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Conserved domains on  [gi|2203696215|ref|WP_240386278|]
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helix-turn-helix transcriptional regulator [Balneola vulgaris]

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];
5-54 4.69e-22

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 79.51  E-value: 4.69e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVFSYS 54
Cdd:COG1476   18 LTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
5-54 4.69e-22

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 79.51  E-value: 4.69e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVFSYS 54
Cdd:COG1476   18 LTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-50 4.20e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.07  E-value: 4.20e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2203696215   5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:smart00530 11 LTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-50 4.87e-13

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: 56.39  E-value: 4.87e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:pfam01381 10 LSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-50 5.35e-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: 56.41  E-value: 5.35e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:cd00093   13 LTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-44 4.89e-06

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: 38.79  E-value: 4.89e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFN 44
Cdd:TIGR03070 16 LTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
5-52 5.11e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 32.46  E-value: 5.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2203696215   5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVFS 52
Cdd:PRK09943   21 LSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFS 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
5-54 4.69e-22

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 79.51  E-value: 4.69e-22
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVFSYS 54
Cdd:COG1476   18 LTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-50 4.20e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 59.07  E-value: 4.20e-14
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2203696215   5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:smart00530 11 LTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-50 4.87e-13

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: 56.39  E-value: 4.87e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:pfam01381 10 LSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-50 5.35e-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: 56.41  E-value: 5.35e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:cd00093   13 LTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
5-52 9.57e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.54  E-value: 9.57e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVFS 52
Cdd:COG1396   21 LTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLG 68
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 5-47 2.02e-10

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: 50.32  E-value: 2.02e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPI 47
Cdd:COG1813   26 LSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISL 68
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-50 9.49e-09

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: 46.55  E-value: 9.49e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEV 50
Cdd:COG3620   31 LSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 5-44 1.27e-07

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 43.64  E-value: 1.27e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFN 44
Cdd:COG3093   23 LSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFG 62
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-51 3.95e-07

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: 41.89  E-value: 3.95e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVF 51
Cdd:pfam12844 13 LTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-44 4.89e-06

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: 38.79  E-value: 4.89e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFN 44
Cdd:TIGR03070 16 LTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 3-22 3.90e-04

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 34.18  E-value: 3.90e-04
                         10        20
                 ....*....|....*....|
gi 2203696215  3 GEMTQQELADKVGVTRQTIN 22
Cdd:cd00092   24 LPLTRQEIADYLGLTRETVS 43
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 5-24 6.65e-04

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 33.58  E-value: 6.65e-04
                         10        20
                 ....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAI 24
Cdd:pfam13545 23 LTQEDLADLLGTTRETVSRV 42
HTH_CRP smart00419
helix_turn_helix, cAMP Regulatory protein;
5-22 7.09e-04

helix_turn_helix, cAMP Regulatory protein;


Pssm-ID: 128696 [Multi-domain]  Cd Length: 48  Bit Score: 33.18  E-value: 7.09e-04
                          10
                  ....*....|....*...
gi 2203696215   5 MTQQELADKVGVTRQTIN 22
Cdd:smart00419  9 LTRQEIAELLGLTRETVS 26
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 5-44 1.23e-03

addiction module antidote protein, HigA family; Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair. [Regulatory functions, DNA interactions, Regulatory functions, Protein interactions, Mobile and extrachromosomal element functions, Other]


Pssm-ID: 274228 [Multi-domain]  Cd Length: 78  Bit Score: 32.97  E-value: 1.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFN 44
Cdd:TIGR02607 19 LSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALG 58
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
5-53 1.41e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 32.81  E-value: 1.41e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAK-YSPSLVLAFKIAHAFNKPIHEVFSY 53
Cdd:COG3655   15 MTKKELAEATGISRATLSRLKNGKaKAVRLDTLEKICKALDCQPGDLLEY 64
parB_part TIGR00180
ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core ...
 3-48 2.59e-03

ParB/RepB/Spo0J family partition protein; This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.


Pssm-ID: 272946 [Multi-domain]  Cd Length: 187  Bit Score: 33.51  E-value: 2.59e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2203696215   3 GEMTQQELADKVGVTRQTI-NAIEAAKYSPSLVLAFKIAHAFNKPIH 48
Cdd:TIGR00180 119 FSMTQEDLAKKIGKSRAHItNLLRLLKLPSEIQSAIPEASGLLSSGH 165
DUF1323 pfam07037
Putative transcription regulator (DUF1323); This family consists of several hypothetical ...
 5-22 4.95e-03

Putative transcription regulator (DUF1323); This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. This family appears to have an HTH domain and is therefore likely to act as a transcriptional regulator.


Pssm-ID: 399786  Cd Length: 122  Bit Score: 32.14  E-value: 4.95e-03
                          10
                  ....*....|....*...
gi 2203696215   5 MTQQELADKVGVTRQTIN 22
Cdd:pfam07037   1 MTPEELAECLGYARQTIN 18
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
5-52 5.11e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 32.46  E-value: 5.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2203696215   5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPIHEVFS 52
Cdd:PRK09943   21 LSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFS 68
Crp COG0664
cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal ...
 5-24 7.35e-03

cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms];


Pssm-ID: 440428 [Multi-domain]  Cd Length: 207  Bit Score: 32.27  E-value: 7.35e-03
                          10        20
                  ....*....|....*....|
gi 2203696215   5 MTQQELADKVGVTRQTINAI 24
Cdd:COG0664   159 LTQEEIASYLGLTRETVSRI 178
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 5-47 7.70e-03

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 31.65  E-value: 7.70e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2203696215   5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHAFNKPI 47
Cdd:PRK13890   19 MTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPL 61
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
5-42 9.45e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 31.10  E-value: 9.45e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2203696215  5 MTQQELADKVGVTRQTINAIEAAKYSPSLVLAFKIAHA 42
Cdd:PRK09726  26 WTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQS 63
 
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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