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Conserved domains on  [gi|2772484915|ref|WP_367294348|]
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helix-turn-helix transcriptional regulator [Latilactobacillus sakei]

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];
1-61 2.42e-17

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.19  E-value: 2.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDML 61
Cdd:COG1476     4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-61 2.42e-17

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.19  E-value: 2.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDML 61
Cdd:COG1476     4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-59 1.77e-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: 62.19  E-value: 1.77e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915   6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:cd00093     4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-59 7.30e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.22  E-value: 7.30e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915    6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-59 1.05e-12

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: 59.86  E-value: 1.05e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915   6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDE 54
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 1-49 1.10e-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: 38.79  E-value: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAI 49
Cdd:TIGR03070   2 QIGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRV 50
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-51 1.36e-04

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 40.22  E-value: 1.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISN 51
Cdd:PRK09706    5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAK 55
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-61 2.42e-17

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 72.19  E-value: 2.42e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDML 61
Cdd:COG1476     4 KLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-74 1.29e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 70.80  E-value: 1.29e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDMLKQDTNYLNKVAND 74
Cdd:COG1396     7 ALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-59 1.77e-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: 62.19  E-value: 1.77e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915   6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:cd00093     4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-59 7.30e-13

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.22  E-value: 7.30e-13
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915    6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDE 55
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-59 1.05e-12

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: 59.86  E-value: 1.05e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915   6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDE 54
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 6-62 2.68e-10

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: 53.83  E-value: 2.68e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2772484915   6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDMLK 62
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQ 60
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-59 2.68e-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: 51.48  E-value: 2.68e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2772484915   2 LATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDD 59
Cdd:COG1813    13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-54 3.17e-08

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 48.39  E-value: 3.17e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYD 54
Cdd:COG2944     6 LTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLRLLEK 59
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 2-60 1.62e-07

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: 46.37  E-value: 1.62e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772484915   2 LATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNY-PDVPMLVAISNLYDLSLDDM 60
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGAER 61
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-61 1.96e-06

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: 44.24  E-value: 1.96e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2772484915   2 LATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDML 61
Cdd:COG3620    18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 12-67 5.05e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.18  E-value: 5.05e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2772484915  12 DLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISNLYDLSLDDMLKQDTNY 67
Cdd:COG3093    20 PLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAY 75
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 1-49 1.10e-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: 38.79  E-value: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAI 49
Cdd:TIGR03070   2 QIGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRV 50
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 1-51 1.36e-04

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 40.22  E-value: 1.36e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTISNWENGKNYPDVPMLVAISN 51
Cdd:PRK09706    5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAK 55
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 6-61 2.53e-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: 2.53e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2772484915   6 LKKRRIDLHLTQQAVADQLHTSRQTISNWENGkNYPDVP-------MLVAISNLYDLSLDDML 61
Cdd:COG1426    10 LRQAREAKGLSLEDVAERTKISVSYLEAIEEG-DFDALPgpvyvrgFLRSYARALGLDPEELL 71
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 1-32 5.38e-03

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: 34.35  E-value: 5.38e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2772484915   1 MLATTLKKRRIDLHLTQQAVADQLHTSRQTIS 32
Cdd:pfam13545   9 ELAARDGGGRIDLPLTQEDLADLLGTTRETVS 40
 
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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