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Conserved domains on  [gi|1216320795|ref|WP_089144481|]
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helix-turn-helix transcriptional regulator [Ligilactobacillus agilis]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10054599)

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
HipB super family cl34252
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
8-49 1.11e-03

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


The actual alignment was detected with superfamily member COG1396:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 37.28  E-value: 1.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1216320795   8 AQRKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLC 49
Cdd:COG1396    14 ELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLA 56
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
8-49 1.11e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 37.28  E-value: 1.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1216320795   8 AQRKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLC 49
Cdd:COG1396    14 ELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLA 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 10-50 2.27e-03

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: 35.61  E-value: 2.27e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1216320795  10 RKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLCA 50
Cdd:cd00093     8 RKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAK 49
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-49 2.50e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.57  E-value: 2.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1216320795   10 RKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLC 49
Cdd:smart00530   6 REEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLA 46
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-49 6.01e-03

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: 34.44  E-value: 6.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1216320795   8 AQRKKLGLTQVTLCQGIC-TQATLSKFERGSQLPSLAILTQLC 49
Cdd:pfam01381   3 ELREELGLSQEELAEKLGvSRSTISKIENGKREPSLETLKKLA 45
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
8-49 1.11e-03

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 37.28  E-value: 1.11e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1216320795   8 AQRKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLC 49
Cdd:COG1396    14 ELRKARGLTQEELAERLgVSRSTISRIERGRRNPSLETLLKLA 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 10-50 2.27e-03

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: 35.61  E-value: 2.27e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1216320795  10 RKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLCA 50
Cdd:cd00093     8 RKEKGLTQEELAEKLgVSRSTISRIENGKRNPSLETLEKLAK 49
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-49 2.50e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.57  E-value: 2.50e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|.
gi 1216320795   10 RKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLC 49
Cdd:smart00530   6 REEKGLTQEELAEKLgVSRSTLSRIENGKRKPSLETLKKLA 46
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 10-51 3.35e-03

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: 35.68  E-value: 3.35e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1216320795  10 RKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLCAR 51
Cdd:COG1813    21 REARGLSQEELAEKLgVSESTIRRIERGEATPSLDTLRKLEKA 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-49 6.01e-03

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: 34.44  E-value: 6.01e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1216320795   8 AQRKKLGLTQVTLCQGIC-TQATLSKFERGSQLPSLAILTQLC 49
Cdd:pfam01381   3 ELREELGLSQEELAEKLGvSRSTISKIENGKREPSLETLKKLA 45
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
10-50 9.67e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.05  E-value: 9.67e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1216320795  10 RKKLGLTQVTLCQGI-CTQATLSKFERGSQLPSLAILTQLCA 50
Cdd:COG1476    13 RKERGLTQEELAELLgVSRQTISAIENGKYNPSLELALKIAR 54
 
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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