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Conserved domains on  [gi|1938362415|ref|YP_009956694|]
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HTH DNA binding protein [Mycobacterium phage Empress]

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 ...
 4-61 2.27e-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.


The actual alignment was detected with superfamily member TIGR02937:

Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 33.86  E-value: 2.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1938362415   4 ADRLAQNRVKRQKVAAEMSELTSEMFDLVKAAYADGMPAPEIARQAGITRGRVYQIIR 61
Cdd:TIGR02937  91 PEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-61 2.27e-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: 33.86  E-value: 2.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1938362415   4 ADRLAQNRVKRQKVAAEMSELTSEMFDLVKAAYADGMPAPEIARQAGITRGRVYQIIR 61
Cdd:TIGR02937  91 PEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
22-63 2.93e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 31.56  E-value: 2.93e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1938362415 22 SELTSEMFDLVKAAYADGMPAPEIARQAGITRGRVYQIIRGE 63
Cdd:pfam02796  4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
 
Name Accession Description Interval E-value
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 4-61 2.27e-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: 33.86  E-value: 2.27e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1938362415   4 ADRLAQNRVKRQKVAAEMSELTSEMFDLVKAAYADGMPAPEIARQAGITRGRVYQIIR 61
Cdd:TIGR02937  91 PEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLK 148
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
22-63 2.93e-03

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 31.56  E-value: 2.93e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1938362415 22 SELTSEMFDLVKAAYADGMPAPEIARQAGITRGRVYQIIRGE 63
Cdd:pfam02796  4 PKLNEEDINEVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
HTH_28 pfam13518
Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is ...
 35-61 3.16e-03

Helix-turn-helix domain; This helix-turn-helix domain is often found in transposases and is likely to be DNA-binding.


Pssm-ID: 463908 [Multi-domain]  Cd Length: 52  Bit Score: 31.79  E-value: 3.16e-03
                         10        20
                 ....*....|....*....|....*..
gi 1938362415 35 AYADGMPAPEIARQAGITRGRVYQIIR 61
Cdd:pfam13518  8 LALEGESIKEAARLFGISRSTVYRWIR 34
 
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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