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Conserved domains on  [gi|16130977|ref|NP_417553|]
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antitoxin/DNA-binding transcriptional repressor HigA [Escherichia coli str. K-12 substr. MG1655]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10009358)

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; similar to Escherichia coli antitoxin HigA, which is an antitoxin component of a type II toxin-antitoxin (TA) system and functions as an mRNA interferase antitoxin

CATH:  1.10.260.40
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244|15808743|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 12-138 3.61e-42

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: 135.73  E-value: 3.61e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130977  12 EKLTAVAPFLAGIQNEEQYTQALELVDHLL----LNDPENPLLDLVCAKITAWEESAPEFAEfnamaqamPGGIAVIRTL 87
Cdd:COG5499   2 TATFNAAPPLKPIRTEADYEAALALIEELLdadeLGTPEGDLLDLLATLIEAYEAKHYPIPP--------PDPIEALKFL 73

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 16130977  88 MDQYGLTLSDL-PEIGSKSMVSRVLSGKRKLTLEHAKKLATRFGISPALFID 138
Cdd:COG5499  74 MEQHGLTQKDLaPEIGSKSRVSEILNGKRSLTLEMIRKLAERFGIPAELFIQ 125
 
Name Accession Description Interval E-value
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 12-138 3.61e-42

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: 135.73  E-value: 3.61e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130977  12 EKLTAVAPFLAGIQNEEQYTQALELVDHLL----LNDPENPLLDLVCAKITAWEESAPEFAEfnamaqamPGGIAVIRTL 87
Cdd:COG5499   2 TATFNAAPPLKPIRTEADYEAALALIEELLdadeLGTPEGDLLDLLATLIEAYEAKHYPIPP--------PDPIEALKFL 73

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 16130977  88 MDQYGLTLSDL-PEIGSKSMVSRVLSGKRKLTLEHAKKLATRFGISPALFID 138
Cdd:COG5499  74 MEQHGLTQKDLaPEIGSKSRVSEILNGKRSLTLEMIRKLAERFGIPAELFIQ 125
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
84-136 2.71e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.13  E-value: 2.71e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 16130977     84 IRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALF 136
Cdd:smart00530   2 LKELREEKGLTQEELAEkLGvSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 84-136 9.10e-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: 43.31  E-value: 9.10e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 16130977  84 IRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALF 136
Cdd:cd00093   4 LKELRKEKGLTQEELAEkLGvSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 84-136 2.03e-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: 42.14  E-value: 2.03e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 16130977    84 IRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALF 136
Cdd:pfam01381   1 LKELREELGLSQEELAEkLGvSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 78-133 4.36e-03

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: 34.13  E-value: 4.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 16130977    78 PGGIaVIRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISP 133
Cdd:TIGR02607   5 PGEI-LLEEFLEPLGLSVRALAKaLGvSRSTLSRIVNGRAAITADMALRLAKALGTSP 61
 
Name Accession Description Interval E-value
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 12-138 3.61e-42

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: 135.73  E-value: 3.61e-42
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130977  12 EKLTAVAPFLAGIQNEEQYTQALELVDHLL----LNDPENPLLDLVCAKITAWEESAPEFAEfnamaqamPGGIAVIRTL 87
Cdd:COG5499   2 TATFNAAPPLKPIRTEADYEAALALIEELLdadeLGTPEGDLLDLLATLIEAYEAKHYPIPP--------PDPIEALKFL 73

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 16130977  88 MDQYGLTLSDL-PEIGSKSMVSRVLSGKRKLTLEHAKKLATRFGISPALFID 138
Cdd:COG5499  74 MEQHGLTQKDLaPEIGSKSRVSEILNGKRSLTLEMIRKLAERFGIPAELFIQ 125
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
84-136 2.71e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 47.13  E-value: 2.71e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 16130977     84 IRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALF 136
Cdd:smart00530   2 LKELREEKGLTQEELAEkLGvSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
73-138 5.88e-07

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 44.60  E-value: 5.88e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16130977  73 MAQAMPGGIAVIRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALFID 138
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAErLGvSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLG 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 84-136 9.10e-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: 43.31  E-value: 9.10e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 16130977  84 IRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALF 136
Cdd:cd00093   4 LKELRKEKGLTQEELAEkLGvSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 84-136 2.03e-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: 42.14  E-value: 2.03e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 16130977    84 IRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALF 136
Cdd:pfam01381   1 LKELREELGLSQEELAEkLGvSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 71-137 2.48e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.18  E-value: 2.48e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130977  71 NAMAQAMPGGIaVIRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISPALFI 137
Cdd:COG3093   2 NKRNPIHPGEI-LREEFLEPLGLSQTELAKaLGvSRQRISEILNGKRAITADTALRLARAFGTSAEFWL 69
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 73-132 7.73e-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: 38.38  E-value: 7.73e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 16130977  73 MAQAMPGGIA-----VIRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGIS 132
Cdd:COG1813   1 MAKESTGELVedygeRIREAREARGLSQEELAEkLGvSESTIRRIERGEATPSLDTLRKLEKALGIS 67
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
73-138 6.28e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 35.98  E-value: 6.28e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 16130977  73 MAQAMPGGIAVIRTlmdQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISP-ALFID 138
Cdd:COG1476   1 MKKKLGNRLKELRK---ERGLTQEELAElLGvSRQTISAIENGKYNPSLELALKIARALGVSLeELFSL 66
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 78-133 4.36e-03

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: 34.13  E-value: 4.36e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 16130977    78 PGGIaVIRTLMDQYGLTLSDLPE-IG-SKSMVSRVLSGKRKLTLEHAKKLATRFGISP 133
Cdd:TIGR02607   5 PGEI-LLEEFLEPLGLSVRALAKaLGvSRSTLSRIVNGRAAITADMALRLAKALGTSP 61
 
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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