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Conserved domains on  [gi|1002400960|ref|WP_061383534|]
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helix-turn-helix domain-containing protein [Salmonella enterica]

Protein Classification

winged helix-turn-helix transcriptional regulator( domain architecture ID 10004391)

winged helix-turn-helix (HTH) transcriptional regulator containing a HxlR family HTH domain; similar to HTH-type transcriptional regulator HxlR, a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|10679470|10908318

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HxlR COG1733
DNA-binding transcriptional regulator, HxlR family [Transcription];
20-112 7.02e-39

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


:

Pssm-ID: 441339  Cd Length: 108  Bit Score: 125.75  E-value: 7.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002400960  20 YTLSLISGKYKMIVMYWLNENKpvMRYNELKRRIGTISFKTLSNTLKELEQDGIINRVEYPQIPPKVEYSLSKRGESLMP 99
Cdd:COG1733    14 RALDVIGGKWKLLILRALLDGP--RRFGELRRSLPGISQKMLTQRLRELEEDGLVERTVYPEVPPRVEYSLTEKGRSLLP 91

                          90
                  ....*....|...
gi 1002400960 100 ILDLMCDWGGKNR 112
Cdd:COG1733    92 VLDALAEWGEEHL 104
 
Name Accession Description Interval E-value
HxlR COG1733
DNA-binding transcriptional regulator, HxlR family [Transcription];
20-112 7.02e-39

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


Pssm-ID: 441339  Cd Length: 108  Bit Score: 125.75  E-value: 7.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002400960  20 YTLSLISGKYKMIVMYWLNENKpvMRYNELKRRIGTISFKTLSNTLKELEQDGIINRVEYPQIPPKVEYSLSKRGESLMP 99
Cdd:COG1733    14 RALDVIGGKWKLLILRALLDGP--RRFGELRRSLPGISQKMLTQRLRELEEDGLVERTVYPEVPPRVEYSLTEKGRSLLP 91

                          90
                  ....*....|...
gi 1002400960 100 ILDLMCDWGGKNR 112
Cdd:COG1733    92 VLDALAEWGEEHL 104
HxlR pfam01638
HxlR-like helix-turn-helix; HxlR, a member of this family, is a DNA-binding protein that acts ...
 24-113 6.75e-37

HxlR-like helix-turn-helix; HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.


Pssm-ID: 460276 [Multi-domain]  Cd Length: 91  Bit Score: 120.10  E-value: 6.75e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002400960  24 LISGKYKMIVMYWLNENKpvMRYNELKRRIGTISFKTLSNTLKELEQDGIINRVEYPQIPPKVEYSLSKRGESLMPILDL 103
Cdd:pfam01638   1 LIGGKWKGLILRELLDGK--KRFSELKRAIPGITQKMLTQRLRELEQDGIINREVYPEVPPKVEYSLTEKGRSLEPILQE 78

                          90
                  ....*....|
gi 1002400960 104 MCDWGGKNRN 113
Cdd:pfam01638  79 LCDWGEEYLE 88
Fur_like cd07153
Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, ...
 46-80 7.05e-03

Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains.


Pssm-ID: 133478 [Multi-domain]  Cd Length: 116  Bit Score: 33.71  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002400960  46 YNELKRRIGTISFKTLSNTLKELEQDGIINRVEYP 80
Cdd:cd07153    23 YERLRKKGPSISLATVYRTLELLEEAGLVREIELG 57
 
Name Accession Description Interval E-value
HxlR COG1733
DNA-binding transcriptional regulator, HxlR family [Transcription];
20-112 7.02e-39

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


Pssm-ID: 441339  Cd Length: 108  Bit Score: 125.75  E-value: 7.02e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002400960  20 YTLSLISGKYKMIVMYWLNENKpvMRYNELKRRIGTISFKTLSNTLKELEQDGIINRVEYPQIPPKVEYSLSKRGESLMP 99
Cdd:COG1733    14 RALDVIGGKWKLLILRALLDGP--RRFGELRRSLPGISQKMLTQRLRELEEDGLVERTVYPEVPPRVEYSLTEKGRSLLP 91

                          90
                  ....*....|...
gi 1002400960 100 ILDLMCDWGGKNR 112
Cdd:COG1733    92 VLDALAEWGEEHL 104
HxlR pfam01638
HxlR-like helix-turn-helix; HxlR, a member of this family, is a DNA-binding protein that acts ...
 24-113 6.75e-37

HxlR-like helix-turn-helix; HxlR, a member of this family, is a DNA-binding protein that acts as a positive regulator of the formaldehyde-inducible hxlAB operon in Bacillus subtilis.


Pssm-ID: 460276 [Multi-domain]  Cd Length: 91  Bit Score: 120.10  E-value: 6.75e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1002400960  24 LISGKYKMIVMYWLNENKpvMRYNELKRRIGTISFKTLSNTLKELEQDGIINRVEYPQIPPKVEYSLSKRGESLMPILDL 103
Cdd:pfam01638   1 LIGGKWKGLILRELLDGK--KRFSELKRAIPGITQKMLTQRLRELEQDGIINREVYPEVPPKVEYSLTEKGRSLEPILQE 78

                          90
                  ....*....|
gi 1002400960 104 MCDWGGKNRN 113
Cdd:pfam01638  79 LCDWGEEYLE 88
FUR pfam01475
Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that ...
 46-79 2.45e-03

Ferric uptake regulator family; This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes. This family is also known as the FUR family.


Pssm-ID: 426280  Cd Length: 121  Bit Score: 34.91  E-value: 2.45e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1002400960  46 YNELKRRIGTISFKTLSNTLKELEQDGIINRVEY 79
Cdd:pfam01475  31 YKELREEDPNISLATVYRTLNLLEEAGLVKRLEF 64
Fur COG0735
Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];
46-78 3.34e-03

Fe2+ or Zn2+ uptake regulation protein Fur/Zur [Inorganic ion transport and metabolism];


Pssm-ID: 440498  Cd Length: 140  Bit Score: 34.93  E-value: 3.34e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1002400960  46 YNELKRRIGTISFKTLSNTLKELEQDGIINRVE 78
Cdd:COG0735    42 YEALRKKGPSISLATVYRTLDLLVEAGLVHRIE 74
Fur_like cd07153
Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, ...
 46-80 7.05e-03

Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators; Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions. For example, PerR, a metal-dependent sensor of hydrogen peroxide. PerR regulates DNA-binding activity through metal-based protein oxidation, and co-ordinates Mn2+ or Fe2+ at its regulatory site. Fur family proteins contain an N-terminal winged-helix DNA-binding domain followed by a dimerization domain; this CD spans both those domains.


Pssm-ID: 133478 [Multi-domain]  Cd Length: 116  Bit Score: 33.71  E-value: 7.05e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1002400960  46 YNELKRRIGTISFKTLSNTLKELEQDGIINRVEYP 80
Cdd:cd07153    23 YERLRKKGPSISLATVYRTLELLEEAGLVREIELG 57
 
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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