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Conserved domains on  [gi|489827228|ref|WP_003730995|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Listeria]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11443570)

helix-turn-helix domain-containing protein such as an XRE (Xenobiotic Response Element) family transcriptional regulator

Gene Ontology:  GO:0003677
PubMed:  37972151

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 1.55e-09

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 48.45  E-value: 1.55e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489827228  1 MSVEHQRFAVAVYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLD 64
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 1.55e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 48.45  E-value: 1.55e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489827228  1 MSVEHQRFAVAVYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLD 64
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-63 2.10e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 44.82  E-value: 2.10e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489827228   12 VYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSlETLKKLAKALGVSLD 54
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-63 6.74e-08

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: 6.74e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 489827228 14 AKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:cd00093   6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLD 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-63 1.46e-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: 42.91  E-value: 1.46e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489827228  12 VYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDASKVR-KEIAEILEIDVD 63
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETlKKLAEALGVSLD 53
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 16-45 2.51e-04

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: 35.29  E-value: 2.51e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 489827228  16 LKAINMKQSDLAKMLGISNPYLSDIINGKR 45
Cdd:TIGR02607 14 LEPLGLSVRALAKALGVSRSTLSRIVNGRA 43
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 20-60 5.47e-04

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 35.11  E-value: 5.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489827228  20 NMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEI 60
Cdd:PRK13890  18 HMTKKELSERSGVSISFLSDLTTGKANPSlKVMEAIADALET 59
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 15-46 6.78e-04

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 35.20  E-value: 6.78e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489827228  15 KLKAINMKQSDLAKMLGISNPYLSDIINGKRD 46
Cdd:NF038310   4 DLESKGITNRKLAKKIGVSKSTLSKFFNGKGE 35
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-63 1.55e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 48.45  E-value: 1.55e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489827228  1 MSVEHQRFAVAVYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:COG1396   1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSlETLLKLAKALGVSLD 64
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-63 2.10e-08

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 44.82  E-value: 2.10e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 489827228   12 VYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSlETLKKLAKALGVSLD 54
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 14-63 6.74e-08

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: 6.74e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 489827228 14 AKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:cd00093   6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSlETLEKLAKALGVSLD 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-63 1.46e-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: 42.91  E-value: 1.46e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489827228  12 VYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDASKVR-KEIAEILEIDVD 63
Cdd:pfam01381  1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETlKKLAEALGVSLD 53
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
17-63 2.08e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 42.91  E-value: 2.08e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 489827228 17 KAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:COG1476  14 KERGLTQEELAELLGVSRQTISAIENGKYNPSlELALKIARALGVSLE 61
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 16-45 4.57e-07

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 42.49  E-value: 4.57e-07
                        10        20        30
                ....*....|....*....|....*....|
gi 489827228 16 LKAINMKQSDLAKMLGISNPYLSDIINGKR 45
Cdd:COG3093  18 LEPLGLSQTELAKALGVSRQRISEILNGKR 47
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-63 2.25e-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: 37.61  E-value: 2.25e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489827228  1 MSVEHQRFAVAVYAKL-----KAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:COG1813   1 MAKESTGELVEDYGERirearEARGLSQEELAEKLGVSESTIRRIERGEATPSlDTLRKLEKALGISLA 69
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-63 3.04e-05

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 37.69  E-value: 3.04e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489827228  4 EHQRFAVAVYAKLKAINMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEIDVD 63
Cdd:COG3620  14 PDDTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTvSTLEKIAEALGKELS 74
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 17-63 1.42e-04

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: 35.34  E-value: 1.42e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489827228  17 KAINMKQSDLAKMLGISNPYLSDIINGKR--DASKVRKeIAEILEIDVD 63
Cdd:pfam12844  9 EERGLTQEELAERLGISRSQLSAIENGKSvpPAETLYK-IAELLGVPAN 56
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
9-44 1.50e-04

Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];


Pssm-ID: 444337  Cd Length: 105  Bit Score: 36.01  E-value: 1.50e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 489827228   9 AVAVYAKLKAINMKQSDLAKMLGISNPYLSDIINGK 44
Cdd:COG5606   34 MAAIRKLIKERGLTQAEAAELLGITQPRVSDLLRGK 69
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 16-45 2.51e-04

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: 35.29  E-value: 2.51e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 489827228  16 LKAINMKQSDLAKMLGISNPYLSDIINGKR 45
Cdd:TIGR02607 14 LEPLGLSVRALAKALGVSRSTLSRIVNGRA 43
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 20-60 5.47e-04

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 35.11  E-value: 5.47e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 489827228  20 NMKQSDLAKMLGISNPYLSDIINGKRDAS-KVRKEIAEILEI 60
Cdd:PRK13890  18 HMTKKELSERSGVSISFLSDLTTGKANPSlKVMEAIADALET 59
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 15-46 6.78e-04

AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR (arbitrium receptor), is a DNA-binding phage regulatory protein that acts as a receptor for a 6-amino acid signaling peptide cleaved from the C-terminus of AimP. AimR controls expression of AimX, the third member of the quorum sensing-like arbitrium system and an inhibitor of phage lysogeny.


Pssm-ID: 468467  Cd Length: 363  Bit Score: 35.20  E-value: 6.78e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489827228  15 KLKAINMKQSDLAKMLGISNPYLSDIINGKRD 46
Cdd:NF038310   4 DLESKGITNRKLAKKIGVSKSTLSKFFNGKGE 35
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
11-62 4.15e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 31.65  E-value: 4.15e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 489827228 11 AVYAKLKAI----NMKQSDLAKMLGISNPYLSDIINGKrdASKVRKE----IAEILEIDV 62
Cdd:COG3655   1 MIYVKLDELlaerGMTKKELAEATGISRATLSRLKNGK--AKAVRLDtlekICKALDCQP 58
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 20-63 5.03e-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: 32.49  E-value: 5.03e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489827228  20 NMKQSDLAKMLGiSNPYLSDIINGKRDASK-VRKEIAEILEIDVD 63
Cdd:COG5499   78 GLTQKDLAPEIG-SKSRVSEILNGKRSLTLeMIRKLAERFGIPAE 121
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
23-45 7.89e-03

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


Pssm-ID: 443351  Cd Length: 68  Bit Score: 31.04  E-value: 7.89e-03
                        10        20
                ....*....|....*....|...
gi 489827228 23 QSDLAKMLGISNPYLSDIINGKR 45
Cdd:COG4197  11 QSALARALGVSQQAVSQWLNGKR 33
 
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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