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Conserved domains on  [gi|2548811777|ref|WP_301600848|]
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sigma-70 family RNA polymerase sigma factor [Curtobacterium flaccumfaciens]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11439701)

sigma-70 family RNA polymerase sigma factor is an initiation factor that promotes the attachment of RNA polymerase to specific initiation sites and is then released

Gene Ontology:  GO:0016987|GO:0003677|GO:0006352|GO:0003899|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 2-221 9.68e-56

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: 179.25  E-value: 9.68e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSRAtHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWA 81
Cdd:COG1191    13 DEEAREELIEEYLPLVKKIASRLAGRL-PAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDEDWV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  82 SRGTRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDA-ARTVAPLDETVHD----LVAADLPLPGDDL 156
Cdd:COG1191    92 PRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAAnAYQLLSLDEPLEDgddlLDLLESGDPEEEL 171

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 157 LETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLAA 221
Cdd:COG1191   172 EHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
 
Name Accession Description Interval E-value
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 2-221 9.68e-56

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: 179.25  E-value: 9.68e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSRAtHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWA 81
Cdd:COG1191    13 DEEAREELIEEYLPLVKKIASRLAGRL-PAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDEDWV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  82 SRGTRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDA-ARTVAPLDETVHD----LVAADLPLPGDDL 156
Cdd:COG1191    92 PRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAAnAYQLLSLDEPLEDgddlLDLLESGDPEEEL 171

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 157 LETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLAA 221
Cdd:COG1191   172 EHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 10-212 1.21e-38

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: 134.71  E-value: 1.21e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  10 IVEHLPLVGYIVADVRSRAT-HLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRGTRKR 88
Cdd:TIGR02479   2 IRRYLPLVKRIAGRLSVGLPsSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  89 IRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDAART-VAPLDETVHD----------LVAADLPLPGDDLL 157
Cdd:TIGR02479  82 ARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALsLVSLDELLESgddggslidrIEDDKSEDPEEELE 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 158 ETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAM 212
Cdd:TIGR02479 162 REELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQAL 216
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 6-220 1.81e-30

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 114.78  E-value: 1.81e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   6 RNAMIVEHLPLVGYIVADVRS-RATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRG 84
Cdd:PRK06288   33 REYLILKYSPLVKYVAGRIAVgMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRS 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  85 TRKRIRETLATQEALSARLGRSVGALEIADAMG--VDKQTAVDAMSDAARTVApLDETVH-----------DLVAADLPL 151
Cdd:PRK06288  113 VRQKARQIERAIAMLEARLGRTPSDEEIADELGisLEEYNSLLSKLSGTSVVS-LNDLWFggdegdevslmDTLESPAAL 191

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 152 PGDDLLETEK-RRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLA 220
Cdd:PRK06288  192 NPDEIAEREEiKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 9-80 2.53e-06

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: 44.12  E-value: 2.53e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2548811777   9 MIVEHLPLVGYIVAdvRSRATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADW 80
Cdd:pfam04542   1 LVERYLPLVYSLAR--RYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 162-215 4.57e-06

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: 42.86  E-value: 4.57e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2548811777 162 RRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLL 215
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 2-221 9.68e-56

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: 179.25  E-value: 9.68e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSRAtHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWA 81
Cdd:COG1191    13 DEEAREELIEEYLPLVKKIASRLAGRL-PAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDEDWV 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  82 SRGTRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDA-ARTVAPLDETVHD----LVAADLPLPGDDL 156
Cdd:COG1191    92 PRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAAnAYQLLSLDEPLEDgddlLDLLESGDPEEEL 171

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 157 LETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLAA 221
Cdd:COG1191   172 EHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 10-212 1.21e-38

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: 134.71  E-value: 1.21e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  10 IVEHLPLVGYIVADVRSRAT-HLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRGTRKR 88
Cdd:TIGR02479   2 IRRYLPLVKRIAGRLSVGLPsSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDELRRLDWVPRSLRQK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  89 IRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDAART-VAPLDETVHD----------LVAADLPLPGDDLL 157
Cdd:TIGR02479  82 ARKLERAIRELEARLGREPTEEEIAEELGMDLKEYRQALNEINALsLVSLDELLESgddggslidrIEDDKSEDPEEELE 161

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 158 ETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAM 212
Cdd:TIGR02479 162 REELREALAEAIESLSEREQLVLSLYYYEELNLKEIGEVLGLTESRVSQIHSQAL 216
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 6-220 1.81e-30

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 114.78  E-value: 1.81e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   6 RNAMIVEHLPLVGYIVADVRS-RATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRG 84
Cdd:PRK06288   33 REYLILKYSPLVKYVAGRIAVgMPQNVEFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDWIPRS 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  85 TRKRIRETLATQEALSARLGRSVGALEIADAMG--VDKQTAVDAMSDAARTVApLDETVH-----------DLVAADLPL 151
Cdd:PRK06288  113 VRQKARQIERAIAMLEARLGRTPSDEEIADELGisLEEYNSLLSKLSGTSVVS-LNDLWFggdegdevslmDTLESPAAL 191

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 152 PGDDLLETEK-RRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLA 220
Cdd:PRK06288  192 NPDEIAEREEiKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAKLA 261
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 3-212 1.55e-29

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 111.48  E-value: 1.55e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   3 RTERNAMIVEHLPLVGYIVADVRSRA-THLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWA 81
Cdd:PRK06986    7 KMDQDELVEQYAPLVKRIALRLKARLpASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDWV 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  82 SRGTRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSD-AARTVAPLDE--TVHDLVAADLPL-----PG 153
Cdd:PRK06986   87 PRSVRRNAREVAQAIRQLEQELGREPTDTEVAEKLGLSLEEYREMLLDtNISQLFSIDElrGEHGDSILVTEDhqdedPL 166

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2548811777 154 DDLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAM 212
Cdd:PRK06986  167 QQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAI 225
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
2-219 3.67e-28

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 108.21  E-value: 3.67e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVrsrATHL----DRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRS 77
Cdd:PRK07670   20 DPDAADELIRRYMPLVHYHVQRI---SVGLpksvSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRK 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  78 ADWASRGTRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDA-ARTVAPLDETVHD----------LVA 146
Cdd:PRK07670   97 EDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVEATMNEGfFANLLSIDEKTHDqddgenvsvtIRD 176

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2548811777 147 ADLPLPGDDLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGL 219
Cdd:PRK07670  177 DKTPTPEEKLLKEELIEELAEKIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
2-205 1.87e-19

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 84.64  E-value: 1.87e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSRAthLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGA----LADD--- 74
Cdd:PRK05572   30 DQEARDTLVEKNLRLVWSVVQRFLNRG--YEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEiqrfLRDDgtv 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  75 --MRSAdwasRGTRKRIRETlatQEALSARLGRSVGALEIADAMGVDKQTAVDAMsDAARTVAPLDETVH---------- 142
Cdd:PRK05572  108 kvSRSL----KETANKIRKD---KDELSKELGREPTIEELAEYLGVTPEEVVLAQ-EASRSPQSIHETVHendgdpitll 179

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2548811777 143 DLVAADlplPGDDLLEtekRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVS 205
Cdd:PRK05572  180 DQIADQ---SEEDWFD---KIALKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGISQVQVS 236
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 6-221 1.10e-17

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 80.05  E-value: 1.10e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   6 RNAMIVEHLPLVGYIVADVRS-RATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRG 84
Cdd:PRK05911   25 RDVLIEFYLPLVKNVAHRLISgMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIIDDLRKQDWVPRS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  85 TRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQ-------TAVDAM-----------SDAARTVApLDETVHDLVA 146
Cdd:PRK05911  105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQelsgwfsSARPALilslneefpcqSDDEAGLA-LEERIADERA 183

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2548811777 147 ADlplpGDDLLE-TEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLAA 221
Cdd:PRK05911  184 ET----GYDVVDkKEFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLRATLSA 255
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 5-220 8.11e-15

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 72.12  E-value: 8.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   5 ERNAMIVEHLPLVGYIVADVRSRAThlDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRG 84
Cdd:PRK07122   41 QRDRIVTRCLPLADHIARRFDGRGE--PRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKV 118

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  85 TRkRIRE-----TLATQEaLSARLGRSVGALEIADAMGVDKQTAVDAM--SDAARTVApLDETVHDLVAADLPLP---GD 154
Cdd:PRK07122  119 PR-RLKElhlrlGRATAE-LSQRLGRAPTASELAAELGMDREEVVEGLvaGSAYNTLS-IDSGGGSGDDDARAIAdtlGD 195

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2548811777 155 ---DLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGLA 220
Cdd:PRK07122  196 vdaGLDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLRDQLE 264
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 24-207 4.87e-14

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 69.95  E-value: 4.87e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  24 VRSRATHLDR------DDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRsadwaSRGTRKRI-------- 89
Cdd:PRK07408   38 VRKEAHRWSNqcsepyEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLR-----DKSPTVRIprrwqelq 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  90 RETLATQEALSARLGRSVGALEIADAMGVDKQTAVDA-MSDAARTVAPLDETVHDLVAADLPLpGDDL---------LET 159
Cdd:PRK07408  113 RQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIkLALQNRTPLSLDAPVNQDEDGSTSL-GDLLpdpryrsfqLAQ 191

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 2548811777 160 EKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQ 207
Cdd:PRK07408  192 EDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRR 239
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
13-206 9.98e-14

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 68.73  E-value: 9.98e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  13 HLPLVGYIVADVRSRATH-LDRDDLAAVGSLALVAAAEAFdptlGVP---FGAYARTRIAGALADDMRSADWASRGTRKR 88
Cdd:PRK12427   24 YLPLVKKVVRQLAFQADSvIDREDMEQIALMGLLEALRRY----GHPdeqFAAYAVHRIRGAILDELRELDWRPRRLRQK 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  89 IRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMS-DAARTVAPLDETVHDLVAADlPLPGDDLLET-EKRRYLR 166
Cdd:PRK12427  100 THKTNDAIREIAKRLGHEPNFEEISAELNLTAEEYQEYLLlENAGTLESLDELLALEAHND-ILQSRDLEENiIIEDNLK 178

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 2548811777 167 AAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQ 206
Cdd:PRK12427  179 QALSQLDEREQLILHLYYQHEMSLKEIALVLDLTEARICQ 218
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 25-219 1.06e-12

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 66.26  E-value: 1.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  25 RSRATHldrDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADWASRGTRkRIRE-----TLATQEaL 99
Cdd:PRK08583   51 KGQSHH---EDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPR-RIKElgpkiKKAVDE-L 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 100 SARLGRSVGALEIADAMGVDKQTAVDAMsDAARTVAPLdeTVHDLVAAD--------LPLPG---DDLLETEKRRYLRAA 168
Cdd:PRK08583  126 TTELQRSPKISEIADRLGVSEEEVLEAM-EMGKSYQAL--SVDHSIEADsdgstvtlLDIVGqqeDGYELTEQRMILEKI 202

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2548811777 169 VEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGL 219
Cdd:PRK08583  203 LPVLSDREKSIIQCTFIENLSQKETGERLGISQMHVSRLQRQAIKKLREAA 253
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 5-219 3.26e-11

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: 60.05  E-value: 3.26e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   5 ERNAMIVEHLPLVGYIVADVRSRatHLDRDDLAAVGSLALVAAAEAFDPtlGVPFGAYARTRIAGALADDMRSadwasrg 84
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGD--DADAEDLVQEAFLKLLEALDRFDP--EGSFKAWLFRIARNLILDYLRR------- 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  85 tRKRIRETLATQEALsarlgrsvgaleiadamgvdkqtavdamsdaartvapldetvhdlvAADLPLPGDDLLETEKRRY 164
Cdd:TIGR02937  71 -KRRLRRELDLLEEL----------------------------------------------LDSDPSPEEELEQEEEREA 103

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 165 LRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGL 219
Cdd:TIGR02937 104 LREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 1-215 4.34e-11

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: 61.61  E-value: 4.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   1 MDRTERNAMIVEHLPLVGYIVADVRSRatHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYA----RTRIAGALADDmr 76
Cdd:COG0568    27 GDEEAKRKLVEANLRLVVSIAKKYQGR--GLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYAtwwiRQAITRAIADQ-- 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  77 sadwaSR---------GTRKRIRETlatQEALSARLGRSVGALEIADAMGVDKQTAVDAMSDAARTV---APLDE----T 140
Cdd:COG0568   103 -----WRtirlpvhmaETLNKLRRA---KRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVsldAPVGDdedsE 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 141 VHDLVAAD-LPLPGDDLLETEKRRYLRAAVEALPERMRFIVEAVY--FGDRSVT--DVAAELGITHSAVSQQRSEAMRLL 215
Cdd:COG0568   175 LGDLLEDEeAPSPEEALEEELLREELREALDTLTEREREILRLRFglDDGEPHTleEIGKEFGVSRERVRQIEAKALRKL 254
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
2-216 9.82e-10

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 57.65  E-value: 9.82e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSRATHLDrdDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGA----LADD--M 75
Cdd:PRK08215   35 DKEAREKLINGNLRLVLSVIQRFNNRGENVD--DLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEirryLRDNnpI 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  76 RsadwASRGTRKRIRETLATQEALSARLGRSVGALEIADAMGVDKQTAVDAMsDAARTVAPLDETV-HDlvaadlplPGD 154
Cdd:PRK08215  113 R----VSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFAL-DAIQDPVSLFEPIyHD--------GGD 179

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 155 -----DLLETEKRR--------YLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSqqRSEAMRLLH 216
Cdd:PRK08215  180 piyvmDQISDEKNKdenwleeiALKEAMKKLNDREKLILNLRFFQGKTQMEVAEEIGISQAQVS--RLEKAALKH 252
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 122-222 1.48e-09

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: 56.16  E-value: 1.48e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 122 TAVDAMSDAARTVAPLDETVHDLvAADLPLPGDDLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITH 201
Cdd:COG1595    79 LAIDHLRKRRRRRELLDELAEEL-PDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                          90       100
                  ....*....|....*....|.
gi 2548811777 202 SAVSQQRSEAMRLLHDGLAAH 222
Cdd:COG1595   158 GTVKSRLSRARKKLREALEEE 178
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 9-160 5.10e-07

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 49.84  E-value: 5.10e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   9 MIVEHLPLVGYIVADVRSRatHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYA----RTRIAGALADDMRSADWASRG 84
Cdd:PRK05949   96 MIEANLRLVVAIAKKYQKR--NMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAywwiRQAITRAIAQQARTIRLPIHI 173

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2548811777  85 TRK--RIREtlaTQEALSARLGRSVGALEIADAMGVDKQTAVDAMSdAARTVAPLDETVHDLVAADLplpgDDLLETE 160
Cdd:PRK05949  174 TEKlnKIKK---TQRELSQKLGRSATPAEIAKELELEPSQIREYLS-MARQPISLDVRVGDNQDTEL----SELLEDE 243
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 2-222 5.27e-07

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 49.65  E-value: 5.27e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVgyIVADVRSRATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADD-MRSADW 80
Cdd:PRK07500   38 DEDALHRIISAHMRLV--ISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYiLRNWSI 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  81 ASRGTRKRIRETLATQEALSARLGRSVGAL-------EIADAMGV--------DKQTAVDAMSDAARTVAPLDETVH--D 143
Cdd:PRK07500  116 VRGGTSSAQKALFFNLRRLRARLAQADEELtkqeihrEIATALGVslsdvemmDARLSGPDASLNAPQSEEDEGRSErmD 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 144 LVAADLPLPGD---DLLETEKRR-YLRAAVEALPERMRFIVEAVYFGDRSVT--DVAAELGITHSAVSQQRSEAMRLLHD 217
Cdd:PRK07500  196 FLVDDSPLPDEqveSSIDGERRRrWLTQALQTLNERELRIIRERRLREDGATleALGEELGISKERVRQIEARALEKLRR 275


                  ....*
gi 2548811777 218 GLAAH 222
Cdd:PRK07500  276 ALLSQ 280
PRK08311 PRK08311
RNA polymerase sigma factor SigI;
2-77 1.52e-06

RNA polymerase sigma factor SigI;


Pssm-ID: 236233 [Multi-domain]  Cd Length: 237  Bit Score: 47.94  E-value: 1.52e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSRATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRS 77
Cdd:PRK08311   16 DEELREELIEEYKPFIAKVVSSVCGRYIDWENDDELSIGLIAFNEAIDSYDEEKGKSFLSFAELVIKRRLIDYFRK 91
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 9-80 2.53e-06

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: 44.12  E-value: 2.53e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2548811777   9 MIVEHLPLVGYIVAdvRSRATHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSADW 80
Cdd:pfam04542   1 LVERYLPLVYSLAR--RYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 162-215 4.57e-06

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: 42.86  E-value: 4.57e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2548811777 162 RRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLL 215
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 3-116 1.51e-05

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 45.54  E-value: 1.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   3 RTERNAMIVEHLPLVGYIVADVRSRATHLDrdDLAAVGSLALVAAAEAFDPTLGVPFGAYA----RTRIAGALADDMRSa 78
Cdd:PRK07406  135 RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQ--DLIQEGSLGLIRAAEKFDHEKGYKFSTYAtwwiRQAITRAIADQSRT- 211

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 2548811777  79 dwasrgtrkrIR------ETLA----TQEALSARLGRSVGALEIADAM 116
Cdd:PRK07406  212 ----------IRlpvhlyETISrikkTTKVLSQEFGRKPTEEEIAESM 249
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 168-215 2.92e-05

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: 40.49  E-value: 2.92e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2548811777 168 AVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLL 215
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 162-215 5.39e-05

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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 40.13  E-value: 5.39e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2548811777 162 RRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLL 215
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 115-217 1.11e-04

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 41.54  E-value: 1.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 115 AMGVDKQTAVDAMSDAARTVAPLDETVHDLVAADLPLPGDDLLEtEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVA 194
Cdd:TIGR02989  56 ARGIARNKVLNYRRKLGRDRLVFDDDLLEALAAEAEPTEAERLS-DDRQALEGCLEKLPERQRELLDLRYQRGQKATALA 134

                          90       100
                  ....*....|....*....|...
gi 2548811777 195 AELGITHSAVSQQRSEAMRLLHD 217
Cdd:TIGR02989 135 EQTGRTVNAVYKALQRIRVSLRE 157
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
130-204 1.29e-04

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 41.64  E-value: 1.29e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 130 AARTVAPLDEtVHDLVAADlplpgdDLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAV 204
Cdd:PRK12539   97 ASLADVPIDD-ADELVAHD------DHAAVESTLDLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAV 164
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 148-219 2.82e-04

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 40.24  E-value: 2.82e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2548811777 148 DLPLPGDDLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGITHSAVSQQRSEAMRLLHDGL 219
Cdd:TIGR02985  90 SEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
2-217 8.48e-04

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 39.93  E-value: 8.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777   2 DRTERNAMIVEHLPLVGYIVADVRSraTHLDRDDLAAVGSLALVAAAEAFDPTLGVPFGAYARTRIAGALADDMRSAdwa 81
Cdd:PRK05803   47 DEEARNILIERNLRLVAHIVKKFEN--TGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEILMHLRNL--- 121

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777  82 srgtrKRIRETLATQealsarlgrsvgaleiaDAMGVDKQ----TAVDAMSDAARTVaplDETVHdlvaadlplpgddlL 157
Cdd:PRK05803  122 -----KKTKKEVSLQ-----------------DPIGVDKEgneiSLIDILGSEEDDV---IEQVE--------------L 162

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2548811777 158 ETEKRRyLRAAVEALPERMRFIVEAVY--FGDRSVT--DVAAELGITHSAVSQQRSEA-MRLLHD 217
Cdd:PRK05803  163 KMEVEK-LYKKIDILDEREKEVIEMRYglGNGKEKTqrEIAKALGISRSYVSRIEKRAlKKLFKE 226
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 140-199 3.32e-03

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 37.75  E-value: 3.32e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2548811777 140 TVHDLVAADLPLPGDDLLETEKRRYLRAAVEALPERMRFIVEAVYFGDRSVTDVAAELGI 199
Cdd:PRK09641  105 TMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDL 164
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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