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Conserved domains on  [gi|2638514629|ref|WP_322500623|]
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sigma-70 family RNA polymerase sigma factor [Streptomyces rochei]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 1001340)

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
PubMed:  33122819|16285916

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE super family cl34313
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 30-163 8.55e-04

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


The actual alignment was detected with superfamily member COG1595:

Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 38.05  E-value: 8.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2638514629  30 DLEQAVWLRLLERLATEGPPRDPYGWLRAA---VRAEARRARRTRRAERPYATEPADAAEREPEQLVLAAARRRALRTAV 106
Cdd:COG1595    46 DLVQETFLRLWRKLDSFRGRGSFRAWLYRIarnLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAAL 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2638514629 107 RRLPGRCPRLIEaLLSPDDLTYREIAGELGISQGSLGPERSRCLGCLRRLLTPEVAA 163
Cdd:COG1595   126 ERLPPRQREVLV-LRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 30-163 8.55e-04

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 38.05  E-value: 8.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2638514629  30 DLEQAVWLRLLERLATEGPPRDPYGWLRAA---VRAEARRARRTRRAERPYATEPADAAEREPEQLVLAAARRRALRTAV 106
Cdd:COG1595    46 DLVQETFLRLWRKLDSFRGRGSFRAWLYRIarnLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAAL 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2638514629 107 RRLPGRCPRLIEaLLSPDDLTYREIAGELGISQGSLGPERSRCLGCLRRLLTPEVAA 163
Cdd:COG1595   126 ERLPPRQREVLV-LRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-157 2.53e-03

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: 36.56  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2638514629  25 GAEPGDLEQAVWLRLLERLATEGPPRDPYGWLRAAVRAEARRARRTRRAERPYATEPADAAERE--PEQLVLAAARRRAL 102
Cdd:TIGR02937  25 DADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLDSDpsPEEELEQEEEREAL 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2638514629 103 RTAVRRLPGRCPRLIEaLLSPDDLTYREIAGELGISQGSLGPERSRCLGCLRRLL 157
Cdd:TIGR02937 105 REALEKLPEREREVLV-LRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 30-163 8.55e-04

DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; DNA-directed RNA polymerase specialized sigma subunit, sigma24 family is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441203 [Multi-domain]  Cd Length: 181  Bit Score: 38.05  E-value: 8.55e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2638514629  30 DLEQAVWLRLLERLATEGPPRDPYGWLRAA---VRAEARRARRTRRAERPYATEPADAAEREPEQLVLAAARRRALRTAV 106
Cdd:COG1595    46 DLVQETFLRLWRKLDSFRGRGSFRAWLYRIarnLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAAL 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2638514629 107 RRLPGRCPRLIEaLLSPDDLTYREIAGELGISQGSLGPERSRCLGCLRRLLTPEVAA 163
Cdd:COG1595   126 ERLPPRQREVLV-LRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGAL 181
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 25-157 2.53e-03

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: 36.56  E-value: 2.53e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2638514629  25 GAEPGDLEQAVWLRLLERLATEGPPRDPYGWLRAAVRAEARRARRTRRAERPYATEPADAAERE--PEQLVLAAARRRAL 102
Cdd:TIGR02937  25 DADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEELLDSDpsPEEELEQEEEREAL 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2638514629 103 RTAVRRLPGRCPRLIEaLLSPDDLTYREIAGELGISQGSLGPERSRCLGCLRRLL 157
Cdd:TIGR02937 105 REALEKLPEREREVLV-LRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
 
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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