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Conserved domains on  [gi|446976872|ref|WP_001054128|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Staphylococcus]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 10787697)

helix-turn-helix (HTH) transcriptional regulator containing a XRE (Xenobiotic Response Element) family HTH domain may act as a transcriptional regulator that controls the expression of genes involved in stress response

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  10473770|2644244
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 7.60e-19

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 76.43  E-value: 7.60e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLVKGT 65
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 7.60e-19

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 76.43  E-value: 7.60e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLVKGT 65
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 1.86e-16

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: 69.89  E-value: 1.86e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446976872   4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-61 1.92e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 67.16  E-value: 1.92e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 446976872     7 IKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDL 61
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 6.85e-15

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: 65.64  E-value: 6.85e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446976872    7 IKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK04140 PRK04140
transcriptional regulator;
4-64 4.09e-06

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 46.00  E-value: 4.09e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446976872   4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVtldDLVKG 64
Cdd:PRK04140 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDV---PLTKP 185
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 4-52 2.26e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 36.45  E-value: 2.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446976872    4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIH--NLLMMCE 52
Cdd:TIGR03830  67 GPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKAldKLLRLLD 117
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 7.60e-19

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 76.43  E-value: 7.60e-19
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLVKGT 65
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 6.70e-18

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 74.26  E-value: 6.70e-18
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLVKGT 65
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGA 70
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-61 1.86e-16

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: 69.89  E-value: 1.86e-16
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 446976872   4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDL 61
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
7-61 1.92e-15

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 67.16  E-value: 1.92e-15
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 446976872     7 IKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDL 61
Cdd:smart00530   2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-61 6.85e-15

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: 65.64  E-value: 6.85e-15
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 446976872    7 IKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDL 61
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-60 6.17e-14

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: 63.42  E-value: 6.17e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 446976872   2 NLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDD 60
Cdd:COG1813   12 DYGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-65 9.30e-10

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: 52.29  E-value: 9.30e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446976872    5 KQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLVKGT 65
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGE 62
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-62 3.00e-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: 3.00e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLV 62
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVL 77
PRK04140 PRK04140
transcriptional regulator;
4-64 4.09e-06

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 46.00  E-value: 4.09e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446976872   4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVtldDLVKG 64
Cdd:PRK04140 128 GDVLREAREELGLSLGELASELGVSRRTISKYENGGMNASIEVAIKLEEILDV---PLTKP 185
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-43 3.11e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 40.30  E-value: 3.11e-05
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 446976872   6 QIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPD 43
Cdd:COG2944   10 EIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPS 47
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-61 4.29e-05

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: 39.82  E-value: 4.29e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446976872    3 LSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDK-SLPDIHNLLMMCELFNVTLDDL 61
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRrGRPSPAVVERLARALGVDGAER 61
PHA01976 PHA01976
helix-turn-helix protein
 1-65 8.73e-05

helix-turn-helix protein


Pssm-ID: 177330 [Multi-domain]  Cd Length: 67  Bit Score: 39.17  E-value: 8.73e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTLDDLVKGT 65
Cdd:PHA01976   1 MSFAIQLIKARNARAWSAPELSRRAGVRHSLIYDFEADKRLPNLKTLLRLADALGVTLDWLCGRC 65
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
4-63 1.60e-04

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 40.98  E-value: 1.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 446976872   4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNvtlDDLVK 63
Cdd:COG1395  129 GEKLRELREERGLSLGELASELGVSRRTISKYERGEMDASIEVALKLEEILG---EPIVK 185
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 3-52 9.98e-04

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 37.53  E-value: 9.98e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 446976872   3 LSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCE 52
Cdd:PRK09706   6 LGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEPTGKNLFALAK 55
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 1-39 1.93e-03

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 35.55  E-value: 1.93e-03
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 446976872   1 MNLSKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDK 39
Cdd:COG1426    4 ETIGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGD 42
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 4-52 2.26e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 36.45  E-value: 2.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 446976872    4 SKQIKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIH--NLLMMCE 52
Cdd:TIGR03830  67 GPEIRRIRKKLGLSQREAAELLGGGVNAFSRYERGEVRPSKAldKLLRLLD 117
TIGR00270 TIGR00270
TIGR00270 family protein; [Hypothetical proteins, Conserved]
 7-58 4.38e-03

TIGR00270 family protein; [Hypothetical proteins, Conserved]


Pssm-ID: 129371 [Multi-domain]  Cd Length: 154  Bit Score: 36.04  E-value: 4.38e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 446976872    7 IKKYRERDGYSQEYLAEKLYVSRQSISNWENDKSLPDIHNLLMMCELFNVTL 58
Cdd:TIGR00270  74 IRREREKRGWSQEQLAKKIQEKESLIKKIENAEIEPEPKVVEKLEKLLKIKL 125
 
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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