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Conserved domains on  [gi|502796709|ref|WP_013031685|]
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helix-turn-helix transcriptional regulator [Nitrosococcus halophilus]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
62-123 2.54e-16

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.95  E-value: 2.54e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 502796709  62 NPLKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDLYPLSE 123
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
62-123 2.54e-16

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.95  E-value: 2.54e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 502796709  62 NPLKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDLYPLSE 123
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 64-118 9.88e-13

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 58.33  E-value: 9.88e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709  64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
64-118 2.06e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.53  E-value: 2.06e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709    64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 64-118 1.02e-09

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 50.62  E-value: 1.02e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709   64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 68-118 4.26e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 44.17  E-value: 4.26e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 502796709  68 RTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:PRK08154  37 RARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL 87
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 64-111 5.06e-04

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 35.71  E-value: 5.06e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 502796709   64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTL 111
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
62-123 2.54e-16

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 67.95  E-value: 2.54e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 502796709  62 NPLKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDLYPLSE 123
Cdd:COG1476    7 NRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
64-118 9.65e-15

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 64.25  E-value: 9.65e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709  64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:COG1396   12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 64-118 9.88e-13

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 58.33  E-value: 9.88e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709  64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
64-118 2.06e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 57.53  E-value: 2.06e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709    64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 64-124 1.72e-10

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 53.49  E-value: 1.72e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502796709  64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDLYPLSEG 124
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDG 82
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 64-118 1.02e-09

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 50.62  E-value: 1.02e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 502796709   64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 68-117 1.25e-09

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 50.71  E-value: 1.25e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 502796709  68 RTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDD 117
Cdd:COG1813   21 REARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 64-118 1.18e-06

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 42.90  E-value: 1.18e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 502796709   64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKG-TIKVLKRIAQTLRVDIDDL 118
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGRpSPAVVERLARALGVDGAER 61
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 64-118 1.77e-06

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 42.53  E-value: 1.77e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 502796709   64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKG-TIKVLKRIAQTLRVDIDDL 118
Cdd:pfam13443   2 LRKLMADRGISKSDLARATGISRATLSRLRKGKPKRvSLDTLDKICDALGCQPGDL 57
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 68-118 4.26e-06

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 44.17  E-value: 4.26e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 502796709  68 RTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDL 118
Cdd:PRK08154  37 RARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL 87
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 71-121 8.37e-06

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 40.73  E-value: 8.37e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 502796709   71 RGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDIDDLYPL 121
Cdd:pfam12844  11 RGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQG 61
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
62-118 9.80e-06

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 40.51  E-value: 9.80e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 502796709  62 NPLKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKG-TIKVLKRIAQTLRVDIDDL 118
Cdd:COG3655    4 VKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAvRLDTLEKICKALDCQPGDL 61
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
61-116 1.50e-05

Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];


Pssm-ID: 441315  Cd Length: 234  Bit Score: 42.47  E-value: 1.50e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502796709  61 ENP---LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERK--GtIKVLKRIAQTLrVDID 116
Cdd:COG1709   21 DDPgetLRKWREDFGISQTELARELGVSPSVISDYESGRRKspG-IAFVKKFVEAL-LEID 79
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
62-113 1.88e-05

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 40.35  E-value: 1.88e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 502796709  62 NPLKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRV 113
Cdd:PRK09726  15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLEL 66
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 64-118 1.05e-04

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 37.86  E-value: 1.05e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 502796709  64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKG------TIKVLKRIAQTLRVDIDDL 118
Cdd:COG1426   10 LRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDAlpgpvyVRGFLRSYARALGLDPEEL 70
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 64-111 5.06e-04

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 35.71  E-value: 5.06e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 502796709   64 LKVWRTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTL 111
Cdd:TIGR03070   7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
PHA01976 PHA01976
helix-turn-helix protein
 68-116 9.29e-03

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 32.62  E-value: 9.29e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 502796709  68 RTYRGLTQAQLAEQVGLSQSHLVTMEKGERKGTIKVLKRIAQTLRVDID 116
Cdd:PHA01976  11 RNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLD 59
 
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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