|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
25-311 |
0e+00 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 502.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 25 TLASHSMLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQE 104
Cdd:PRK06596 2 TKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 105 GNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQEL 184
Cdd:PRK06596 82 GNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEEL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 185 NVKREEVAEMETRLSGGDIALEGQI-DDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEA 263
Cdd:PRK06596 162 GVSEEEVREMESRLSGQDASLDAPIdDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEA 241
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 490657882 264 RWLNVDddgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311
Cdd:PRK06596 242 RWLDDD-----KSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAAA 284
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
37-309 |
6.90e-165 |
|
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: 459.05 E-value: 6.90e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 37 GNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRF 116
Cdd:TIGR02392 1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 117 DPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKKGTQA-FTPEEIDGLAQELNVKREEVAEME 195
Cdd:TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQGwLNPEEVEAIAEELGVSEREVREME 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 196 TRLSGGDIALEGQIDDGEESY-APIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARWLNVDddgsg 274
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGgAPIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD----- 235
|
250 260 270
....*....|....*....|....*....|....*
gi 490657882 275 GSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAA 309
Cdd:TIGR02392 236 KLTLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
41-311 |
2.03e-108 |
|
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: 2.03e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 41 AYIQAVNRIPLLSAEEERQYATEYReQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQ 120
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 121 NVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQ-----RKLFFNLrSHKKGTQAfTPEEIdglAQELNVKREEVAEME 195
Cdd:COG0568 80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlnklRRAKRQL-LQELGREP-TPEEI---AEELGVPEEKVREML 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 196 tRLSGGDIALEGQIDDGEESyAPIAYLADSHNEPTAVLAARQrdmLQTDGIARALESLDARSRRIIEARWLNVDDDgsgG 275
Cdd:COG0568 155 -RLAREPVSLDAPVGDDEDS-ELGDLLEDEEAPSPEEALEEE---LLREELREALDTLTEREREILRLRFGLDDGE---P 226
|
250 260 270
....*....|....*....|....*....|....*.
gi 490657882 276 STLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311
Cdd:COG0568 227 HTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
76-145 |
1.37e-18 |
|
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: 78.40 E-value: 1.37e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 76 LVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWR 145
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
246-304 |
1.93e-07 |
|
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: 47.10 E-value: 1.93e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 490657882 246 IARALESLDARSRRIIEARWLNvdddgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:cd06171 4 LEEALDKLPEREREVILLRFGE-------GLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
25-311 |
0e+00 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 502.40 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 25 TLASHSMLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQE 104
Cdd:PRK06596 2 TKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQE 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 105 GNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKKGTQAFTPEEIDGLAQEL 184
Cdd:PRK06596 82 GNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGWLNPEEVEMVAEEL 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 185 NVKREEVAEMETRLSGGDIALEGQI-DDGEESYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEA 263
Cdd:PRK06596 162 GVSEEEVREMESRLSGQDASLDAPIdDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERSRDIIEA 241
|
250 260 270 280
....*....|....*....|....*....|....*....|....*...
gi 490657882 264 RWLNVDddgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311
Cdd:PRK06596 242 RWLDDD-----KSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAAA 284
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
37-309 |
6.90e-165 |
|
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: 459.05 E-value: 6.90e-165
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 37 GNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRF 116
Cdd:TIGR02392 1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 117 DPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHKKGTQA-FTPEEIDGLAQELNVKREEVAEME 195
Cdd:TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQGwLNPEEVEAIAEELGVSEREVREME 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 196 TRLSGGDIALEGQIDDGEESY-APIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARWLNVDddgsg 274
Cdd:TIGR02392 161 SRLSGQDMSLNASIDDDEDDGgAPIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDD----- 235
|
250 260 270
....*....|....*....|....*....|....*
gi 490657882 275 GSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAA 309
Cdd:TIGR02392 236 KLTLQELAAEYGVSAERIRQIEKNAMKKLKAALAA 270
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
41-311 |
2.03e-108 |
|
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: 2.03e-108
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 41 AYIQAVNRIPLLSAEEERQYATEYReQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQ 120
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQ-AGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 121 NVRLVSYAIHWIKAEIHEYILRNWRMVKVATTKAQ-----RKLFFNLrSHKKGTQAfTPEEIdglAQELNVKREEVAEME 195
Cdd:COG0568 80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAEtlnklRRAKRQL-LQELGREP-TPEEI---AEELGVPEEKVREML 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 196 tRLSGGDIALEGQIDDGEESyAPIAYLADSHNEPTAVLAARQrdmLQTDGIARALESLDARSRRIIEARWLNVDDDgsgG 275
Cdd:COG0568 155 -RLAREPVSLDAPVGDDEDS-ELGDLLEDEEAPSPEEALEEE---LLREELREALDTLTEREREILRLRFGLDDGE---P 226
|
250 260 270
....*....|....*....|....*....|....*.
gi 490657882 276 STLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311
Cdd:COG0568 227 HTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
50-309 |
1.22e-70 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 220.68 E-value: 1.22e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 50 PLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAI 129
Cdd:PRK07500 19 PYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 130 HWIKAEIHEYILRNWRMVKVATTKAQRKLFFNLRSHK----KGTQAFTPEEIDG-LAQELNVKREEVAEMETRLSGGDIA 204
Cdd:PRK07500 99 WWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRarlaQADEELTKQEIHReIATALGVSLSDVEMMDARLSGPDAS 178
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 205 LEG-QIDDGEESYAPIAYLADSHNEP-----TAVLAARQRDMLQtdgiaRALESLDARSRRIIEARWLNVDddgsgGSTL 278
Cdd:PRK07500 179 LNApQSEEDEGRSERMDFLVDDSPLPdeqveSSIDGERRRRWLT-----QALQTLNERELRIIRERRLRED-----GATL 248
|
250 260 270
....*....|....*....|....*....|.
gi 490657882 279 HDLAAEFGVSAERIRQIEASAMKKMRTALAA 309
Cdd:PRK07500 249 EALGEELGISKERVRQIEARALEKLRRALLS 279
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
42-304 |
4.77e-36 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 132.80 E-value: 4.77e-36
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 42 YIQAVNRIPLLSAEEERQYATEYrEQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQN 121
Cdd:PRK09210 101 YLKEIGRVPLLTAEEEIELAKRI-EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKG 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 122 VRLVSYAIHWIKAEIHEYILRNWRMVK-----VAT----TKAQRKLFFNLrshkkgTQAFTPEEIdglAQELNVKREEVA 192
Cdd:PRK09210 180 FKFSTYATWWIRQAITRAIADQARTIRipvhmVETinklIRVQRQLLQEL------GREPTPEEI---AEEMDMPPEKVR 250
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 193 EMeTRLSGGDIALEGQIddGEESyapiaylaDSH-------NEPTAVLAARQRDML--QTDGIaraLESLDARSRRIIEA 263
Cdd:PRK09210 251 EI-LKIAQEPVSLETPI--GEED--------DSHlgdfiedQDATSPADHAAYELLkeQLEDV---LDTLTDREENVLRL 316
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 490657882 264 RW-LnvdDDGSgGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK09210 317 RFgL---DDGR-TRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
47-308 |
3.72e-31 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 118.90 E-value: 3.72e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 47 NRI---PLLSAEEERQYATEYReQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVR 123
Cdd:PRK05657 60 NEIgysPLLTAEEEVYFARRAL-RGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFR 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 124 LVSYAIHWIKAEIHEYILRNWRMVKV---------ATTKAQRKLffnlrSHKKGTQAfTPEEIdglAQELNVKREEVAEM 194
Cdd:PRK05657 139 FSTYATWWIRQTIERAIMNQTRTIRLpvhvvkelnVYLRAAREL-----EHKLDHEP-SAEEI---AELLDKPVDDVSRM 209
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 195 ---ETRLSGGDIALEGqidDGEESYAPIayLADSHNEPTAVLAArQRDMLQTdgIARALESLDARSRRIIEARW-LNvdd 270
Cdd:PRK05657 210 lalNERITSLDTPLGG---DPEKSLLDI--LADEQENGPEDTTQ-DDDMKQS--IVKWLFELNDKQREVLARRFgLL--- 278
|
250 260 270
....*....|....*....|....*....|....*...
gi 490657882 271 dGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALA 308
Cdd:PRK05657 279 -GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
56-309 |
2.59e-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: 114.54 E-value: 2.59e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 56 EERQYATEYReQNNLDAARRLVLSHLRLVVSVARNYLG-YGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKA 134
Cdd:COG1191 1 DLEELLRRYQ-EGDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 135 EI------HEYILRNWRMVKVATTKAQRKLffnlrSHKKGtQAFTPEEIdglAQELNVKREEVAEMETRLSGGDIA-LEG 207
Cdd:COG1191 80 AIldylrdEDWVPRSVRELARKIEEAIEEL-----EQELG-REPTDEEI---AEELGISLEEVQEALEAANAYQLLsLDE 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 208 QIDDGEEsyapiayLADSHNEPTAVLAARQRDMLQTdgIARALESLDARSRRIIEARWLnvdddgsGGSTLHDLAAEFGV 287
Cdd:COG1191 151 PLEDGDD-------LLDLLESGDPEEELEHEELREA--LAEAIEQLPERERLVLSLYYF-------EELTLKEIAEVLGV 214
|
250 260
....*....|....*....|..
gi 490657882 288 SAERIRQIEASAMKKMRTALAA 309
Cdd:COG1191 215 SESRVSRLHKKALARLREYLKE 236
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
52-311 |
2.96e-28 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 110.98 E-value: 2.96e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 52 LSAEEERQYATEYREQNnldAARR-LVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIH 130
Cdd:PRK07921 69 LSEARKRDLAAVVRDGE---AARRhLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATW 145
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 131 WIKAEIHEYILRNWRMV-----------KVATTKaqRKLFFNLrshkkGTQAfTPEEidgLAQELNVKREEVAEMeTRLS 199
Cdd:PRK07921 146 WIRQAITRGMADQSRTIrlpvhlveqvnKLARIK--RELHQQL-----GREA-TDEE---LAEESGIPEEKIADL-LEHS 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 200 GGDIALEGQIddGEESYAPIA-YLADShnEPTAVLAARQRDMLQTDgIARALESLDARSRRIIEARW-LnvdDDGSgGST 277
Cdd:PRK07921 214 RDPVSLDMPV--GSDEEAPLGdFIEDS--EATSAENAVIAGLLHTD-IRSVLATLDEREQQVIRLRFgL---DDGQ-PRT 284
|
250 260 270
....*....|....*....|....*....|....*....
gi 490657882 278 LHDLAAEFGVSAERIRQIEASAMKKMRTA-----LAAYA 311
Cdd:PRK07921 285 LDQIGKLFGLSRERVRQIEREVMSKLRNGeradrLRSYA 323
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
38-304 |
5.68e-25 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 104.31 E-value: 5.68e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 38 NIDAYIQAVNRIPLLSAEEERQ---------YATEYREQN-NLDAARR----------------LVLSHLRLVVSVARNY 91
Cdd:PRK05901 212 PVKAYLKQIGKVKLLNAEEEVElakrieaglYAEELLAEGeKLDPELRrdlqwigrdgkraknhLLEANLRLVVSLAKRY 291
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 92 LGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEI---------------HeyilrnwrMVKVAT--TKA 154
Cdd:PRK05901 292 TNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAItramadqartiripvH--------MVETINklGRI 363
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 155 QRKLffnlrshkkgTQAF----TPEEidgLAQELNVKREEVAEMEtRLSGGDIALEGQI-DDGEESYAPiaYLADSHNEp 229
Cdd:PRK05901 364 EREL----------LQELgrepTPEE---LAKEMGFTPEKVREIQ-KYNREPISLDKTIgKEGDSQFGD--FIEDSEAV- 426
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490657882 230 TAVLAARQRdMLQtDGIARALESLDARSRRIIEARWlNVDDDGSggSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK05901 427 SPVDAVSFT-LLQ-DQLQEVLETLSEREAGVIRMRF-GLTDGQP--KTLDEIGQVYGVTRERIRQIESKTLRKLR 496
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
39-304 |
2.75e-23 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 98.32 E-value: 2.75e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 39 IDAYIQAVNRIPLLSAEEE----RQYAT-----EYREQNNLD------------------------------AARRLVLS 79
Cdd:PRK07406 65 IRVYLQEIGRIRLLRPDEEielaRKIADlleleELREQFESElgrepsdkewaelvdmplpkfrrrlmlgrrAKEKMVQS 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 80 HLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVATtkaqrKLF 159
Cdd:PRK07406 145 NLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLY 219
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 160 FNLRSHKKGTQAftpeeidgLAQELNVK--REEVAE-ME---------TRLSGGDIALEGQIDDGEESYAPIAYLADSHN 227
Cdd:PRK07406 220 ETISRIKKTTKV--------LSQEFGRKptEEEIAEsMEmtieklrfiAKSAQLPISLETPIGKEEDSRLGDFIEADGET 291
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490657882 228 EPTAVlaarQRDMLQTDgIARALESLDARSRRIIEARWlNVDDDGSggSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK07406 292 PEDDV----AKNLLRED-LEGVLATLSPRERDVLRLRY-GLDDGRM--KTLEEIGQIFNVTRERIRQIEAKALRKLR 360
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
70-304 |
1.71e-22 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 96.48 E-value: 1.71e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 70 LDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVK- 148
Cdd:PRK07598 174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRl 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 149 -VATT-------KAQRKLffnlrSHKKGTqafTPeEIDGLAQELNVKREEVAEMETRLSgGDIALEGQI-DDGEESYAPI 219
Cdd:PRK07598 254 pVHITeklnkikKAQRKI-----SQEKGR---TP-TIEDIAQELEMTPTQVREVLLRVP-RSVSLETKVgKDKDTELGDL 323
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 220 AYLADSHNEPTAVLAARQRDMLQTdgiaraLESLDARSRRIIEARWlnvdddGSGGSTLHDLaAEFG----VSAERIRQI 295
Cdd:PRK07598 324 LETDDISPEEMLMRESLQRDLQHL------LADLTSRERDVIRMRF------GLADGHTYSL-AEIGraldLSRERVRQI 390
|
....*....
gi 490657882 296 EASAMKKMR 304
Cdd:PRK07598 391 ESKALQKLR 399
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
43-304 |
9.70e-20 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 86.54 E-value: 9.70e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 43 IQAVN--RIPLLSAEEERQYATEYReQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQ 120
Cdd:PRK08215 8 ICGVNtsKLPVLKNEEMRELFERMQ-NGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQ 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 121 NVRLVSYAIHWIKAEIHEYiLRNWRMVKVATT---KAQRKLFFNLRSHKKGTQAFTPEEIdglAQELNVKREEVAEmetr 197
Cdd:PRK08215 87 NVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSlrdIAYKALQVREKLINENSKEPTVEEI---AKELEVPREEVVF---- 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 198 lsggdiALEGqIDDGEESYAPI-------AYLADShneptaVLAARQRDMLQTDGIA--RALESLDARSRRIIEARWLNv 268
Cdd:PRK08215 159 ------ALDA-IQDPVSLFEPIyhdggdpIYVMDQ------ISDEKNKDENWLEEIAlkEAMKKLNDREKLILNLRFFQ- 224
|
250 260 270
....*....|....*....|....*....|....*.
gi 490657882 269 dddgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK08215 225 ------GKTQMEVAEEIGISQAQVSRLEKAALKHMR 254
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
41-304 |
2.75e-19 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 86.35 E-value: 2.75e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 41 AYIQAVNRIPLLSAEEERQYA--------------------------TEYREQNNLD-------------AARRLVLSHL 81
Cdd:PRK07405 12 TYLREIGRVPLLTHEEEILYGkqvqrlvalqeireelaeelgreptdAEWAKAAKLSeeelrsaiaegeaAKRKMVEANL 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 82 RLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV---------ATT 152
Cdd:PRK07405 92 RLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLpihiteklnKIK 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 153 KAQRKLffnlrSHKKGTQAFTPEeidgLAQELNVKREEVAEMETRlSGGDIALEGQIDDGEESYAPiAYLADSHNEPT-- 230
Cdd:PRK07405 172 KAQRQL-----SQQLGRAATIGE----LAEELELTPKQVREYLER-ARQPLSLDLRVGDNQDTELG-ELLEDTGASPEdf 240
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490657882 231 AVLAARQRDmlqtdgIARALESLDARSRRIIEARWLNVDDDgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK07405 241 ATQSSLQLD------LERLMEDLTPQQKEVIALRFGLEDGQ---PLTLAKIGERLNISRERVRQIEREALSKLR 305
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
76-145 |
1.37e-18 |
|
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: 78.40 E-value: 1.37e-18
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 76 LVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWR 145
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
72-304 |
2.87e-17 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 82.15 E-value: 2.87e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 72 AARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEI--------------- 136
Cdd:PRK05658 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsiadqartiripv 460
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 137 H--EYIlrNwRMVKVattkaQRKLFfnlrsHKKGTQAfTPEEidgLAQEL-----------NVKREEvaemetrlsggdI 203
Cdd:PRK05658 461 HmiETI--N-KLNRI-----SRQML-----QEIGREP-TPEE---LAERLgmpedkvrkvlKIAKEP------------I 511
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 204 ALEGQIDDGEesyapiaylaDSH-----NEPTAVL---AARQRDMLQTdgIARALESLDARSRRIIEARWlnvdddGSGG 275
Cdd:PRK05658 512 SLETPIGDDE----------DSHlgdfiEDKNAELpidAAIQESLREA--TTDVLASLTPREAKVLRMRF------GIDM 573
|
250 260 270
....*....|....*....|....*....|..
gi 490657882 276 STLHDL---AAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK05658 574 NTDHTLeevGKQFDVTRERIRQIEAKALRKLR 605
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
42-304 |
3.77e-17 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 80.27 E-value: 3.77e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 42 YIQAVNRIPLLSAEEERQY--------------------------ATEYREQNNLD-------------AARRLVLSHLR 82
Cdd:PRK05949 23 YLHEIGRVPLLTHEQEIVYgkqvqqmmslleakealakklgrepsLPEWAEAVNLSetelkqtlkqgkrAKQKMIEANLR 102
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 83 LVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV---------ATTK 153
Cdd:PRK05949 103 LVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLpihiteklnKIKK 182
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 154 AQRKLffnlrSHKKGTQAfTPEEIdglAQELNVKREEVAEMETrLSGGDIALEGQIDDGEESYAPiAYLADSHNEPTAVL 233
Cdd:PRK05949 183 TQREL-----SQKLGRSA-TPAEI---AKELELEPSQIREYLS-MARQPISLDVRVGDNQDTELS-ELLEDEGPSPDQYI 251
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490657882 234 AarqRDMLQTDgIARALESLDARSRRIIEARW-LNvddDGSGGStLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK05949 252 T---QELLRQD-LNNLLAELTPQQREVLTLRFgLE---DGKELS-LAKVGERLNLSRERVRQLEHQALAHLR 315
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
71-309 |
5.51e-16 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 76.16 E-value: 5.51e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 71 DAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYiLRNWRMVKVA 150
Cdd:PRK05572 32 EARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVS 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 151 -----TTKAQRKLFFNLRshKKGTQAFTPEEIdglAQELNVKREEVAeMETRLSGGDIALEGQI--DDGeesyAPIaYLA 223
Cdd:PRK05572 111 rslkeTANKIRKDKDELS--KELGREPTIEEL---AEYLGVTPEEVV-LAQEASRSPQSIHETVheNDG----DPI-TLL 179
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 224 DSHNEPTavlaarQRDMLqtDGIA--RALESLDARSRRIIEARWLNvdddgsgGSTLHDLAAEFGVSAERIRQIEASAMK 301
Cdd:PRK05572 180 DQIADQS------EEDWF--DKIAlkEAIRELDERERLIVYLRYFK-------DKTQSEVAKRLGISQVQVSRLEKKILK 244
|
....*...
gi 490657882 302 KMRTALAA 309
Cdd:PRK05572 245 QMKEKLDE 252
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
52-307 |
4.21e-13 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 67.80 E-value: 4.21e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 52 LSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131
Cdd:PRK08583 10 LTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPT 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 132 IKAEIHEYIL-RNW-----RMVKVATTKAqrklffnlrshKKGTQAFTPE-----EIDGLAQELNVKREEVAE-METRLS 199
Cdd:PRK08583 90 IIGEIKRYLRdKTWsvhvpRRIKELGPKI-----------KKAVDELTTElqrspKISEIADRLGVSEEEVLEaMEMGKS 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 200 ---------------GGDIAL---EGQIDDGEESyapiayladshneptavlaARQRDMLQtdgiaRALESLDARSRRII 261
Cdd:PRK08583 159 yqalsvdhsieadsdGSTVTLldiVGQQEDGYEL-------------------TEQRMILE-----KILPVLSDREKSII 214
|
250 260 270 280
....*....|....*....|....*....|....*....|....*.
gi 490657882 262 EARWLnvdDDGSGGSTLHDLaaefGVSAERIRQIEASAMKKMRTAL 307
Cdd:PRK08583 215 QCTFI---ENLSQKETGERL----GISQMHVSRLQRQAIKKLREAA 253
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
52-303 |
1.43e-12 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 66.12 E-value: 1.43e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 52 LSAEEERQYATEYREqNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHW 131
Cdd:PRK05803 31 LSEEEERKYLELMKE-GDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARC 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 132 IKAEIheyilrnwrmvkvattkaqrklFFNLRSHKKgtqaftpeeidglaqelnvkreevaemeTRlsgGDIALEGQID- 210
Cdd:PRK05803 110 IENEI----------------------LMHLRNLKK----------------------------TK---KEVSLQDPIGv 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 211 --DGEEsyapIAYLADSHNEPTAVLAARQRDMlQTDGIARALESLDARSRRIIEARW-LnvddDGSGGSTLHDLAAEFGV 287
Cdd:PRK05803 137 dkEGNE----ISLIDILGSEEDDVIEQVELKM-EVEKLYKKIDILDEREKEVIEMRYgL----GNGKEKTQREIAKALGI 207
|
250
....*....|....*.
gi 490657882 288 SAERIRQIEASAMKKM 303
Cdd:PRK05803 208 SRSYVSRIEKRALKKL 223
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
49-308 |
1.46e-12 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 66.63 E-value: 1.46e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 49 IPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVArNYLGYGLP----HGDLIQEGNIGLMKAVKRFDPAQNVRL 124
Cdd:PRK06288 9 IPKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVA-GRIAVGMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKF 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 125 VSYAIHWIKAEIH------EYILRNWRMVKVATTKAQRKLFFNLRshkkgtQAFTPEEIdglAQELNVKREEVAEMETRL 198
Cdd:PRK06288 88 KTYAVTRIRGAIFdelrsiDWIPRSVRQKARQIERAIAMLEARLG------RTPSDEEI---ADELGISLEEYNSLLSKL 158
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 199 SGGD-IALEGQIDDGEESYAPiaYLADSHNEPTA---VLAARQRDMLQTdgIARALESLDARSRRIIEARWLNvdddgsg 274
Cdd:PRK06288 159 SGTSvVSLNDLWFGGDEGDEV--SLMDTLESPAAlnpDEIAEREEIKRV--IVEAIKTLPEREKKVLILYYYE------- 227
|
250 260 270
....*....|....*....|....*....|....
gi 490657882 275 GSTLHDLAAEFGVSAERIRQIEASAMKKMRTALA 308
Cdd:PRK06288 228 DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
71-307 |
3.39e-12 |
|
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: 63.52 E-value: 3.39e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 71 DAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRlvSYAIHWIKAEIHEYIlrnwrmvkva 150
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIARNLILDYL---------- 68
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 151 ttkaqrklffnlrSHKKGTQAFTPEEIDGLAQELNVKREEVAEMETRLsggdialegqiddgeesyapiayladshnept 230
Cdd:TIGR02937 69 -------------RRKRRLRRELDLLEELLDSDPSPEEELEQEEEREA-------------------------------- 103
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490657882 231 avlaarqrdmlqtdgIARALESLDARSRRIIEARWLNvdddgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307
Cdd:TIGR02937 104 ---------------LREALEKLPEREREVLVLRYLE-------GLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
75-308 |
3.14e-11 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 62.49 E-value: 3.14e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 75 RLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVAttKA 154
Cdd:PRK07122 44 RIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVP--RR 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 155 QRKLFFNL-RSHKKGTQ----AFTPEEidgLAQELNVKREEVAEMetrLSGGD----IALEGQIDDGEESYAPIA-YLAD 224
Cdd:PRK07122 122 LKELHLRLgRATAELSQrlgrAPTASE---LAAELGMDREEVVEG---LVAGSayntLSIDSGGGSGDDDARAIAdTLGD 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 225 shnEPTAVLAARQRDMLQTdgiarALESLDARSRRIIEARWLnvdddgsGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:PRK07122 196 ---VDAGLDQIENREALRP-----LLAALPERERTVLVLRFF-------ESMTQTQIAERVGISQMHVSRLLAKTLARLR 260
|
....
gi 490657882 305 TALA 308
Cdd:PRK07122 261 DQLE 264
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
50-143 |
3.91e-11 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 61.80 E-value: 3.91e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 50 PLLSAEEErQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAI 129
Cdd:PRK08301 32 PPLSKEEE-EYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110
|
90
....*....|....
gi 490657882 130 HWIKAEIHEYILRN 143
Cdd:PRK08301 111 RCIENEILMYLRRN 124
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
64-310 |
4.42e-11 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 61.94 E-value: 4.42e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 64 YREQNNLDAARRLVLSHLRLVVSVARNyLGYGLPHG----DLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEY 139
Cdd:PRK05911 16 YWSTQEIEYRDVLIEFYLPLVKNVAHR-LISGMPSHvkteDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDD 94
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 140 iLRNWRMVKVATTKAQRKLFFNLRSHKkgtQAFTPEEIDG-LAQELNVKREEVAE-METRLSGGDIALEGQ---IDDGEE 214
Cdd:PRK05911 95 -LRKQDWVPRSVHQKANKLADAMDSLR---QSLGKEPTDGeLCEYLNISQQELSGwFSSARPALILSLNEEfpcQSDDEA 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 215 SYAPIAYLADSHNEpTAVLAARQRDMLQTdgIARALESLDARSRRIIEARWLNvdddgsgGSTLHDLAAEFGVSAERIRQ 294
Cdd:PRK05911 171 GLALEERIADERAE-TGYDVVDKKEFSSI--LAEAILALEEKERKVMALYYYE-------ELVLKEIGKILGVSESRVSQ 240
|
250
....*....|....*.
gi 490657882 295 IEASAMKKMRTALAAY 310
Cdd:PRK05911 241 IHSKALLKLRATLSAF 256
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
75-289 |
1.53e-10 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 60.32 E-value: 1.53e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 75 RLVLSHLRLVVSVARNYLGY-GLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEY---------ILRNW 144
Cdd:PRK07408 29 QLVELNLGLVRKEAHRWSNQcSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYlrdksptvrIPRRW 108
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 145 RMVKVATTKAQRKLffnlrSHKKGTQAfTPEEIdglAQELNVKREEVAEME------TRLSggdiaLEGQIDDGEESYAP 218
Cdd:PRK07408 109 QELQRQAKKVRQEL-----RQELGRQP-TDQEI---AQALDISLEEWQEIKlalqnrTPLS-----LDAPVNQDEDGSTS 174
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490657882 219 IA-YLADSHnepTAVLAARQRDMLQtdgIARALESLDARSRRIIEARWlnvdddgsggstLHDL----AAE-FGVSA 289
Cdd:PRK07408 175 LGdLLPDPR---YRSFQLAQEDRIR---LQQALAQLEERTREVLEFVF------------LHDLtqkeAAErLGISP 233
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
74-311 |
8.80e-10 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 57.94 E-value: 8.80e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 74 RRLVLsHL--RLVVSVARNylgyglphgDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRN-W------ 144
Cdd:PRK06986 22 KRIAL-RLkaRLPASVDLD---------DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLdWvprsvr 91
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 145 ---RMVKVATTKAQRKLffnlrshkkGTQAfTPEEIdglAQELNVKREEVAEMETRLSGGDIAlegQIDD--GEESYAPI 219
Cdd:PRK06986 92 rnaREVAQAIRQLEQEL---------GREP-TDTEV---AEKLGLSLEEYREMLLDTNISQLF---SIDElrGEHGDSIL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 220 AYLADSHNEPTAVLAarqRDMLQtDGIARALESLDARSRRII-----EArwLNvdddgsggstLHDLAAEFGVSAERIRQ 294
Cdd:PRK06986 156 VTEDHQDEDPLQQLE---DEELR-EALVEAIESLPEREQLVLslyyqEE--LN----------LKEIGAVLGVSESRVSQ 219
|
250
....*....|....*..
gi 490657882 295 IEASAMKKMRTALAAYA 311
Cdd:PRK06986 220 IHSQAIKRLRARLGEWT 236
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
249-304 |
5.57e-09 |
|
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: 51.27 E-value: 5.57e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*.
gi 490657882 249 ALESLDARSRRIIEARWLnvdddgsGGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:pfam04545 1 ALASLPPRERQVLVLRYG-------EGLTLEEIGERLGISRERVRQIEKRALRKLR 49
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
246-304 |
1.93e-07 |
|
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: 47.10 E-value: 1.93e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 490657882 246 IARALESLDARSRRIIEARWLNvdddgsgGSTLHDLAAEFGVSAERIRQIEASAMKKMR 304
Cdd:cd06171 4 LEEALDKLPEREREVILLRFGE-------GLSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
83-118 |
7.03e-05 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 42.97 E-value: 7.03e-05
10 20 30
....*....|....*....|....*....|....*.
gi 490657882 83 LVVSVARNYLGYGLPHGDLIQEGNIGLMKAVKRFDP 118
Cdd:PRK08295 36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDK 71
|
|
| Sigma70_r1_2 |
pfam00140 |
Sigma-70 factor, region 1.2; |
39-66 |
4.68e-04 |
|
Sigma-70 factor, region 1.2;
Pssm-ID: 425482 [Multi-domain] Cd Length: 34 Bit Score: 36.91 E-value: 4.68e-04
10 20
....*....|....*....|....*...
gi 490657882 39 IDAYIQAVNRIPLLSAEEERQYATEYRE 66
Cdd:pfam00140 3 VRLYLKEIGRIPLLTAEEEVELAKRIEA 30
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
55-307 |
4.84e-04 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 40.80 E-value: 4.84e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 55 EEERQYATEYREQNNLDAARRLVLSHLRLV-VSVARnyLGYGLPHG----DLIQEGNIGLMKAVKRFDPAQNVRLVSYAI 129
Cdd:PRK07670 6 YEEQKLWDRWKEERDPDAADELIRRYMPLVhYHVQR--ISVGLPKSvskdDLKSLGMLGLYDALEKFDPSRDLKFDTYAS 83
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 130 HWIKAEI------HEYILRNWR----MVKVATTKAQRKLffnLRShkkgtqaFTPEEIdglAQELNVKREEV-AEMETRL 198
Cdd:PRK07670 84 FRIRGAIidglrkEDWLPRSMRektkKVEAAIEKLEQRY---MRN-------VTPKEV---AAELGMTEEEVeATMNEGF 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 490657882 199 SGGDIALEGQIDDGEESYAPIAYLADSHNEP--TAVLAARQRDMLqtdgiARALESLDARSRRIIEarwLNVDDDgsggS 276
Cdd:PRK07670 151 FANLLSIDEKTHDQDDGENVSVTIRDDKTPTpeEKLLKEELIEEL-----AEKIKQLSEKEQLVIS---LFYKEE----L 218
|
250 260 270
....*....|....*....|....*....|.
gi 490657882 277 TLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307
Cdd:PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249
|
|
| |
