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Conserved domains on  [gi|1119200272|ref|WP_072209206|]
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MULTISPECIES: HigA family addiction module antitoxin [Pantoea]

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 ...
 23-106 6.66e-29

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


:

Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 100.65  E-value: 6.66e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1119200272  23 MAMHNPPHPGGFITE-YLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGIAARLWLAMQAAFDLHKA 101
Cdd:COG3093     1 MNKRNPIHPGEILREeFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLA 80


                  ....*
gi 1119200272 102 RENTD 106
Cdd:COG3093    81 RQKAG 85
 
Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 23-106 6.66e-29

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 100.65  E-value: 6.66e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1119200272  23 MAMHNPPHPGGFITE-YLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGIAARLWLAMQAAFDLHKA 101
Cdd:COG3093     1 MNKRNPIHPGEILREeFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLA 80


                  ....*
gi 1119200272 102 RENTD 106
Cdd:COG3093    81 RQKAG 85
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 27-103 8.67e-25

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: 89.60  E-value: 8.67e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1119200272  27 NPPHPGGFIT-EYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGIAARLWLAMQAAFDLHKARE 103
Cdd:TIGR02607   1 NPAHPGEILLeEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIAEQ 78
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
34-84 5.48e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 5.48e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1119200272   34 FITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 32-84 1.23e-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: 45.24  E-value: 1.23e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1119200272  32 GGFITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 35-84 2.82e-07

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: 44.45  E-value: 2.82e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1119200272  35 ITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGV 50
PRK04140 PRK04140
transcriptional regulator;
31-79 3.49e-05

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 41.77  E-value: 3.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1119200272  31 PGGF--------ITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLE 79
Cdd:PRK04140  119 PGGFyvkidgdvLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLE 175
 
Name Accession Description Interval E-value
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 23-106 6.66e-29

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 100.65  E-value: 6.66e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1119200272  23 MAMHNPPHPGGFITE-YLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGIAARLWLAMQAAFDLHKA 101
Cdd:COG3093     1 MNKRNPIHPGEILREeFLEPLGLSQTELAKALGVSRQRISEILNGKRAITADTALRLARAFGTSAEFWLNLQAAYDLWLA 80


                  ....*
gi 1119200272 102 RENTD 106
Cdd:COG3093    81 RQKAG 85
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 27-103 8.67e-25

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: 89.60  E-value: 8.67e-25
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1119200272  27 NPPHPGGFIT-EYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGIAARLWLAMQAAFDLHKARE 103
Cdd:TIGR02607   1 NPAHPGEILLeEFLEPLGLSVRALAKALGVSRSTLSRIVNGRAAITADMALRLAKALGTSPEFWLNLQNAYDLWIAEQ 78
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
34-84 5.48e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.36  E-value: 5.48e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1119200272   34 FITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGV 51
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 32-84 1.23e-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: 45.24  E-value: 1.23e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1119200272  32 GGFITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGV 53
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 35-84 2.82e-07

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: 44.45  E-value: 2.82e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1119200272  35 ITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGV 50
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
45-79 6.22e-06

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 41.05  E-value: 6.22e-06
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1119200272  45 SLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLE 79
Cdd:COG4197    10 SQSALARALGVSQQAVSQWLNGKRRVPAERCLAIE 44
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 32-84 2.39e-05

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: 39.54  E-value: 2.39e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1119200272  32 GGFITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:COG1813    14 GERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGI 66
PRK04140 PRK04140
transcriptional regulator;
31-79 3.49e-05

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 41.77  E-value: 3.49e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1119200272  31 PGGF--------ITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLE 79
Cdd:PRK04140  119 PGGFyvkidgdvLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLE 175
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
32-84 3.52e-05

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 39.59  E-value: 3.52e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1119200272  32 GGFITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:COG1396     9 GERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGV 61
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 32-78 9.80e-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: 38.04  E-value: 9.80e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1119200272  32 GGFITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRL 78
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKI 47
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
27-79 1.75e-04

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 39.43  E-value: 1.75e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1119200272  27 NPP----HPGGF--------ITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLE 79
Cdd:COG1395   112 EPPliyaAPGGLyvkidgekLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLE 176
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
37-79 6.73e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 33.19  E-value: 6.73e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1119200272  37 EYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAvspemAVRLE 79
Cdd:COG3655     8 ELLAERGMTKKELAEATGISRATLSRLKNGKAK-----AVRLD 45
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
35-84 7.40e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 32.90  E-value: 7.40e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1119200272  35 ITEYLEDNNVSLRKMAKDLGVSPAALSKVASGKAAVSPEMAVRLEAGLGI 84
Cdd:COG1476     9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGV 58
 
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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