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Conserved domains on  [gi|1122345417|ref|WP_074030473|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Serratia]

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];
1-67 7.84e-12

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.08  E-value: 7.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1122345417  1 MNNIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDIFPPQ 67
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG-----VSLEELFSLE 67
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-67 7.84e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.08  E-value: 7.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1122345417  1 MNNIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDIFPPQ 67
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG-----VSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 1-63 9.13e-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: 48.70  E-value: 9.13e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1122345417  1 MNNIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDI 63
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALG-----VSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-63 5.50e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.74  E-value: 5.50e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1122345417   3 NIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDI 63
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALG-----VSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-63 4.37e-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: 44.45  E-value: 4.37e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1122345417  8 RKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDI 63
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALG-----VSLDEL 55
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 8-33 1.20e-04

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: 37.23  E-value: 1.20e-04
                          10        20
                  ....*....|....*....|....*.
gi 1122345417   8 RKKLGLSQSALASLIGWTTSRLSNYE 33
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYE 99
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-67 7.84e-12

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.08  E-value: 7.84e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1122345417  1 MNNIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDIFPPQ 67
Cdd:COG1476    6 GNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALG-----VSLEELFSLE 67
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 1-63 9.13e-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: 48.70  E-value: 9.13e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1122345417  1 MNNIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDI 63
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALG-----VSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
3-63 5.50e-09

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 46.74  E-value: 5.50e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1122345417   3 NIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDI 63
Cdd:smart00530  1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALG-----VSLDEL 56
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
2-64 1.16e-08

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 46.53  E-value: 1.16e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1122345417  2 NNIAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDIF 64
Cdd:COG1396   10 ERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALG-----VSLDELL 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 8-63 4.37e-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: 44.45  E-value: 4.37e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 1122345417  8 RKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALNslgaeVTLDDI 63
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALG-----VSLDEL 55
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
4-47 8.56e-07

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 41.46  E-value: 8.56e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 1122345417  4 IAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLI 47
Cdd:COG2944   11 IRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALKLL 54
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 4-52 1.76e-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: 38.85  E-value: 1.76e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 1122345417  4 IAVHRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALN 52
Cdd:COG3620   22 LRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALG 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 7-58 4.66e-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: 36.74  E-value: 4.66e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 1122345417  7 HRKKLGLSQSALASLIGWTTSRLSNYEI-EIRTPSLDDSRLIVSALNSLGAEV 58
Cdd:pfam13560  9 LRERAGLSQEALARRLGVSRSTLSRLETgRRGRPSPAVVERLARALGVDGAER 61
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 8-33 1.20e-04

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: 37.23  E-value: 1.20e-04
                          10        20
                  ....*....|....*....|....*.
gi 1122345417   8 RKKLGLSQSALASLIGWTTSRLSNYE 33
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYE 99
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 8-52 3.85e-04

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: 34.53  E-value: 3.85e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 1122345417  8 RKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALN 52
Cdd:COG1813   21 REARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALG 65
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 7-52 6.32e-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: 31.49  E-value: 6.32e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 1122345417  7 HRKKLGLSQSALASLIGWTTSRLSNYEIEIRTPSLDDSRLIVSALN 52
Cdd:pfam12844  7 AREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
 
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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