|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
271-516 |
2.27e-51 |
|
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 440334 [Multi-domain] Cd Length: 268 Bit Score: 176.01 E-value: 2.27e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 271 KKIEIG-RAARNKLIKHNLRLVLFVMNKYFHeftNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRS 349
Cdd:COG0568 22 RRIQAGdEEAKRKLVEANLRLVVSIAKKYQG---RGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRA 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 350 -MTTSNFTRVPFGL-ESVRVeIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSkhSVTQEEfinG 427
Cdd:COG0568 99 iADQWRTIRLPVHMaETLNK-LRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDA--PVGDDE---D 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 428 ITDVDGVGANNSRQPA------LLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALM 501
Cdd:COG0568 173 SELGDLLEDEEAPSPEealeeeLLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALR 252
|
250
....*....|....*
gi 1063733635 502 KLKHQARVDYLRQYI 516
Cdd:COG0568 253 KLRHPLRSRKLRDYL 267
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
238-516 |
2.43e-50 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 176.51 E-value: 2.43e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 238 LLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFVMNKYFHEftnGPKFQDLCQAGMR 317
Cdd:PRK07406 96 LEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNR---GLSFQDLIQEGSL 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 318 GLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKIT 396
Cdd:PRK07406 173 GLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTiRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMT 252
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 397 PERYREVLRAAKPVLSLNSkhSVTQEE------FI--NGITDVDGVGANnsrqpaLLRLALDDVLDSLKPKESLVIRQRY 468
Cdd:PRK07406 253 IEKLRFIAKSAQLPISLET--PIGKEEdsrlgdFIeaDGETPEDDVAKN------LLREDLEGVLATLSPRERDVLRLRY 324
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1063733635 469 GLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYI 516
Cdd:PRK07406 325 GLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
366-439 |
2.59e-14 |
|
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Pssm-ID: 427997 [Multi-domain] Cd Length: 78 Bit Score: 68.01 E-value: 2.59e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063733635 366 RVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQEEFING-ITDVDGVGANNS 439
Cdd:pfam04539 3 LNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDlLEDDDIESPEEA 77
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
278-506 |
5.51e-09 |
|
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Pssm-ID: 274357 [Multi-domain] Cd Length: 158 Bit Score: 55.05 E-value: 5.51e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 278 AARNKLIKHNLRLVLFVMNKYFhefTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRlsTYGLFWIRHAIIRSMTTSNFTR 357
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIARNLILDYLRRKRRLR 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 358 VpfglesvrveiykaktelwfemgrppTEDEVVERLKITPERYREVLRAAkpvlslnskhsvtqeefingitdvdgvgan 437
Cdd:TIGR02937 76 R--------------------------ELDLLEELLDSDPSPEEELEQEE------------------------------ 99
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 438 nsrqpalLRLALDDVLDSLKPKESLVIRQRYGldgkGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQ 506
Cdd:TIGR02937 100 -------EREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
446-504 |
2.17e-05 |
|
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
Pssm-ID: 100119 [Multi-domain] Cd Length: 55 Bit Score: 42.09 E-value: 2.17e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 446 RLALDDVLDSLKPKESLVIRQRYGldgkGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
238-280 |
2.34e-03 |
|
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Pssm-ID: 427997 [Multi-domain] Cd Length: 78 Bit Score: 36.81 E-value: 2.34e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1063733635 238 LLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAAR 280
Cdd:pfam04539 6 IKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPV 48
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
271-516 |
2.27e-51 |
|
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 440334 [Multi-domain] Cd Length: 268 Bit Score: 176.01 E-value: 2.27e-51
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 271 KKIEIG-RAARNKLIKHNLRLVLFVMNKYFHeftNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRS 349
Cdd:COG0568 22 RRIQAGdEEAKRKLVEANLRLVVSIAKKYQG---RGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRA 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 350 -MTTSNFTRVPFGL-ESVRVeIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSkhSVTQEEfinG 427
Cdd:COG0568 99 iADQWRTIRLPVHMaETLNK-LRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDA--PVGDDE---D 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 428 ITDVDGVGANNSRQPA------LLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALM 501
Cdd:COG0568 173 SELGDLLEDEEAPSPEealeeeLLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALR 252
|
250
....*....|....*
gi 1063733635 502 KLKHQARVDYLRQYI 516
Cdd:COG0568 253 KLRHPLRSRKLRDYL 267
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
238-516 |
2.43e-50 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 176.51 E-value: 2.43e-50
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 238 LLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFVMNKYFHEftnGPKFQDLCQAGMR 317
Cdd:PRK07406 96 LEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNR---GLSFQDLIQEGSL 172
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 318 GLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKIT 396
Cdd:PRK07406 173 GLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTiRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMT 252
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 397 PERYREVLRAAKPVLSLNSkhSVTQEE------FI--NGITDVDGVGANnsrqpaLLRLALDDVLDSLKPKESLVIRQRY 468
Cdd:PRK07406 253 IEKLRFIAKSAQLPISLET--PIGKEEdsrlgdFIeaDGETPEDDVAKN------LLREDLEGVLATLSPRERDVLRLRY 324
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1063733635 469 GLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYI 516
Cdd:PRK07406 325 GLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
218-517 |
4.15e-45 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 161.16 E-value: 4.15e-45
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 218 PVLSSTEHAWLFKLMQPMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFVMNK 297
Cdd:PRK05949 31 PLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKK 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 298 YFHEftnGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKAKTEL 376
Cdd:PRK05949 111 YQKR---NMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTiRLPIHITEKLNKIKKTQREL 187
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 377 WFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSL 456
Cdd:PRK05949 188 SQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQELLRQDLNNLLAEL 267
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1063733635 457 KPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHqaRVDYLRQYIV 517
Cdd:PRK05949 268 TPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR--RRANVKEYLA 326
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
218-504 |
1.68e-40 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 148.37 E-value: 1.68e-40
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 218 PVLSSTEHAWLFKLMQPMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLFVMNK 297
Cdd:PRK07405 21 PLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGEAAKRKMVEANLRLVVSVAKK 100
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 298 YFHEFTNgpkFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKAKTEL 376
Cdd:PRK07405 101 YLKRNVD---LLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTiRLPIHITEKLNKIKKAQRQL 177
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 377 WFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSL 456
Cdd:PRK07405 178 SQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTGASPEDFATQSSLQLDLERLMEDL 257
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 1063733635 457 KPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:PRK07405 258 TPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
234-516 |
1.21e-39 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 148.48 E-value: 1.21e-39
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 234 PMKALLEVKDVLQKSLGREP-------------------------REAEIAgeiNMTAGEVKKKIEIGRAARNKLIKHNL 288
Cdd:PRK07598 109 PYLRLIEVRERLTSELGHRPslerwaktadisladlkptlaegkrRWAEIA---KLTVEELEQIQKQGLRAKEHMIKANL 185
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 289 RLVLFVMNKYFHEftnGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRV 367
Cdd:PRK07598 186 RLVVSVAKKYQNR---GLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTiRLPVHITEKLN 262
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 368 EIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALLRL 447
Cdd:PRK07598 263 KIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDISPEEMLMRESLQR 342
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 448 ALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYI 516
Cdd:PRK07598 343 DLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYL 411
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
276-515 |
3.02e-38 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 142.56 E-value: 3.02e-38
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 276 GRAARNKLIKHNLRLVLFVMNKYFhefTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNF 355
Cdd:PRK07921 84 GEAARRHLLEANLRLVVSLAKRYT---GRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSR 160
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 356 T-RVPFGL-ESVRvEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSvTQEEFING--ITDV 431
Cdd:PRK07921 161 TiRLPVHLvEQVN-KLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVG-SDEEAPLGdfIEDS 238
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 432 DGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDY 511
Cdd:PRK07921 239 EATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADR 318
|
....
gi 1063733635 512 LRQY 515
Cdd:PRK07921 319 LRSY 322
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
268-516 |
3.44e-34 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 132.42 E-value: 3.44e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 268 EVKKKIEIG-RAARNKLIKHNLRLVLFVMNKYFhefTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAI 346
Cdd:PRK09210 118 ELAKRIEEGdEEAKQRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAI 194
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 347 IRSMTTSNFT-RVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSkhSVTQEE-- 423
Cdd:PRK09210 195 TRAIADQARTiRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLET--PIGEEDds 272
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 424 ----FINgitdvDGVGANNSRQPA--LLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEV 497
Cdd:PRK09210 273 hlgdFIE-----DQDATSPADHAAyeLLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347
|
250
....*....|....*....
gi 1063733635 498 KALMKLKHQARVDYLRQYI 516
Cdd:PRK09210 348 KALRKLRHPSRSKQLKDFL 366
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
49-516 |
4.08e-34 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 134.74 E-value: 4.08e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 49 PPREQVLIPAEKHNEKKRevTRRKPCKTPKKPLSLEHNSAPSCSLGVDYNEAAARLESIYKLSPATTTLVEDDVEDGGSK 128
Cdd:PRK05901 11 AAEEEAKKKLKKLAAKSK--SKGFITKEEIKEALESKKKTPEQIDQVLIFLSGMVKDTDDATESDIPKKKTKTAAKAAAA 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 129 AKVSRRRKRKESGEEKKVVVRNNVKKEKRMSLDKRIALKRNVQEKPVVA----SVDKKVTKRQQEEEKIERLVRDYSASN 204
Cdd:PRK05901 89 KAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDddddLDDDDIDDDDDDEDDDEDDDDDDVDDE 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 205 DIVSLDWKKMKIPPVLSSTEHAWLFKLMQPMKALLE--------VKDVLqKSLGREP-----REAEIAGEIN-------- 263
Cdd:PRK05901 169 DEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAkltatadpVKAYL-KQIGKVKllnaeEEVELAKRIEaglyaeel 247
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 264 MTAGE---------VKKKIEIGRAARNKLIKHNLRLVLFVMNKYfhefTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFR 333
Cdd:PRK05901 248 LAEGEkldpelrrdLQWIGRDGKRAKNHLLEANLRLVVSLAKRY----TNrGLSFLDLIQEGNLGLIKAVEKFDYTKGYK 323
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 334 LSTYGLFWIRHAIIRSMTTSNFT-RVPfglesVR-VE----IYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAA 407
Cdd:PRK05901 324 FSTYATWWIRQAITRAMADQARTiRIP-----VHmVEtinkLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYN 398
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 408 KPVLSLNSkhSVTQEE------FI---NGITDVDGVGANnsrqpaLLRLALDDVLDSLKPKESLVIRQRYGL-DGKgDRT 477
Cdd:PRK05901 399 REPISLDK--TIGKEGdsqfgdFIedsEAVSPVDAVSFT------LLQDQLQEVLETLSEREAGVIRMRFGLtDGQ-PKT 469
|
490 500 510
....*....|....*....|....*....|....*....
gi 1063733635 478 LGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYI 516
Cdd:PRK05901 470 LDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFL 508
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
277-504 |
5.03e-30 |
|
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 440804 [Multi-domain] Cd Length: 236 Bit Score: 117.23 E-value: 5.03e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 277 RAARNKLIKHNLRLVLFVMNKYFHEFtnGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAII---RSMtts 353
Cdd:COG1191 14 EEAREELIEEYLPLVKKIASRLAGRL--PAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILdylRDE--- 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 354 nfTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAK--PVLSLnskhsvtQEEFINGITDV 431
Cdd:COG1191 89 --DWVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSL-------DEPLEDGDDLL 159
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063733635 432 DGVGANNSRQPAL---LRLALDDVLDSLKPKESLVIRQRYgldgKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:COG1191 160 DLLESGDPEEELEheeLREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALARLR 231
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
119-516 |
2.82e-29 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 121.82 E-value: 2.82e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 119 EDDVEDGGSKAKVSRRRKRKESGEEKKVVVRNnVKKEKRMSLDKRIAlKRNVQEKPVVASVDKKVTKRQQ---EEEKIER 195
Cdd:PRK05658 198 EEEEEDENDDSLAADESELPEKVLEKFKALAK-QYKKLRKAQEKKVE-GRLAQHKKYAKLREKLKEELKSlrlTSKQIDE 275
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 196 LVRDYSASND-IVSLDWKKMKIPPVL-------------SSTEHAWLFKLMQPMK----ALLEVKDVLQKSLGREpreAE 257
Cdd:PRK05658 276 LVEQLRDINKrVRGQERELLRLVERLkmprkdflklfqgNELDITWLEKEIASGKpwseFLVRVYDEIKKLQQEL---EA 352
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 258 IAGEINMTAGEVKK---KIEIG----RAARNKLIKHNLRLVLFVMNKYfhefTN-GPKFQDLCQAGMRGLITAIDRFEPK 329
Cdd:PRK05658 353 IEEETGLTIEELKEinrQISKGeakaRRAKKEMVEANLRLVISIAKKY----TNrGLQFLDLIQEGNIGLMKAVDKFEYR 428
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 330 RKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPfglesvrV-------EIYKAKTELWFEMGRPPTEDEVVERLKITPERYR 401
Cdd:PRK05658 429 RGYKFSTYATWWIRQAITRSIADQARTiRIP-------VhmietinKLNRISRQMLQEIGREPTPEELAERLGMPEDKVR 501
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 402 EVLRAAKPVLSLNSkhSVTQEE------FI---NGITDVDGVGANNsrqpalLRLALDDVLDSLKPKESLVIRQRYGLDG 472
Cdd:PRK05658 502 KVLKIAKEPISLET--PIGDDEdshlgdFIedkNAELPIDAAIQES------LREATTDVLASLTPREAKVLRMRFGIDM 573
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 1063733635 473 KGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYI 516
Cdd:PRK05658 574 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFL 617
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
278-504 |
1.15e-23 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 101.57 E-value: 1.15e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 278 AARNKLIKHNLRLVLFVMNKYfhefTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRS-MTTSNF 355
Cdd:PRK05657 86 AARQRMIESNLRLVVKIAKRY----LNrGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAiMNQTRT 161
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 356 TRVPfglesVRV-----EIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSV-TQEEFINGIT 429
Cdd:PRK05657 162 IRLP-----VHVvkelnVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGdPEKSLLDILA 236
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063733635 430 DVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:PRK05657 237 DEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
268-506 |
7.61e-22 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 94.65 E-value: 7.61e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 268 EVKKKIEIGRA----ARNKLIKHNLRLVLFVMNKyfheFTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWI 342
Cdd:PRK05572 18 ENKELIKKSQDgdqeARDTLVEKNLRLVWSVVQR----FLNrGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMI 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 343 RHAIIRSMTTSNFTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPEryrEVLRAAKPVLSLNSKHSVTQE 422
Cdd:PRK05572 94 IGEIQRFLRDDGTVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPE---EVVLAQEASRSPQSIHETVHE 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 423 EFINGITDVDGVgANNSRQPALLRLALDDVLDSLKPKESLVIRQRYgldgKGDRTLGEIAGNLNISREMVRKHEVKALMK 502
Cdd:PRK05572 171 NDGDPITLLDQI-ADQSEEDWFDKIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQVSRLEKKILKQ 245
|
....
gi 1063733635 503 LKHQ 506
Cdd:PRK05572 246 MKEK 249
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
279-506 |
4.34e-18 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 83.46 E-value: 4.34e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 279 ARNKLIKHNLRLVLFVMNKYfhEFTnGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAI---IRSmttsnf 355
Cdd:PRK05803 50 ARNILIERNLRLVAHIVKKF--ENT-GEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEIlmhLRN------ 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 356 trvpfgLESVRVEIykaktelwfemgrpptedevverlkitperyrevlraakpvlSLNSKHSVTQEEfiNGITDVDGVG 435
Cdd:PRK05803 121 ------LKKTKKEV------------------------------------------SLQDPIGVDKEG--NEISLIDILG 150
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063733635 436 ANNSRQPALLRLALD-----DVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQ 506
Cdd:PRK05803 151 SEEDDVIEQVELKMEveklyKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
268-504 |
5.54e-16 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 77.68 E-value: 5.54e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 268 EVKKKIEIG-RAARNKLIKHNLRLVLFVMNKyfheFTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHA 345
Cdd:PRK08215 26 ELFERMQNGdKEAREKLINGNLRLVLSVIQR----FNNrGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGE 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 346 IIRSMTTSNFTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLnskhsvtQEEFI 425
Cdd:PRK08215 102 IRRYLRDNNPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSL-------FEPIY 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 426 NGITD----VDGVGANNSRQPALLR-LALDDVLDSLKPKESLVIRQRYgLDGKgdrTLGEIAGNLNISREMVRKHEVKAL 500
Cdd:PRK08215 175 HDGGDpiyvMDQISDEKNKDENWLEeIALKEAMKKLNDREKLILNLRF-FQGK---TQMEVAEEIGISQAQVSRLEKAAL 250
|
....
gi 1063733635 501 MKLK 504
Cdd:PRK08215 251 KHMR 254
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
366-439 |
2.59e-14 |
|
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Pssm-ID: 427997 [Multi-domain] Cd Length: 78 Bit Score: 68.01 E-value: 2.59e-14
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1063733635 366 RVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQEEFING-ITDVDGVGANNS 439
Cdd:pfam04539 3 LNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDlLEDDDIESPEEA 77
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
280-504 |
3.21e-14 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 72.73 E-value: 3.21e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 280 RNKLIKHNLRLVLFVMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFtrVP 359
Cdd:PRK05911 25 RDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDW--VP 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 360 FGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKP--VLSLNSKHS--------VTQEEFI---N 426
Cdd:PRK05911 103 RSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPalILSLNEEFPcqsddeagLALEERIadeR 182
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1063733635 427 GITDVDGVgannSRQPALLRLAldDVLDSLKPKEslviRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:PRK05911 183 AETGYDVV----DKKEFSSILA--EAILALEEKE----RKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
277-504 |
3.90e-14 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 72.76 E-value: 3.90e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 277 RAARNKLIKHNLRLVLFVMNKYFHeftNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAI---------- 346
Cdd:PRK07500 39 EDALHRIISAHMRLVISMAGKFRR---FGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIqdyilrnwsi 115
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 347 IRSMTTSNFTRVPFGLESVRVEIYKAKTELwfemGRPPTEDEVVERLKItPERYREVL--RAAKPVLSLNSKHSVTQEEf 424
Cdd:PRK07500 116 VRGGTSSAQKALFFNLRRLRARLAQADEEL----TKQEIHREIATALGV-SLSDVEMMdaRLSGPDASLNAPQSEEDEG- 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 425 inGITDVDGVgANNSRQPA----------LLRLALDDVLDSLKPKESLVIRQRYgLDGKGdRTLGEIAGNLNISREMVRK 494
Cdd:PRK07500 190 --RSERMDFL-VDDSPLPDeqvessidgeRRRRWLTQALQTLNERELRIIRERR-LREDG-ATLEALGEELGISKERVRQ 264
|
250
....*....|
gi 1063733635 495 HEVKALMKLK 504
Cdd:PRK07500 265 IEARALEKLR 274
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
280-416 |
1.19e-12 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 68.02 E-value: 1.19e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 280 RNKLIKHNLRLVlfvmNKYFHEFTNGPK--FQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAI---IRSmtTSN 354
Cdd:PRK07408 27 RNQLVELNLGLV----RKEAHRWSNQCSepYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIqhyLRD--KSP 100
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1063733635 355 FTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAA--KPVLSLNSK 416
Cdd:PRK07408 101 TVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALqnRTPLSLDAP 164
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
279-510 |
8.48e-12 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 65.49 E-value: 8.48e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 279 ARNKLIKHNLRLVLFVMNKY-----FHEftngpkfqDLCQAGMRGLITAIDRFEPK--RKFRlstygLFWIRHAI----- 346
Cdd:PRK08583 30 AQEKLVKHYKNLVESLAYKYskgqsHHE--------DLVQVGMVGLLGAIRRYDPSfgRSFE-----AFAVPTIIgeikr 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 347 -IRSMTTSnfTRVPFGLESVRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAKPVLSLNSKHSVTQEEFI 425
Cdd:PRK08583 97 yLRDKTWS--VHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDG 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 426 NGITDVDGVGA-NNSRQPALLRLALDDVLDSLKPKESLVIRQRYgLDGKGDRTLGEIAGnlnISREMVRKHEVKALMKLK 504
Cdd:PRK08583 175 STVTLLDIVGQqEDGYELTEQRMILEKILPVLSDREKSIIQCTF-IENLSQKETGERLG---ISQMHVSRLQRQAIKKLR 250
|
....*.
gi 1063733635 505 HQARVD 510
Cdd:PRK08583 251 EAAFLD 256
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
278-504 |
9.87e-12 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 65.58 E-value: 9.87e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 278 AARnKLIKHNLRLVLFVMNKYFHEftnGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAI----IRSM--- 350
Cdd:PRK06596 49 AAK-QLVLSHLRFVVHIARGYRGY---GLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIheyiLRNWriv 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 351 ---TTSNFTRVPFGLEsvrveiyKAKTEL-WFemgRPPTEDEVVERLKITPERYREV-LRAAKPVLSLN-------SKHS 418
Cdd:PRK06596 125 kvaTTKAQRKLFFNLR-------KAKKRLgWL---NPEEVEMVAEELGVSEEEVREMeSRLSGQDASLDapiddddEESG 194
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 419 VTQEEFINGITDVDGVGANNSRQpALLRLALDDVLDSLKPKESLVIRQRYGLDGKgdRTLGEIAGNLNISREMVRKHEVK 498
Cdd:PRK06596 195 APQDYLEDKSSDPADVLEEDNWE-DQRRALLADALEGLDERSRDIIEARWLDDDK--STLQELAAEYGVSAERVRQIEKN 271
|
....*.
gi 1063733635 499 ALMKLK 504
Cdd:PRK06596 272 AMKKLK 277
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
283-348 |
1.90e-11 |
|
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation.
Pssm-ID: 427998 [Multi-domain] Cd Length: 71 Bit Score: 59.52 E-value: 1.90e-11
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063733635 283 LIKHNLRLVLFVMNKYFHeftNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIR 348
Cdd:pfam04542 1 LVERYLPLVYSLARRYLG---DGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIID 63
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
280-504 |
4.75e-11 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 63.17 E-value: 4.75e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 280 RNKLIKHNLRLVLFVMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFtrVP 359
Cdd:PRK06288 33 REYLILKYSPLVKYVAGRIAVGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDW--IP 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 360 fglESVRV---EIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLR--AAKPVLSLNSKHSVTQEEfiNGITDVDGV 434
Cdd:PRK06288 111 ---RSVRQkarQIERAIAMLEARLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDLWFGGDEG--DEVSLMDTL 185
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1063733635 435 GANNSRQPALL------RLALDDVLDSLKPKESLVIRQRYgldgKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:PRK06288 186 ESPAALNPDEIaereeiKRVIVEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLR 257
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
452-505 |
3.21e-10 |
|
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.
Pssm-ID: 461347 [Multi-domain] Cd Length: 50 Bit Score: 55.51 E-value: 3.21e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 1063733635 452 VLDSLKPKESLVIRQRYGldgkGDRTLGEIAGNLNISREMVRKHEVKALMKLKH 505
Cdd:pfam04545 1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
277-505 |
3.40e-09 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 57.36 E-value: 3.40e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 277 RAARNKLIKHNLRLVLFVMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNft 356
Cdd:PRK07670 21 PDAADELIRRYMPLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKED-- 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 357 RVPfglESVRVEIYK---AKTELWFEMGRPPTEDEVVERLKITPEryrEVLRAAKP-----VLSLNSKHSVTQEEFINGI 428
Cdd:PRK07670 99 WLP---RSMREKTKKveaAIEKLEQRYMRNVTPKEVAAELGMTEE---EVEATMNEgffanLLSIDEKTHDQDDGENVSV 172
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 429 T--DVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRYgldgKGDRTLGEIAGNLNISREMVRKHEVKALMKLKH 505
Cdd:PRK07670 173 TirDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
278-506 |
5.51e-09 |
|
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Pssm-ID: 274357 [Multi-domain] Cd Length: 158 Bit Score: 55.05 E-value: 5.51e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 278 AARNKLIKHNLRLVLFVMNKYFhefTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRlsTYGLFWIRHAIIRSMTTSNFTR 357
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYL---GDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIARNLILDYLRRKRRLR 75
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 358 VpfglesvrveiykaktelwfemgrppTEDEVVERLKITPERYREVLRAAkpvlslnskhsvtqeefingitdvdgvgan 437
Cdd:TIGR02937 76 R--------------------------ELDLLEELLDSDPSPEEELEQEE------------------------------ 99
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 438 nsrqpalLRLALDDVLDSLKPKESLVIRQRYGldgkGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQ 506
Cdd:TIGR02937 100 -------EREALREALEKLPEREREVLVLRYL----EGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
310-464 |
1.64e-08 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 55.24 E-value: 1.64e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 310 DLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAI---IRSMTTsnftrVPfglESVRV---EIYKAKTELWFEMGRP 383
Cdd:PRK06986 40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldeLRSLDW-----VP---RSVRRnarEVAQAIRQLEQELGRE 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 384 PTEDEVVERLKITPERYREVLRA--AKPVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPAlLRLALDDVLDSLKPKES 461
Cdd:PRK06986 112 PTDTEVAEKLGLSLEEYREMLLDtnISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLEDEE-LREALVEAIESLPEREQ 190
|
...
gi 1063733635 462 LVI 464
Cdd:PRK06986 191 LVL 193
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
271-337 |
2.80e-06 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 48.70 E-value: 2.80e-06
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 271 KKIEIGR-AARNKLIKHNLRLVLFVMNKyfheFTN-GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTY 337
Cdd:PRK08301 44 NKLPKGDeAVRSLLIERNLRLVVYIARK----FENtGINIEDLISIGTIGLIKAVNTFNPEKKIKLATY 108
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
305-506 |
3.33e-06 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 48.62 E-value: 3.33e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 305 GPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRVEIYKAKTELWFEMGRP 383
Cdd:PRK07122 64 GEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSvKVPRRLKELHLRLGRATAELSQRLGRA 143
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063733635 384 PTEDEVVERLKITPERYREVLRA--AKPVLSLNSKHSVTQEE---FINGITDVDGVGANNSRQPALLRLalddvLDSLKP 458
Cdd:PRK07122 144 PTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGSGDDDaraIADTLGDVDAGLDQIENREALRPL-----LAALPE 218
|
170 180 190 200
....*....|....*....|....*....|....*....|....*...
gi 1063733635 459 KESLVIRQRYgldgKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQ 506
Cdd:PRK07122 219 RERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
446-504 |
2.17e-05 |
|
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
Pssm-ID: 100119 [Multi-domain] Cd Length: 55 Bit Score: 42.09 E-value: 2.17e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 1063733635 446 RLALDDVLDSLKPKESLVIRQRYGldgkGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
445-506 |
1.88e-03 |
|
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 441203 [Multi-domain] Cd Length: 181 Bit Score: 39.59 E-value: 1.88e-03
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1063733635 445 LRLALDDVLDSLKPKESLVIRQRYgLDGKgdrTLGEIAGNLNISREMVRKHEVKALMKLKHQ 506
Cdd:COG1595 117 LLEALLAALERLPPRQREVLVLRY-LEGL---SYAEIAEILGISEGTVKSRLSRARKKLREA 174
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
238-280 |
2.34e-03 |
|
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
Pssm-ID: 427997 [Multi-domain] Cd Length: 78 Bit Score: 36.81 E-value: 2.34e-03
10 20 30 40
....*....|....*....|....*....|....*....|...
gi 1063733635 238 LLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAAR 280
Cdd:pfam04539 6 IKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPV 48
|
|
| |
