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Conserved domains on  [gi|489518368|ref|WP_003423177|]
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helix-turn-helix transcriptional regulator [Clostridioides difficile]

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];
1-59 3.31e-19

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 73.34  E-value: 3.31e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 489518368  1 MKTKVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-59 3.31e-19

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 73.34  E-value: 3.31e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 489518368  1 MKTKVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-59 4.52e-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: 57.56  E-value: 4.52e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368  4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 1.01e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 1.01e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368    4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-59 3.57e-11

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: 52.54  E-value: 3.57e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489518368   5 VREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-56 3.90e-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: 44.96  E-value: 3.90e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489518368   5 VREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTI 56
Cdd:TIGR03070  7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
PRK04140 PRK04140
transcriptional regulator;
4-77 2.97e-04

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 37.14  E-value: 2.97e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489518368   4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEELCCLKENKEMEDKKHESKE 77
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTKPIDILEKVRDDEVTPEDPE 203
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-59 3.31e-19

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 73.34  E-value: 3.31e-19
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 489518368  1 MKTKVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:COG1476   5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEEL 63
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-59 4.52e-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: 57.56  E-value: 4.52e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368  4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
4-59 1.01e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.37  E-value: 1.01e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368    4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-59 1.46e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 56.93  E-value: 1.46e-12
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368  4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:COG1396  11 RLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDEL 66
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 5-59 3.57e-11

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: 52.54  E-value: 3.57e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489518368   5 VREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 4-58 2.66e-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: 48.01  E-value: 2.66e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 489518368  4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEE 58
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 5-56 3.90e-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: 44.96  E-value: 3.90e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489518368   5 VREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTI 56
Cdd:TIGR03070  7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALGLEL 58
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-66 5.23e-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: 45.40  E-value: 5.23e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489518368  5 VREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEELCCLKENK 66
Cdd:COG3620  22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGK 83
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-59 3.31e-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: 42.66  E-value: 3.31e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368   4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWL 58
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 6-77 2.89e-06

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.95  E-value: 2.89e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489518368  6 REFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEELCCLKENKEMEDKKHESKE 77
Cdd:COG3093  15 EEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLARQKAGE 86
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-59 1.10e-05

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: 38.66  E-value: 1.10e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489518368   6 REFRTNMGLTQQQLADLVHVSNRTIISIEK-EQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:pfam13560  7 RRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAER 61
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 6-57 2.98e-05

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: 37.98  E-value: 2.98e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489518368   6 REFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIE 57
Cdd:TIGR02607 11 EEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPE 62
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
3-43 1.10e-04

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.45  E-value: 1.10e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 489518368  3 TKVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLM 43
Cdd:COG2944   9 EEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGA 49
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 6-39 1.73e-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: 35.94  E-value: 1.73e-04
                        10        20        30
                ....*....|....*....|....*....|....
gi 489518368  6 REFRTNMGLTQQQLADLVHVSNRTIISIEKEQYS 39
Cdd:COG1426  11 RQAREAKGLSLEDVAERTKISVSYLEAIEEGDFD 44
PRK04140 PRK04140
transcriptional regulator;
4-77 2.97e-04

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 37.14  E-value: 2.97e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489518368   4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEELCCLKENKEMEDKKHESKE 77
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPLTKPIDILEKVRDDEVTPEDPE 203
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 4-59 6.89e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 36.09  E-value: 6.89e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 489518368   4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEEL 59
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL 87
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
7-58 1.01e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 35.54  E-value: 1.01e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489518368   7 EFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTIEE 58
Cdd:PRK09943  14 EIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSE 65
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 4-51 3.23e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 33.67  E-value: 3.23e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 489518368   4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQV 51
Cdd:PRK09706   9 RIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKA 56
HTH_25 pfam13413
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-39 3.46e-03

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433187 [Multi-domain]  Cd Length: 62  Bit Score: 32.47  E-value: 3.46e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 489518368   6 REFRTNMGLTQQQLADLVHVSNRTIISIEKEQYS 39
Cdd:pfam13413  3 RAAREARGLSLEDVAERTKIRPRYLEALEEDDFD 36
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-56 3.68e-03

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 34.04  E-value: 3.68e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489518368   4 KVREFRTNMGLTQQQLADLVHVSNRTIISIEKEQYSPSLMLAYRMAQVFGTTI 56
Cdd:COG1395  131 KLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPI 183
 
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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