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Conserved domains on  [gi|1774348485|gb|QGF61058|]
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helix-turn-helix domain-containing protein [Listeria monocytogenes]

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];
4-68 2.27e-20

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 77.58  E-value: 2.27e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774348485   4 NKFVGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDFFPE 68
Cdd:COG1476     2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-68 2.27e-20

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 77.58  E-value: 2.27e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774348485   4 NKFVGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDFFPE 68
Cdd:COG1476     2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-65 5.11e-17

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: 68.73  E-value: 5.11e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDF 65
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-65 1.04e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 67.93  E-value: 1.04e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1774348485   10 KIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDF 65
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-65 2.11e-16

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: 67.18  E-value: 2.11e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1774348485  11 IKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDF 65
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK04140 PRK04140
transcriptional regulator;
8-104 1.89e-08

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 50.24  E-value: 1.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLD------DFFPERNLPPVDErlvti 81
Cdd:PRK04140  128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTkpidilEKVRDDEVTPEDP----- 202

                          90       100
                  ....*....|....*....|...
gi 1774348485  82 aahiDDDVTEEEMRDILAYIEMK 104
Cdd:PRK04140  203 ----EEDPFEKEILNVLTRLGFD 221
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 7-62 1.37e-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: 42.26  E-value: 1.37e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1774348485   7 VGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRL 62
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
4-68 2.27e-20

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 77.58  E-value: 2.27e-20
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774348485   4 NKFVGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDFFPE 68
Cdd:COG1476     2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSL 66
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-66 2.82e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 70.03  E-value: 2.82e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1774348485   2 ELNKFVGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDFF 66
Cdd:COG1396     3 TLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 8-65 5.11e-17

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: 68.73  E-value: 5.11e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDF 65
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
10-65 1.04e-16

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 67.93  E-value: 1.04e-16
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1774348485   10 KIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDF 65
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 11-65 2.11e-16

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: 67.18  E-value: 2.11e-16
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1774348485  11 IKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDF 65
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-64 6.76e-14

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: 61.11  E-value: 6.76e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1774348485   2 ELNKFVGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDD 64
Cdd:COG1813     8 ELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 8-59 1.23e-09

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: 49.98  E-value: 1.23e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFN 59
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 7-70 1.34e-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: 48.09  E-value: 1.34e-08
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1774348485   7 VGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDFFPERN 70
Cdd:COG3620    18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDD 81
PRK04140 PRK04140
transcriptional regulator;
8-104 1.89e-08

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 50.24  E-value: 1.89e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLD------DFFPERNLPPVDErlvti 81
Cdd:PRK04140  128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTkpidilEKVRDDEVTPEDP----- 202

                          90       100
                  ....*....|....*....|...
gi 1774348485  82 aahiDDDVTEEEMRDILAYIEMK 104
Cdd:PRK04140  203 ----EEDPFEKEILNVLTRLGFD 221
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 8-44 7.95e-08

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: 45.60  E-value: 7.95e-08
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDR 44
Cdd:pfam13560   3 GARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRR 39
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
8-98 9.36e-08

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 48.29  E-value: 9.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFN----KRLDDFFPERNLPPVDERlvtiaa 83
Cdd:COG1395   129 GEKLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGepivKPIDILEGAEDLEEAEPT------ 202

                          90
                  ....*....|....*
gi 1774348485  84 hiDDDVTEEEMRDIL 98
Cdd:COG1395   203 --PEDPEEEEILEVL 215
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 14-59 2.83e-07

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 44.41  E-value: 2.83e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1774348485  14 YREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFN 59
Cdd:COG3093    17 FLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFG 62
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 7-62 1.37e-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: 42.26  E-value: 1.37e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1774348485   7 VGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRL 62
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 7-46 4.42e-06

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: 40.94  E-value: 4.42e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1774348485   7 VGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKA 46
Cdd:COG1426     6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDA 45
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
9-66 1.69e-04

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 37.04  E-value: 1.69e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1774348485   9 NKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKA-NQDVLFELAKIFNKRLDDFF 66
Cdd:COG3655     4 VKLDELLAERGMTKKELAEATGISRATLSRLKNGKAKAvRLDTLEKICKALDCQPGDLL 62
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 7-43 6.02e-04

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: 36.45  E-value: 6.02e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1774348485   7 VGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGD 43
Cdd:TIGR03830  66 TGPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGE 102
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
8-84 1.76e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 35.93  E-value: 1.76e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1774348485   8 GNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKIFNKRLDDFFPERNLPpvDERLVTIAAH 84
Cdd:PRK09943    9 GKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFFSEPEKP--DEPQVVINQD 83
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-57 6.16e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 34.06  E-value: 6.16e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1774348485   4 NKFVGNKIKQYREERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFELAKI 57
Cdd:PRK09706    3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKA 56
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
17-103 8.03e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 33.26  E-value: 8.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1774348485  17 ERGLNQEALAEKLHTTRQTISRYENGDRKANQDVLFelakifnkrlddffpernlppvDERLVTIAAHIDDDVTEEEMRD 96
Cdd:COG2522    26 ERGLSQSEIAKLLGITQAAVSQYLSGKRGASERIEF----------------------DEEIKELIEELAEGLASGKPED 83


                  ....*..
gi 1774348485  97 ILAYIEM 103
Cdd:COG2522    84 ALAEICR 90
 
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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