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Conserved domains on  [gi|493782203|ref|WP_006730585|]
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DNA-directed RNA polymerase sigma-70 factor [Lactobacillus iners]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK08295 super family cl32289
RNA polymerase sporulation sigma factor SigH;
1-72 9.03e-10

RNA polymerase sporulation sigma factor SigH;


The actual alignment was detected with superfamily member PRK08295:

Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 55.30  E-value: 9.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493782203   1 MSDSELIMRVKQKDNDALQQLFVRYKPVVNKIKAQYYVRNYDYQDWDQEAMIVCYEACCLYDFERNSQFGAF 72
Cdd:PRK08295   9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-72 9.03e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 55.30  E-value: 9.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493782203   1 MSDSELIMRVKQKDNDALQQLFVRYKPVVNKIKAQYYVRNYDYQDWDQEAMIVCYEACCLYDFERNSQFGAF 72
Cdd:PRK08295   9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-108 3.19e-05

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: 41.95  E-value: 3.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493782203   16 DALQQLFVRYKPVVNKIKAQYYVRNYDYQDWDQEAMIVCYEACCLYDFERNsqFGAFYKTKFTNHVRSLLRyelaKRREA 95
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIARNLILDYLR----RKRRL 74

                          90
                  ....*....|...
gi 493782203   96 NRTAISYEYGNDA 108
Cdd:TIGR02937  75 RRELDLLEELLDS 87
 
Name Accession Description Interval E-value
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
1-72 9.03e-10

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 55.30  E-value: 9.03e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 493782203   1 MSDSELIMRVKQKDNDALQQLFVRYKPVVNKIKAQYYVRNYDYQDWDQEAMIVCYEACCLYDFERNSQFGAF 72
Cdd:PRK08295   9 LEDEELVELARSGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSF 80
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 16-108 3.19e-05

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: 41.95  E-value: 3.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493782203   16 DALQQLFVRYKPVVNKIKAQYYVRNYDYQDWDQEAMIVCYEACCLYDFERNsqFGAFYKTKFTNHVRSLLRyelaKRREA 95
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGS--FKAWLFRIARNLILDYLR----RKRRL 74

                          90
                  ....*....|...
gi 493782203   96 NRTAISYEYGNDA 108
Cdd:TIGR02937  75 RRELDLLEELLDS 87
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 1-96 2.80e-03

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 36.84  E-value: 2.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 493782203   1 MSDSELIMRVKQK---DNDALQQLFVRYKPVVNKIKAQYYVRNYDYQDWDQEAMI-VCYEaccLYDFERNSQFGAFYKTK 76
Cdd:PRK09640   8 LNDEELVARVHVElfhVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLkVLYG---LKNFEGKSKFKTWLYSI 84

                         90       100
                 ....*....|....*....|
gi 493782203  77 FTNHVRSLLRYELAKRREAN 96
Cdd:PRK09640  85 TYNECITQYRKERRKRRLMD 104
 
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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