|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
1-284 |
0e+00 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 539.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 1 MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK06596 1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596 81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 161 LGVTSKDVREMESRMAAQDMTFDLsSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDII 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASLDA-PIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDII 239
|
250 260 270 280
....*....|....*....|....*....|....*....|....
gi 1314861348 241 RARWLDeDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:PRK06596 240 EARWLD-DDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
14-284 |
1.40e-167 |
|
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]
Pssm-ID: 274107 [Multi-domain] Cd Length: 270 Bit Score: 464.83 E-value: 1.40e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 14 GNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392 1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVTSKDVREME 172
Cdd:TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 173 SRMAAQDMTFDLSSDDDSDSQPmAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDnKST 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG-APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KLT 238
|
250 260 270
....*....|....*....|....*....|..
gi 1314861348 253 LQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:TIGR02392 239 LQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
18-284 |
7.10e-109 |
|
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: 315.84 E-value: 7.10e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 18 SYIRAANAWPMLSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVTSKDVREMEs 173
Cdd:COG0568 80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 174 RMAAQDMTFDlssdddsdsqpmAPVlyLQDKSSNFADGIEDDNW---EEQAANR-----LTDAMQGLDERSQDIIRARW- 244
Cdd:COG0568 155 RLAREPVSLD------------APV--GDDEDSELGDLLEDEEApspEEALEEEllreeLREALDTLTEREREILRLRFg 220
|
250 260 270 280
....*....|....*....|....*....|....*....|
gi 1314861348 245 LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:COG0568 221 LDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
53-123 |
3.88e-17 |
|
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: 74.16 E-value: 3.88e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314861348 53 LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
223-279 |
1.97e-10 |
|
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: 55.19 E-value: 1.97e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1314861348 223 NRLTDAMQGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:cd06171 2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
1-284 |
0e+00 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 539.76 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 1 MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK06596 1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVEMVARE 160
Cdd:PRK06596 81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEE 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 161 LGVTSKDVREMESRMAAQDMTFDLsSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDII 240
Cdd:PRK06596 161 LGVSEEEVREMESRLSGQDASLDA-PIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDII 239
|
250 260 270 280
....*....|....*....|....*....|....*....|....
gi 1314861348 241 RARWLDeDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:PRK06596 240 EARWLD-DDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
14-284 |
1.40e-167 |
|
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]
Pssm-ID: 274107 [Multi-domain] Cd Length: 270 Bit Score: 464.83 E-value: 1.40e-167
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 14 GNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:TIGR02392 1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 94 NPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-GWFNQDEVEMVARELGVTSKDVREME 172
Cdd:TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLqGWLNPEEVEAIAEELGVSEREVREME 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 173 SRMAAQDMTFDLSSDDDSDSQPmAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDnKST 252
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGG-APIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD-KLT 238
|
250 260 270
....*....|....*....|....*....|..
gi 1314861348 253 LQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:TIGR02392 239 LQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
18-284 |
7.10e-109 |
|
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: 315.84 E-value: 7.10e-109
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 18 SYIRAANAWPMLSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEV 97
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 98 GVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQ--RKlffnLRKTKQRL--GWFNQDEVEMVARELGVTSKDVREMEs 173
Cdd:COG0568 80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlNK----LRRAKRQLlqELGREPTPEEIAEELGVPEEKVREML- 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 174 RMAAQDMTFDlssdddsdsqpmAPVlyLQDKSSNFADGIEDDNW---EEQAANR-----LTDAMQGLDERSQDIIRARW- 244
Cdd:COG0568 155 RLAREPVSLD------------APV--GDDEDSELGDLLEDEEApspEEALEEEllreeLREALDTLTEREREILRLRFg 220
|
250 260 270 280
....*....|....*....|....*....|....*....|
gi 1314861348 245 LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:COG0568 221 LDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRS 260
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
17-284 |
1.70e-66 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 209.12 E-value: 1.70e-66
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 17 DSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPE 96
Cdd:PRK07500 9 RSMIRSAMKAPYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPD 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 97 VGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREM 171
Cdd:PRK07500 89 REVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLaqadeELTKQEIHREIATALGVSLSDVEMM 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 172 ESRMAAQDMTFDlSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKs 251
Cdd:PRK07500 169 DARLSGPDASLN-APQSEEDEGRSERMDFLVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGA- 246
|
250 260 270
....*....|....*....|....*....|...
gi 1314861348 252 TLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:PRK07500 247 TLEALGEELGISKERVRQIEARALEKLRRALLS 279
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
45-284 |
7.22e-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: 112.61 E-value: 7.22e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 45 GDLEAAKTLILSHLRFVVHIARNYAG-YGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEI------HEYV 117
Cdd:COG1191 12 GDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAIldylrdEDWV 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 118 LRNWRIVKVATTKAQRKLFfnlrktkQRLGWFNQDEvEmVARELGVTSKDVREMESRMAAqdmtfdlssdddsdsqpmAP 197
Cdd:COG1191 92 PRSVRELARKIEEAIEELE-------QELGREPTDE-E-IAEELGISLEEVQEALEAANA------------------YQ 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 198 VLYLQDKSSN---FADGIEDDNWEEQAANR-----LTDAMQGLDERSQDIIRARWLDEDnksTLQELADRYGVSAERVRQ 269
Cdd:COG1191 145 LLSLDEPLEDgddLLDLLESGDPEEELEHEelreaLAEAIEQLPERERLVLSLYYFEEL---TLKEIAEVLGVSESRVSR 221
|
250
....*....|....*
gi 1314861348 270 LEKNAMKKLRAAIEA 284
Cdd:COG1191 222 LHKKALARLREYLKE 236
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
27-279 |
6.56e-29 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 113.16 E-value: 6.56e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 27 PMLSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK09210 109 PLLTAEEEIELAKRIE-EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAT 187
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 107 HWIKAEIHEYV---LRNWRI-VKVATT-----KAQRKLFfnlrktkQRLGwfNQDEVEMVARELGVTSKDVREMEsRMAA 177
Cdd:PRK09210 188 WWIRQAITRAIadqARTIRIpVHMVETinkliRVQRQLL-------QELG--REPTPEEIAEEMDMPPEKVREIL-KIAQ 257
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 178 QDMTFDlssdddsdsQPMApvlylQDKSSNFADGIEDDNWE--EQAANR------LTDAMQGLDERSQDIIRARW-LDED 248
Cdd:PRK09210 258 EPVSLE---------TPIG-----EEDDSHLGDFIEDQDATspADHAAYellkeqLEDVLDTLTDREENVLRLRFgLDDG 323
|
250 260 270
....*....|....*....|....*....|.
gi 1314861348 249 NKSTLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:PRK09210 324 RTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
27-279 |
1.90e-28 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 110.82 E-value: 1.90e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 27 PMLSADEERALAeKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK05657 66 PLLTAEEEVYFA-RRALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 107 HWIKAEIHEYVLRNWRIVKV---------ATTKAQRKLFFNLRKtkqrlgwfnQDEVEMVARELGVTSKDVREMES---R 174
Cdd:PRK05657 145 WWIRQTIERAIMNQTRTIRLpvhvvkelnVYLRAARELEHKLDH---------EPSAEEIAELLDKPVDDVSRMLAlneR 215
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 175 MAAQDMTFDLssdddsdsqpmapvlylqDKSSNFADGIEDDNW---EEQAANR----LTDA-MQGLDERSQDIIRARW-L 245
Cdd:PRK05657 216 ITSLDTPLGG------------------DPEKSLLDILADEQEngpEDTTQDDdmkqSIVKwLFELNDKQREVLARRFgL 277
|
250 260 270
....*....|....*....|....*....|....
gi 1314861348 246 DEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:PRK05657 278 LGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
46-280 |
2.94e-25 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 102.50 E-value: 2.94e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 46 DLEAAKT-LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIV 124
Cdd:PRK07921 83 DGEAARRhLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTI 162
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 125 K--VATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVARELGVTSKDVREM--ESR-MAAQDMtfdlssdddsdsqpmaPVl 199
Cdd:PRK07921 163 RlpVHLVEQVNKLARIKRELHQQLG--REATDEELAEESGIPEEKIADLleHSRdPVSLDM----------------PV- 223
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 200 yLQDKSSNFADGIEDDNW--EEQA--ANRLTDAMQG----LDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQL 270
Cdd:PRK07921 224 -GSDEEAPLGDFIEDSEAtsAENAviAGLLHTDIRSvlatLDEREQQVIRLRFgLDDGQPRTLDQIGKLFGLSRERVRQI 302
|
250
....*....|
gi 1314861348 271 EKNAMKKLRA 280
Cdd:PRK07921 303 EREVMSKLRN 312
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
27-283 |
2.29e-22 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 93.09 E-value: 2.29e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 27 PMLSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK08215 17 PVLKNEEMRELFERMQ-NGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 107 HWIKAEIHEYvLRNWRIVKVatTKAQRKLFFNLRKTKQRLGWFNQDE--VEMVARELGVTSKDVreMESRMAAQDmtfdl 184
Cdd:PRK08215 96 PMIIGEIRRY-LRDNNPIRV--SRSLRDIAYKALQVREKLINENSKEptVEEIAKELEVPREEV--VFALDAIQD----- 165
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 185 ssdddsdsqPMA---PV-------LYLQDKSSNfaDGIEDDNWEEQAAnrLTDAMQGLDERSQDIIRARWLDednKSTLQ 254
Cdd:PRK08215 166 ---------PVSlfePIyhdggdpIYVMDQISD--EKNKDENWLEEIA--LKEAMKKLNDREKLILNLRFFQ---GKTQM 229
|
250 260
....*....|....*....|....*....
gi 1314861348 255 ELADRYGVSAERVRQLEKNAMKKLRAAIE 283
Cdd:PRK08215 230 EVAEEIGISQAQVSRLEKAALKHMRKYIQ 258
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
27-279 |
9.18e-21 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 91.59 E-value: 9.18e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 27 PMLSADEERALA----------EKLHYHGDLEA---------------AK-TLILSHLRFVVHIARNYAGYGLPQADLIQ 80
Cdd:PRK05901 224 KLLNAEEEVELAkrieaglyaeELLAEGEKLDPelrrdlqwigrdgkrAKnHLLEANLRLVVSLAKRYTNRGLSFLDLIQ 303
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 81 EGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK-----VAT----TKAQRKLFfnlrktkQRLGWFNQ 151
Cdd:PRK05901 304 EGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRipvhmVETinklGRIERELL-------QELGREPT 376
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 152 DEvEMvARELGVTSKDVREMesRMAAQDmtfdlssdddsdsqpmaPV-LylqDKS------SNFADGIEDDNWE--EQAA 222
Cdd:PRK05901 377 PE-EL-AKEMGFTPEKVREI--QKYNRE-----------------PIsL---DKTigkegdSQFGDFIEDSEAVspVDAV 432
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1314861348 223 NR--LTDAMQ----GLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:PRK05901 433 SFtlLQDQLQevleTLSEREAGVIRMRFgLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLR 496
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
47-279 |
1.90e-19 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 87.23 E-value: 1.90e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 47 LEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK- 125
Cdd:PRK07598 174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRl 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 126 -VATT-------KAQRKLFFNLRKTKQrlgwfnqdeVEMVARELGVTSKDVREMESRMaaqdmtfdlssdddsdsqPMAP 197
Cdd:PRK07598 254 pVHITeklnkikKAQRKISQEKGRTPT---------IEDIAQELEMTPTQVREVLLRV------------------PRSV 306
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 198 VLYL---QDKSSNFADGIEDDN-------WEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKS-TLQELADRYGVSAER 266
Cdd:PRK07598 307 SLETkvgKDKDTELGDLLETDDispeemlMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTySLAEIGRALDLSRER 386
|
250
....*....|...
gi 1314861348 267 VRQLEKNAMKKLR 279
Cdd:PRK07598 387 VRQIESKALQKLR 399
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
27-284 |
5.54e-18 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 81.17 E-value: 5.54e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 27 PMLSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK05572 12 PQLKDEENKELIKKSQ-DGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAV 90
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 107 HWIKAEIHEYvLRNWRIVKVatTKAQRKLFFNLRKTKQRLG-WFNQD-EVEMVARELGVTSKDVremesrMAAQDMTFDL 184
Cdd:PRK05572 91 PMIIGEIQRF-LRDDGTVKV--SRSLKETANKIRKDKDELSkELGREpTIEELAEYLGVTPEEV------VLAQEASRSP 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 185 SSDDDSDSQPMAPVLYLQDKssnFADGIEDDnWEEQAAnrLTDAMQGLDERSQDIIRARWLDEDNKStlqELADRYGVSA 264
Cdd:PRK05572 162 QSIHETVHENDGDPITLLDQ---IADQSEED-WFDKIA--LKEAIRELDERERLIVYLRYFKDKTQS---EVAKRLGISQ 232
|
250 260
....*....|....*....|
gi 1314861348 265 ERVRQLEKNAMKKLRAAIEA 284
Cdd:PRK05572 233 VQVSRLEKKILKQMKEKLDE 252
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
15-278 |
9.68e-18 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 79.99 E-value: 9.68e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 15 NLDSYIrAANAWPM-LSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:PRK05803 17 FLVSYV-KNNSFPQpLSEEEERKYLELMK-EGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESF 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 94 NPEVGVRLVSFAVHWIKAEIheyvLRNWRivkvattkaqrklffNLRKTKQRLgwFNQDevemvarELGVtSKDVREMEs 173
Cdd:PRK05803 95 DAGKGTKLATYAARCIENEI----LMHLR---------------NLKKTKKEV--SLQD-------PIGV-DKEGNEIS- 144
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 174 rmaaqdmtfdlssdddsdsqpmapvlyLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARW-LDEDNKST 252
Cdd:PRK05803 145 ---------------------------LIDILGSEEDDVIEQVELKMEVEKLYKKIDILDEREKEVIEMRYgLGNGKEKT 197
|
250 260
....*....|....*....|....*.
gi 1314861348 253 LQELADRYGVSAERVRQLEKNAMKKL 278
Cdd:PRK05803 198 QREIAKALGISRSYVSRIEKRALKKL 223
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
53-123 |
3.88e-17 |
|
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: 74.16 E-value: 3.88e-17
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1314861348 53 LILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
48-279 |
6.29e-17 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 79.03 E-value: 6.29e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 48 EAAK-TLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKV 126
Cdd:PRK07405 80 EAAKrKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRL 159
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 127 ---------ATTKAQRKLffnlrktKQRLGwfNQDEVEMVARELGVTSKDVREMESRmAAQDMTFDLSSDddsdsqpmap 197
Cdd:PRK07405 160 pihiteklnKIKKAQRQL-------SQQLG--RAATIGELAEELELTPKQVREYLER-ARQPLSLDLRVG---------- 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 198 vlylQDKSSNFADGIEDD-----NWEEQAANR--LTDAMQGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQ 269
Cdd:PRK07405 220 ----DNQDTELGELLEDTgaspeDFATQSSLQldLERLMEDLTPQQKEVIALRFgLEDGQPLTLAKIGERLNISRERVRQ 295
|
250
....*....|
gi 1314861348 270 LEKNAMKKLR 279
Cdd:PRK07405 296 IEREALSKLR 305
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
49-279 |
3.08e-16 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 77.19 E-value: 3.08e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 49 AAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK--V 126
Cdd:PRK05949 92 AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRlpI 171
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 127 ATTKAQRKLFFNLRKTKQRLGwfNQDEVEMVARELGVTSKDVREMESrMAAQDMTFDLssdDDSDSQPMAPVLYLQDkss 206
Cdd:PRK05949 172 HITEKLNKIKKTQRELSQKLG--RSATPAEIAKELELEPSQIREYLS-MARQPISLDV---RVGDNQDTELSELLED--- 242
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1314861348 207 nfaDGIEDDNWEEQAANR--LTDAMQGLDERSQDIIRARWLDEDNKS-TLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:PRK05949 243 ---EGPSPDQYITQELLRqdLNNLLAELTPQQREVLTLRFGLEDGKElSLAKVGERLNLSRERVRQLEHQALAHLR 315
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
27-123 |
3.08e-16 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 76.05 E-value: 3.08e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 27 PMLSADEERALAEKLHyHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAV 106
Cdd:PRK08301 32 PPLSKEEEEYLLNKLP-KGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110
|
90
....*....|....*..
gi 1314861348 107 HWIKAEIHEYVLRNWRI 123
Cdd:PRK08301 111 RCIENEILMYLRRNNKV 127
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
49-279 |
3.25e-16 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 77.52 E-value: 3.25e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 49 AAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVkvat 128
Cdd:PRK07406 137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTI---- 212
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 129 tkaqrKLFFNLRKTKQRLgwfnQDEVEMVARELGVTSKDvREMESRMaaqDMTFDLSSDDDSDSQ-PMA---PVLYLQDk 204
Cdd:PRK07406 213 -----RLPVHLYETISRI----KKTTKVLSQEFGRKPTE-EEIAESM---EMTIEKLRFIAKSAQlPISletPIGKEED- 278
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 205 sSNFADGIEDD--NWEEQAANR-----LTDAMQGLDERSQDIIRARW-LDEDNKSTLQELADRYGVSAERVRQLEKNAMK 276
Cdd:PRK07406 279 -SRLGDFIEADgeTPEDDVAKNllredLEGVLATLSPRERDVLRLRYgLDDGRMKTLEEIGQIFNVTRERIRQIEAKALR 357
|
...
gi 1314861348 277 KLR 279
Cdd:PRK07406 358 KLR 360
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
29-282 |
1.88e-15 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 73.96 E-value: 1.88e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 29 LSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHW 108
Cdd:PRK08583 10 LTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPT 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 109 IKAEIHEYvLRN--W-------------RIVKVA---TTKAQRklffnlrktkqrlgwfnQDEVEMVARELGVTSKDVRE 170
Cdd:PRK08583 90 IIGEIKRY-LRDktWsvhvprrikelgpKIKKAVdelTTELQR-----------------SPKISEIADRLGVSEEEVLE 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 171 -MESRMAAQDMTFDlssdddsdsqpmAPVLYLQDKSS-NFAD--GIEDDNWEEqaANR---LTDAMQGLDERSQDIIRAR 243
Cdd:PRK08583 152 aMEMGKSYQALSVD------------HSIEADSDGSTvTLLDivGQQEDGYEL--TEQrmiLEKILPVLSDREKSIIQCT 217
|
250 260 270
....*....|....*....|....*....|....*....
gi 1314861348 244 WLdeDNKSTlQELADRYGVSAERVRQLEKNAMKKLRAAI 282
Cdd:PRK08583 218 FI--ENLSQ-KETGERLGISQMHVSRLQRQAIKKLREAA 253
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
48-282 |
4.66e-14 |
|
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: 68.14 E-value: 4.66e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 48 EAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVgvRLVSFAVHWIKAEIHEYvlrnwrivkva 127
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDY----------- 67
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 128 ttkaqrklffnLRKTKQRLGWFNQDEVEmvarelgvtskdvremesrmaaqdmtfdlssdddsdsqpmapvlylqdksSN 207
Cdd:TIGR02937 68 -----------LRRKRRLRRELDLLEEL--------------------------------------------------LD 86
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1314861348 208 FADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLRAAI 282
Cdd:TIGR02937 87 SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEG---LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
228-280 |
1.49e-12 |
|
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: 60.90 E-value: 1.49e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|...
gi 1314861348 228 AMQGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLRA 280
Cdd:pfam04545 1 ALASLPPRERQVLVLRYGEG---LTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
77-278 |
1.82e-12 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 65.71 E-value: 1.82e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 77 DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEY---------VLRNWRIVKVATTKAQRKLffnlrktKQRLG 147
Cdd:PRK07408 55 DLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYlrdksptvrIPRRWQELQRQAKKVRQEL-------RQELG 127
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 148 wfNQDEVEMVARELGVTSKDVREMesRMAAQDMTfdlssdddsdsqPM---APVLYLQDKSSNFADGIEDDNWEEQAAN- 223
Cdd:PRK07408 128 --RQPTDQEIAQALDISLEEWQEI--KLALQNRT------------PLsldAPVNQDEDGSTSLGDLLPDPRYRSFQLAq 191
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1314861348 224 ----RLTDAMQGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERV-RQLEK--NAMKKL 278
Cdd:PRK07408 192 edriRLQQALAQLEERTREVLEFVFLHD---LTQKEAAERLGISPVTVsRRVKKglDQLKKL 250
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
63-283 |
3.59e-12 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 64.80 E-value: 3.59e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 63 HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVAttKAQRKLFFNLRKT 142
Cdd:PRK07122 55 HIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP--RRLKELHLRLGRA 132
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 143 ----KQRLGwfNQDEVEMVARELGVTSKDVRE-MESRMAAQDMTFDlssdddsdsqpmAPVLYLQDKSSNFADGIED-DN 216
Cdd:PRK07122 133 taelSQRLG--RAPTASELAAELGMDREEVVEgLVAGSAYNTLSID------------SGGGSGDDDARAIADTLGDvDA 198
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1314861348 217 WEEQAANR--LTDAMQGLDERSQDIIRARWLDednKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283
Cdd:PRK07122 199 GLDQIENReaLRPLLAALPERERTVLVLRFFE---SMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
48-93 |
5.98e-11 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 62.50 E-value: 5.98e-11
10 20 30 40
....*....|....*....|....*....|....*....|....*.
gi 1314861348 48 EAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRF 93
Cdd:PRK05658 380 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 425
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
223-279 |
1.97e-10 |
|
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: 55.19 E-value: 1.97e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 1314861348 223 NRLTDAMQGLDERSQDIIRARWLDEdnkSTLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:cd06171 2 ERLEEALDKLPEREREVILLRFGEG---LSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
46-284 |
3.69e-10 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 59.25 E-value: 3.69e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 46 DLEAAKTLILSHLRFVVHIARNYAGyGLPQ----ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYvLRNW 121
Cdd:PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLIS-GMPShvktEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDD-LRKQ 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 122 RIVKVATTKAQRKLFFNLRKTKQRLGwfnqdevemvaRElgVTSKDVREMeSRMAAQDMTfdlssDDDSDSQPmAPVLYL 201
Cdd:PRK05911 99 DWVPRSVHQKANKLADAMDSLRQSLG-----------KE--PTDGELCEY-LNISQQELS-----GWFSSARP-ALILSL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 202 QDKSSNFADG---------IEDDNWE--------EQAANRLTDAMQGLDERSQDIIRARWLDEdnkSTLQELADRYGVSA 264
Cdd:PRK05911 159 NEEFPCQSDDeaglaleerIADERAEtgydvvdkKEFSSILAEAILALEEKERKVMALYYYEE---LVLKEIGKILGVSE 235
|
250 260
....*....|....*....|
gi 1314861348 265 ERVRQLEKNAMKKLRAAIEA 284
Cdd:PRK05911 236 SRVSQIHSKALLKLRATLSA 255
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
51-280 |
4.69e-10 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 58.32 E-value: 4.69e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 51 KTLILSHLRFVVHIARNYAGYgLPQA----DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN-W--RI 123
Cdd:PRK06986 11 DELVEQYAPLVKRIALRLKAR-LPASvdldDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdWvpRS 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 124 VKvattKAQRKLFFNLRKTKQRLGwFNQDEVEmVARELGVTSKDVREM-----ESRMAAQDmtfDLSSDDDSDSQPMApv 198
Cdd:PRK06986 90 VR----RNAREVAQAIRQLEQELG-REPTDTE-VAEKLGLSLEEYREMlldtnISQLFSID---ELRGEHGDSILVTE-- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 199 lylQDKSSNFADGIEDDNWEEqaanRLTDAMQGLDERSQDIIRARWLDEDNkstLQELADRYGVSAERVRQLEKNAMKKL 278
Cdd:PRK06986 159 ---DHQDEDPLQQLEDEELRE----ALVEAIESLPEREQLVLSLYYQEELN---LKEIGAVLGVSESRVSQIHSQAIKRL 228
|
..
gi 1314861348 279 RA 280
Cdd:PRK06986 229 RA 230
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
32-280 |
1.17e-07 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 51.61 E-value: 1.17e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 32 DEERALAEKLHYHGDLEAAKTLILSHLRFVVHIArNYAGYGLP----QADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVH 107
Cdd:PRK06288 15 QDETELWREYKKTGDPKIREYLILKYSPLVKYVA-GRIAVGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVT 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 108 WIKAEIHEYvLR--NW--RIVKVATTKAQRKLFFnlrkTKQRLGWfNQDEVEmVARELGVTSKDVREMESRMAAQDMTfd 183
Cdd:PRK06288 94 RIRGAIFDE-LRsiDWipRSVRQKARQIERAIAM----LEARLGR-TPSDEE-IADELGISLEEYNSLLSKLSGTSVV-- 164
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 184 lssdddsdsqPMAPVLYLQDKSSNFA--DGIED---DNWE-----EQAANRLTDAMQGLDERSQDIIRARWLDEdnkSTL 253
Cdd:PRK06288 165 ----------SLNDLWFGGDEGDEVSlmDTLESpaaLNPDeiaerEEIKRVIVEAIKTLPEREKKVLILYYYED---LTL 231
|
250 260
....*....|....*....|....*..
gi 1314861348 254 QELADRYGVSAERVRQLEKNAMKKLRA 280
Cdd:PRK06288 232 KEIGKVLGVTESRISQLHTKAVLQLRA 258
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
45-104 |
8.20e-07 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 48.75 E-value: 8.20e-07
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 45 GDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEvgvRLVSF 104
Cdd:PRK08295 21 GDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKD---KLSSF 77
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
33-283 |
7.29e-05 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 43.11 E-value: 7.29e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 33 EERALAEKLHYHGDLEAAKTLILSHLRFV-VHIARNYAGygLPQA----DLIQEGNIGLMKAVRRFNPEVGVRLVSFAVH 107
Cdd:PRK07670 7 EEQKLWDRWKEERDPDAADELIRRYMPLVhYHVQRISVG--LPKSvskdDLKSLGMLGLYDALEKFDPSRDLKFDTYASF 84
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 108 WIKAEIHEYVLRNWRIVKVATTKAqRKLFFNLRKTKQRLGwfNQDEVEMVARELGVTSKDV-REMESRMAAQDMTFDlss 186
Cdd:PRK07670 85 RIRGAIIDGLRKEDWLPRSMREKT-KKVEAAIEKLEQRYM--RNVTPKEVAAELGMTEEEVeATMNEGFFANLLSID--- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 187 dddsdsqpmaPVLYLQDKSSNFADGIEDDNW---EEQAANR-----LTDAMQGLDERSQDIIRARWLDEdnkSTLQELAD 258
Cdd:PRK07670 159 ----------EKTHDQDDGENVSVTIRDDKTptpEEKLLKEelieeLAEKIKQLSEKEQLVISLFYKEE---LTLTEIGQ 225
|
250 260
....*....|....*....|....*
gi 1314861348 259 RYGVSAERVRQLEKNAMKKLRAAIE 283
Cdd:PRK07670 226 VLNLSTSRISQIHSKALFKLKKLLE 250
|
|
| PRK12427 |
PRK12427 |
FliA/WhiG family RNA polymerase sigma factor; |
77-279 |
2.00e-03 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 183523 [Multi-domain] Cd Length: 231 Bit Score: 38.69 E-value: 2.00e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 77 DLIQEGNIGLMKAVRRFN-PEVGvrLVSFAVHWIKAEI-HEYVLRNWRIVKVATTKAQRKLFfnLRKTKQRLGwfNQDEV 154
Cdd:PRK12427 47 DMEQIALMGLLEALRRYGhPDEQ--FAAYAVHRIRGAIlDELRELDWRPRRLRQKTHKTNDA--IREIAKRLG--HEPNF 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 155 EMVARELGVTSKDVREMESRMAAQDMtfdlssdddsdsQPMAPVLYLQdkssNFADGIEDDNWEEQAANR--LTDAMQGL 232
Cdd:PRK12427 121 EEISAELNLTAEEYQEYLLLENAGTL------------ESLDELLALE----AHNDILQSRDLEENIIIEdnLKQALSQL 184
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 1314861348 233 DERSQDIIRARWLDEDNkstLQELADRYGVSAERVRQLEKNAMKKLR 279
Cdd:PRK12427 185 DEREQLILHLYYQHEMS---LKEIALVLDLTEARICQLNKKIAQKIK 228
|
|
| RpoE |
COG1595 |
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ... |
209-284 |
2.35e-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: 38.05 E-value: 2.35e-03
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1314861348 209 ADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDnksTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284
Cdd:COG1595 105 AADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGL---SYAEIAEILGISEGTVKSRLSRARKKLREALEE 177
|
|
| TelA |
pfam05816 |
Toxic anion resistance protein (TelA); This family consists of several prokaryotic TelA like ... |
1-92 |
4.85e-03 |
|
Toxic anion resistance protein (TelA); This family consists of several prokaryotic TelA like proteins. TelA and KlA are associated with tellurite resistance and plasmid fertility inhibition.
Pssm-ID: 461748 Cd Length: 330 Bit Score: 37.88 E-value: 4.85e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1314861348 1 MTDKMQSLALAPVGNLDSYIRAANA-WPMLSADEERALAEKLHYHGDLEAAKTL-----ILSHLRFVVH---IARNYAGY 71
Cdd:pfam05816 117 MLDQMYEKNLEYFKELEKYIAAGELkLEELDAELLPELEAKAAASGDPEDAQALrdlrqALFRLEQRIHdleLQRAVSIQ 196
|
90 100
....*....|....*....|.
gi 1314861348 72 GLPQADLIQEGNIGLMKAVRR 92
Cdd:pfam05816 197 TAPQIRLVQNNNQELIEKIQS 217
|
|
| |
