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Conserved domains on  [gi|2188370094|ref|WP_236888142|]
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helix-turn-helix transcriptional regulator [Dehalococcoides mccartyi]

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];
3-57 3.54e-10

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.85  E-value: 3.54e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSPVLRRLILENMpEYTFDDLFIIEE 57
Cdd:COG1476   15 ERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARAL-GVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-57 3.54e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.85  E-value: 3.54e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSPVLRRLILENMpEYTFDDLFIIEE 57
Cdd:COG1476   15 ERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARAL-GVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-39 7.73e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 48.67  E-value: 7.73e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2188370094   3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:smart00530  8 EKGLTQEELAEKLGVSRSTLSRIENGKRKPSLeTLKKL 45
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-39 3.85e-09

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: 47.16  E-value: 3.85e-09
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:cd00093   10 EKGLTQEELAEKLGVSRSTISRIENGKRNPSLeTLEKL 47
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 3-39 1.54e-08

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: 45.22  E-value: 1.54e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIENGKREPSLeTLKKL 44
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 5-34 8.06e-05

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: 36.44  E-value: 8.06e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 2188370094  5 NLSQRDLAEKIGFSRSHLSHIINGRREPSP 34
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIVNGRAAITA 47
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 1-31 2.08e-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: 37.12  E-value: 2.08e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2188370094   1 MSRKNLSQRDLAEKIGFSRSHLSHIINGRRE 31
Cdd:NF038310    5 LESKGITNRKLAKKIGVSKSTLSKFFNGKGE 35
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 1-33 6.49e-03

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 32.42  E-value: 6.49e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2188370094   1 MSRKNLSQRDLAEKIGFSRSHLSHIINGRREPS 33
Cdd:PRK13890   14 LDERHMTKKELSERSGVSISFLSDLTTGKANPS 46
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
3-57 3.54e-10

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 49.85  E-value: 3.54e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSPVLRRLILENMpEYTFDDLFIIEE 57
Cdd:COG1476   15 ERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARAL-GVSLEELFSLEE 68
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-39 7.73e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 48.67  E-value: 7.73e-10
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 2188370094   3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:smart00530  8 EKGLTQEELAEKLGVSRSTLSRIENGKRKPSLeTLKKL 45
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
3-39 3.31e-09

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 47.68  E-value: 3.31e-09
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:COG1396   18 ARGLTQEELAERLGVSRSTISRIERGRRNPSLeTLLKL 55
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 3-39 3.85e-09

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: 47.16  E-value: 3.85e-09
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:cd00093   10 EKGLTQEELAEKLGVSRSTISRIENGKRNPSLeTLEKL 47
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 3-39 1.54e-08

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: 45.22  E-value: 1.54e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSP-VLRRL 39
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIENGKREPSLeTLKKL 44
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 1-34 3.74e-08

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


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 45.19  E-value: 3.74e-08
                         10        20        30
                 ....*....|....*....|....*....|....
gi 2188370094  1 MSRKNLSQRDLAEKIGFSRSHLSHIINGRREPSP 34
Cdd:COG3093   18 LEPLGLSQTELAKALGVSRQRISEILNGKRAITA 51
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-40 6.80e-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: 44.16  E-value: 6.80e-08
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSPVLRRLI 40
Cdd:COG1813   23 ARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKL 60
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
3-46 3.14e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 42.23  E-value: 3.14e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPSPVLRRLI--LENMPE 46
Cdd:COG2944   17 RLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLLrlLEKHPE 62
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 3-39 9.34e-06

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: 38.66  E-value: 9.34e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRRE-PSP-VLRRL 39
Cdd:pfam13560 12 RAGLSQEALARRLGVSRSTLSRLETGRRGrPSPaVVERL 50
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-40 9.43e-06

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: 39.23  E-value: 9.43e-06
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRREPS-PVLRRLI 40
Cdd:COG3620   28 ELGLSQLPVAELVGVSQSDILRIESGKRDPTvSTLEKIA 66
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 2-34 5.43e-05

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: 36.50  E-value: 5.43e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 2188370094  2 SRKNLSQRDLAEKIGFSRSHLSHIINGRREPSP 34
Cdd:pfam12844  9 EERGLTQEELAERLGISRSQLSAIENGKSVPPA 41
antidote_HigA TIGR02607
addiction module antidote protein, HigA family; Members of this family form a distinct clade ...
 5-34 8.06e-05

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: 36.44  E-value: 8.06e-05
                         10        20        30
                 ....*....|....*....|....*....|
gi 2188370094  5 NLSQRDLAEKIGFSRSHLSHIINGRREPSP 34
Cdd:TIGR02607 18 GLSVRALAKALGVSRSTLSRIVNGRAAITA 47
lysogeny_AimR NF038310
AimR family lysis-lysogeny pheromone receptor; The founding member of this family, AimR ...
 1-31 2.08e-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: 37.12  E-value: 2.08e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2188370094   1 MSRKNLSQRDLAEKIGFSRSHLSHIINGRRE 31
Cdd:NF038310    5 LESKGITNRKLAKKIGVSKSTLSKFFNGKGE 35
HigA COG5499
Antitoxin component HigA of the HigAB toxin-antitoxin module, contains an N-terminal HTH ...
 1-33 7.98e-04

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: 34.81  E-value: 7.98e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2188370094   1 MSRKNLSQRDLAEKIGfSRSHLSHIINGRREPS 33
Cdd:COG5499    74 MEQHGLTQKDLAPEIG-SKSRVSEILNGKRSLT 105
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 3-38 1.26e-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: 33.24  E-value: 1.26e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 2188370094  3 RKNLSQRDLAEKIGFSRSHLSHIINGRRE--PSPVLRR 38
Cdd:COG1426   16 AKGLSLEDVAERTKISVSYLEAIEEGDFDalPGPVYVR 53
PRK13890 PRK13890
conjugal transfer protein TrbA; Provisional
 1-33 6.49e-03

conjugal transfer protein TrbA; Provisional


Pssm-ID: 237547 [Multi-domain]  Cd Length: 120  Bit Score: 32.42  E-value: 6.49e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2188370094   1 MSRKNLSQRDLAEKIGFSRSHLSHIINGRREPS 33
Cdd:PRK13890   14 LDERHMTKKELSERSGVSISFLSDLTTGKANPS 46
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 1-29 9.09e-03

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: 30.97  E-value: 9.09e-03
                         10        20
                 ....*....|....*....|....*....
gi 2188370094  1 MSRKNLSQRDLAEKIGFSRSHLSHIINGR 29
Cdd:pfam13443  6 MADRGISKSDLARATGISRATLSRLRKGK 34
 
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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