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Conserved domains on  [gi|446729127|ref|WP_000806440|]
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MULTISPECIES: HigA family addiction module antitoxin [Escherichia]

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 ...
 7-84 9.33e-33

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: 109.24  E-value: 9.33e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446729127    7 KPTTPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNLQAAVDLWEVEN 84
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIAEQ 78
 
Name Accession Description Interval E-value
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 7-84 9.33e-33

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: 109.24  E-value: 9.33e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446729127    7 KPTTPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNLQAAVDLWEVEN 84
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIAEQ 78
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 5-87 1.26e-32

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 109.13  E-value: 1.26e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446729127   5 TRKPTTPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNLQAAVDLWEVEN 84
Cdd:COG3093    3 KRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLARQ 82


                 ...
gi 446729127  85 NMR 87
Cdd:COG3093   83 KAG 85
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-70 1.42e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.13  E-value: 1.42e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 446729127    16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW 70
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-70 8.26e-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: 45.22  E-value: 8.26e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446729127   16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW 70
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 16-70 3.39e-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: 3.39e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446729127  16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW 70
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
PRK04140 PRK04140
transcriptional regulator;
15-65 7.05e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 34.45  E-value: 7.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446729127  15 LLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDT 65
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDV 180
 
Name Accession Description Interval E-value
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 7-84 9.33e-33

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: 109.24  E-value: 9.33e-33
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 446729127    7 KPTTPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNLQAAVDLWEVEN 84
Cdd:TIGR02607   1 NPAHPGEILLEEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIAEQ 78
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 5-87 1.26e-32

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 109.13  E-value: 1.26e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446729127   5 TRKPTTPGDILLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNLQAAVDLWEVEN 84
Cdd:COG3093    3 KRNPIHPGEILREEFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLARQ 82


                 ...
gi 446729127  85 NMR 87
Cdd:COG3093   83 KAG 85
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
16-70 1.42e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.13  E-value: 1.42e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 446729127    16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW 70
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 16-70 8.26e-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: 45.22  E-value: 8.26e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446729127   16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW 70
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 16-70 3.39e-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: 3.39e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446729127  16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW 70
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
16-68 4.23e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 43.68  E-value: 4.23e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446729127  16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVD 68
Cdd:COG1476    9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLE 61
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
23-69 4.83e-05

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 38.82  E-value: 4.83e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 446729127  23 LDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDF 69
Cdd:COG1396   19 RGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDE 65
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 16-73 5.37e-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: 33.03  E-value: 5.37e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 446729127   16 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFWLNL 73
Cdd:pfam12844   4 LRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQG 61
PRK04140 PRK04140
transcriptional regulator;
15-65 7.05e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 34.45  E-value: 7.05e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 446729127  15 LLYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDT 65
Cdd:PRK04140 130 VLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDV 180
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 7-63 9.48e-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: 33.27  E-value: 9.48e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446729127   7 KPTTPGDILLYeYLEPLDLKINELAELLhVHRNSVSALINNNRKLTTEMAFRLAKVF 63
Cdd:COG5499   62 PPPDPIEALKF-LMEQHGLTQKDLAPEI-GSKSRVSEILNGKRSLTLEMIRKLAERF 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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