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Conserved domains on  [gi|500952952|ref|WP_012030621|]
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HigA family addiction module antitoxin [Dichelobacter nodosus]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10006927)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain, similar to Proteus vulgaris antitoxin HigA that binds to its own promoter and regulates transcription of the higB/higA operon and functions as the antitoxin component of a type II toxin-antitoxin (TA) system that counteracts the effect of the HigB toxin

CATH:  1.10.10.10
Gene Ontology:  GO:0003700|GO:0003677|GO:0006355
PubMed:  10473770|15808743
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 3-89 1.42e-28

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


:

Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 98.73  E-value: 1.42e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500952952   3 KMKNPPHPGLMLKVMYLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAFpKHSASFWLRAQAGYALSRV 82
Cdd:COG3093    2 NKRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAF-GTSAEFWLNLQAAYDLWLA 80


                 ....*..
gi 500952952  83 NPHCADK 89
Cdd:COG3093   81 RQKAGEE 87
 
Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 3-89 1.42e-28

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 98.73  E-value: 1.42e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500952952   3 KMKNPPHPGLMLKVMYLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAFpKHSASFWLRAQAGYALSRV 82
Cdd:COG3093    2 NKRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAF-GTSAEFWLNLQAAYDLWLA 80


                 ....*..
gi 500952952  83 NPHCADK 89
Cdd:COG3093   81 RQKAGEE 87
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 6-79 1.65e-26

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: 93.07  E-value: 1.65e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500952952    6 NPPHPGLMLKVMYLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAFpKHSASFWLRAQAGYAL 79
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKAL-GTSPEFWLNLQNAYDL 73
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 18-62 3.60e-08

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: 45.99  E-value: 3.60e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 500952952   18 YLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:pfam01381   4 LREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEAL 48
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
18-62 6.42e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.20  E-value: 6.42e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 500952952    18 YLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:smart00530   5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 22-62 2.70e-07

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: 43.70  E-value: 2.70e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 500952952  22 LGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:cd00093   11 KGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
 
Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 3-89 1.42e-28

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 98.73  E-value: 1.42e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 500952952   3 KMKNPPHPGLMLKVMYLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAFpKHSASFWLRAQAGYALSRV 82
Cdd:COG3093    2 NKRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAF-GTSAEFWLNLQAAYDLWLA 80


                 ....*..
gi 500952952  83 NPHCADK 89
Cdd:COG3093   81 RQKAGEE 87
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 6-79 1.65e-26

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: 93.07  E-value: 1.65e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 500952952    6 NPPHPGLMLKVMYLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAFpKHSASFWLRAQAGYAL 79
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKAL-GTSPEFWLNLQNAYDL 73
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 18-62 3.60e-08

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: 45.99  E-value: 3.60e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 500952952   18 YLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:pfam01381   4 LREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEAL 48
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
18-62 6.42e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 45.20  E-value: 6.42e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 500952952    18 YLEPLGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:smart00530   5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 22-62 2.70e-07

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: 43.70  E-value: 2.70e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 500952952  22 LGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:cd00093   11 KGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKAL 51
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 22-62 5.55e-04

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: 35.30  E-value: 5.55e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 500952952  22 LGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:COG1813   24 RGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKAL 64
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
22-62 1.79e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.05  E-value: 1.79e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 500952952  22 LGLNITETAEKLDMPRSALSEIVNAKRAISPEVAVKLEKAF 62
Cdd:COG1476   16 RGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARAL 56
 
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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