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Conserved domains on  [gi|399498830|ref|YP_006560589|]
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sigma-70 family RNA polymerase sigma factor [Salmonella phage vB_SemP_Emek]

Protein Classification

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]; ...
 67-94 8.63e-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: 36.13  E-value: 8.63e-04
                         10        20
                 ....*....|....*....|....*...
gi 399498830  67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:COG1595  143 GLSYAEIAEILGISEGTVKSRLSRARKK 170
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 67-94 8.63e-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: 36.13  E-value: 8.63e-04
                         10        20
                 ....*....|....*....|....*...
gi 399498830  67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:COG1595  143 GLSYAEIAEILGISEGTVKSRLSRARKK 170
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 67-94 1.57e-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: 35.40  E-value: 1.57e-03
                          10        20
                  ....*....|....*....|....*...
gi 399498830   67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:TIGR02937 126 GLSYKEIAEILGISVGTVKRRLKRARKK 153
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 67-94 2.05e-03

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: 33.20  E-value: 2.05e-03
                         10        20
                 ....*....|....*....|....*...
gi 399498830  67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:pfam08281 26 GLSYAEIAELLGISEGTVKSRLSRARKK 53
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 63-94 2.40e-03

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 33.27  E-value: 2.40e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 399498830   63 LISSGYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:smart00421 14 LLAEGLTNKEIAERLGISEKTVKTHLSNIMRK 45
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 67-94 8.63e-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: 36.13  E-value: 8.63e-04
                         10        20
                 ....*....|....*....|....*...
gi 399498830  67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:COG1595  143 GLSYAEIAEILGISEGTVKSRLSRARKK 170
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 67-94 1.57e-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: 35.40  E-value: 1.57e-03
                          10        20
                  ....*....|....*....|....*...
gi 399498830   67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:TIGR02937 126 GLSYKEIAEILGISVGTVKRRLKRARKK 153
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
63-94 2.03e-03

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 35.50  E-value: 2.03e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 399498830  63 LISSGYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:COG2771  138 LLAEGLTLKEIARILGISERTVRTHLKRIYRK 169
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 67-94 2.05e-03

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: 33.20  E-value: 2.05e-03
                         10        20
                 ....*....|....*....|....*...
gi 399498830  67 GYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:pfam08281 26 GLSYAEIAELLGISEGTVKSRLSRARKK 53
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 63-94 2.40e-03

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 33.27  E-value: 2.40e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 399498830   63 LISSGYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:smart00421 14 LLAEGLTNKEIAERLGISEKTVKTHLSNIMRK 45
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 63-94 2.90e-03

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 34.48  E-value: 2.90e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 399498830  63 LISSGYTQRNVAKILGRSEESVKSRLSRLRKK 94
Cdd:COG2197   80 LLAEGLSNKEIAERLGISERTVKTHVSNILRK 111
 
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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