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Conserved domains on  [gi|970269053|ref|WP_058651676|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Enterobacter]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11466506)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 31-93 5.63e-12

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: 56.57  E-value: 5.63e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELSIDVTLPNGK 93
Cdd:COG3620  21 ALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
 
Name Accession Description Interval E-value
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 31-93 5.63e-12

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: 56.57  E-value: 5.63e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELSIDVTLPNGK 93
Cdd:COG3620  21 ALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
32-84 3.87e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 48.28  E-value: 3.87e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 970269053   32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELS 84
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 31-84 2.47e-08

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: 46.39  E-value: 2.47e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELS 84
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 7-88 3.00e-08

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 46.45  E-value: 3.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970269053   7 LMAQQSAESQERIAAKVEVMRRIvalNQLRDELNISQTELAVAMGVKQPTVAKIEQP-GNDPRLSTLKRYVSALGGELSI 85
Cdd:pfam13744  1 VFADLGFEDAEELQAKAQLARAI---ARLIEGRGLSQQEAAALLGIAQPKVSALLKGkLSRFSLDKLLDFLTALGQDVEI 77


                 ...
gi 970269053  86 DVT 88
Cdd:pfam13744 78 VVK 80
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 31-83 2.57e-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: 2.57e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970269053  31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGEL 83
Cdd:TIGR03070  6 LVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
31-80 1.16e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 34.96  E-value: 1.16e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALG 80
Cdd:PRK09726 16 AMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLE 65
 
Name Accession Description Interval E-value
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 31-93 5.63e-12

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: 56.57  E-value: 5.63e-12
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELSIDVTLPNGK 93
Cdd:COG3620  21 ALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
32-84 3.87e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 48.28  E-value: 3.87e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 970269053   32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELS 84
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 31-84 2.47e-08

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: 46.39  E-value: 2.47e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELS 84
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56
HTH_37 pfam13744
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.
 7-88 3.00e-08

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain.


Pssm-ID: 433449 [Multi-domain]  Cd Length: 80  Bit Score: 46.45  E-value: 3.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 970269053   7 LMAQQSAESQERIAAKVEVMRRIvalNQLRDELNISQTELAVAMGVKQPTVAKIEQP-GNDPRLSTLKRYVSALGGELSI 85
Cdd:pfam13744  1 VFADLGFEDAEELQAKAQLARAI---ARLIEGRGLSQQEAAALLGIAQPKVSALLKGkLSRFSLDKLLDFLTALGQDVEI 77


                 ...
gi 970269053  86 DVT 88
Cdd:pfam13744 78 VVK 80
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
32-80 1.58e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.60  E-value: 1.58e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 970269053 32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALG 80
Cdd:COG1396  12 LRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALG 60
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 32-84 3.23e-07

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: 43.30  E-value: 3.23e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970269053  32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELS 84
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
26-80 5.82e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 42.91  E-value: 5.82e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 970269053 26 MRRIVALN--QLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALG 80
Cdd:COG1476   1 MKKKLGNRlkELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG 57
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 34-80 2.26e-04

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: 36.45  E-value: 2.26e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 970269053 34 QLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALG 80
Cdd:COG1813  19 EAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALG 65
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 31-83 2.57e-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: 2.57e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970269053  31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGEL 83
Cdd:TIGR03070  6 LVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 32-80 4.95e-04

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: 35.20  E-value: 4.95e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 970269053  32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQ-PGNDPRLSTLKRYVSALG 80
Cdd:pfam13560  6 LRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALG 55
COG1709 COG1709
Predicted transcriptional regulator,contains XRE-type HTH domain [Transcription];
36-86 9.30e-04

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


Pssm-ID: 441315  Cd Length: 234  Bit Score: 36.31  E-value: 9.30e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 970269053  36 RDELNISQTELAVAMGVKQPTVAKIE-----QPGndprLSTLKRYVSALggeLSID 86
Cdd:COG1709   31 REDFGISQTELARELGVSPSVISDYEsgrrkSPG----IAFVKKFVEAL---LEID 79
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
31-80 1.16e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 34.96  E-value: 1.16e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 970269053 31 ALNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALG 80
Cdd:PRK09726 16 AMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLE 65
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
34-73 1.72e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 33.75  E-value: 1.72e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 970269053 34 QLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLK 73
Cdd:COG2944  13 ALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALK 52
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 32-80 1.85e-03

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: 33.80  E-value: 1.85e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 970269053  32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALG 80
Cdd:pfam12844  4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
32-84 8.45e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 33.61  E-value: 8.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 970269053  32 LNQLRDELNISQTELAVAMGVKQPTVAKIEQPGNDPRLSTLKRYVSALGGELS 84
Cdd:PRK09943  12 LSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLS 64
 
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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