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Conserved domains on  [gi|2263815688|ref|WP_253196509|]
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sigma factor-like helix-turn-helix DNA-binding protein [Klebsiella pneumoniae]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 10550549)

sigma-70 family RNA polymerase sigma factor; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

PubMed:  11931761

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 10-44 8.66e-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: 39.75  E-value: 8.66e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2263815688  10 FLAAREEGKTYREIAEEFGMNVRSVERRgVRLARQ 44
Cdd:pfam08281  19 FLLRYLEGLSYAEIAELLGISEGTVKSR-LSRARK 52
 
Name Accession Description Interval E-value
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 10-44 8.66e-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: 39.75  E-value: 8.66e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2263815688  10 FLAAREEGKTYREIAEEFGMNVRSVERRgVRLARQ 44
Cdd:pfam08281  19 FLLRYLEGLSYAEIAELLGISEGTVKSR-LSRARK 52
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 10-44 8.01e-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: 8.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2263815688  10 FLAAREEGKTYREIAEEFGMNVRSVERRgVRLARQ 44
Cdd:TIGR02937 119 LVLRYLEGLSYKEIAEILGISVGTVKRR-LKRARK 152
 
Name Accession Description Interval E-value
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 10-44 8.66e-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: 39.75  E-value: 8.66e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2263815688  10 FLAAREEGKTYREIAEEFGMNVRSVERRgVRLARQ 44
Cdd:pfam08281  19 FLLRYLEGLSYAEIAELLGISEGTVKSR-LSRARK 52
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 10-44 8.01e-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: 8.01e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2263815688  10 FLAAREEGKTYREIAEEFGMNVRSVERRgVRLARQ 44
Cdd:TIGR02937 119 LVLRYLEGLSYKEIAEILGISVGTVKRR-LKRARK 152
 
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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