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Conserved domains on  [gi|613390029|gb|EZZ93895|]
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hypothetical protein W395_00962 [Staphylococcus aureus VET0057R]

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];
1-72 7.60e-12

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


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 59.63  E-value: 7.60e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613390029   1 MAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP-SYILHRISDE 72
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSlDELLGGADEE 73
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 7.60e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 59.63  E-value: 7.60e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613390029   1 MAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP-SYILHRISDE 72
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSlDELLGGADEE 73
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-62 4.90e-10

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: 54.10  E-value: 4.90e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 613390029   9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-62 1.82e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.74  E-value: 1.82e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 613390029    12 IKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-62 2.09e-05

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: 40.99  E-value: 2.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 613390029   12 IKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 9-52 3.14e-04

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 38.02  E-value: 3.14e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 613390029    9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEI 52
Cdd:TIGR03070   4 GILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKV 47
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
5-42 3.57e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 35.73  E-value: 3.57e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 613390029   5 PTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHEN 42
Cdd:PRK09726  10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47
 
Name Accession Description Interval E-value
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-72 7.60e-12

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 59.63  E-value: 7.60e-12
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 613390029   1 MAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP-SYILHRISDE 72
Cdd:COG1396    1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSlDELLGGADEE 73
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-62 4.90e-10

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: 54.10  E-value: 4.90e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 613390029   9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVS 54
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 1-62 5.57e-08

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: 48.78  E-value: 5.57e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 613390029   1 MAELPTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:COG1813    6 TGELVEDYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGIS 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
12-62 1.82e-07

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.74  E-value: 1.82e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|.
gi 613390029    12 IKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVS 52
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
9-62 5.70e-07

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 45.99  E-value: 5.70e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 613390029   9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVS 59
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 9-53 6.48e-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: 46.55  E-value: 6.48e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 613390029   9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIE 53
Cdd:COG3620   19 GEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLE 63
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
9-45 1.80e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 41.46  E-value: 1.80e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 613390029   9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNR 45
Cdd:COG2944    8 PEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRR 44
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-62 2.09e-05

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: 40.99  E-value: 2.09e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 613390029   12 IKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP 62
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVS 51
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 5-47 4.37e-05

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 40.95  E-value: 4.37e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 613390029   5 PTHYGTIIK-TLRKYMKLTQSKLSERTGFSQNTISNHENGNRNI 47
Cdd:COG3093    6 PIHPGEILReEFLEPLGLSQTELAKALGVSRQRISEILNGKRAI 49
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 9-52 3.14e-04

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 38.02  E-value: 3.14e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 613390029    9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEI 52
Cdd:TIGR03070   4 GILVRARRKALGLTQADLADLAGVGLRFIRDLENGKPTVRLDKV 47
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 9-67 7.86e-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: 36.88  E-value: 7.86e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 613390029    9 GTIIKTLRKYMKLTQSKLSERTGFSQNTISNHENGNRNIGVNEIEIYGKGLGIP-SYILH 67
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPaNWLLQ 60
PRK09726 PRK09726
type II toxin-antitoxin system antitoxin HipB;
5-42 3.57e-03

type II toxin-antitoxin system antitoxin HipB;


Pssm-ID: 182049  Cd Length: 88  Bit Score: 35.73  E-value: 3.57e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 613390029   5 PTHYGTIIKTLRKYMKLTQSKLSERTGFSQNTISNHEN 42
Cdd:PRK09726  10 PTQLANAMKLVRQQNGWTQSELAKKIGIKQATISNFEN 47
 
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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