVFEIRDNKLQMELIPErlrgetasfdieangkvyVEKGRRITarhirqlekddIKHIEVPVEYIAGKVAAkdy 301
Cdd:pfam04563 234 ---FELICYDVNDQQLQEELLPS------------------LEEGFKIR-----------IQTQEQALDYIGGRGRA--- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 302 ideatgelicpanmelsldllaklsqsghkrietlftndldhgpyisetvrvdptndrlsalveIYRMMRPGEPPTREAA 381
Cdd:pfam04563 279 ----------------------------------------------------------------IFRMGRPREPRIKYAE 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 382 ESLFENLFFSEDRYDLSAVGRMKFnrsllrdeiegsgilskddIIEVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:pfam04563 295 EILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLA 355
|
490 500 510 520
....*....|....*....|....*....|....*....|.
gi 490254324 462 NQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISA 500
Cdd:pfam04563 356 SLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1340 |
9.60e-87 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 307.27 E-value: 9.60e-87
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 31 QLDSFQKFIEQdpegqyGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVK----------ECQIRGVTYSAPLRVKL 100
Cdd:PRK08565 18 HLDSYNDFIER------GLQEIVDEFGEIKTEIPGLKIVLGKIRVGEPEIKEAdgserpitpmEARLRNLTYAAPLYLTM 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 101 RLVIYEREapegtvkdIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQLHRSPG-V 155
Cdd:PRK08565 92 IPVENGIE--------YEPEEVKIGDLPIMVKSkicplsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrV 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 156 FFDSDKgkthSSGKVLYNARIIPYRG---SWLDFEFDPKDNLFVRIDR-RRKLPATIILRALNYTTEQ-ILDLFFEkvvf 230
Cdd:PRK08565 164 LVDKGE----AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRALGLETDRdIVYAVSL---- 235
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 231 eirDNKLQMELIPerlrgetaSFdieangkvyvEKGRRItarhirqlekddIKHIEVPVEYIAGKVAAkdyideatGEli 310
Cdd:PRK08565 236 ---DPEIQQELLP--------SL----------EQASSI------------AATVEDALDYIGKRVAI--------GQ-- 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 311 cPANMELsldllaklsqsghKRIETLftndLDHG--PYIsetvrvdptndrlsalveiyrmmrpGEPPTREAAESLFenl 388
Cdd:PRK08565 273 -PREYRI-------------ERAEQI----LDKYllPHL-------------------------GTSPEDRIKKAYF--- 306
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 389 ffsedrydlsaVGRMkfnrsllrdeiegsgilskddiievMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGL 468
Cdd:PRK08565 307 -----------LGQM-------------------------ASKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAF 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 469 VRVERAVKERL----SLG---DLDTLMPQDMINAKPISA-AVKEFFGS-SQLSQFMDQNNPLSEITHKRRIsaLGPggLT 539
Cdd:PRK08565 351 KQLVKDLKYQLeksyARGrklDLRAIVRPDIITERIRHAlATGNWVGGrTGVSQLLDRTNYLSTLSHLRRV--VSP--LS 426
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 540 RERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQtneygfletpyrkVTNGVVTDEI----------HYLSAI 609
Cdd:PRK08565 427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQ-------------ISVGVDEEEVeeilyelgvvPVEEAR 493
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 610 EEGN------YViaqaNSNL---DENGH-FVEDLVTCRSKGESSlfsrdqvdymdvstqQVVSVGaslipFLEHDDANRA 679
Cdd:PRK08565 494 EEEYiswsrvYL----NGRLigyHPDGEeLAEKIRELRRSGKIS---------------DEVNVA-----YIETGEINEV 549
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 680 LMGANMQRQAVPTL--RADKPLVGtgMERAVAVDSGVTAVAK--RGGTVQYVDASR---IVIKVNEDEMYPGEAGIDIY- 751
Cdd:PRK08565 550 YVNCDSGRVRRPLIvvENGKPKLT--REHVEKLKKGELTFDDlvKMGVIEYLDAEEeenAYVALDPEDLTPEHTHLEIWp 627
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 752 --------NLTKYTRSNQ---NTCINQMPCVSLGEPI--------ERGDVL------------------ADGPStdlgel 794
Cdd:PRK08565 628 pailgitaSIIPYPEHNQsprNTYQAAMAKQSLGLYAanfrirtdTRGHLLhypqrplvqtraleiigyNDRPA------ 701
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 795 alGQNMRVAFMPWNGYNFEDSILVSERVVqeDR-------FTTIHIQELacvsrdTKLGPEEITADIP--NV----GEAA 861
Cdd:PRK08565 702 --GQNAVVAVLSYTGYNIEDAIIMNKASI--ERglarstfFRTYETEER------KYPGGQEDKIEIPepNVrgyrGEEY 771
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 862 LSKLDESGIVYIGAEVTGGDILVGKVTPKgetQLTPEEKLLRAIFGEKasdvKDSSLRVPNGVSGTVidvqvftrdgvek 941
Cdd:PRK08565 772 YRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----RDTSVTVRHGEKGIV------------- 831
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 942 DKraleieemqlkqakkdlseelqileaglfsriyaVLVSGGVEAEKLdklprdrwlelgltdeekqnqleqlaeqydel 1021
Cdd:PRK08565 832 DT----------------------------------VLITESPEGNKL-------------------------------- 845
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1022 khefekkleakrrkitqgddlapgvlkiVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPL 1101
Cdd:PRK08565 846 ----------------------------VKVRVRDLRIPELGDKFASRHGQKGVIGMLVPQEDMPFTEDGIVPDLIINPH 897
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1102 GVPSRMNIGQILEThlgmaakgIGDKINAMlkqqqevaklrefiqraydlgadvrqkvdlntfsdeevlrlaenlrKGMP 1181
Cdd:PRK08565 898 AIPSRMTVGQLLES--------IAGKVAAL----------------------------------------------EGRF 923
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1182 I-ATPvFDGAKEAEI-KELLQLGDLPtSGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPL 1259
Cdd:PRK08565 924 VdATP-FYGEPEEELrKELLKLGYKP-DGTEVMYDGRTGEKIKAPIFIGVVYYQKLHHMVADKIHARARGPVQILTRQPT 1001
|
1370 1380 1390 1400 1410 1420 1430 1440
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1260 GGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvngRTKMY--------------KNI----VDGN----HQMEp 1317
Cdd:PRK08565 1002 EGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD----KTTIYvcelcghiawydrrKNKyvcpIHGDkgniSPVE- 1076
|
1450 1460
....*....|....*....|...
gi 490254324 1318 gMPESFNVLLKEIRSLGINIELE 1340
Cdd:PRK08565 1077 -VSYAFKLLLQELMSMGISPRLK 1098
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
594-1341 |
1.49e-58 |
|
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: 213.35 E-value: 1.49e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 594 VTNGVvtdeIHYLSAIEEGNYVIAQansnldenghFVEDLvtcrskgesslfsRDQVDYMDVSTQQVVSVGASLIPFLEH 673
Cdd:TIGR03670 87 VKQGV----IEYLDAEEEENAYIAL----------DPEEL-------------TPEHTHLEIDPSAILGIIASTIPYPEH 139
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 674 DDANRALMGANMQRQAVPTLRADKPLvgtgmeravAVDSgvtavakRGGTVQYvdasrivikvnedemyPgeagidiynl 753
Cdd:TIGR03670 140 NQSPRNTMGAAMAKQSLGLYAANYRI---------RLDT-------RGHLLHY----------------P---------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 754 tkytrsnqntcinQMPCVSlgepiERGDVLadgpsTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHI 833
Cdd:TIGR03670 178 -------------QKPLVK-----TRVLEL-----IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFF 234
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 834 QELACVSRDTKLGPE-EITADIPNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTPkgetqltP---EEkllRAI 905
Cdd:TIGR03670 235 RTYEAEERRYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LRE 304
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 906 FGEKASDVKDSSLRVPNGVSGTVidvqvftrdgvekDKraleieemqlkqakkdlseelqileaglfsriyaVLVSGGVE 985
Cdd:TIGR03670 305 FGLVTERRRDTSVTVRHGEKGIV-------------DK----------------------------------VIITETEE 337
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 986 AEKLdklprdrwlelgltdeekqnqleqlaeqydelkhefekkleakrrkitqgddlapgvlkiVKVYLAVKRRIQPGDK 1065
Cdd:TIGR03670 338 GNKL------------------------------------------------------------VKVRVRDLRIPELGDK 357
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1066 MAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILEThlgmaakgIGDKINAMlkqqqevaklrefi 1145
Cdd:TIGR03670 358 FASRHGQKGVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM--------IAGKVAAL-------------- 415
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1146 qraydlgadvrqkvdlntfsdeevlrlaenlrKGMPI-ATPvFDGAKEAEI-KELLQLGDLPTsGQITLFDGRTGEQFER 1223
Cdd:TIGR03670 416 --------------------------------EGRRVdGTP-FEGEPEEELrKELLKLGFKPD-GKEVMYDGITGEKLEA 461
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1224 PVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV----- 1298
Cdd:TIGR03670 462 EIFIGVIYYQKLHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESDKYvvyvc 541
|
730 740 750 760 770
....*....|....*....|....*....|....*....|....*....|....*...
gi 490254324 1299 ---------NGRTKMYKNIVDGN----HQMEpgMPESFNVLLKEIRSLGI--NIELED 1341
Cdd:TIGR03670 542 encghiaweDKRKGTAYCPVCGEtgdiSPVE--MSYAFKLLLDELKSLGIspRLELGD 597
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
603-1341 |
2.06e-48 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 183.62 E-value: 2.06e-48
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 603 IHYLSAIEEGNYVIAQANSNLDENgHfvedlvtcrskgesslfsrdqvDYMDVSTQQVVSVGASLIPFLEHDDANRALMG 682
Cdd:PRK07225 98 IEYLDAEEEENAYIAVYEEDLTEE-H----------------------THLEIDPSLILGIGAGMIPYPEHNASPRITMG 154
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 683 ANMQRQA--VPT----LRADKplvgtgmeravavdsgvtavakRGGTVQYVDASRIVIKVNEdemypgEAGIDiynltky 756
Cdd:PRK07225 155 AGMIKQSlgLPAanykLRPDT----------------------RGHLLHYPQVPLVKTQTQE------IIGFD------- 199
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 757 trsnqntcinqmpcvslgepiERgdvladgPStdlgelalGQNMRVAFMPWNGYNFEDSILVSERVV------------- 823
Cdd:PRK07225 200 ---------------------ER-------PA--------GQNFVVAVMSYEGYNIEDALIMNKASIerglgrshffrty 243
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 824 ----------QEDRFTTihiqelacvsrdtklgPEEitadipNV----GEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Cdd:PRK07225 244 egeerrypggQEDRFEI----------------PDK------DVrgyrGEEAYRHLDEDGLVNPETEVKEGDVLIGKTSP 301
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 890 kgetqltP---EEKllrAIFGEKASDVKDSSLRVPNGVSGTVidvqvftrdgvekdkraleieemqlkqakkDlseelqi 966
Cdd:PRK07225 302 -------PrflEEP---DDFGISPEKRRETSVTMRSGEEGIV------------------------------D------- 334
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 967 leaglfsriyAVLVSGGVEAEKLDKLpRDRwlelgltdeekqnqleqlaeqyDELKHEFekkleakrrkitqgddlapgv 1046
Cdd:PRK07225 335 ----------TVILTETEEGSRLVKV-RVR----------------------DLRIPEL--------------------- 360
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1047 lkivkvylavkrriqpGDKMAGRHGNKGVISKINPIEDMPHDANGTPVDIVLNPLGVPSRMNIGQILEThlgmaakgIGD 1126
Cdd:PRK07225 361 ----------------GDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLEM--------IGG 416
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1127 KINAMLKQqqevaklrefiqraydlgadvrqKVDlntfsdeevlrlaenlrkgmpiATPvFDGAKEAEIKELLQLGDLPT 1206
Cdd:PRK07225 417 KVGSLEGR-----------------------RVD----------------------GTA-FSGEDEEDLREALEKLGFEH 450
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1207 SGQITLFDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Cdd:PRK07225 451 TGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAML 530
|
730 740 750 760 770 780 790
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490254324 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
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490254324 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 |
4.34e-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: 127.87 E-value: 4.34e-35
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 490254324 591 YRKVTNGVVTDEIHYLSAIEEGNYVIAQANSNLDENGHFVEDLVTCRSKGESSLFSRDQVDYMDVS 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 |
1.91e-34 |
|
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp. The clamp region (C-terminal) contains a zinc-binding motif. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription.
Pssm-ID: 461355 [Multi-domain] Cd Length: 87 Bit Score: 126.93 E-value: 1.91e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 1266 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVNGRTKMYKN-----IVDGNHQMEPG-MPESFNVLLKEIRSLGI 1335
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGyIPESFKLLFQELQSLGI 80
|
....*..
gi 490254324 1336 NIELEDE 1342
Cdd:pfam04560 81 DPRLLLE 87
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
31-580 |
1.47e-27 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 118.51 E-value: 1.47e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 31 QLDSFQKFIEqdpegqYGLEAAFRSVFPIQSYSGNSE-LQYVSYRLGEPVfdVKECQ------------IRGVTYSAPLR 97
Cdd:PRK09606 22 HIDSYNDFVD------NGLQKIIDEQGPIETEIEDGVyVELGKIRVGKPV--VKEADgsereiypmearLRNLTYSAPLY 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 98 vkLRLVIYEREAPEGTVkdikeqEVYMGEIPLM-----------TDN-------------GTFVINGTERVIVSQLHRSP 153
Cdd:PRK09606 94 --LEMSPVEGGEEEEPE------EVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERVLMTLEDLAP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 154 GVF---FDSDKGKTHSSGKVL-----YNARIIPYRGswldfefdpKDNL----FVRIDRRrkLPATIILRALNYTTEqil 221
Cdd:PRK09606 166 NKIlveKDERYGDRIEVAKVFsqrrgYRALVTVERN---------RDGLlevsFPSVPGS--IPFVILMRALGLETD--- 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 222 dlffEKVVFEIRDNKlqmeliperlrgETASFDIEangkvyvekgrritarhirQLEKDDIKHIEVPVEYIAGKVA---A 298
Cdd:PRK09606 232 ----EEIVEAVSDDP------------EIVKFMLE-------------------NLEEAEVDTQEEALEYIGKRVApgqT 276
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 299 KDYideatgelicpanmelsldllaKLsqsghKRIETLFTNdldhgpYISETVRVDPtNDRLSALVEIYRMmrpgepptr 378
Cdd:PRK09606 277 KEY----------------------RI-----KRAEYVIDR------YLLPHLGVEP-EVRRAKAHYLGRM--------- 313
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 379 eaAESLFEnlffsedrydlsavgrmkfnrsllrdeiegsgilskddiievmkklidIRNGKGEVDDIDHLGNRRIRSVGE 458
Cdd:PRK09606 314 --AEACFE------------------------------------------------LALGRREEDDKDHYANKRLKLAGD 343
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 459 MAENQFRVGLVRVERAVK---ERlslgdldtlmpQDMINAKP-ISAAVKE----------------FFGSSQLSQFMDQN 518
Cdd:PRK09606 344 LMEDLFRVAFNRLARDVKyqlER-----------ANMRNRELsIKTAVRSdvlterlehamatgnwVGGRTGVSQLLDRT 412
|
570 580 590 600 610 620
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490254324 519 NPLSEITHKRRISAlgpgGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQ 580
Cdd:PRK09606 413 DYMATLSHLRRVVS----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMVE 470
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
151-454 |
9.71e-10 |
|
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Pssm-ID: 398318 [Multi-domain] Cd Length: 185 Bit Score: 59.28 E-value: 9.71e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 151 RSPGVFFDSDKGKTHSSGKvlYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQ-ILDLffekVV 229
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIAT--YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSDReILDR----LC 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 230 FEIRDNKLQMELIPErlrgetasfdieangkvyvekgrritarhirqlekddikhievpveyiagkvaAKDYIDEATGEL 309
Cdd:pfam04561 75 YDFNDPQMLELLKPE-----------------------------------------------------LEEAENIYTQEE 101
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490254324 310 icpanmelsldllaklsqsghkrietlftndldhgpyisetvrvdptndrlsALVEIYRM--MRPGEPPTREAAESLFEN 387
Cdd:pfam04561 102 ----------------------------------------------------ALDYIGKGfaLRRGEEPRLQRAREILYS 129
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490254324 388 LFfsedrydlsavGRMKFNRSLLRDEIEGSGILSKDDIIEVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Cdd:pfam04561 130 RD-----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| HMG-box_IXR1-like_rpt1 |
cd22011 |
first high mobility group (HMG)-box found in Saccharomyces cerevisiae intrastrand cross-link ... |
989-1029 |
6.15e-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: 39.83 E-value: 6.15e-04
10 20 30 40
....*....|....*....|....*....|....*....|....
gi 490254324 989 LDKLPRDRWLelGLTDEEKQ---NQLEQLAEQYDELKHEFEKKL 1029
Cdd:cd22011 32 LSKRAAEQWR--SLTLAEKQpyyDEVEVLKKQYDVEKEEYEKEL 73
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
290-344 |
6.08e-03 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 41.21 E-value: 6.08e-03
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 490254324 290 EYIAGKVAAKDYIDEATGELICPANMELSLDLLAKLSQSGHKRIE--TLFTNDLDHG 344
Cdd:PRK00566 804 ERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVKirSVLTCETRHG 860
|
|
| |
