|
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: 2244.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1 MGYSYTEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRD-PEGQQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 80 FDVRECQIRGTTYAAPLRVKLRLVSYDkdaapgtIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILNLFFDKVIFQIEdnkllm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKE------ 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 240 dlvperlrgetatfdivangktyvevgrritarhiralekdnvtqVEVPTEYIVGKVAAKDYVDLETGEVICPANGEISL 319
Cdd:PRK00405 227 ---------------------------------------------IEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 320 EIlaklsqagyktietlftndldYGPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 400 VGRMKFNRSLGIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 480 SLGDLEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 560 PIETPEGPNIGLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgE 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-Y 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 640 HGESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVA 719
Cdd:PRK00405 560 KGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVA 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 720 KRGGTIQYVDASRIVVKVneDETVAGEAGIDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQ 799
Cdd:PRK00405 640 KRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQ 717
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 800 NMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVK 879
Cdd:PRK00405 718 NVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVK 797
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 880 GGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRdgvekdkraleieemqlkqakk 959
Cdd:PRK00405 798 PGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR---------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 960 dlveeleileaglfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkIIQ 1039
Cdd:PRK00405 856 -----------------------------------------------------------------------------IEQ 858
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1040 GDDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLG 1119
Cdd:PRK00405 859 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLG 938
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1120 LAAKGIGDQInamikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlrkglplATPVFDGAHEEEIKGLL 1199
Cdd:PRK00405 939 WAAKGLGIKF-----------------------------------------------------ATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1200 ELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1402578118 1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDEE 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: 1864.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 8 KKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRDPE----GQQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPVFDVR 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 84 ECQIRGTTYAAPLRVKLRLVSYDKDaapgTIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEED----GTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTteeilnlffdkvifqiednkllmdlvp 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 244 erlrgetatfdivangktyvevgrritarhiralekdnvtqvevpteyivgkvaakdyvdletgevicpangeisleila 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 324 klsqagyktIETLFTNDLDYGPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 404 KFNRSLGIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 484 LEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 564 PEGPNIGLINSLAVYARTNDYGFLETPYRKVVNGQV--TEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRGEhG 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYR-G 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 642 ESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVAKR 721
Cdd:TIGR02013 519 EITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKR 598
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 722 GGTIQYVDASRIVVKVNEDETvAGEAGIDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNM 801
Cdd:TIGR02013 599 GGVVEYVDAKRIVIRYDEDEE-EPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNV 677
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 802 RVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGG 881
Cdd:TIGR02013 678 LVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAG 757
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 882 DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdl 961
Cdd:TIGR02013 758 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE----------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 962 veeleileaglfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiQGD 1041
Cdd:TIGR02013 815 -----------------------------------------------------------------------------QGD 817
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1042 DLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLA 1121
Cdd:TIGR02013 818 ELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWA 897
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1122 AKGIGdqinamikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlRKGLPLATPVFDGAHEEEIKGLLEL 1201
Cdd:TIGR02013 898 GKRLG--------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1202 GGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
gi 1402578118 1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDL 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: 1630.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 12 RKDFGKRPQVLNVPYLLTIQLDSFDKFIQrdpegqQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPVFDVRECQIRGTT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLE------EGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 92 YAAPLRVKLRLVSYDkdaapgtIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 172 YNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTT-EEILNLFFDKVIFqiednkllmdlvperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQ-------------------- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 251 atfdivangktyvevgrritarhiralekdnvtqvevpteyivgkvaakdyvdletgevicpangeisleilaklsqagy 330
Cdd:COG0085 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 331 ktietlftndldygPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSAVGRMKFNRSLG 410
Cdd:COG0085 205 --------------EYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 411 IEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLEAVTPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 491 DLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 571 LINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgEHGESGLYRPEE 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR-YRGEEVLVPPEE 509
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 651 IHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmekpvaldsgvavvakrggtiqyvda 730
Cdd:COG0085 510 VDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------ 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 731 srivvkvnedetvageagiDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNMRVAFMPWNG 810
Cdd:COG0085 560 -------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEG 620
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 811 YNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTP 890
Cdd:COG0085 621 YNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTP 700
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 891 KGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlveeleilea 970
Cdd:COG0085 701 KGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE-------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 971 glfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiQGDDLAPGVLKV 1050
Cdd:COG0085 749 --------------------------------------------------------------------EGDELPPGVNKL 760
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1051 VKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAAKgigdqin 1130
Cdd:COG0085 761 VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1131 amikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlRKGLPLATPVFDGAHEEEIKGLLELGGLPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1211 TLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|...
gi 1402578118 1291 LTVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINID-LDEE 1342
Cdd:COG0085 948 LTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEvLSED 1000
|
|
| 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: 880.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 27 LLTIQLDSFDKFIQrdpegqQGLEAAFRSVFPIVS--NNGNTELQYVSYRLGEPV---------FDVRECQIRGTTYAAP 95
Cdd:cd00653 1 LVKQQIDSFNYFLN------VGLQEIVKSIPPITDtdDDGRLKLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 96 LRVKLRLVSYDKDaapgtikDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDNlyaridrrrklpatiilralnytteeilnlffdk 227
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKD---------------------------------- 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 228 vifqiednkllmdlvperlrgetatfdivangktyvevgrRITARHiralekdnvtqvevpteyivgkvaakdyvdletg 307
Cdd:cd00653 189 ----------------------------------------RIYVRI---------------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 308 evicpangeisleilaklsqagyktietlftndldygPYIsdtlrvdpttDRLSALVEIYRmmrpgepptkeaaeglfdn 387
Cdd:cd00653 195 -------------------------------------DLK----------RQEEALKYIGK------------------- 208
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 388 lffspdrydlsavgrmKFnrslgieettgsgilskEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIG 467
Cdd:cd00653 209 ----------------RF-----------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSG 255
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 468 LVRVERAVKERLS--LGDLEAVTPQDLINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEVTHKRRISAl 533
Cdd:cd00653 256 LKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS- 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 534 gpGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYARTNdyGFLETPYRKVVngqvteeieylsaieegk 613
Cdd:cd00653 335 --LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------------ 392
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 614 yiiaqansnlddelrftdtfvtcrgehgesglyrpEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPT 693
Cdd:cd00653 393 -----------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 694 ----------------LRADKPLVGTGMEKPVALdsgvavvakrggtiqyvdasrivvkvnedetvageagidiynlvky 757
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIAF---------------------------------------------- 471
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 758 trsnqntcinqipcvklgepiergeiladgpstdlGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQEL 837
Cdd:cd00653 472 -----------------------------------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 838 SCVARDTKLGSEEIT-ADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 916
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 917 SSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlveeleileaglfarvrnvlisggmdaaqldkldrt 996
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 997 kwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiqgddLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGV 1076
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1077 ISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAAKgigdqinamikqkqdveklrgyiqkaydlgggs 1156
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1157 qkvdlstftdeevmrlaqnlRKGLPLATPVFDGAHEEEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLN 1236
Cdd:cd00653 693 --------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLK 752
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------- 1309
Cdd:cd00653 753 HMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcr 832
|
1370 1380 1390
....*....|....*....|....*....|....
gi 1402578118 1310 ---SGNQQMDPGTPESFNVIMKEIRSLGINIDLD 1340
Cdd:cd00653 833 lckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
718-1264 |
2.49e-164 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 495.90 E-value: 2.49e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 718 VAKRGGTIQYVDASRIVVKVNEdetvaGEAGIDIYNLVKYTRSNQNT---CINQIPCVKLGEpIERGeiladgpstDLGE 794
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAG---------GFGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 795 LALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQElsCVARDTKLG-SEEITADIPNVGEAALSKLDESGIVY 873
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGpIEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 874 IGAEVKGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFtrdgvekdkraleieemq 953
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 954 lkqakkdlveeleileaglfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevk 1033
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1034 rgkiiqgdDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQI 1113
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1114 LETHLGLAAKGigdqinamikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlrKGLPLATPVFDGAHE- 1192
Cdd:pfam00562 272 LETHLGKAAAL-----------------------------------------------------LGVFVDATPFDGASTe 298
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1402578118 1193 -EEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562 299 vEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| rpoB |
PRK00405 |
DNA-directed RNA polymerase subunit beta; Reviewed |
1-1342 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta; Reviewed
Pssm-ID: 234749 [Multi-domain] Cd Length: 1112 Bit Score: 2244.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1 MGYSYTEKKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRD-PEGQQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPV 79
Cdd:PRK00405 1 MVYSYTGKKRIRKSFGKIKEVLELPNLLEIQLDSFDWFLQLDvPPEDEGLEEVFRSIFPIEDFNGNLSLEFVSYELGEPK 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 80 FDVRECQIRGTTYAAPLRVKLRLVSYDkdaapgtIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDS 159
Cdd:PRK00405 81 YDVEECKERGLTYSAPLRVKLRLINKE-------TGEIKEQEVYMGDIPLMTENGTFIINGTERVIVSQLHRSPGVYFDH 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 160 DKGKThSSGKVLYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILNLFFDKVIFQIEdnkllm 239
Cdd:PRK00405 154 DKDKT-SSGKLLYSARIIPYRGSWLEFEFDPKDILYVRIDRRRKLPVTVLLRALGYSDEEILDLFYEKEEFGKE------ 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 240 dlvperlrgetatfdivangktyvevgrritarhiralekdnvtqVEVPTEYIVGKVAAKDYVDLETGEVICPANGEISL 319
Cdd:PRK00405 227 ---------------------------------------------IEVPVEYLLGKVLAEDIVDEETGEVLAEANDEITE 261
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 320 EIlaklsqagyktietlftndldYGPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSA 399
Cdd:PRK00405 262 EL---------------------DGPYIRNTLEKDPTSSREEALVEIYRRLRPGEPPTVEAARSLLENLFFDPKRYDLSK 320
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 400 VGRMKFNRSLGIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERL 479
Cdd:PRK00405 321 VGRYKLNKKLGLDEDEDVRVLTKEDIIATIKYLINLRNGKGEVDDIDHLGNRRVRSVGELLQNQFRIGLSRMERAVRERM 400
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 480 SLGDLEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVC 559
Cdd:PRK00405 401 SLQDLDTLTPQDLINAKPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRIC 480
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 560 PIETPEGPNIGLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgE 639
Cdd:PRK00405 481 PIETPEGPNIGLINSLATYARVNEYGFIETPYRKVVDGKVTDEIVYLTADEEDNYVIAQANAPLDEDGRFVDELVTAR-Y 559
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 640 HGESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVA 719
Cdd:PRK00405 560 KGEFVLVPPEEVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRPEAPLVGTGMERRVARDSGAVVVA 639
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 720 KRGGTIQYVDASRIVVKVneDETVAGEAGIDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQ 799
Cdd:PRK00405 640 KRDGVVEYVDASRIVVRV--EELDPGEDGVDIYNLIKFQRSNQNTCINQRPIVKVGDRVEKGDVLADGPSTDNGELALGQ 717
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 800 NMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVK 879
Cdd:PRK00405 718 NVLVAFMPWNGYNFEDAILISERLVKEDVFTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDESGIVRIGAEVK 797
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 880 GGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRdgvekdkraleieemqlkqakk 959
Cdd:PRK00405 798 PGDILVGKVTPKGETELTPEEKLLRAIFGEKARDVKDTSLRVPHGEEGTVIDVKVFTR---------------------- 855
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 960 dlveeleileaglfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkIIQ 1039
Cdd:PRK00405 856 -----------------------------------------------------------------------------IEQ 858
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1040 GDDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLG 1119
Cdd:PRK00405 859 GDELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSRILPVEDMPYLEDGTPVDIVLNPLGVPSRMNIGQILETHLG 938
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1120 LAAKGIGDQInamikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlrkglplATPVFDGAHEEEIKGLL 1199
Cdd:PRK00405 939 WAAKGLGIKF-----------------------------------------------------ATPVFDGAKEEEIKELL 965
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1200 ELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK00405 966 EEAGLPEDGKTTLYDGRTGEPFDRPVTVGYMYMLKLHHLVDDKIHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1045
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1402578118 1280 AYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDEE 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: 1864.72 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 8 KKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRDPE----GQQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPVFDVR 83
Cdd:TIGR02013 1 KKRIRIDFGKIPEVLEVPNLLEIQLDSYDWFLQQDTPpekrKEEGLEEVFKSIFPIEDYTGNIELEYLSYRLGEPKYSVE 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 84 ECQIRGTTYAAPLRVKLRLVSYDKDaapgTIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGk 163
Cdd:TIGR02013 81 ECKERGLTYSAPLKVKLRLINKEED----GTKEIKEQDVYMGDIPLMTDRGTFIINGAERVVVSQLHRSPGVFFSSEKD- 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 164 THSSGKVLYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTteeilnlffdkvifqiednkllmdlvp 243
Cdd:TIGR02013 156 TTKSGKVLFSARIIPYRGSWLEFETDKKDVLYVRIDRKRKLPATVLLRALGYT--------------------------- 208
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 244 erlrgetatfdivangktyvevgrritarhiralekdnvtqvevpteyivgkvaakdyvdletgevicpangeisleila 323
Cdd:TIGR02013 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 324 klsqagyktIETLFTNDLDYGPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSAVGRM 403
Cdd:TIGR02013 209 ---------IDTLILNRLGSGEYIRNTLRKDPTNSEEEALVEIYRKLRPGEPPTVEAARSLLENLFFDPKRYDLGRVGRY 279
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 404 KFNRSLGIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGD 483
Cdd:TIGR02013 280 KLNKKLGLDVPESIGVLTKEDIIATIKYLIKLRNGKGEIDDIDHLGNRRIRSVGELLQNQFRVGLARMERIVRERMSTQD 359
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 484 LEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIET 563
Cdd:TIGR02013 360 TDTLTPQDLINAKPISAAIKEFFGSSQLSQFMDQTNPLAELTHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIET 439
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 564 PEGPNIGLINSLAVYARTNDYGFLETPYRKVVNGQV--TEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRGEhG 641
Cdd:TIGR02013 440 PEGPNIGLINSLSTYARVNEYGFIETPYRKVKDGKVvvTDEIDYLTADEEDNYVIAQANAPLDENGRFVEDLVVARYR-G 518
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 642 ESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVAKR 721
Cdd:TIGR02013 519 EITLVSPDQVDYMDVSPKQVVSVAASLIPFLEHDDANRALMGSNMQRQAVPLLRSEAPLVGTGMEAKVARDSGAVIVAKR 598
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 722 GGTIQYVDASRIVVKVNEDETvAGEAGIDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNM 801
Cdd:TIGR02013 599 GGVVEYVDAKRIVIRYDEDEE-EPDGGIDIYRLLKYQRSNQDTCINQRPIVSVGDRVEAGDVLADGPSTDLGELALGRNV 677
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 802 RVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGG 881
Cdd:TIGR02013 678 LVAFMPWNGYNYEDAILISERLVKDDVFTSIHIEEYEVEARDTKLGPEEITRDIPNVSEEALRNLDENGIVRIGAEVKAG 757
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 882 DILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdl 961
Cdd:TIGR02013 758 DILVGKVTPKGETELTPEEKLLRAIFGEKARDVRDTSLRVPPGVEGTVIDVKVFSRE----------------------- 814
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 962 veeleileaglfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiQGD 1041
Cdd:TIGR02013 815 -----------------------------------------------------------------------------QGD 817
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1042 DLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLA 1121
Cdd:TIGR02013 818 ELPPGVNKLVKVYIAQKRKIQVGDKMAGRHGNKGVVSKILPIEDMPFLEDGTPVDIVLNPLGVPSRMNIGQILETHLGWA 897
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1122 AKGIGdqinamikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlRKGLPLATPVFDGAHEEEIKGLLEL 1201
Cdd:TIGR02013 898 GKRLG--------------------------------------------------RKGVPIATPVFDGASEEEIKEYLEK 927
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1202 GGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1281
Cdd:TIGR02013 928 AGLPRDGKVRLYDGRTGEQFDRPVTVGYMYMLKLHHLVDDKMHARSTGPYSLVTQQPLGGKAQFGGQRFGEMEVWALEAY 1007
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|....*...
gi 1402578118 1282 GAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDL 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: 1630.20 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 12 RKDFGKRPQVLNVPYLLTIQLDSFDKFIQrdpegqQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPVFDVRECQIRGTT 91
Cdd:COG0085 1 RWSFAKIKEPLELPNLLEIQLDSFNWFLE------EGLQEIFDEISPIEDFTGNLSLEFGDYRLGEPKYTPEECKERDLT 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 92 YAAPLRVKLRLVSYDkdaapgtIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVL 171
Cdd:COG0085 75 YAAPLYVKVRLVNKE-------TGEIKEQEVFMGDFPLMTDSGTFIINGTERVIVSQLVRSPGVYFVEEEDK---SGKDL 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 172 YNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTT-EEILNLFFDKVIFqiednkllmdlvperlrget 250
Cdd:COG0085 145 YSAKVIPSRGAWLEFETDKDGTIYVRIDRKRKIPVTVLLRALGLETdEEILEAFGDDPIQ-------------------- 204
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 251 atfdivangktyvevgrritarhiralekdnvtqvevpteyivgkvaakdyvdletgevicpangeisleilaklsqagy 330
Cdd:COG0085 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 331 ktietlftndldygPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSAVGRMKFNRSLG 410
Cdd:COG0085 205 --------------EYILATLEKDNTKTQEEALLEIYRKLRPGEPPTIERAEQLLDNLFFDPKRYDLAHVGRYKINKKLG 270
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 411 IEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLEAVTPQ 490
Cdd:COG0085 271 LDVPPEDRVLTAEDIVATIKYLLELHLGEREPDDIDHLGNRRVRLVGELLQNQFRVGLSRMERVVRERMTTQDVEAITPQ 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 491 DLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIG 570
Cdd:COG0085 351 SLINIRPVVAAIKEFFGSSQLSQFMDQTNPLSELTHKRRLSALGPGGLSRERAGFEVRDVHPSHYGRMCPIETPEGPNIG 430
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 571 LINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgEHGESGLYRPEE 650
Cdd:COG0085 431 LIGSLALYARVNEYGFIETPYRKVENGKVTDEIEYLTADEEENYYIAQANAPLDEDGNFLEERVLVR-YRGEEVLVPPEE 509
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 651 IHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmekpvaldsgvavvakrggtiqyvda 730
Cdd:COG0085 510 VDYMDVSPKQIVSVATSLIPFLEHDDANRALMGANMQRQAVPLLRPEAPL------------------------------ 559
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 731 srivvkvnedetvageagiDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNMRVAFMPWNG 810
Cdd:COG0085 560 -------------------LHYPLQKFQRSNQGTCINQRPIVRVGDRVEKGDVLADGPATDNGELALGQNLLVAFMPWEG 620
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 811 YNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTP 890
Cdd:COG0085 621 YNYEDAIIISERLVKDDVLTSIHIEEYEIEARDTKLGPEEITRDIPNVSEEALRNLDEDGIIRIGAEVKGGDILVGKVTP 700
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 891 KGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlveeleilea 970
Cdd:COG0085 701 KGETELTPEERLLRAIFGEKAREVRDTSLRVPHGEKGKVIDVKVFSRE-------------------------------- 748
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 971 glfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiQGDDLAPGVLKV 1050
Cdd:COG0085 749 --------------------------------------------------------------------EGDELPPGVNKL 760
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1051 VKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAAKgigdqin 1130
Cdd:COG0085 761 VRVYVAQKRKIEVGDKLAGRHGNKGVISRILPQEDMPFLEDGTPVDIVLNPLGVPSRMNVGQVLETHLGWAAA------- 833
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1131 amikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlRKGLPLATPVFDGAHEEEIKGLLELGGLPTSGQI 1210
Cdd:COG0085 834 ----------------------------------------------LLGRRVATPVFDGAPEEEIRELLEKAGLPPDGKE 867
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1211 TLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEM 1290
Cdd:COG0085 868 VLYDGRTGEPFDNPVTVGYMYYLKLHHMVDDKIHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQER 947
|
1290 1300 1310 1320 1330
....*....|....*....|....*....|....*....|....*....|...
gi 1402578118 1291 LTVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINID-LDEE 1342
Cdd:COG0085 948 LTIKSDDVCGRVKVYEAIVKGENIPEPGIPESFKVLLKELQSLGLDVEvLSED 1000
|
|
| PRK14844 |
PRK14844 |
DNA-directed RNA polymerase subunit beta/beta'; |
27-1341 |
0e+00 |
|
DNA-directed RNA polymerase subunit beta/beta';
Pssm-ID: 173305 [Multi-domain] Cd Length: 2836 Bit Score: 1408.60 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 27 LLTIQLDSFDKFIQRDpEGQQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPVFDVRECQIRGTTYAAPLRVKLRLV--- 103
Cdd:PRK14844 32 LVKVQKESYDSFTPKN-KGNERLEVIFHTIFPINDPLHRATIEFISCRVDDPKYDESECIKRGITFSAQVIASIRLVimq 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 104 -------------SYDKDAAPGTIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKV 170
Cdd:PRK14844 111 dgisldeyksikeSGDHSKLATVIKSIEEQEVHFCELPMMTDKGTFIINGVEKVIVSQMHRSPGVFFDSDKGKTYNSGKL 190
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 171 LYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILNLFFDKVIFQIEDNKLLMDLVPERLRGET 250
Cdd:PRK14844 191 IYSARVIPYRGSWLDIEFDVKDHLYFRIDRKRKLPISVLLKALGLSNNDILDRFYEKIKYIKHKDGWKVPFVPDKFKGVR 270
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 251 ATFDIV-ANGKTYVEVGRRITARHIRALEKDNVTQVEVPTEYIVGKVAAKDYVDLETGEVICPANGEISLEILAKLSQAG 329
Cdd:PRK14844 271 LPFDLMdVEGNVLLKANVRITSRLAKKLYDNELKEYLVPFDSICGLFLAEDLIDSASSTKILSAGESIKLEDIKKLELLS 350
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 330 YKTIETLFTNDLDYGPYISDTLRVDPTTDRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSAVGRMKFNRSL 409
Cdd:PRK14844 351 IDEISVLNIDNLSVGPYILNTLFLDENMSYQDALYEIYKVLRPGEVPVLEIVEEFFRNLFFSPEYYDLSNIGRLKLNSYL 430
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 410 GIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLEAVTP 489
Cdd:PRK14844 431 GLNYDEDLTVLTHEDIIEIVRKIVLLRDGQGSVDDIDHLGNRRVRSVGEFIENQFRTGLLKLERAVVDSMSTSSLDKVSP 510
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 490 QDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNI 569
Cdd:PRK14844 511 SDFINPKVLTNVLRDFFNSSQLSQFMDQTNPLSEITHKRRLSALGPGGLTRERAGFEVRDVHPTHYGRICPIETPEGQNI 590
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 570 GLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgEHGESGLYRPE 649
Cdd:PRK14844 591 GLINSLAIYARINKYGFIESPYRKVVNRVVTDQIEYLSAIDEGLYYIADTSAKLDENNCFVDDMLYCR-YAGSFVMVSSD 669
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 650 EIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVAKRGGTIQYVD 729
Cdd:PRK14844 670 QVSYIDVSPKQVISVAASLIPFLENDDANRALMGSNMQRQAVPLLKPTAPLVATGMESFVASGSGAVVLAKRDGIVDSSD 749
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 730 ASRIVVKVNEDETVaGEAGIDIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNMRVAFMPWN 809
Cdd:PRK14844 750 SNSIVIRAFDKERV-NYLDVDIYHLRKFQRSNHNTCINQKPLVCVGDYVKEGDVIADGPAINSGELALGQNLLVAFMSWQ 828
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 810 GYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVT 889
Cdd:PRK14844 829 GYNFEDSIIISSEVVKKDLFTSIHIEEFECVVHDTPLGSEKITRAIPGVNEENLYHLDDSGIVKIGTRVGPGYILVGKVT 908
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 890 PKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLVEELEILE 969
Cdd:PRK14844 909 PKPSLSLPPETKLLMTIFGEKSFDCADSSLYTSPDVEGTVIDVQVFTRRGVEENERALLIKQKEINDFEKERDYIINVTS 988
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 970 AGLFARVRNVLI-SGGMDAAQLDKLDRTKWLEQTLSDeekqsqlEQLAEQYEELRKDFEHKL-------EVKRGKIIQGD 1041
Cdd:PRK14844 989 EYFYDELKKLLInSGSQDREKFDSIEREQWWGIGLKN-------QSISEQVKSLKKDFDEKVshaiaqfKRKVEKLHEGY 1061
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1042 DLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLA 1121
Cdd:PRK14844 1062 DLPQGVSMSVKVFIAVKHSLQPGDKMAGRHGNKGVISRVVPVEDMPYLEDGTPVDIILNPLGVPSRMNVGQILETHVGWA 1141
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1122 AKGIG----------------------------------------------------------------DQINAMIKQ-- 1135
Cdd:PRK14844 1142 CKKLGekvgnildeinkiksafckgirslnddnftkfaaayldnkkienidddeitasvlntpnknalnDELNELVENyl 1221
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1136 ---KQDVEKLRGYIQKAYDLGGG-SQKVDLSTFTDEEVMRLAQNLRKGLPLATPVFDGAHEEEIKGLLELGGLPTSGQIT 1211
Cdd:PRK14844 1222 nscKSAYSNLRNFLIEVYSCGSNvSICNNIRDISDNNLIEFARKLRDGIPVAAPVFEGPKDEQIAKLFELAGLDNSGQAV 1301
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1212 LYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEML 1291
Cdd:PRK14844 1302 LYDGCSGEKFDRKVTVGYMYMLKLHHLVDGKIHARSVGPYSLVTQQPLGGKSHFGGQRFGEMECWALQAYGAAYTLQEML 1381
|
1370 1380 1390 1400 1410
....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1292 TVKSDDVNGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINIDLDE 1341
Cdd:PRK14844 1382 TVKSDDINGRVKIYESIIKGDSNFECGIPESFNVMIKELRSLCLNVDLKQ 1431
|
|
| 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: 1401.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 8 KKRIRKDFGKRPQVLNVPYLLTIQLDSFDKFIQRDPEGQQGLEAAFRSVFPIVSNNGNTELQYVSYRLGEPVFDVRECQI 87
Cdd:PRK09603 8 KNRLRADFTKTPTDLEVPNLLLLQRDSYDSFLYSKDGKESGIEKVFKSIFPIQDEHNRITLEYAGCEFGKSKYTVREAME 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 88 RGTTYAAPLRVKLRLVSYDKDAAPG---TIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKT 164
Cdd:PRK09603 88 RGITYSIPLKIKVRLILWEKDTKSGeknGIKDIKEQSIFIREIPLMTERTSFIINGVERVVVNQLHRSPGVIFKEEESST 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 165 hSSGKVLYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILNLFFDKVIFQIEDNKLLMDLVPE 244
Cdd:PRK09603 168 -SLNKLIYTGQIIPDRGSWLYFEYDSKDVLYARINKRRKVPVTILFRAMDYQKQDIIKMFYPLVKVRYENDKYLIPFASL 246
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 245 RLRGEtATFDIV-ANGKTYVEVGRRITARHIRALEKDNVTQVEVPTEYIVGKVAAKDYVDLEtgevicpangEISLEILA 323
Cdd:PRK09603 247 DANQR-MEFDLKdPQGKIILLAGKKLTSRKIKELKENHLEWVEYPMDILLNRHLAEPVMVGK----------EVLLDMLT 315
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 324 KLSQAGYKTI------ETLFTNDLDYGPYIS---------DTLRVDPTTDRLS-----ALVEIYRMMRPGEPPTKEAAEG 383
Cdd:PRK09603 316 QLDKNKLEKIhdlgvqEFVIINDLALGHDASiihsfsadsESLKLLKQTEKIDdenalAAIRIHKVMKPGDPVTTEVAKQ 395
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 384 LFDNLFFSPDRYDLSAVGRMKFNRSLGIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQ 463
Cdd:PRK09603 396 FVKKLFFDPERYDLTMVGRMKMNHKLGLHVPDYITTLTHEDIITTVKYLMKIKNNQGKIDDRDHLGNRRIRAVGELLANE 475
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 464 FRIGLVRVERAVKERLSL--GDLEAVTPQDLINAKPISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRE 541
Cdd:PRK09603 476 LHSGLVKMQKTIKDKLTTmsGAFDSLMPHDLVNSKMITSTIMEFFMGGQLSQFMDQTNPLSEVTHKRRLSALGEGGLVKD 555
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 542 RAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANS 621
Cdd:PRK09603 556 RVGFEARDVHPTHYGRICPIETPEGQNIGLINTLSTFTRVNDLGFIEAPYKKVVDGKVVGETIYLTAIQEDSHIIAPAST 635
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 622 NLDDELRFTDTFVTCRGEhGESGLYRPEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLV 701
Cdd:PRK09603 636 PIDEEGNILGDLIETRVE-GEIVLNEKSKVTLMDLSSSMLVGVAASLIPFLEHDDANRALMGTNMQRQAVPLLRSDAPIV 714
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 702 GTGMEKPVALDSGVAVVAKRGGTIQYVDASRIVVkVNEDETvagEAGIDIYNLVKYTRSNQNTCINQIPCVKLGEPIERG 781
Cdd:PRK09603 715 GTGIEKIIARDSWGAIKANRAGVVEKIDSKNIYI-LGEGKE---EAYIDAYSLQKNLRTNQNTSFNQVPIVKVGDKVEAG 790
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 782 EILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEA 861
Cdd:PRK09603 791 QIIADGPSMDRGELALGKNVRVAFMPWNGYNFEDAIVVSERITKDDIFTSTHIYEKEVDARELKHGVEEFTADIPDVKEE 870
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 862 ALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDGVE 941
Cdd:PRK09603 871 ALAHLDESGIVKVGTYVSAGMILVGKTSPKGEIKSTPEERLLRAIFGDKAGHVVNKSLYCPPSLEGTVIDVKVFTKKGYE 950
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 942 KDKRALEIEEMQLKQAKKDLVEELEILEAGLFARVRNVL----------ISGGM--DAAQLDKLDRTKWLEQTLS----- 1004
Cdd:PRK09603 951 KDARVLSAYEEEKAKLDMEHFDRLTMLNREELLRVSSLLsqaileepfsHNGKDykEGDQIPKEEIASINRFTLAslvkk 1030
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1005 -DEEKQSQLEQLAEQYEELRKDFEHKLEVKRgKIIQGDDLAP-GVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINP 1082
Cdd:PRK09603 1031 ySKEVQNHYEITKNNFLEQKKVLGEEHEEKL-SILEKDDILPnGVIKKVKLYIATKRKLKVGDKMAGRHGNKGIVSNIVP 1109
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1083 VEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAAKGIGDQINAMIKQ--KQDVEKLRGY---IQKAYDLGGGSQ 1157
Cdd:PRK09603 1110 VADMPYTADGEPVDIVLNPLGVPSRMNIGQILEMHLGLVGKEFGKQIASMLEDktKDFAKELRAKmleIANAINEKDPLT 1189
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1158 KVDLSTFTDEEVMRLAQNLRKGLPLATPVFDGAHEEEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNH 1237
Cdd:PRK09603 1190 IHALENCSDEELLEYAKDWSKGVKMAIPVFEGISQEKFYKLFELAKIAMDGKMDLYDGRTGEKMRERVNVGYMYMIKLHH 1269
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1238 LVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQQMDP 1317
Cdd:PRK09603 1270 LVDEKVHARSTGPYSLVTHQPVGGKALFGGQRFGEMEVWALEAYGAAHTLKEMLTIKSDDIRGRENAYRAIAKGEQVGES 1349
|
1370 1380
....*....|....*....|..
gi 1402578118 1318 GTPESFNVIMKEIRSLGINIDL 1339
Cdd:PRK09603 1350 EIPETFYVLTKELQSLALDINI 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: 1057.97 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 25 PYLLTIQLDSFDKFIQrdpegqQGLEAAFRSVFPIVSNNGNTELQYVS--YRLGEPVFDVRECQIRGTTYAAPLRVKLRL 102
Cdd:CHL00001 13 PGFNQIQFEGFCRFID------QGLTEELSKFPKIEDTDQEIEFQLFVetYQLVEPLIKERDAVYESLTYSSELYVPAGL 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 103 VSYDKdaapgtiKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKthsSGKVLYNARIIPYRGS 182
Cdd:CHL00001 87 IWKKS-------RDMQEQTVFIGNIPLMNSLGTFIINGIYRVVINQILRSPGIYYRSELDH---NGISVYTGTIISDWGG 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 183 WLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEIL-NLFFDKVIFQIEDNKllmdlvperlrgetatfdivangkt 261
Cdd:CHL00001 157 RLELEIDRKARIWARVSRKQKISILVLLSAMGLNLREILdNVCYPEIFLSFLNDK------------------------- 211
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 262 yvevgrritarhiralEKDNVTQVEvpteyivgkvaakdyvdletgevicpangeisleilaklsqagyktietlftndl 341
Cdd:CHL00001 212 ----------------EKKKIGSKE------------------------------------------------------- 220
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 342 dygpyisdtlrvdpttdrlSALVEIYRMM--RPGEPPTKEAAEGLFDNLFFSPdRYDLSAVGRMKFNRSLGIEETTGSGI 419
Cdd:CHL00001 221 -------------------NAILEFYQQFacVGGDPVFSESLCKELQKKFFQQ-RCELGRIGRRNMNRKLNLDIPENNTF 280
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 420 LSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLS--LGDLEAVTPQDLINAKP 497
Cdd:CHL00001 281 LLPQDVLAAADYLIGMKFGMGTLDDIDHLKNKRIRSVADLLQDQFGLALNRLENAVRGTICgaIRRKLIPTPQNLVTSTP 360
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 498 ISAAVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAV 577
Cdd:CHL00001 361 LTTTYESFFGSHPLSQFLDQTNPLTEIVHGRKLSSLGPGGLTGRTASFRVRDIHPSHYGRICPIDTSEGINAGLIGSLAI 440
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 578 YARTNDYGFLETPYRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDE---------LRFTDTFVTcrgehgesglYRP 648
Cdd:CHL00001 441 HARIGHWGSLESPFYEISERSKEERMVYLSPSEDEYYMIAAGNSLALNQgiqeeqvvpARYRQEFLT----------IAW 510
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 649 EEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVAKRGGTIQYV 728
Cdd:CHL00001 511 EQIHLRSIFPFQYFSIGASLIPFLEHNDANRALMGSNMQRQAVPLSRSEKCIVGTGLERQVALDSGVVAIAEHEGKIIYT 590
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 729 DASRIVVKVNEDETvageagidIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNMRVAFMPW 808
Cdd:CHL00001 591 DTDKIILSGNGDTL--------SIPLVMYQRSNKNTCMHQKPQVRRGKCVKKGQILADGAATVGGELALGKNVLVAYMPW 662
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 809 NGYNFEDSMLVSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKV 888
Cdd:CHL00001 663 EGYNFEDAVLISERLVYEDIYTSFHIRKYEIQTHVTSQGPERITKEIPHLEAHLLRNLDKNGIVMLGSWVETGDILVGKL 742
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 889 TPK--GETQLTPEEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVqvftrdgvekdkraleieemqlkqakkdlveele 966
Cdd:CHL00001 743 TPQeaEESSYAPEGRLLRAIFGIQVSTSKETCLKLPIGGRGRVIDV---------------------------------- 788
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 967 ileaglfarvrnvlisggmdaaqldkldrtKWleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiIQGDDLAPG 1046
Cdd:CHL00001 789 ------------------------------RW---------------------------------------IQKKGGSSY 799
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1047 VLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAAkgig 1126
Cdd:CHL00001 800 NPETIHVYILQKREIQVGDKVAGRHGNKGIISKILPRQDMPYLQDGTPVDMVLNPLGVPSRMNVGQIFECLLGLAG---- 875
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1127 dqinamikqkqdveklrGYIQKAYDLgggsqkvdlstftdeevmrlaqnlrkglplaTPvFDGAHEEEIKGLLELGGLPT 1206
Cdd:CHL00001 876 -----------------DLLNRHYRI-------------------------------AP-FDERYEQEASRKLVFSELYE 906
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1207 SGQIT---------------LYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG 1271
Cdd:CHL00001 907 ASKQTanpwvfepeypgksrLFDGRTGDPFEQPVTIGKAYILKLIHQVDDKIHARSSGPYALVTQQPLRGRSKQGGQRVG 986
|
1290 1300 1310 1320 1330 1340
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1402578118 1272 EMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVSGNQQMDP-GTPESFNVIMKEIRSLGINID 1338
Cdd:CHL00001 987 EMEVWALEGFGVAYILQEMLTYKSDHIRARQEVLGAIITGGTIPKPeDAPESFRLLVRELRSLALELN 1054
|
|
| rpoB |
CHL00207 |
RNA polymerase beta subunit; Provisional |
23-1337 |
0e+00 |
|
RNA polymerase beta subunit; Provisional
Pssm-ID: 214397 [Multi-domain] Cd Length: 1077 Bit Score: 1057.39 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 23 NVPYLLTIQLDSFDKFIQrdpegqQGLEAAFRSVFPIVSNNGNTELQYVS--YRLGEPVFDVRECQIRGTTYAAPLRVKL 100
Cdd:CHL00207 6 ALPDFLEIQRTSFCWFLN------EGLNEELNIFSKIFDYTGNLELLLFGknYKLKYPKYNLLSAKSYDSNYSIQIYLPL 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 101 RLVSYDkdaapgtIKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHssgKVLYNARIIPYR 180
Cdd:CHL00207 80 KFINLK-------TNKIKFINYLIGNLPKMTQRGTFIINGLERVIVSQIIRSPGIYFKKEIKKNS---NKIYSATLIPNR 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 181 GSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTTEEILNlffdkvifqiednkllmdlvperlrgetatfdivanGK 260
Cdd:CHL00207 150 GSWIKFELDKNKEIWIRIDKNRKKPLIIFLKALGLTDQDIYS------------------------------------RL 193
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 261 TYvevgrritarhiralekdnvtqvevpteyivgkvaakdyvdletgevicpangeisleilaklsqagYKTIETLFTND 340
Cdd:CHL00207 194 TK-------------------------------------------------------------------SEFLKKLKPIL 206
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 341 LDYGPYIsdtlrvdpttdRLSALVEIYRMMRPGEPPTKEAAEGLFDNLFFSPDRYDLSAVGRMKFNRSLGIEETTGSGIL 420
Cdd:CHL00207 207 LNSNSYT-----------NEEILLEIYKNLSPIEPATVNDANQNLFSRFFDPKNYDLGKVGRYKINNKLNLNIPERVRNL 275
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 421 SKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGLVRVERAVKERLSLGDLEAVTPQDLINAKPISA 500
Cdd:CHL00207 276 TYEDILSIIDKLINLKINKGNFDDIDHLKNRRVRSVGELLQNQFRIGLKRLERILRNRMTICDIDSLSKFNLINPKPLIA 355
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 501 AVKEFFGSSQLSQFMDQNNPLSEVTHKRRISALGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYAR 580
Cdd:CHL00207 356 LIREFFGSSQLSQYMDQTNPLSELTHKRRISILGPGGLDKDRISFAVRDIHPSHYGRICPIETPEGPNCGLIGSLATNAR 435
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 581 TNDYGFLETPYRKVVNGQV--TEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgEHGESGLYRPEEIHYMDVST 658
Cdd:CHL00207 436 INKFGFIETPFYKVINGKVkkFGNPIYLTADSEDLYRIAPNDINLNKNNYFKKNIIPVR-YKQEFKTVNPSKVDFIAISP 514
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 659 QQIVSVAAALIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMEKPVALDSGVAVVAKRGGTIQYVDASRIVVKVN 738
Cdd:CHL00207 515 IQVFSIAESLIPFLEHNDANRALMGSNMQRQAVPLLYPEKPIVGTGYEKQIALDSGMTIISLTEGIVVSVSAYKIIIQDD 594
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 739 EDETVageagidIYNLVKYTRSNQNTCINQIPCVKLGEPIERGEILADGPSTDLGELALGQNMRVAFMPWNGYNFEDSML 818
Cdd:CHL00207 595 NNRYI-------HYYLQKYQRSNQNTCINYRPIVWVGEKINIGQILADGSDIDNSELALGQNVLVAYMPWEGYNFEDAIL 667
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 819 VSERVVQEDRFTTIHIQELSCVARDTKLGSEEITADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTP 898
Cdd:CHL00207 668 INKRLVYEDLFTSIHIEKYEIELRQTKLGSEEITRNIPNVSEYSLKNLDENGIISIGSKVLAGDILVGKITPKGESDQLP 747
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 899 EEKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlveeleileaglfarvrn 978
Cdd:CHL00207 748 EGKLLRAIFGEKAKDVKDTSLRMPNGGYGRVIKVEIFSRS---------------------------------------- 787
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 979 vlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiQGDDLAPGVLKVVKVYLAVK 1058
Cdd:CHL00207 788 ------------------------------------------------------------KGDELKFGYYLKIRVFIAQI 807
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1059 RQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAakgiGDQINAMIKQkqd 1138
Cdd:CHL00207 808 RKIQVGDKLAGRHGNKGIISRILPRQDMPYLPDGTPPDIILNPLGVPSRMNVGQLFECLLGLA----GDNLNKRFKI--- 880
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1139 veklrgyiqkaydlgggsqkVDLSTFTDEEVMRLAQNlrKGLPLATpvfdgaheeEIKGLLELGGLPTSGQITLYDGRTG 1218
Cdd:CHL00207 881 --------------------LPFDEMYGSEYSRILIN--NKLNQAS---------IKNNEYWLFNSYHPGKMVLRDGRTG 929
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1219 EKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDV 1298
Cdd:CHL00207 930 YKFKNPVTVGIAYMLKLIHLVDDKIHARTTGPYSLVTQQPLGGKAQHGGQRFGEMEVWALEAFGAAYTLKELLTIKSDDM 1009
|
1290 1300 1310
....*....|....*....|....*....|....*....
gi 1402578118 1299 NGRTKMYKNIVSGNQQMDPGTPESFNVIMKEIRSLGINI 1337
Cdd:CHL00207 1010 QGRNETLNAIVKGQPIPKPGTPESFKVLMRELQSLGLDI 1048
|
|
| 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: 880.75 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 27 LLTIQLDSFDKFIQrdpegqQGLEAAFRSVFPIVS--NNGNTELQYVSYRLGEPV---------FDVRECQIRGTTYAAP 95
Cdd:cd00653 1 LVKQQIDSFNYFLN------VGLQEIVKSIPPITDtdDDGRLKLKFGDIYLGKPKveeggvtrkLTPNECRLRDLTYSAP 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 96 LRVKLRLVSYDKDaapgtikDIKEQEVYMGEIPLMTD------------------------NGTFVINGTERVIVSQLHR 151
Cdd:cd00653 75 LYVDIRLTVNDKG-------KIKEQEVFIGEIPIMLRsklcnlngltpeeliklgecpldpGGYFIINGTEKVIINQEQR 147
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 152 SPGVFFDSDkgkthSSGKVLYNARIIP----YRGSWLDFEFDPKDNlyaridrrrklpatiilralnytteeilnlffdk 227
Cdd:cd00653 148 SPNVIIVED-----SKGKRIYTKTSIPsyspYRGSWLEVKSDKKKD---------------------------------- 188
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 228 vifqiednkllmdlvperlrgetatfdivangktyvevgrRITARHiralekdnvtqvevpteyivgkvaakdyvdletg 307
Cdd:cd00653 189 ----------------------------------------RIYVRI---------------------------------- 194
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 308 evicpangeisleilaklsqagyktietlftndldygPYIsdtlrvdpttDRLSALVEIYRmmrpgepptkeaaeglfdn 387
Cdd:cd00653 195 -------------------------------------DLK----------RQEEALKYIGK------------------- 208
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 388 lffspdrydlsavgrmKFnrslgieettgsgilskEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIG 467
Cdd:cd00653 209 ----------------RF-----------------EDLIYMIRKLILLVLGKGKLDDIDHLGNKRVRLAGELLQNLFRSG 255
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 468 LVRVERAVKERLS--LGDLEAVTPQDLINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEVTHKRRISAl 533
Cdd:cd00653 256 LKRLEREVKEKLQkqLSKKKDLTPQLLINSKPITSGIKEFLATGNwgskrflmqrsgLSQVLDRLNPLSELSHKRRISS- 334
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 534 gpGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYARTNdyGFLETPYRKVVngqvteeieylsaieegk 613
Cdd:cd00653 335 --LGLFRERKGFEVRDLHPSHWGRICPIETPEGENCGLVKNLALMARIS--GRIERPYRIVE------------------ 392
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 614 yiiaqansnlddelrftdtfvtcrgehgesglyrpEEIHYMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQAVPT 693
Cdd:cd00653 393 -----------------------------------KEVTHIEISPSQILSVAASLIPFPEHNQSPRNLYQSNMQKQAVGT 437
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 694 ----------------LRADKPLVGTGMEKPVALdsgvavvakrggtiqyvdasrivvkvnedetvageagidiynlvky 757
Cdd:cd00653 438 palnqqyrmdtklyllLYPQKPLVGTGIEEYIAF---------------------------------------------- 471
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 758 trsnqntcinqipcvklgepiergeiladgpstdlGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQEL 837
Cdd:cd00653 472 -----------------------------------GELPLGQNAIVAVMSYSGYNFEDAIIINKSSVDRGFFRSIHYKKY 516
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 838 SCVARDTKLGSEEIT-ADIPNVGEAALSKLDESGIVYIGAEVKGGDILVGKVTPKGETQLTPeekllraIFGEKASDVKD 916
Cdd:cd00653 517 EIELRKTKNGPEEITrGDIPNVSEEKLKNLDEDGIIRPGARVEPGDILVGKITPKGETESTP-------IFGEKARDVRD 589
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 917 SSLRVPNSVSGTVIDVQVFTRDgvekdkraleieemqlkqakkdlveeleileaglfarvrnvlisggmdaaqldkldrt 996
Cdd:cd00653 590 TSLKYPGGEKGIVDDVKIFSRE---------------------------------------------------------- 611
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 997 kwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiqgddLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGV 1076
Cdd:cd00653 612 ----------------------------------------------LNDGGNKLVKVYIRQKRKPQIGDKFASRHGQKGV 645
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1077 ISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILETHLGLAAKgigdqinamikqkqdveklrgyiqkaydlgggs 1156
Cdd:cd00653 646 ISKILPQEDMPFTEDGIPPDIILNPHGFPSRMTIGQLLESLLGKAGA--------------------------------- 692
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1157 qkvdlstftdeevmrlaqnlRKGLPLATPVFDGAHEEEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLN 1236
Cdd:cd00653 693 --------------------LLGKFGDATPFDGAEEEDISELLGEAGLNYYGKEVLYDGRTGEPLEAPIFVGPVYYQRLK 752
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIV------- 1309
Cdd:cd00653 753 HMVDDKIHARSTGPYSLLTRQPLKGRSRGGGQRFGEMERDALIAHGAAYLLQERLTIKSDDVVARVCVKCGIIlsanlcr 832
|
1370 1380 1390
....*....|....*....|....*....|....
gi 1402578118 1310 ---SGNQQMDPGTPESFNVIMKEIRSLGINIDLD 1340
Cdd:cd00653 833 lckKGTNISKVGIPYAFKLLFQELQSMNIDPRLK 866
|
|
| RNA_pol_Rpb2_6 |
pfam00562 |
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of ... |
718-1264 |
2.49e-164 |
|
RNA polymerase Rpb2, domain 6; RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion. This domain is also involved in binding to Rpb1 and Rpb3. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).
Pssm-ID: 459854 [Multi-domain] Cd Length: 371 Bit Score: 495.90 E-value: 2.49e-164
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 718 VAKRGGTIQYVDASRIVVKVNEdetvaGEAGIDIYNLVKYTRSNQNT---CINQIPCVKLGEpIERGeiladgpstDLGE 794
Cdd:pfam00562 1 VASLIPFVDHNQSPRNTYQCAM-----GKQAMGIYTLNKFYRSDQNTyvlCYPQKPLVKTGA-VEAG---------GFGE 65
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 795 LALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQElsCVARDTKLG-SEEITADIPNVGEAALSKLDESGIVY 873
Cdd:pfam00562 66 LPLGQNAIVAVMSYTGYNQEDAIIINKSSVDRGFFTSIHIKE--IEARKTKLGpIEEITRDIPNVSEEALKKLDEDGIVR 143
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 874 IGAEVKGGDILVGKVtpkGETQLTpeeKLLRAIFGEKASDVKDSSLRVPNSVSGTVIDVQVFtrdgvekdkraleieemq 953
Cdd:pfam00562 144 VGAEVKPGDILVGKV---GPTELT---KLLRAIFGEKARDVKDTSLKVPPGEEGVVDDVIVF------------------ 199
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 954 lkqakkdlveeleileaglfarvrnvlisggmdaaqldkldrtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevk 1033
Cdd:pfam00562 --------------------------------------------------------------------------------
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1034 rgkiiqgdDLAPGVLKVVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQI 1113
Cdd:pfam00562 200 --------ELPPGGIKMVKVYIRQKRKPEVGDKFASRHGQKGVVSRILPQEDMPFTEDGIPPDIILNPHGVPSRMTIGQL 271
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1114 LETHLGLAAKGigdqinamikqkqdveklrgyiqkaydlgggsqkvdlstftdeevmrlaqnlrKGLPLATPVFDGAHE- 1192
Cdd:pfam00562 272 LETHLGKAAAL-----------------------------------------------------LGVFVDATPFDGASTe 298
|
490 500 510 520 530 540 550
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1402578118 1193 -EEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQ 1264
Cdd:pfam00562 299 vEDIGELLEKAGYNYYGKEVLYDGRTGEPFEAPIFVGPIYYQKLKHMVDDKIHARSTGPYSLLTRQPLGGRAR 371
|
|
| RNA_pol_Rpb2_1 |
pfam04563 |
RNA polymerase beta subunit; RNA polymerases catalyze the DNA dependent polymerization of RNA. ... |
26-500 |
3.40e-97 |
|
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: 317.40 E-value: 3.40e-97
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 26 YLLTIQLDSFDKFIQRDPEGQQGLEAAFRSVFPIVSNNGNT---ELQYVSYRLGEPVFDVR----------ECQIRGTTY 92
Cdd:pfam04563 1 GLVRQQLDSFNEFVDNDLQKIIDENALIESEFEIQHPGENGdklSLKFGQIRLGKPMFDETdgstreiypqECRLRNLTY 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 93 AAPLRVKLRLVSYDKdaapgtiKDIKEQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQ 148
Cdd:pfam04563 81 SAPLYVDLELSVYNG-------EDIKPIEVFIGRLPIMLRSnacilsgateselvklgecpldpgGYFIINGSEKVIVAQ 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 149 LHRS---PGVFFDSDKGKTHSSGKVLYNARI--IPYRGSWLDF-EFDPKDNLYARIDRRRK-LPATIILRALNYTTEEIL 221
Cdd:pfam04563 154 EHRSrnhPIVFKKADPKKRGSVASVRSSAEIsvRPDSTSWVNVlEYLSNGTIYFKFPYIKKeIPIVIILRALGFTSDREI 233
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 222 nlfFDKVIFQIEDNKLLMDLVPErlrgetatfdivangktyVEVGRRItarhiralekdNVTQVEVPTEYIVGKVAAkdy 301
Cdd:pfam04563 234 ---FELICYDVNDQQLQEELLPS------------------LEEGFKI-----------RIQTQEQALDYIGGRGRA--- 278
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 302 vdletgevicpangeisleilaklsqagyktietlftndldygpyisdtlrvdpttdrlsalveIYRMMRPGEPPTKEAA 381
Cdd:pfam04563 279 ----------------------------------------------------------------IFRMGRPREPRIKYAE 294
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 382 EGLFDNLFFSPDRYDLSAVGRMKFnrslgieettgsgilskedIVNVMRKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAE 461
Cdd:pfam04563 295 EILQKEVLPHLGTYELDETKKAYF-------------------IGYMIRRLLLLALGRREVDDRDHLGNKRLRLAGPLLA 355
|
490 500 510 520
....*....|....*....|....*....|....*....|.
gi 1402578118 462 NQFRIGLVRVERAVKERL--SLGDLEAVTPQDLINAKPISA 500
Cdd:pfam04563 356 SLFRVLFKKLVRDVRERLqkVLGSPDDLMLQLLVNAKPITS 396
|
|
| PRK08565 |
PRK08565 |
DNA-directed RNA polymerase subunit B; Provisional |
31-1305 |
2.76e-89 |
|
DNA-directed RNA polymerase subunit B; Provisional
Pssm-ID: 236291 [Multi-domain] Cd Length: 1103 Bit Score: 314.59 E-value: 2.76e-89
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 31 QLDSFDKFIQRdpeGQQGLEAAFRSVFPIVsnnGNTELQYVSYRLGEPVFDV----------RECQIRGTTYAAPLRVKL 100
Cdd:PRK08565 18 HLDSYNDFIER---GLQEIVDEFGEIKTEI---PGLKIVLGKIRVGEPEIKEadgserpitpMEARLRNLTYAAPLYLTM 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 101 RLVsydkdaAPGTIKdiKEQEVYMGEIPLMT----DN--------------------GTFVINGTERVIVSQLHRSPG-V 155
Cdd:PRK08565 92 IPV------ENGIEY--EPEEVKIGDLPIMVkskiCPlsglspdelieigedpkdpgGYFIINGSERVIVSQEDLAPNrV 163
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 156 FFDSDKgkthSSGKVLYNARIIPYRG---SWLDFEFDPKDNLYARIDR-RRKLPATIILRALnytteeilnlffdkvifq 231
Cdd:PRK08565 164 LVDKGE----AGSSITHTAKVISSRAgyrAQVTVERRKDGTIYVSFPAvPGKIPFVILMRAL------------------ 221
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 232 iednkllmdlvperlrgetatfdivangktyvevgrritarhirALEKDnvtqvevptEYIVGKVAAKDyvdletgevic 311
Cdd:PRK08565 222 --------------------------------------------GLETD---------RDIVYAVSLDP----------- 237
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 312 pangEISLEILAKLSQAGyktietlftndldygpyisdtlRVDPTTDrlSALVEIYRMMRPGEPPTK--EAAEGLFDNLF 389
Cdd:PRK08565 238 ----EIQQELLPSLEQAS----------------------SIAATVE--DALDYIGKRVAIGQPREYriERAEQILDKYL 289
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 390 fspdrydLSAVGRMKFNRslgieettgsgiLSKEDIVNVM-RKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQFRIGL 468
Cdd:PRK08565 290 -------LPHLGTSPEDR------------IKKAYFLGQMaSKLLELYLGRREPDDKDHYANKRLRLAGDLLAELFRVAF 350
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 469 VRVERAVKERL----SLG---DLEAVTPQDLINAKPISA-AVKEFFGS-SQLSQFMDQNNPLSEVTHKRRIsaLGPggLT 539
Cdd:PRK08565 351 KQLVKDLKYQLeksyARGrklDLRAIVRPDIITERIRHAlATGNWVGGrTGVSQLLDRTNYLSTLSHLRRV--VSP--LS 426
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 540 RERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYAR----TNDYGFLETPYRK-VVNGQVTEEIEYLSA------ 608
Cdd:PRK08565 427 RGQPHFEARDLHGTQWGRICPFETPEGPNCGLVKNLALMAQisvgVDEEEVEEILYELgVVPVEEAREEEYISWsrvyln 506
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 609 ------IEEGKYIIA-------------QANSNLDDELRFTDTFVTCRG----------EHGESGLYR------------ 647
Cdd:PRK08565 507 grligyHPDGEELAEkirelrrsgkisdEVNVAYIETGEINEVYVNCDSgrvrrplivvENGKPKLTRehveklkkgelt 586
|
730 740 750 760 770 780 790 800
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 648 --------------------------PEEI---H-YMDVSTQQIVSVAAALIPFLEHDDANRALMGANMQRQA--VPT-- 693
Cdd:PRK08565 587 fddlvkmgvieyldaeeeenayvaldPEDLtpeHtHLEIWPPAILGITASIIPYPEHNQSPRNTYQAAMAKQSlgLYAan 666
|
810 820 830 840 850 860 870 880
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 694 --LRAD----------KPLVGT-GMEkpvaldsgvavvakrggtiqyvdasrivvkvnedetvageagidiynLVKYTrs 760
Cdd:PRK08565 667 frIRTDtrghllhypqRPLVQTrALE-----------------------------------------------IIGYN-- 697
|
890 900 910 920 930 940 950 960
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 761 nqntcinqipcvklgepiergeilaDGPStdlgelalGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCV 840
Cdd:PRK08565 698 -------------------------DRPA--------GQNAVVAVLSYTGYNIEDAIIMNKASIERGLARSTFFRTYETE 744
|
970 980 990 1000 1010 1020 1030 1040
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 841 ARDTKLGSE-EITADIPNV----GEAALSKLDESGIVYIGAEVKGGDILVGKVTPKgetQLTPEEKLLRAIFGEKasdvK 915
Cdd:PRK08565 745 ERKYPGGQEdKIEIPEPNVrgyrGEEYYRKLDEDGIVSPEVEVKGGDVLIGKTSPP---RFLEELEELSLGLQER----R 817
|
1050 1060 1070 1080 1090 1100 1110 1120
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 916 DSSlrvpnsvsgtvidvqVFTRDGvekdkraleieemqlkqakkdlveeleilEAGLfarVRNVLISggmdaaqlDKLDR 995
Cdd:PRK08565 818 DTS---------------VTVRHG-----------------------------EKGI---VDTVLIT--------ESPEG 842
|
1130 1140 1150 1160 1170 1180 1190 1200
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 996 TKwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiqgddlapgvlkVVKVYLAVKRQIQPGDKMAGRHGNKG 1075
Cdd:PRK08565 843 NK----------------------------------------------------LVKVRVRDLRIPELGDKFASRHGQKG 870
|
1210 1220 1230 1240 1250 1260 1270 1280
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1076 VISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEThlgLAAKgigdqinamikqkqdVEKLRGyiqkaydlggg 1155
Cdd:PRK08565 871 VIGMLVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLES---IAGK---------------VAALEG----------- 921
|
1290 1300 1310 1320 1330 1340 1350 1360
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1156 sQKVDlstftdeevmrlaqnlrkglplATPvFDGAHEEEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKL 1235
Cdd:PRK08565 922 -RFVD----------------------ATP-FYGEPEEELRKELLKLGYKPDGTEVMYDGRTGEKIKAPIFIGVVYYQKL 977
|
1370 1380 1390 1400 1410 1420 1430
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1236 NHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvngRTKMY 1305
Cdd:PRK08565 978 HHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGHGAAMLLKERLLDSSD----KTTIY 1043
|
|
| rpoB_arch |
TIGR03670 |
DNA-directed RNA polymerase subunit B; This model represents the archaeal version of ... |
603-1305 |
1.06e-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: 214.12 E-value: 1.06e-58
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 603 IEYLSAIEEGKYIIAQANSNLddelrftdtfvtcrgehgesglyRPEEIHyMDVSTQQIVSVAAALIPFLEHDDANRALM 682
Cdd:TIGR03670 92 IEYLDAEEEENAYIALDPEEL-----------------------TPEHTH-LEIDPSAILGIIASTIPYPEHNQSPRNTM 147
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 683 GANMQRQAVPTLRADKPLvgtgmekpvALDSgvavvakRGGTIQYVdasrivvkvnedetvageagidiynlvkytrsnq 762
Cdd:TIGR03670 148 GAAMAKQSLGLYAANYRI---------RLDT-------RGHLLHYP---------------------------------- 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 763 ntcinQIPCVKlgepiERGEILadgpsTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVVQEDRFTTIHIQELSCVAR 842
Cdd:TIGR03670 178 -----QKPLVK-----TRVLEL-----IGYDDRPAGQNFVVAVMSYEGYNIEDALIMNKASIERGLARSTFFRTYEAEER 242
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 843 DTKLGSE-EITADIPNV----GEAALSKLDESGIVYIGAEVKGGDILVGKVTPkgetqltP---EEkllRAIFGEKASDV 914
Cdd:TIGR03670 243 RYPGGQEdRFEIPEPDVrgyrGEEAYKHLDEDGIVYPEVEVKGGDVLIGKTSP-------PrflEE---LREFGLVTERR 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 915 KDSSLRVPNSVSGtVIDvqvftrdgvekdkraleieemqlkqakkdlveeleileaglfarvrNVLISGGMDAAqldkld 994
Cdd:TIGR03670 313 RDTSVTVRHGEKG-IVD----------------------------------------------KVIITETEEGN------ 339
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 995 rtkwleqtlsdeekqsqleqlaeqyeelrkdfehklevkrgkiiqgddlapgvlKVVKVYLAVKRQIQPGDKMAGRHGNK 1074
Cdd:TIGR03670 340 ------------------------------------------------------KLVKVRVRDLRIPELGDKFASRHGQK 365
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1075 GVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEThlgLAAKgigdqinamikqkqdVEKLRGyiqkaydlgg 1154
Cdd:TIGR03670 366 GVIGMIVPQEDMPFTEDGIVPDLIINPHAIPSRMTVGQLLEM---IAGK---------------VAALEG---------- 417
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1155 gsQKVDlstftdeevmrlaqnlrkglplATPvFDGAHEEEIKGLLELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLK 1234
Cdd:TIGR03670 418 --RRVD----------------------GTP-FEGEPEEELRKELLKLGFKPDGKEVMYDGITGEKLEAEIFIGVIYYQK 472
|
650 660 670 680 690 700 710
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1402578118 1235 LNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDdvngRTKMY 1305
Cdd:TIGR03670 473 LHHMVADKIHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLIGHGAAMLLKERLLDESD----KYVVY 539
|
|
| PRK07225 |
PRK07225 |
DNA-directed RNA polymerase subunit B'; Validated |
593-1298 |
3.77e-50 |
|
DNA-directed RNA polymerase subunit B'; Validated
Pssm-ID: 235972 [Multi-domain] Cd Length: 605 Bit Score: 188.63 E-value: 3.77e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 593 KVVNGQVTEE-------IEYLSAIEEGKYIIAQANSNLddelrftdtfvtcrgehgesglyRPEEIHyMDVSTQQIVSVA 665
Cdd:PRK07225 81 KLKNGELTFDdlvkqgvIEYLDAEEEENAYIAVYEEDL-----------------------TEEHTH-LEIDPSLILGIG 136
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 666 AALIPFLEHDDANRALMGANMQRQAVPTLRADKPLvgtgmeKPvalDSgvavvakRGGTIQYVdasrivvkvnedetvag 745
Cdd:PRK07225 137 AGMIPYPEHNASPRITMGAGMIKQSLGLPAANYKL------RP---DT-------RGHLLHYP----------------- 183
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 746 eagidiynlvkytrsnqntcinQIPCVKLgEPIErgeiladgpSTDLGELALGQNMRVAFMPWNGYNFEDSMLVSERVV- 824
Cdd:PRK07225 184 ----------------------QVPLVKT-QTQE---------IIGFDERPAGQNFVVAVMSYEGYNIEDALIMNKASIe 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 825 ----------------------QEDRFTtihiqelscvardtkLGSEEITAdipNVGEAALSKLDESGIVYIGAEVKGGD 882
Cdd:PRK07225 232 rglgrshffrtyegeerrypggQEDRFE---------------IPDKDVRG---YRGEEAYRHLDEDGLVNPETEVKEGD 293
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 883 ILVGKVTPkgetqltP---EEKllrAIFGEKASDVKDSSLRVPNSVSGTVidvqvftrdgvekdkraleieemqlkqakk 959
Cdd:PRK07225 294 VLIGKTSP-------PrflEEP---DDFGISPEKRRETSVTMRSGEEGIV------------------------------ 333
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 960 DLVeeleileaglfarvrnvlisggmdaaqldkldrtkwleqTLSDEEKQSQLeqlaeqyeelrkdfehklevkrgkiiq 1039
Cdd:PRK07225 334 DTV---------------------------------------ILTETEEGSRL--------------------------- 347
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1040 gddlapgvlkvVKVYLAVKRQIQPGDKMAGRHGNKGVISKINPVEDMPYDENGQPVDIVLNPLGVPSRMNIGQILEthlg 1119
Cdd:PRK07225 348 -----------VKVRVRDLRIPELGDKFASRHGQKGVIGLIVPQEDMPFTESGVVPDLIINPHAIPSRMTVGHVLE---- 412
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1120 laakgigdqinaMIKQKqdVEKLRGyiqkaydlgggsQKVDlstftdeevmrlaqnlrkglplATPvFDGAHEEEIKGLL 1199
Cdd:PRK07225 413 ------------MIGGK--VGSLEG------------RRVD----------------------GTA-FSGEDEEDLREAL 443
|
650 660 670 680 690 700 710 720
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1200 ELGGLPTSGQITLYDGRTGEKFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALE 1279
Cdd:PRK07225 444 EKLGFEHTGKEVMYDGITGEKIEAEIFVGVIYYQKLHHMVANKLHARSRGPVQVLTRQPTEGRAREGGLRFGEMERDVLI 523
|
730
....*....|....*....
gi 1402578118 1280 AYGAAYTLQEMLTVKSDDV 1298
Cdd:PRK07225 524 GHGAAMLLKERLLDESDKV 542
|
|
| RNA_pol_Rpb2_3 |
pfam04565 |
RNA polymerase Rpb2, domain 3; RNA polymerases catalyze the DNA dependent polymerization of ... |
513-580 |
2.63e-35 |
|
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: 128.41 E-value: 2.63e-35
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1402578118 513 QFMDQNNPLSEVTHKRRISAlGPGGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYAR 580
Cdd:pfam04565 1 QVLDRTNYLSTLSHLRRVNS-PRGGLFREMKTTEVRDLHPSHWGRICPVETPEGPNCGLVKHLALYAR 67
|
|
| RNA_pol_Rpb2_7 |
pfam04560 |
RNA polymerase Rpb2, domain 7; RNA polymerases catalyze the DNA dependent polymerization of ... |
1266-1342 |
1.07e-30 |
|
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: 116.15 E-value: 1.07e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 1266 GGQRFGEMEVWALEAYGAAYTLQEMLTVKSD----DVNGRTKMYKN-----IVSGNQQMDPGT-PESFNVIMKEIRSLGI 1335
Cdd:pfam04560 1 GGLRFGEMERWALIAYGAAHTLQERLTIKSDayevDVCGRCGLYAAynkcpICKGETDISPGYiPESFKLLFQELQSLGI 80
|
....*..
gi 1402578118 1336 NIDLDEE 1342
Cdd:pfam04560 81 DPRLLLE 87
|
|
| RNA_pol_Rpb2_45 |
pfam10385 |
RNA polymerase beta subunit external 1 domain; RNA polymerases catalyze the DNA-dependent ... |
591-657 |
1.11e-28 |
|
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: 109.76 E-value: 1.11e-28
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1402578118 591 YRKVVNGQVTEEIEYLSAIEEGKYIIAQANSNLDDELRFTDTFVTCRgEHGESGLYRPEEIHYMDVS 657
Cdd:pfam10385 1 YRKVEDGKVTDEIVYLTADEEDGYVIAQANAPLDEDGRFVDERVSAR-YRGEFPLVPPEEVDYMDVS 66
|
|
| PRK09606 |
PRK09606 |
DNA-directed RNA polymerase subunit B''; Validated |
31-579 |
1.02e-26 |
|
DNA-directed RNA polymerase subunit B''; Validated
Pssm-ID: 236587 [Multi-domain] Cd Length: 494 Bit Score: 115.82 E-value: 1.02e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 31 QLDSFDKFIQRdpegqqGLEAAFRSVFPIVSNNGNTE-LQYVSYRLGEPVfdVRECQ------------IRGTTYAAPLR 97
Cdd:PRK09606 22 HIDSYNDFVDN------GLQKIIDEQGPIETEIEDGVyVELGKIRVGKPV--VKEADgsereiypmearLRNLTYSAPLY 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 98 VKLRLVSYDKDAAPgtikdikeQEVYMGEIPLM-----------TDN-------------GTFVINGTERVIVSQLHRSP 153
Cdd:PRK09606 94 LEMSPVEGGEEEEP--------EEVYIGELPVMvgskicnlyglSEEelievgedpldpgGYFIVNGSERVLMTLEDLAP 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 154 GVF---FDSDKGKTHSSGKVL-----YNARIIpyrgswldFEFDPKDNLYARIDR-RRKLPATIILRALNYTTEEilnlf 224
Cdd:PRK09606 166 NKIlveKDERYGDRIEVAKVFsqrrgYRALVT--------VERNRDGLLEVSFPSvPGSIPFVILMRALGLETDE----- 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 225 fdKVIFQIEDNKllmdlvperlrgETATFdIVANgktyvevgrritarhiraLEKDNVTQVEVPTEYIVGKVAAKdyvdl 304
Cdd:PRK09606 233 --EIVEAVSDDP------------EIVKF-MLEN------------------LEEAEVDTQEEALEYIGKRVAPG----- 274
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 305 ETGEvicpangeisleilaklsqagyktietlftndldygpyisdtlrvdpttdrlsalveiYRMMRpgepptkeaAEGL 384
Cdd:PRK09606 275 QTKE----------------------------------------------------------YRIKR---------AEYV 287
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 385 FDNLFFSpdrydlsavgrmkfnrSLGIEEttgSGILSKEDIVNVM-RKLIDIRNGRGEVDDIDHLGNRRIRSVGEMAENQ 463
Cdd:PRK09606 288 IDRYLLP----------------HLGVEP---EVRRAKAHYLGRMaEACFELALGRREEDDKDHYANKRLKLAGDLMEDL 348
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 464 FRIGLVRVERAVK---ER-------LSLGdlEAVTPqDLINAKPISA-AVKEFFGS-SQLSQFMDQNNPLSEVTHKRRIS 531
Cdd:PRK09606 349 FRVAFNRLARDVKyqlERanmrnreLSIK--TAVRS-DVLTERLEHAmATGNWVGGrTGVSQLLDRTDYMATLSHLRRVV 425
|
570 580 590 600
....*....|....*....|....*....|....*....|....*...
gi 1402578118 532 AlgpgGLTRERAGFEVRDVHATHYGRVCPIETPEGPNIGLINSLAVYA 579
Cdd:PRK09606 426 S----PLSRSQPHFEARDLHPTQWGRICPSETPEGPNCGLVKNFAQMV 469
|
|
| RNA_pol_Rpb2_2 |
pfam04561 |
RNA polymerase Rpb2, domain 2; RNA polymerases catalyze the DNA dependent polymerization of ... |
151-454 |
2.85e-12 |
|
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: 66.60 E-value: 2.85e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 151 RSPGVFFDSDKGKTHSSGKvlYNARIIPYRGSWLDFEFDPKDNLYARIDRRRKLPATIILRALNYTT-EEILNLffdkVI 229
Cdd:pfam04561 1 RSNGIYVEKELDKNGIIAT--YTSSLISNRGSWLKLEIDGKTLIWSRPSKKRKIPIVIFLKALGLVSdREILDR----LC 74
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 230 FQIEDNKLLMDLVPErlrgetatfdivangktyvevgrritarhiralekdnvtqvevpteyivgkvaakdyvdLETGEV 309
Cdd:pfam04561 75 YDFNDPQMLELLKPE-----------------------------------------------------------LEEAEN 95
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1402578118 310 ICpangeisleilaklsqagykTIETlftndldygpyisdtlrvdpttdrlsALVEIYRM--MRPGEPPTKEAAEGLFDN 387
Cdd:pfam04561 96 IY--------------------TQEE--------------------------ALDYIGKGfaLRRGEEPRLQRAREILYS 129
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1402578118 388 LFfspdrydlsavGRMKFNRSLGIEETTGSGILSKEDIVNVMRKLIDIRNGRGEVDDIDHLGNRRIR 454
Cdd:pfam04561 130 RD-----------PKYNLNKHLGLNEPFENERLKAQDILYMIDRLLNLKLGRRKPDDIDHLGNKRVR 185
|
|
| PRK00566 |
PRK00566 |
DNA-directed RNA polymerase subunit beta'; Provisional |
290-334 |
4.22e-05 |
|
DNA-directed RNA polymerase subunit beta'; Provisional
Pssm-ID: 234794 [Multi-domain] Cd Length: 1156 Bit Score: 48.14 E-value: 4.22e-05
10 20 30 40
....*....|....*....|....*....|....*....|....*
gi 1402578118 290 EYIVGKVAAKDYVDLETGEVICPANGEISLEILAKLSQAGYKTIE 334
Cdd:PRK00566 804 ERILGRVLAEDVVDPETGEVIVPAGTLIDEEIADKIEEAGIEEVK 848
|
|
| |
