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Conserved domains on  [gi|2070269245|gb|QXR34216|]
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HigA family addiction module antidote protein (plasmid) [Enterobacter hormaechei]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10021105)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 7-82 6.12e-29

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: 100.00  E-value: 6.12e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2070269245   7 KPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEV 82
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIA 76
 
Name Accession Description Interval E-value
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 7-82 6.12e-29

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: 100.00  E-value: 6.12e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2070269245   7 KPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEV 82
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIA 76
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 5-82 3.57e-28

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 98.34  E-value: 3.57e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2070269245   5 TRKPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEV 82
Cdd:COG3093     3 KRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLA 80
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-66 3.44e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 43.66  E-value: 3.44e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2070269245   16 LYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTT 66
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-70 2.43e-06

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: 41.76  E-value: 2.43e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2070269245  16 LYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFW 70
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 24-70 4.38e-06

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: 41.00  E-value: 4.38e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2070269245  24 GLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFW 70
Cdd:cd00093    12 GLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
 
Name Accession Description Interval E-value
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 7-82 6.12e-29

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: 100.00  E-value: 6.12e-29
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2070269245   7 KPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEV 82
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIA 76
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 5-82 3.57e-28

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 98.34  E-value: 3.57e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2070269245   5 TRKPSTVGDIILYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFWLNIQQSVDLWEV 82
Cdd:COG3093     3 KRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLA 80
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-66 3.44e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 43.66  E-value: 3.44e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 2070269245   16 LYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTT 66
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-70 2.43e-06

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: 41.76  E-value: 2.43e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2070269245  16 LYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFW 70
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 24-70 4.38e-06

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: 41.00  E-value: 4.38e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2070269245  24 GLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFW 70
Cdd:cd00093    12 GLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
24-66 1.66e-05

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 39.83  E-value: 1.66e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2070269245  24 GLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTT 66
Cdd:COG1476    17 GLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVS 59
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
24-66 3.32e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.51  E-value: 3.32e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2070269245  24 GLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTT 66
Cdd:COG1396    20 GLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 16-72 3.82e-03

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: 33.42  E-value: 3.82e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2070269245  16 LYEYLEPSGLKINDLAEMLNVHRNSASALVNNNRKLSTDMAFRLAKAFDTTAKFWLN 72
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQ 60
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 13-63 5.74e-03

Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH domain [Defense mechanisms];


Pssm-ID: 444250  Cd Length: 127  Bit Score: 34.04  E-value: 5.74e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2070269245  13 DIILYeYLEPSGLKINDLAEMLNvHRNSASALVNNNRKLSTDMAFRLAKAF 63
Cdd:COG5499    68 EALKF-LMEQHGLTQKDLAPEIG-SKSRVSEILNGKRSLTLEMIRKLAERF 116
 
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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