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Conserved domains on  [gi|446332250|ref|WP_000410105|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Enterobacteriaceae]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-84 2.44e-14

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 63.48  E-value: 2.44e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446332250  11 SRLNDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQESSE 84
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-84 2.44e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 63.48  E-value: 2.44e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446332250  11 SRLNDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQESSE 84
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 14-135 1.02e-13

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 63.33  E-value: 1.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446332250  14 NDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQESS---------E 84
Cdd:PRK09706   3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDEDKQptppvplnqP 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446332250  85 LWLNESQRKLLELFNQLPGSEQQRMIELFEVRLKEIDEYVEKYLRGRLKDN 135
Cdd:PRK09706  83 VELSEDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARKRSA 133
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 20-75 1.03e-11

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: 56.02  E-value: 1.03e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446332250  20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPEL 75
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-75 1.16e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.99  E-value: 1.16e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446332250    20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPEL 75
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 21-75 9.93e-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: 51.00  E-value: 9.93e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446332250   21 LKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPEL 75
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 28-86 2.77e-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: 39.91  E-value: 2.77e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446332250   28 LGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISpPELLFGEQESSELW 86
Cdd:TIGR02607  17 LGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTS-PEFWLNLQNAYDLW 74
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
11-84 2.44e-14

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 63.48  E-value: 2.44e-14
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446332250  11 SRLNDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQESSE 84
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELP 75
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 14-135 1.02e-13

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 63.33  E-value: 1.02e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446332250  14 NDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQESS---------E 84
Cdd:PRK09706   3 NLTLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAKALQCSPTWLLFGDEDKQptppvplnqP 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446332250  85 LWLNESQRKLLELFNQLPGSEQQRMIELFEVRLKEIDEYVEKYLRGRLKDN 135
Cdd:PRK09706  83 VELSEDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLKARKRSA 133
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 20-75 1.03e-11

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: 56.02  E-value: 1.03e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 446332250  20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPEL 75
Cdd:cd00093    3 RLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
20-75 1.16e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.99  E-value: 1.16e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 446332250    20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPEL 75
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
14-80 2.08e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 55.62  E-value: 2.08e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446332250  14 NDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQ 80
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 21-75 9.93e-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: 51.00  E-value: 9.93e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446332250   21 LKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPEL 75
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 5-81 1.03e-09

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: 51.94  E-value: 1.03e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446332250   5 NEKIAASRLNDKIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQE 81
Cdd:COG3620    6 SRDVVTVSPDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDG 82
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-74 7.99e-08

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: 46.47  E-value: 7.99e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446332250   1 MEKENEKIAASRLNDkiamRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPE 74
Cdd:COG1813    1 MAKESTGELVEDYGE----RIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 17-75 1.31e-07

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: 1.31e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446332250   17 IAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRN-VGVHDAVVLGKALGISPPEL 75
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGAER 61
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 26-87 3.53e-06

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 42.49  E-value: 3.53e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446332250  26 QKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISpPELLFGEQESSELWL 87
Cdd:COG3093   19 EPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTS-AEFWLNLQAAYDLWL 79
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 20-81 2.41e-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: 39.58  E-value: 2.41e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446332250   20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPELLFGEQE 81
Cdd:pfam12844   3 RLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 28-86 2.77e-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: 39.91  E-value: 2.77e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 446332250   28 LGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISpPELLFGEQESSELW 86
Cdd:TIGR02607  17 LGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTS-PEFWLNLQNAYDLW 74
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
20-84 1.45e-04

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 39.78  E-value: 1.45e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446332250  20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLGKALGISPPElLFGEQESSE 84
Cdd:PRK09943  11 RLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLSLSE-FFSEPEKPD 74
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 20-108 2.94e-04

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 39.17  E-value: 2.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446332250  20 RLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVhdaVVL---GKALGISPPELLFGEQESSELWlnesqRKLLE 96
Cdd:PRK08154  32 RVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSI---LLLrrvARALGCSLADLLGDVDTSSPDW-----LLIRE 103

                         90
                 ....*....|..
gi 446332250  97 LFNQLPGSEQQR 108
Cdd:PRK08154 104 LLEQASPAQLAR 115
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
18-54 7.72e-04

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 35.68  E-value: 7.72e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 446332250  18 AMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSR 54
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRR 44
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 16-76 7.70e-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: 33.24  E-value: 7.70e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446332250  16 KIAMRLKERRQKLGLSQGKLAEICGWTQSRIGNYEAGSRNVGVHDAVVLG------KALGISPPELL 76
Cdd:COG1426    5 TIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDFDALPGPVYVRGflrsyaRALGLDPEELL 71
 
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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