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Conserved domains on  [gi|515665454|ref|WP_017098054|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Vibrio]

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];
22-77 1.73e-12

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 57.17  E-value: 1.73e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKI 77
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
22-77 1.73e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 57.17  E-value: 1.73e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKI 77
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 23-78 1.58e-11

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: 54.48  E-value: 1.58e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454  23 GEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 22-77 3.32e-10

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: 51.12  E-value: 3.32e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454   22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKI 77
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
26-78 7.83e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.82  E-value: 7.83e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 515665454    26 IKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 26-78 1.78e-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: 49.08  E-value: 1.78e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 515665454   26 IKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
15-99 2.00e-04

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 36.88  E-value: 2.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515665454  15 QVFTPSLLGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKISIQPWQdlDASVSSQEK 94
Cdd:PRK09726   6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK--NASPESTEQ 83


                 ....*
gi 515665454  95 GNDVW 99
Cdd:PRK09726  84 QDLEW 88
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
22-77 1.73e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 57.17  E-value: 1.73e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKI 77
Cdd:COG1476    5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
22-78 3.04e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.93  E-value: 3.04e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:COG1396    8 LGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLD 64
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 23-78 1.58e-11

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: 54.48  E-value: 1.58e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454  23 GEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLD 56
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 22-77 3.32e-10

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: 51.12  E-value: 3.32e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454   22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKI 77
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 22-78 6.48e-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: 51.17  E-value: 6.48e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELS 74
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
26-78 7.83e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 49.82  E-value: 7.83e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 515665454    26 IKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 26-78 1.78e-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: 49.08  E-value: 1.78e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 515665454   26 IKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 22-78 1.25e-06

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: 42.23  E-value: 1.25e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 23-78 8.56e-05

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: 37.27  E-value: 8.56e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 515665454   23 GEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKIS 78
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPAN 56
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
19-57 1.25e-04

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.84  E-value: 1.25e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 515665454  19 PSLLGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQG 57
Cdd:COG2944    4 KPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQG 42
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
15-99 2.00e-04

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 36.88  E-value: 2.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 515665454  15 QVFTPSLLGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQGSSDIKLTSLMKVVSALGIKISIQPWQdlDASVSSQEK 94
Cdd:PRK09726   6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTLCDAK--NASPESTEQ 83


                 ....*
gi 515665454  95 GNDVW 99
Cdd:PRK09726  84 QDLEW 88
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 22-57 1.03e-03

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: 34.43  E-value: 1.03e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 515665454   22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQG 57
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETG 37
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 22-57 7.72e-03

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: 32.47  E-value: 7.72e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 515665454  22 LGEAIKAKRTQSKITQQDAALLSGVSKQTYIKIEQG 57
Cdd:COG1426    6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEG 41
 
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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