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Conserved domains on  [gi|447051561|ref|WP_001128817|]
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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];
1-66 2.25e-23

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 83.36  E-value: 2.25e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561  1 MPLKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVLFWFED 66
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 2.25e-23

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 83.36  E-value: 2.25e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561  1 MPLKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVLFWFED 66
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.77e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.61  E-value: 1.77e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561    6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-61 1.19e-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: 58.33  E-value: 1.19e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561  6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 1.29e-12

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: 55.62  E-value: 1.29e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 447051561   7 MKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 8-54 1.88e-07

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: 42.65  E-value: 1.88e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 447051561   8 KEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVL 54
Cdd:TIGR03070  8 RARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 16-61 6.97e-06

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 40.12  E-value: 6.97e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 447051561  16 MSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:PRK13890  19 MTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLL 64
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-66 2.25e-23

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 83.36  E-value: 2.25e-23
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561  1 MPLKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVLFWFED 66
Cdd:COG1476   3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-61 1.77e-14

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 60.61  E-value: 1.77e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561    6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-62 5.79e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 5.79e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 447051561  1 MPLKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVLF 62
Cdd:COG1396   6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-61 1.19e-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: 58.33  E-value: 1.19e-13
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561  6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:cd00093   3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 1.29e-12

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: 55.62  E-value: 1.29e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 447051561   7 MKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 6-62 3.51e-10

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: 3.51e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 447051561   6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVLF 62
Cdd:pfam12844  3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 6-59 4.06e-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: 49.94  E-value: 4.06e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 447051561  6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIE 59
Cdd:COG1813  16 RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 8-54 1.88e-07

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: 42.65  E-value: 1.88e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 447051561   8 KEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVL 54
Cdd:TIGR03070  8 RARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKVLRVLDAL 54
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-61 2.07e-07

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: 43.47  E-value: 2.07e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 447051561  1 MPLKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:COG3620  16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAV 76
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 6-62 2.96e-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: 40.17  E-value: 2.96e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 447051561  6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYD------IAKVLKAPIEVLF 62
Cdd:COG1426   9 LLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVrgflrsYARALGLDPEELL 71
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 16-61 6.97e-06

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 40.12  E-value: 6.97e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 447051561  16 MSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:PRK13890  19 MTKKELSERSGVSISFLSDLTTGKANPSLKVMEAIADALETPLPLL 64
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 9-63 1.27e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 38.64  E-value: 1.27e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 447051561  9 EYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEvlFW 63
Cdd:COG3093  16 EFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAE--FW 68
HTH_Crp_2 pfam13545
Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain ...
 3-32 1.98e-05

Crp-like helix-turn-helix domain; This family represents a crp-like helix-turn-helix domain that is likely to bind DNA.


Pssm-ID: 463917 [Multi-domain]  Cd Length: 68  Bit Score: 37.82  E-value: 1.98e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 447051561   3 LKTRMKEYRVKLSMSQEDLANEVGVRRETI 32
Cdd:pfam13545 10 LAARDGGGRIDLPLTQEDLADLLGTTRETV 39
PRK04140 PRK04140
transcriptional regulator;
6-58 2.84e-05

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 39.46  E-value: 2.84e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 447051561   6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPI 58
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDVPL 182
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
5-43 4.77e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 36.84  E-value: 4.77e-05
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 447051561  5 TRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPS 43
Cdd:COG2944   9 EEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
6-58 9.38e-05

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 37.89  E-value: 9.38e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 447051561   6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPI 58
Cdd:COG1395  131 KLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILGEPI 183
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 6-61 1.64e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 37.24  E-value: 1.64e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 447051561   6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLKAPIEVL 61
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSILLLRRVARALGCSLADL 87
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 6-61 9.91e-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: 33.27  E-value: 9.91e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 447051561   6 RMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYN-PSFKLTYDIAKVLKAPIEVL 61
Cdd:pfam13560  5 RLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGAER 61
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 3-66 1.70e-03

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 34.06  E-value: 1.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 447051561   3 LKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVLK-APIEVLFWFED 66
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQcSPTWLLFGDED 70
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
2-62 3.75e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 32.04  E-value: 3.75e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 447051561  2 PLKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGK-YNPSFKLTYDIAKVLKAPIEVLF 62
Cdd:COG3655   1 MIYVKLDELLAERGMTKKELAEATGISRATLSRLKNGKaKAVRLDTLEKICKALDCQPGDLL 62
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
3-54 6.67e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 31.87  E-value: 6.67e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 447051561  3 LKTRMKEYRVKLSMSQEDLANEVGVRRETIGNLENGKYNPSFKLTYDIAKVL 54
Cdd:PRK09726 13 LANAMKLVRQQNGWTQSELAKKIGIKQATISNFENNPDNTTLTTFFKILQSL 64
 
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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