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Conserved domains on  [gi|446351911|ref|WP_000429766|]
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MULTISPECIES: helix-turn-helix domain-containing protein [Staphylococcus]

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];
4-64 2.51e-13

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 2.51e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446351911   4 NKVRKILSENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-64 2.51e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 2.51e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446351911   4 NKVRKILSENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
11-68 4.45e-12

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: 56.02  E-value: 4.45e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446351911  11 SENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVPKSRI 68
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-64 4.03e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 53.68  E-value: 4.03e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446351911    13 NLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
14-64 2.03e-09

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: 49.08  E-value: 2.03e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446351911   14 LQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
14-43 6.47e-03

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: 34.43  E-value: 6.47e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 446351911  14 LQELMNDKNIDQRELAEAIGVSQPTVSNWI 43
Cdd:NF038310   1 IKNDLESKGITNRKLAKKIGVSKSTLSKFF 30
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
4-64 2.51e-13

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 60.01  E-value: 2.51e-13
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446351911   4 NKVRKILSENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:COG1396    2 STLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVS 62
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
11-68 4.45e-12

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: 56.02  E-value: 4.45e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446351911  11 SENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVPKSRI 68
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-64 4.03e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 53.68  E-value: 4.03e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|..
gi 446351911    13 NLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
7-64 7.94e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 53.31  E-value: 7.94e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446351911   7 RKILSENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:COG1476    2 KKKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVS 59
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
14-64 2.03e-09

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: 49.08  E-value: 2.03e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446351911   14 LQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
13-63 1.02e-07

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 45.13  E-value: 1.02e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446351911  13 NLQELMNDKNIDQRELAEAIGVSQPTVSNWIQ-QTKYPRIKRIQQLADYFNV 63
Cdd:COG3655    5 KLDELLAERGMTKKELAEATGISRATLSRLKNgKAKAVRLDTLEKICKALDC 56
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
13-63 1.10e-07

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 44.84  E-value: 1.10e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446351911   13 NLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQT-KYPRIKRIQQLADYFNV 63
Cdd:pfam13443   1 KLRKLMADRGISKSDLARATGISRATLSRLRKGKpKRVSLDTLDKICDALGC 52
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
10-62 2.64e-07

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: 45.01  E-value: 2.64e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 446351911  10 LSENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFN 62
Cdd:COG3620   18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALG 70
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
10-64 3.65e-07

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: 43.77  E-value: 3.65e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 446351911  10 LSENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVP 64
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
25-53 7.92e-05

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


Pssm-ID: 443351  Cd Length: 68  Bit Score: 37.58  E-value: 7.92e-05
                         10        20
                 ....*....|....*....|....*....
gi 446351911  25 QRELAEAIGVSQPTVSNWIQQTKYPRIKR 53
Cdd:COG4197   11 QSALARALGVSQQAVSQWLNGKRRVPAER 39
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
9-43 3.46e-04

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 36.33  E-value: 3.46e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446351911   9 ILSEnlqELMNDKNIDQRELAEAIGVSQPTVSNWI 43
Cdd:COG3093   12 ILRE---EFLEPLGLSQTELAKALGVSRQRISEIL 43
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
14-64 6.11e-04

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 35.20  E-value: 6.11e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446351911   14 LQELMNDKNIDQRELAEAIGVSQPTVSnWIQQTKYPRIKR--IQQLADYFNVP 64
Cdd:pfam13560   6 LRRLRERAGLSQEALARRLGVSRSTLS-RLETGRRGRPSPavVERLARALGVD 57
YdaS_antitoxin pfam15943
Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family ...
25-47 6.16e-04

Putative antitoxin of bacterial toxin-antitoxin system, YdaS/YdaT; YdaS_antitoxin is a family of putative bacterial antitoxins, neutralising the toxin YdaT, family pfam06254.


Pssm-ID: 435033  Cd Length: 65  Bit Score: 35.40  E-value: 6.16e-04
                          10        20
                  ....*....|....*....|...
gi 446351911   25 QRELAEAIGVSQPTVSNWIQQTK 47
Cdd:pfam15943  11 QKALAEALGVTQQAVSQWLHGKK 33
COG3398 COG3398
Predicted transcriptional regulator, contains two HTH domains [Transcription];
1-40 6.60e-04

Predicted transcriptional regulator, contains two HTH domains [Transcription];


Pssm-ID: 442625 [Multi-domain]  Cd Length: 159  Bit Score: 36.78  E-value: 6.60e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446351911   1 MENNKVRKILSEnlqeLMNDKNIDQRELAEAIGVSQPTVS 40
Cdd:COG3398   94 LRRETPRRILLY----LLENPGATNKELAEELGISRSTVS 129
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
12-68 1.51e-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: 34.19  E-value: 1.51e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 446351911   12 ENLQELMNDKNIDQRELAEAIGVSQPTVSNWIQQTKYPRIKRIQQLADYFNVPKSRI 68
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWL 58
COG5606 COG5606
Predicted DNA-binding protein, XRE-type HTH domain [General function prediction only];
2-41 1.77e-03

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


Pssm-ID: 444337  Cd Length: 105  Bit Score: 34.86  E-value: 1.77e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446351911   2 ENNKVRKILSENLQELMNDKNIDQRELAEAIGVSQPTVSN 41
Cdd:COG5606   25 EELKLKAQLMAAIRKLIKERGLTQAEAAELLGITQPRVSD 64
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
22-50 2.54e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 33.75  E-value: 2.54e-03
                         10        20
                 ....*....|....*....|....*....
gi 446351911  22 NIDQRELAEAIGVSQPTVSNWIQQTKYPR 50
Cdd:COG2944   19 GLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
HTH_AsnC-type pfam13404
AsnC-type helix-turn-helix domain;
7-53 4.10e-03

AsnC-type helix-turn-helix domain;


Pssm-ID: 433180 [Multi-domain]  Cd Length: 41  Bit Score: 32.73  E-value: 4.10e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 446351911    7 RKILsenlQELMNDKNIDQRELAEAIGVSQPTVSNwiqqtkypRIKR 53
Cdd:pfam13404   5 RKIL----RLLQEDARISFAELAERVGLSESTVLR--------RIRR 39
Spo0J COG1475
Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, ...
14-41 4.60e-03

Chromosome segregation protein Spo0J, contains ParB-like nuclease domain [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441084 [Multi-domain]  Cd Length: 241  Bit Score: 34.96  E-value: 4.60e-03
                         10        20
                 ....*....|....*....|....*...
gi 446351911  14 LQELMNDKNIDQRELAEAIGVSQPTVSN 41
Cdd:COG1475  112 YQRLLEEFGLTQEEIAERLGKSRSEVSN 139
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
14-43 6.47e-03

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: 34.43  E-value: 6.47e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 446351911  14 LQELMNDKNIDQRELAEAIGVSQPTVSNWI 43
Cdd:NF038310   1 IKNDLESKGITNRKLAKKIGVSKSTLSKFF 30
HTH_ASNC smart00344
helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase ...
7-57 7.80e-03

helix_turn_helix ASNC type; AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli)


Pssm-ID: 214628 [Multi-domain]  Cd Length: 108  Bit Score: 33.26  E-value: 7.80e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 446351911     7 RKILSEnlqeLMNDKNIDQRELAEAIGVSQPTVSNwiqqtkypRIKRIQQL 57
Cdd:smart00344   6 RKILEE----LQKDARISLAELAKKVGLSPSTVHN--------RVKRLEEE 44
 
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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