|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
40-299 |
7.30e-46 |
|
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: 156.37 E-value: 7.30e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 40 IKEIGNYQVLSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHpdIEFDDLVQEGNEGMLRAMEDFNPALG 119
Cdd:COG0568 3 LREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRG--LPLLDLIQEGNLGLMKAVEKFDPERG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 120 YCFSTYAFWWI----------QKRMLgiickkrsgpfKIPNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEI 189
Cdd:COG0568 81 FRFSTYATWWIrqaitraiadQWRTI-----------RLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEK 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 190 VIRHNVYYKRatTMTLDIdTINEDigiSNSSHDD---KSAIPSINEMVIEDLNYEI---WLifdEVLNPKQKMVLNLCFG 263
Cdd:COG0568 150 VREMLRLARE--PVSLDA-PVGDD---EDSELGDlleDEEAPSPEEALEEELLREElreAL---DTLTEREREILRLRFG 220
|
250 260 270
....*....|....*....|....*....|....*.
gi 1209279056 264 LLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:COG0568 221 LDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRH 256
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
69-310 |
1.55e-29 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 116.51 E-value: 1.55e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 69 RDYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIICKKrSGPFKI 148
Cdd:PRK07598 177 KEHMIKANLRLVVSVAKKYQNR--GLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQ-SRTIRL 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 149 PNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRATTMTL----DIDTINEDIgisnSSHDDK 224
Cdd:PRK07598 254 PVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETkvgkDKDTELGDL----LETDDI 329
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 225 SaiPSiNEMVIEDLNYEIWLIFDEvLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKKCDYKD 304
Cdd:PRK07598 330 S--PE-EMLMRESLQRDLQHLLAD-LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRN 405
|
....*.
gi 1209279056 305 EIFNLL 310
Cdd:PRK07598 406 RIRDYL 411
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
79-300 |
4.66e-18 |
|
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Pssm-ID: 274153 [Multi-domain] Cd Length: 224 Bit Score: 81.55 E-value: 4.66e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 79 LVLSIARKYKNKHPD-IEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIICKKRSGPFKIPNYVNQFNL 157
Cdd:TIGR02479 8 LVKRIAGRLSVGLPSsVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKARKLER 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 158 KYVELEdkylQMYNRPPSVEEVVKELDVTSEIVirHNVYYKRATTMTLDIDTINEDIGISNSSHD---DKSAIPSINEMV 234
Cdd:TIGR02479 88 AIRELE----ARLGREPTEEEIAEELGMDLKEY--RQALNEINALSLVSLDELLESGDDGGSLIDrieDDKSEDPEEELE 161
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 235 IEDLNYEIWLIFDEvLNPKQKMVLNLcfglldgkVYLH----KEIAKALMITTERVSQIKEEAIKKLKKC 300
Cdd:TIGR02479 162 REELREALAEAIES-LSEREQLVLSL--------YYYEelnlKEIGEVLGLTESRVSQIHSQALKKLRAK 222
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
72-135 |
5.60e-14 |
|
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: 66.07 E-value: 5.60e-14
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1209279056 72 LFHVNVGLVLSIARKYKNKHPDIEfdDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRML 135
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAE--DLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAII 62
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
248-298 |
1.12e-05 |
|
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
Pssm-ID: 100119 [Multi-domain] Cd Length: 55 Bit Score: 42.09 E-value: 1.12e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1209279056 248 EVLNPKQKMVLNLCFGllDGKVYlhKEIAKALMITTERVSQIKEEAIKKLK 298
Cdd:cd06171 9 DKLPEREREVILLRFG--EGLSY--EEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
40-299 |
7.30e-46 |
|
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: 156.37 E-value: 7.30e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 40 IKEIGNYQVLSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHpdIEFDDLVQEGNEGMLRAMEDFNPALG 119
Cdd:COG0568 3 LREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRG--LPLLDLIQEGNLGLMKAVEKFDPERG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 120 YCFSTYAFWWI----------QKRMLgiickkrsgpfKIPNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEI 189
Cdd:COG0568 81 FRFSTYATWWIrqaitraiadQWRTI-----------RLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEK 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 190 VIRHNVYYKRatTMTLDIdTINEDigiSNSSHDD---KSAIPSINEMVIEDLNYEI---WLifdEVLNPKQKMVLNLCFG 263
Cdd:COG0568 150 VREMLRLARE--PVSLDA-PVGDD---EDSELGDlleDEEAPSPEEALEEELLREElreAL---DTLTEREREILRLRFG 220
|
250 260 270
....*....|....*....|....*....|....*.
gi 1209279056 264 LLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:COG0568 221 LDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRH 256
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
53-299 |
3.74e-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: 114.15 E-value: 3.74e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 53 ESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDiEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQK 132
Cdd:COG1191 1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPA-ELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRG 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 133 RMLGIICKKRsgpfKIPNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRATTMTLDiDTINE 212
Cdd:COG1191 80 AILDYLRDED----WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANAYQLLSLD-EPLED 154
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 213 DIGISNSSHDDKSAIPSINEMVIEDLNYEIwlifdEVLNPKQKMVLNLcfglldgkVYLH----KEIAKALMITTERVSQ 288
Cdd:COG1191 155 GDDLLDLLESGDPEEELEHEELREALAEAI-----EQLPERERLVLSL--------YYFEeltlKEIAEVLGVSESRVSR 221
|
250
....*....|.
gi 1209279056 289 IKEEAIKKLKK 299
Cdd:COG1191 222 LHKKALARLRE 232
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
69-310 |
1.55e-29 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 116.51 E-value: 1.55e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 69 RDYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIICKKrSGPFKI 148
Cdd:PRK07598 177 KEHMIKANLRLVVSVAKKYQNR--GLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQ-SRTIRL 253
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 149 PNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRATTMTL----DIDTINEDIgisnSSHDDK 224
Cdd:PRK07598 254 PVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETkvgkDKDTELGDL----LETDDI 329
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 225 SaiPSiNEMVIEDLNYEIWLIFDEvLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKKCDYKD 304
Cdd:PRK07598 330 S--PE-EMLMRESLQRDLQHLLAD-LTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRN 405
|
....*.
gi 1209279056 305 EIFNLL 310
Cdd:PRK07598 406 RIRDYL 411
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
40-298 |
1.48e-28 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 113.16 E-value: 1.48e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 40 IKEIGNYQVLSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALG 119
Cdd:PRK09210 102 LKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGR--GMLFLDLIQEGNMGLMKAVEKFDYRKG 179
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 120 YCFSTYAFWWI-QKRMLGIICKKRSgpFKIP-NYVNQFNlKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIViRhnvyy 197
Cdd:PRK09210 180 FKFSTYATWWIrQAITRAIADQART--IRIPvHMVETIN-KLIRVQRQLLQELGREPTPEEIAEEMDMPPEKV-R----- 250
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 198 krattmtlDIDTINED-------IGISNSSH------DDKSAIPS---INEMVIEDLnyeiwlifDEVLN---PKQKMVL 258
Cdd:PRK09210 251 --------EILKIAQEpvsletpIGEEDDSHlgdfieDQDATSPAdhaAYELLKEQL--------EDVLDtltDREENVL 314
|
250 260 270 280
....*....|....*....|....*....|....*....|
gi 1209279056 259 NLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLK 298
Cdd:PRK09210 315 RLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
76-299 |
1.52e-27 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 109.46 E-value: 1.52e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 76 NVGLVLSIARKYKNKHPDIEfdDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIICKKrSGPFKIPNYVNQF 155
Cdd:PRK07405 90 NLRLVVSVAKKYLKRNVDLL--DLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEK-SRTIRLPIHITEK 166
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 156 NLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVirhNVYYKRA-TTMTLDI------DT----INEDIGISNSSHDDK 224
Cdd:PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQV---REYLERArQPLSLDLrvgdnqDTelgeLLEDTGASPEDFATQ 243
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1209279056 225 SAIPSINEMVIEDlnyeiwlifdevLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:PRK07405 244 SSLQLDLERLMED------------LTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
76-299 |
1.33e-25 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 104.15 E-value: 1.33e-25
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 76 NVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIICKKRSG---PFKIPNYV 152
Cdd:PRK05949 100 NLRLVVAIAKKYQKR--NMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTirlPIHITEKL 177
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 153 NQFNLKYVELEdkylQMYNRPPSVEEVVKELDVTSEiVIRHNVYYKRaTTMTLDIDT-INEDIGISNSSHDDKSAiPSI- 230
Cdd:PRK05949 178 NKIKKTQRELS----QKLGRSATPAEIAKELELEPS-QIREYLSMAR-QPISLDVRVgDNQDTELSELLEDEGPS-PDQy 250
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1209279056 231 --NEMVIEDLNYeiWLifdEVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:PRK05949 251 itQELLRQDLNN--LL---AELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLRR 316
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
42-299 |
3.99e-24 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 100.03 E-value: 3.99e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 42 EIGNYQVLSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALGYC 121
Cdd:PRK05657 61 EIGYSPLLTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNR--GLALLDLIEEGNLGLIRAVEKFDPERGFR 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 122 FSTYAFWWI-QKRMLGIICKKRSgpFKIPNYV----NQFNLKYVELEDKylqmYNRPPSVEEVVKELDVTSEIVIRHNVY 196
Cdd:PRK05657 139 FSTYATWWIrQTIERAIMNQTRT--IRLPVHVvkelNVYLRAARELEHK----LDHEPSAEEIAELLDKPVDDVSRMLAL 212
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 197 YKRATTM--TLDIDTineDIGISNSSHDDKSAIPsiNEMVIEDlnyEI------WLifdEVLNPKQKMVLNLCFGLLDGK 268
Cdd:PRK05657 213 NERITSLdtPLGGDP---EKSLLDILADEQENGP--EDTTQDD---DMkqsivkWL---FELNDKQREVLARRFGLLGYE 281
|
250 260 270
....*....|....*....|....*....|.
gi 1209279056 269 VYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:PRK05657 282 AATLEDVAREIGLTRERVRQIQVEALRRLRE 312
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
69-304 |
1.77e-23 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 98.26 E-value: 1.77e-23
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 69 RDYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWI-QKRMLGIICKKRSgpFK 147
Cdd:PRK07921 88 RRHLLEANLRLVVSLAKRYTGR--GMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIrQAITRGMADQSRT--IR 163
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 148 IP-NYVNQFNlKYVELEDKYLQMYNRPPSVEEVVKELDVTSEivirhnvyyKRATTMTLDIDTINEDIGISNSSH----- 221
Cdd:PRK07921 164 LPvHLVEQVN-KLARIKRELHQQLGREATDEELAEESGIPEE---------KIADLLEHSRDPVSLDMPVGSDEEaplgd 233
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 222 --DDKSAIPSINEMVIEDLNYEIWLIFDeVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:PRK07921 234 fiEDSEATSAENAVIAGLLHTDIRSVLA-TLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312
|
....*
gi 1209279056 300 CDYKD 304
Cdd:PRK07921 313 GERAD 317
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
69-298 |
2.71e-22 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 96.99 E-value: 2.71e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 69 RDYLFHVNVGLVLSIARKYKNKHPDieFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWI----------QKRmlgII 138
Cdd:PRK05901 273 KNHLLEANLRLVVSLAKRYTNRGLS--FLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIrqaitramadQAR---TI 347
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 139 ckkrsgpfKIP-NYVNQFNlKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVirhnVYYKRattmtLDIDTINED--IG 215
Cdd:PRK05901 348 --------RIPvHMVETIN-KLGRIERELLQELGREPTPEELAKEMGFTPEKV----REIQK-----YNREPISLDktIG 409
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 216 ISNSSH-----DDKSAIpSINEMVIEDLNYEiwlIFDEVLN---PKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVS 287
Cdd:PRK05901 410 KEGDSQfgdfiEDSEAV-SPVDAVSFTLLQD---QLQEVLEtlsEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIR 485
|
250
....*....|.
gi 1209279056 288 QIKEEAIKKLK 298
Cdd:PRK05901 486 QIESKTLRKLR 496
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
60-298 |
5.30e-20 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 89.46 E-value: 5.30e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 60 RYKHGEKdLRDYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIIC 139
Cdd:PRK07406 130 RLMLGRR-AKEKMVQSNLRLVVSIAKKYMNR--GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIA 206
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 140 KKrSGPFKIPNYVNQfNLKYVELEDKYL-QMYNRPPSVEEVVKELDVTSEIVirhnvyykR--ATTMTLDI--------- 207
Cdd:PRK07406 207 DQ-SRTIRLPVHLYE-TISRIKKTTKVLsQEFGRKPTEEEIAESMEMTIEKL--------RfiAKSAQLPIsletpigke 276
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 208 ------DTINEDIgisNSSHDDKSaipsiNEMVIEDLnyEIWLifdEVLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMI 281
Cdd:PRK07406 277 edsrlgDFIEADG---ETPEDDVA-----KNLLREDL--EGVL---ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNV 343
|
250
....*....|....*..
gi 1209279056 282 TTERVSQIKEEAIKKLK 298
Cdd:PRK07406 344 TRERIRQIEAKALRKLR 360
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
79-300 |
4.66e-18 |
|
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Pssm-ID: 274153 [Multi-domain] Cd Length: 224 Bit Score: 81.55 E-value: 4.66e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 79 LVLSIARKYKNKHPD-IEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIICKKRSGPFKIPNYVNQFNL 157
Cdd:TIGR02479 8 LVKRIAGRLSVGLPSsVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQKARKLER 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 158 KYVELEdkylQMYNRPPSVEEVVKELDVTSEIVirHNVYYKRATTMTLDIDTINEDIGISNSSHD---DKSAIPSINEMV 234
Cdd:TIGR02479 88 AIRELE----ARLGREPTEEEIAEELGMDLKEY--RQALNEINALSLVSLDELLESGDDGGSLIDrieDDKSEDPEEELE 161
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 235 IEDLNYEIWLIFDEvLNPKQKMVLNLcfglldgkVYLH----KEIAKALMITTERVSQIKEEAIKKLKKC 300
Cdd:TIGR02479 162 REELREALAEAIES-LSEREQLVLSL--------YYYEelnlKEIGEVLGLTESRVSQIHSQALKKLRAK 222
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
48-299 |
2.15e-17 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 80.38 E-value: 2.15e-17
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 48 VLSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIefDDLVQEGNEGMLRAMEDFNPALGYCFSTYAF 127
Cdd:PRK08215 18 VLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENV--DDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 128 WWIQ---KRMLgiickKRSGPFKIPNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIrhnvyykrattmt 204
Cdd:PRK08215 96 PMIIgeiRRYL-----RDNNPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVV------------- 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 205 LDIDTINEDIGISNS-SHDDKSAIPSINEMVIEDLNYEIWLifDEV--------LNPKQKMVLNLCFglLDGKVYLhkEI 275
Cdd:PRK08215 158 FALDAIQDPVSLFEPiYHDGGDPIYVMDQISDEKNKDENWL--EEIalkeamkkLNDREKLILNLRF--FQGKTQM--EV 231
|
250 260
....*....|....*....|....
gi 1209279056 276 AKALMITTERVSQIKEEAIKKLKK 299
Cdd:PRK08215 232 AEEIGISQAQVSRLEKAALKHMRK 255
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
40-300 |
2.23e-16 |
|
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: 77.71 E-value: 2.23e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 40 IKEIGNYQVLSKQESLNLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKN---KHPDiefddLVQEGNEGMLRAMEDFN 115
Cdd:TIGR02392 7 IRAVNRIPMLTPEEEYQLAKRLReHGDLDAAKKLVLSHLRFVVKIARGYRGyglPQAD-----LIQEGNIGLMKAVKRFD 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 116 PALGYCFSTYAFWWIQKRMLGIICKKRSgPFKIPNYVNQ----FNLKYVEledKYLQMYNRPPSVEEVVKELDVTSEIVI 191
Cdd:TIGR02392 82 PERGVRLVSFAVHWIKAEIHEYILRNWR-LVKVATTKAQrklfFNLRKMK---KRLQGWLNPEEVEAIAEELGVSEREVR 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 192 RHNVYYkRATTMTLDidtinedigISNSSHDDKSAIPsINEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGL------- 264
Cdd:TIGR02392 158 EMESRL-SGQDMSLN---------ASIDDDEDDGGAP-IAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLdarsrri 226
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 1209279056 265 ------LDGKVYLHkEIAKALMITTERVSQIKEEAIKKLKKC 300
Cdd:TIGR02392 227 iearwlDDDKLTLQ-ELAAEYGVSAERIRQIEKNAMKKLKAA 267
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
29-305 |
1.92e-15 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 74.21 E-value: 1.92e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 29 PMAYPEGNTFEikeignyQVLSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIefDDLVQEGNEGML 108
Cdd:PRK05803 18 LVSYVKNNSFP-------QPLSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDV--DDLISIGTIGLI 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 109 RAMEDFNPALGYCFSTYAFWWIQKRMLGIIckkRSgpfkipnyvNQFNLKYVELEDkylqmynrPPSVEevvKEldvTSE 188
Cdd:PRK05803 89 KAIESFDAGKGTKLATYAARCIENEILMHL---RN---------LKKTKKEVSLQD--------PIGVD---KE---GNE 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 189 IVIrhnvyykrattmtLDIDTINEDigisnsshddksaipSINEMVieDLNYEIWLIFD--EVLNPKQKMVLNLCFGLLD 266
Cdd:PRK05803 143 ISL-------------IDILGSEED---------------DVIEQV--ELKMEVEKLYKkiDILDEREKEVIEMRYGLGN 192
|
250 260 270
....*....|....*....|....*....|....*....
gi 1209279056 267 GKVYLHKEIAKALMITTERVSQIKEEAIKKLKKCDYKDE 305
Cdd:PRK05803 193 GKEKTQREIAKALGISRSYVSRIEKRALKKLFKELYRAE 231
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
72-135 |
5.60e-14 |
|
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: 66.07 E-value: 5.60e-14
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1209279056 72 LFHVNVGLVLSIARKYKNKHPDIEfdDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRML 135
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAE--DLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAII 62
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
67-300 |
1.26e-13 |
|
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: 67.37 E-value: 1.26e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 67 DLRDYLFHVNVGLVLSIARKYKNKHPDIEfdDLVQEGNEGMLRAMEDFNPalGYCFSTYAFWWIQKRMLGIICKKRsgpf 146
Cdd:TIGR02937 1 EAFEELYERYLPLVYRYARRYLGDDADAE--DLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRRKR---- 72
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 147 kipnyvnqfnlKYVELEDKYLQMYNRPPSVEEvvkeldvtseivirhnvyykrattmtldidtinedigisnsshddksa 226
Cdd:TIGR02937 73 -----------RLRRELDLLEELLDSDPSPEE------------------------------------------------ 93
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1209279056 227 ipsinEMVIEDLNYEIWLIFDEvLNPKQKMVLNLCFglLDGkvYLHKEIAKALMITTERVSQIKEEAIKKLKKC 300
Cdd:TIGR02937 94 -----ELEQEEEREALREALEK-LPEREREVLVLRY--LEG--LSYKEIAEILGISVGTVKRRLKRARKKLREL 157
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
51-188 |
1.82e-13 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 69.18 E-value: 1.82e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 51 KQESLNLFQRYKHGEK-DLRDYLFHVNVGLVLSIARKYKNKHPDiEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWW 129
Cdd:PRK07408 8 KSETMELLRAYQQNPSiALRNQLVELNLGLVRKEAHRWSNQCSE-PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPY 86
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*....
gi 1209279056 130 IQKRMLGIIcKKRSGPFKIPNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSE 188
Cdd:PRK07408 87 IRGEIQHYL-RDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPTDQEIAQALDISLE 144
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
39-298 |
1.17e-12 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 68.28 E-value: 1.17e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 39 EIKEIGNYQVLSKQESLNLFQRYKHGEKDLR---DYLFHVNVGLVLSIARKYKNKhpDIEFDDLVQEGNEGMLRAMEDFN 115
Cdd:PRK05658 349 ELEAIEEETGLTIEELKEINRQISKGEAKARrakKEMVEANLRLVISIAKKYTNR--GLQFLDLIQEGNIGLMKAVDKFE 426
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 116 PALGYCFSTYAFWWI----------QKRMLgiickkrsgpfKIP-NYVNQFNlKYVELEDKYLQMYNRPPSVEEVVKELD 184
Cdd:PRK05658 427 YRRGYKFSTYATWWIrqaitrsiadQARTI-----------RIPvHMIETIN-KLNRISRQMLQEIGREPTPEELAERLG 494
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 185 vtseivirhnvyykrattMTLD-IDTI----------------NEDigisnsSH-----DDKSAIPSINEMVIEDLNYEI 242
Cdd:PRK05658 495 ------------------MPEDkVRKVlkiakepisletpigdDED------SHlgdfiEDKNAELPIDAAIQESLREAT 550
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1209279056 243 wlifDEV---LNPKQKMVLNLCFGLLDGkvYLH--KEIAKALMITTERVSQIKEEAIKKLK 298
Cdd:PRK05658 551 ----TDVlasLTPREAKVLRMRFGIDMN--TDHtlEEVGKQFDVTRERIRQIEAKALRKLR 605
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
24-300 |
1.61e-12 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 66.74 E-value: 1.61e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 24 ARSIKPMAYPEGNTFE--IKEIGNYQVLSKQESLNLFQRYK-HGEKD---------LRdylfhvnvgLVLSIARKYKnkH 91
Cdd:PRK06596 2 TKALQLLALSPEGNLDayIQAVNKIPMLTAEEEYMLAKRLReHGDLEaakqlvlshLR---------FVVHIARGYR--G 70
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 92 PDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIqkrmlgiickKRSgpfkIPNYV-------------NQ---- 154
Cdd:PRK06596 71 YGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWI----------KAE----IHEYIlrnwrivkvattkAQrklf 136
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 155 FNLKYVEledKYLQMYNrPPSVEEVVKELDVTSEIVIRHNvyyKR--ATTMTLDIdTINEDIGISNSSHD---DKSAIPs 229
Cdd:PRK06596 137 FNLRKAK---KRLGWLN-PEEVEMVAEELGVSEEEVREME---SRlsGQDASLDA-PIDDDDEESGAPQDyleDKSSDP- 207
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1209279056 230 inEMVIEDLNYEIW---LIFD--EVLNPKQKMVLNlCFGLLDGKVYLHkEIAKALMITTERVSQIKEEAIKKLKKC 300
Cdd:PRK06596 208 --ADVLEEDNWEDQrraLLADalEGLDERSRDIIE-ARWLDDDKSTLQ-ELAAEYGVSAERVRQIEKNAMKKLKAA 279
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
61-300 |
2.51e-12 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 65.25 E-value: 2.51e-12
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 61 YKHGEKDLRDYLFHVNVGLVLSIARKYKNKHP-DIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKRMLGIIc 139
Cdd:PRK06986 2 YTAEGKMDQDELVEQYAPLVKRIALRLKARLPaSVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDEL- 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 140 kkRSGPFkIPNYVNQfNLKYVELE-DKYLQMYNRPPSVEEVVKELDVTSE----IVIRHNVYykraTTMTLD-IDTINED 213
Cdd:PRK06986 81 --RSLDW-VPRSVRR-NAREVAQAiRQLEQELGREPTDTEVAEKLGLSLEeyreMLLDTNIS----QLFSIDeLRGEHGD 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 214 IGISNSSHDDKSAIPSI-NEMVIEDLNYEIwlifdEVLNPKQKMVLNLcfglldgkvYLH-----KEIAKALMITTERVS 287
Cdd:PRK06986 153 SILVTEDHQDEDPLQQLeDEELREALVEAI-----ESLPEREQLVLSL---------YYQeelnlKEIGAVLGVSESRVS 218
|
250
....*....|...
gi 1209279056 288 QIKEEAIKKLKKC 300
Cdd:PRK06986 219 QIHSQAIKRLRAR 231
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
57-299 |
1.71e-10 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 60.44 E-value: 1.71e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 57 LFQRYKH------GEKDLRDYLFHVN-------VGLVLSIARkyknkhpdiefDDLVQEGNEGMLRAMEDFNPALGYCFS 123
Cdd:PRK07670 11 LWDRWKEerdpdaADELIRRYMPLVHyhvqrisVGLPKSVSK-----------DDLKSLGMLGLYDALEKFDPSRDLKFD 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 124 TYAFWWIQKRMLGIICKK----RSGPFKIpnyvnqfnlKYVE-LEDKYLQMYNRPPSVEEVVKELDVTSEIVirhnvyyk 198
Cdd:PRK07670 80 TYASFRIRGAIIDGLRKEdwlpRSMREKT---------KKVEaAIEKLEQRYMRNVTPKEVAAELGMTEEEV-------- 142
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 199 rATTM-------TLDID---TINEDI-GISNSSHDDKSAIPS---INEMVIEDLNYEIwlifdEVLNPKQKMVLNLcfgl 264
Cdd:PRK07670 143 -EATMnegffanLLSIDektHDQDDGeNVSVTIRDDKTPTPEeklLKEELIEELAEKI-----KQLSEKEQLVISL---- 212
|
250 260 270
....*....|....*....|....*....|....*....
gi 1209279056 265 ldgkVYLHK----EIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:PRK07670 213 ----FYKEEltltEIGQVLNLSTSRISQIHSKALFKLKK 247
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
49-134 |
2.09e-10 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 60.43 E-value: 2.09e-10
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 49 LSKQESLNLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKN-KHPdieFDDLVQEGNEGMLRAMEDFNPALGYCFSTYA 126
Cdd:PRK07500 21 LEREEEHALAYRWKdHRDEDALHRIISAHMRLVISMAGKFRRfGLP---MNDLIQEGYVGLLEAAARFEPDREVRFSTYA 97
|
....*...
gi 1209279056 127 FWWIQKRM 134
Cdd:PRK07500 98 TWWIRASI 105
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
57-298 |
1.94e-09 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 57.39 E-value: 1.94e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 57 LFQRYKH-GEKDLRDYLFHVNVGLVLSIARKYK-NKHPDIEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFwwiqKRM 134
Cdd:PRK06288 20 LWREYKKtGDPKIREYLILKYSPLVKYVAGRIAvGMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAV----TRI 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 135 LGIICKKRSGPFKIPNYVNQfnlKYVELEDKYLQMYN---RPPSVEEVVKELDVTSEIVirHNVYYKRATTMTLDIDTI- 210
Cdd:PRK06288 96 RGAIFDELRSIDWIPRSVRQ---KARQIERAIAMLEArlgRTPSDEEIADELGISLEEY--NSLLSKLSGTSVVSLNDLw 170
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 211 -----NEDIGISNSSHDDKSAIPsinEMVIEDlnYEIWLIFDEVLNP---KQKMVLNLCF--GLldgkvyLHKEIAKALM 280
Cdd:PRK06288 171 fggdeGDEVSLMDTLESPAALNP---DEIAER--EEIKRVIVEAIKTlpeREKKVLILYYyeDL------TLKEIGKVLG 239
|
250
....*....|....*...
gi 1209279056 281 ITTERVSQIKEEAIKKLK 298
Cdd:PRK06288 240 VTESRISQLHTKAVLQLR 257
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
49-298 |
7.69e-09 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 55.47 E-value: 7.69e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 49 LSKQESLNLFQRY-KHGEKDLRDYLFHVNVGLVLSIARKY-KNKHPDiefDDLVQEGNEGMLRAMEDFNPALGYCFSTYA 126
Cdd:PRK08583 10 LTKEEVNKWIAEYqENQDEEAQEKLVKHYKNLVESLAYKYsKGQSHH---EDLVQVGMVGLLGAIRRYDPSFGRSFEAFA 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 127 FWWIQ---KRML-----GIICKKRS---GPfKIPNYVNQFNlkyVELEdkylqmynRPPSVEEVVKELDVTSEIVIrhnv 195
Cdd:PRK08583 87 VPTIIgeiKRYLrdktwSVHVPRRIkelGP-KIKKAVDELT---TELQ--------RSPKISEIADRLGVSEEEVL---- 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 196 yykRATTMTLDIDTINEDIGISNSShdDKSAIPSINEMVIEDLNYE-------IWLIFdEVLNPKQKMVLNLCFglLDGK 268
Cdd:PRK08583 151 ---EAMEMGKSYQALSVDHSIEADS--DGSTVTLLDIVGQQEDGYElteqrmiLEKIL-PVLSDREKSIIQCTF--IENL 222
|
250 260 270
....*....|....*....|....*....|
gi 1209279056 269 VylHKEIAKALMITTERVSQIKEEAIKKLK 298
Cdd:PRK08583 223 S--QKETGERLGISQMHVSRLQRQAIKKLR 250
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
65-298 |
1.60e-08 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 54.62 E-value: 1.60e-08
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 65 EKDLRDYLFHVNVGLVLSIARKYKNKHPD-IEFDDLVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKrmlGIICKKRS 143
Cdd:PRK05911 21 EIEYRDVLIEFYLPLVKNVAHRLISGMPShVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKA---AIIDDLRK 97
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 144 GPFkIPNYVNQFNLKYVELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRATTMTLdidtiNEDigisNSSHDD 223
Cdd:PRK05911 98 QDW-VPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILSL-----NEE----FPCQSD 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1209279056 224 KSAIPSINEMVIEDLNYEIWLIFD------------EVLNPKQKMVLNLCFglLDGKVYlhKEIAKALMITTERVSQIKE 291
Cdd:PRK05911 168 DEAGLALEERIADERAETGYDVVDkkefssilaeaiLALEEKERKVMALYY--YEELVL--KEIGKILGVSESRVSQIHS 243
|
....*..
gi 1209279056 292 EAIKKLK 298
Cdd:PRK05911 244 KALLKLR 250
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
248-299 |
1.21e-07 |
|
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: 47.42 E-value: 1.21e-07
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|..
gi 1209279056 248 EVLNPKQKMVLNLCFGlldgKVYLHKEIAKALMITTERVSQIKEEAIKKLKK 299
Cdd:pfam04545 3 ASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
248-298 |
1.12e-05 |
|
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).
Pssm-ID: 100119 [Multi-domain] Cd Length: 55 Bit Score: 42.09 E-value: 1.12e-05
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|.
gi 1209279056 248 EVLNPKQKMVLNLCFGllDGKVYlhKEIAKALMITTERVSQIKEEAIKKLK 298
Cdd:cd06171 9 DKLPEREREVILLRFG--EGLSY--EEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
49-126 |
4.06e-05 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 44.08 E-value: 4.06e-05
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1209279056 49 LSKQESLNLFQRYKHGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEfdDLVQEGNEGMLRAMEDFNPALGYCFSTYA 126
Cdd:PRK08301 34 LSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIE--DLISIGTIGLIKAVNTFNPEKKIKLATYA 109
|
|
| |
