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Conserved domains on  [gi|446460506|ref|WP_000538360|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Bacillus]

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];
1-65 1.71e-24

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 86.06  E-value: 1.71e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446460506  1 MGVKNKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIFTLE 65
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 1.71e-24

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 86.06  E-value: 1.71e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446460506  1 MGVKNKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIFTLE 65
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.36e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 63.31  E-value: 1.36e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446460506    6 KIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 3.61e-15

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: 3.61e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 446460506  5 NKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 9.84e-14

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: 58.71  E-value: 9.84e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446460506   7 IKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 16-59 6.18e-06

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: 39.52  E-value: 6.18e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446460506  16 ITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVE 59
Cdd:TIGR02607 19 LSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPE 62
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
5-56 7.50e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 39.58  E-value: 7.50e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 446460506  5 NKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGV 56
Cdd:PRK09726 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLEL 66
NadS NF041265
NadS family protein;
7-43 2.69e-03

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 32.84  E-value: 2.69e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 446460506  7 IKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPS 43
Cdd:NF041265 35 VKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPT 71
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 1.71e-24

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 86.06  E-value: 1.71e-24
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446460506  1 MGVKNKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIFTLE 65
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 4.61e-16

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 65.40  E-value: 4.61e-16
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 446460506  1 MGVKNKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIFT 63
Cdd:COG1396   6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLG 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.36e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 63.31  E-value: 1.36e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 446460506    6 KIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 5-61 3.61e-15

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: 3.61e-15
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 446460506  5 NKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:cd00093   2 ERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 9.84e-14

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: 58.71  E-value: 9.84e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446460506   7 IKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 6-60 1.19e-10

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: 51.09  E-value: 1.19e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 446460506  6 KIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEE 60
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 6-66 5.39e-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: 46.90  E-value: 5.39e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446460506   6 KIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIFTLEL 66
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEG 63
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 9-59 2.27e-08

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 45.57  E-value: 2.27e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 446460506  9 ELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVE 59
Cdd:COG3093  16 EFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE 66
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 7-65 8.43e-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: 44.63  E-value: 8.43e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 446460506  7 IKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIFTLE 65
Cdd:COG3620  22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVD 80
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 16-59 6.18e-06

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: 39.52  E-value: 6.18e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 446460506  16 ITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVE 59
Cdd:TIGR02607 19 LSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPE 62
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
5-56 7.50e-06

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 39.58  E-value: 7.50e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 446460506  5 NKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGV 56
Cdd:PRK09726 15 NAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSLEL 66
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 7-55 1.02e-05

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: 38.41  E-value: 1.02e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 446460506   7 IKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFG 55
Cdd:TIGR03070  7 VRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDALG 55
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 6-65 3.86e-05

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 37.14  E-value: 3.86e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446460506   6 KIKELRKQHHITQVEMAKAMQVTRQTIVAIEN-HHYNPSLELSLKIAKYFGVKVEEIFTLE 65
Cdd:pfam13443  1 KLRKLMADRGISKSDLARATGISRATLSRLRKgKPKRVSLDTLDKICDALGCQPGDLLEYV 61
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 7-61 8.52e-04

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: 8.52e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446460506   7 IKELRKQHHITQVEMAKAMQVTRQTIVAIEN-HHYNPSLELSLKIAKYFGVKVEEI 61
Cdd:pfam13560  6 LRRLRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAER 61
PRK04140 PRK04140
transcriptional regulator;
5-58 9.81e-04

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 35.22  E-value: 9.81e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 446460506   5 NKIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKV 58
Cdd:PRK04140 129 DVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
NadS NF041265
NadS family protein;
7-43 2.69e-03

NadS family protein;


Pssm-ID: 469165  Cd Length: 94  Bit Score: 32.84  E-value: 2.69e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 446460506  7 IKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPS 43
Cdd:NF041265 35 VKAIRAQLNVSQAEMAKALGTSVDTIKSWESKRRNPT 71
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
6-62 3.82e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 33.23  E-value: 3.82e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446460506   6 KIKELRKQHHITQVEMAKAMQVTRQTIVAIENHHYNPSLELSLKIAKYFGVKVEEIF 62
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFF 67
 
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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