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Conserved domains on  [gi|447019960|ref|WP_001097216|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Enterobacterales]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10650117)

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
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-68 1.85e-10

Helix-turn-helix XRE-family like proteins;


:

Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.75  E-value: 1.85e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 447019960   20 FRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-68 1.85e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.75  E-value: 1.85e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 447019960   20 FRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
21-68 2.18e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 52.31  E-value: 2.18e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 447019960 21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:COG1396  16 RKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSL 63
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 21-68 4.88e-10

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: 50.62  E-value: 4.88e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 447019960  21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSL 52
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 20-68 5.18e-10

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: 50.63  E-value: 5.18e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 447019960 20 FRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:cd00093   7 LRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 21-68 2.64e-08

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: 46.11  E-value: 2.64e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 447019960  21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
12-70 8.79e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 40.35  E-value: 8.79e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 447019960 12 QLRPVLIGFRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEIVL 70
Cdd:PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL 70
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-68 1.85e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 51.75  E-value: 1.85e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 447019960   20 FRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSL 53
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
21-68 2.18e-10

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 52.31  E-value: 2.18e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 447019960 21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:COG1396  16 RKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSL 63
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
17-68 2.35e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 51.77  E-value: 2.35e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 447019960 17 LIGFRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:COG1476   9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSL 60
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 21-68 4.88e-10

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: 50.62  E-value: 4.88e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 447019960  21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSL 52
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 20-68 5.18e-10

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: 50.63  E-value: 5.18e-10
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 447019960 20 FRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:cd00093   7 LRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 13-68 1.55e-08

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: 47.71  E-value: 1.55e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 447019960 13 LRPVLIGFRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:COG3620  18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKEL 73
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 21-68 2.64e-08

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: 46.11  E-value: 2.64e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 447019960  21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:TIGR03070 11 RKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
12-70 8.79e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 40.35  E-value: 8.79e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 447019960 12 QLRPVLIGFRKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEIVL 70
Cdd:PRK09726 12 QLANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLELSMTL 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 21-68 2.67e-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: 38.42  E-value: 2.67e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 447019960  21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEI 68
Cdd:pfam12844  8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPA 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 21-69 1.35e-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: 36.84  E-value: 1.35e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 447019960 21 RKANGLTQKDVSERLGITQQTYARLEANPASAGFERLFRVFSVLGVEIV 69
Cdd:COG1813  21 REARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 20-68 2.13e-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: 33.66  E-value: 2.13e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 447019960  20 FRKANGLTQKDVSERLGITQQTYARLE---ANPASAGF-ERLFRVFSVLGVEI 68
Cdd:pfam13560  9 LRERAGLSQEALARRLGVSRSTLSRLEtgrRGRPSPAVvERLARALGVDGAER 61
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 21-60 3.15e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 34.14  E-value: 3.15e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 447019960   21 RKANGLTQKDVSERLGITQQTYARLE--ANPASAGFERLFRV 60
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYErgEVRPSKALDKLLRL 115
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 21-48 7.87e-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: 7.87e-03
                        10        20
                ....*....|....*....|....*...
gi 447019960 21 RKANGLTQKDVSERLGITQQTYARLEAN 48
Cdd:COG1426  14 REAKGLSLEDVAERTKISVSYLEAIEEG 41
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
22-73 7.91e-03

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 32.93  E-value: 7.91e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 447019960  22 KANGLTQKDVSERLGITQQTYARLeANPASAGF--ERLFRVFSVLG--VEIVLSSR 73
Cdd:COG5606   42 KERGLTQAEAAELLGITQPRVSDL-LRGKISKFslDKLVNMLARLGqdVEIVVRPA 96
 
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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