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Conserved domains on  [gi|2498494916|ref|WP_280946495|]
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helix-turn-helix domain-containing protein [Saccharophagus degradans]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10578545)

helix-turn-helix (HTH) domain-containing protein may function in DNA binding; similar to excisionase

CATH:  1.10.1660.10
Gene Ontology:  GO:0003677
PubMed:  15808743

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 13-62 3.40e-16

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


:

Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 64.79  E-value: 3.40e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFKVGGSWRFKREDIERWIEEGK 62
Cdd:pfam12728  2 LTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLERRR 51
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 13-62 3.40e-16

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 64.79  E-value: 3.40e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFKVGGSWRFKREDIERWIEEGK 62
Cdd:pfam12728  2 LTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLERRR 51
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
6-66 3.97e-15

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 62.25  E-value: 3.97e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2498494916  6 NETTDQILTLKEVAAYLKLADKTAYKLAADGKLP-GFKVGG-SWRFKREDIERWIEEGKSRGK 66
Cdd:COG3311    2 SLPPDRLLRLKEVAELLGVSRSTIYRLIKKGEFPkPVKLGGrSVRWRESEVEAWLAARIAASR 64
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 13-60 1.20e-11

DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General]


Pssm-ID: 200128  Cd Length: 49  Bit Score: 53.37  E-value: 1.20e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFKVGGSWRFKREDIERWIEE 60
Cdd:TIGR01764  2 LTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRHYRIPREDVDEYLEQ 49
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 13-56 6.15e-04

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 33.71  E-value: 6.15e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFK-VGGSWRFKREDIER 56
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRtPGGHRRFPEEDLER 45
 
Name Accession Description Interval E-value
HTH_17 pfam12728
Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.
 13-62 3.40e-16

Helix-turn-helix domain; This domain is a DNA-binding helix-turn-helix domain.


Pssm-ID: 463684 [Multi-domain]  Cd Length: 51  Bit Score: 64.79  E-value: 3.40e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFKVGGSWRFKREDIERWIEEGK 62
Cdd:pfam12728  2 LTVEEAAELLGVSRRTVYRLIRSGELPAAKIGRRWRIRKSDLEEWLERRR 51
AlpA COG3311
DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];
6-66 3.97e-15

DNA-binding transcriptional regulator AlpA [Transcription, Mobilome: prophages, transposons];


Pssm-ID: 442540 [Multi-domain]  Cd Length: 64  Bit Score: 62.25  E-value: 3.97e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2498494916  6 NETTDQILTLKEVAAYLKLADKTAYKLAADGKLP-GFKVGG-SWRFKREDIERWIEEGKSRGK 66
Cdd:COG3311    2 SLPPDRLLRLKEVAELLGVSRSTIYRLIKKGEFPkPVKLGGrSVRWRESEVEAWLAARIAASR 64
excise TIGR01764
DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein ...
 13-60 1.20e-11

DNA binding domain, excisionase family; An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376). [Unknown function, General]


Pssm-ID: 200128  Cd Length: 49  Bit Score: 53.37  E-value: 1.20e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFKVGGSWRFKREDIERWIEE 60
Cdd:TIGR01764  2 LTVEEAAEYLGVSKSTVYRLIEEGELPAYRVGRHYRIPREDVDEYLEQ 49
HTH_MerR-trunc cd04762
Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family ...
 13-56 6.15e-04

Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins; Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.


Pssm-ID: 133390 [Multi-domain]  Cd Length: 49  Bit Score: 33.71  E-value: 6.15e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2498494916 13 LTLKEVAAYLKLADKTAYKLAADGKLPGFK-VGGSWRFKREDIER 56
Cdd:cd04762    1 LTTKEAAELLGVSPSTLRRWVKEGKLKAIRtPGGHRRFPEEDLER 45
 
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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