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Conserved domains on  [gi|1238239309|gb|PAM75891|]
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sigma-70 family RNA polymerase sigma factor [Bacillus subtilis]

Protein Classification

sigma-70 RNA polymerase sigma factor region 4 domain-containing protein( domain architecture ID 1001861)

sigma-70 RNA polymerase sigma factor region 4 domain-containing protein which may or may not bind DNA or function as a sigma factor.

Gene Ontology:  GO:0003677|GO:0016987|GO:0006352
PubMed:  1597408

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
sigma70-ECF super family cl37189
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-188 3.84e-07

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.


The actual alignment was detected with superfamily member TIGR02937:

Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 47.73  E-value: 3.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238239309  18 FEEVRERFLPMVYKTMKqansKFMFNQVEEEDFQQELELELWRAYEAYDSDtgYCFTTYLYpklrKGVRNATYSRYAQKN 97
Cdd:TIGR02937   3 FEELYERYLPLVYRYAR----RYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLF----RIARNLILDYLRRKR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238239309  98 QSNGVFsisspigDDDLKIEDMLAANDTSFDNIATNELLSIILKNVKEDEMDLLkIIIDVKNNPVNAYAKKHGLTRQAAN 177
Cdd:TIGR02937  73 RLRREL-------DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVL-VLRYLEGLSYKEIAEILGISVGTVK 144

                         170
                  ....*....|.
gi 1238239309 178 QRVIKLKKKLR 188
Cdd:TIGR02937 145 RRLKRARKKLR 155
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-188 3.84e-07

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: 47.73  E-value: 3.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238239309  18 FEEVRERFLPMVYKTMKqansKFMFNQVEEEDFQQELELELWRAYEAYDSDtgYCFTTYLYpklrKGVRNATYSRYAQKN 97
Cdd:TIGR02937   3 FEELYERYLPLVYRYAR----RYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLF----RIARNLILDYLRRKR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238239309  98 QSNGVFsisspigDDDLKIEDMLAANDTSFDNIATNELLSIILKNVKEDEMDLLkIIIDVKNNPVNAYAKKHGLTRQAAN 177
Cdd:TIGR02937  73 RLRREL-------DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVL-VLRYLEGLSYKEIAEILGISVGTVK 144

                         170
                  ....*....|.
gi 1238239309 178 QRVIKLKKKLR 188
Cdd:TIGR02937 145 RRLKRARKKLR 155
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 23-97 1.49e-05

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: 41.42  E-value: 1.49e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1238239309  23 ERFLPMVYKTMKqansKFMFNQVEEEDFQQELELELWRAYEAYDSDTGYCFTTYLYPKlrkgVRNATYSRYAQKN 97
Cdd:pfam04542   3 ERYLPLVYSLAR----RYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTI----IRNAIIDYLRKQR 69
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 49-92 7.38e-03

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 36.39  E-value: 7.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1238239309  49 DFQQELELELWRAYEAYDSDTGYCFTTYLYPKLRKGVRN--ATYSR 92
Cdd:PRK07598  204 DLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRaiATQSR 249
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 18-188 3.84e-07

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: 47.73  E-value: 3.84e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238239309  18 FEEVRERFLPMVYKTMKqansKFMFNQVEEEDFQQELELELWRAYEAYDSDtgYCFTTYLYpklrKGVRNATYSRYAQKN 97
Cdd:TIGR02937   3 FEELYERYLPLVYRYAR----RYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLF----RIARNLILDYLRRKR 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238239309  98 QSNGVFsisspigDDDLKIEDMLAANDTSFDNIATNELLSIILKNVKEDEMDLLkIIIDVKNNPVNAYAKKHGLTRQAAN 177
Cdd:TIGR02937  73 RLRREL-------DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVL-VLRYLEGLSYKEIAEILGISVGTVK 144

                         170
                  ....*....|.
gi 1238239309 178 QRVIKLKKKLR 188
Cdd:TIGR02937 145 RRLKRARKKLR 155
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 23-97 1.49e-05

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: 41.42  E-value: 1.49e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1238239309  23 ERFLPMVYKTMKqansKFMFNQVEEEDFQQELELELWRAYEAYDSDTGYCFTTYLYPKlrkgVRNATYSRYAQKN 97
Cdd:pfam04542   3 ERYLPLVYSLAR----RYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTI----IRNAIIDYLRKQR 69
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 49-92 7.38e-03

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 36.39  E-value: 7.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1238239309  49 DFQQELELELWRAYEAYDSDTGYCFTTYLYPKLRKGVRN--ATYSR 92
Cdd:PRK07598  204 DLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRaiATQSR 249
 
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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