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Conserved domains on  [gi|2788144534|gb|XEH74460|]
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helix-turn-helix transcriptional regulator (plasmid) [Edwardsiella tarda]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10650117)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator

CATH:  1.10.10.10
Gene Ontology:  GO:0003677
PubMed:  15808743|2644244|8831795
SCOP:  4000362

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-64 6.93e-12

Helix-turn-helix XRE-family like proteins;


:

Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.99  E-value: 6.93e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534    5 RLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKL---GVS-RSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-64 6.93e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.99  E-value: 6.93e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534    5 RLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKL---GVS-RSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-64 9.09e-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: 55.64  E-value: 9.09e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2788144534   4 KRLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:cd00093     2 ERLKELRKEKGLTQEELAEKL---GVS-RSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 2.13e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 55.39  E-value: 2.13e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534   1 MVPKRLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYFYTIDDD 70
Cdd:COG1396     7 ALGERLRELRKARGLTQEELAERL---GVS-RSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-64 1.58e-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: 49.85  E-value: 1.58e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2788144534   6 LREAREASGLSQGKLAELIGlegVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:pfam01381   1 LKELREELGLSQEELAEKLG---VS-RSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 5-63 6.45e-04

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 37.79  E-value: 6.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534   5 RLREAREASGLSQGKLAELIGLEGVSLN-SRLSNYEVGRFTPSFDFVVRVAKVLDYPECY 63
Cdd:PRK13355    7 RLKQAMKARGLKQEDLVHAAEARGVKLGkSHISQYVSGKTGPRRDVLPFLAAILGVSEDW 66
 
Name Accession Description Interval E-value
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
5-64 6.93e-12

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 55.99  E-value: 6.93e-12
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534    5 RLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:smart00530   1 RLKELREEKGLTQEELAEKL---GVS-RSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-64 9.09e-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: 55.64  E-value: 9.09e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2788144534   4 KRLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:cd00093     2 ERLKELRKEKGLTQEELAEKL---GVS-RSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-70 2.13e-11

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 55.39  E-value: 2.13e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534   1 MVPKRLREAREASGLSQGKLAELIgleGVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYFYTIDDD 70
Cdd:COG1396     7 ALGERLRELRKARGLTQEELAERL---GVS-RSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADE 72
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-69 5.39e-11

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 54.08  E-value: 5.39e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2788144534   1 MVPKRLREAREASGLSQGKLAELIgleGVSLNSrLSNYEVGRFTPSFDFVVRVAKVLDYPECYFYTIDD 69
Cdd:COG1476     4 KLGNRLKELRKERGLTQEELAELL---GVSRQT-ISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 2-58 7.63e-10

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: 51.09  E-value: 7.63e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2788144534   2 VPKRLREAREASGLSQGKLAELIgleGVSLnSRLSNYEVGRFTPSFDFVVRVAKVLD 58
Cdd:COG1813    13 YGERIREAREARGLSQEELAEKL---GVSE-STIRRIERGEATPSLDTLRKLEKALG 65
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 6-64 1.58e-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: 49.85  E-value: 1.58e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2788144534   6 LREAREASGLSQGKLAELIGlegVSlNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYF 64
Cdd:pfam01381   1 LKELREELGLSQEELAEKLG---VS-RSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 4-66 4.28e-09

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: 48.82  E-value: 4.28e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2788144534   4 KRLREAREASGLSQGKLAELIGLEGvslnSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYFYT 66
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISR----SQLSAIENGKSVPPAETLYKIAELLGVPANWLLQ 60
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 5-58 1.12e-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: 42.90  E-value: 1.12e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2788144534   5 RLREAREASGLSQGKLAELIGLEGvslnSRLSNYEVGR-FTPSFDFVVRVAKVLD 58
Cdd:pfam13560   5 RLRRLRERAGLSQEALARRLGVSR----STLSRLETGRrGRPSPAVVERLARALG 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 2-70 9.44e-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: 38.46  E-value: 9.44e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2788144534   2 VPKRLREAREASGLSQGKLAELIgleGVSLNSrLSNYEVGRFTPSFDFVVRVAKVLDYPECYFYTIDDD 70
Cdd:COG3620    18 LGEALRLMRKELGLSQLPVAELV---GVSQSD-ILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDG 82
COG1395 COG1395
Predicted transcriptional regulator [Transcription];
3-58 6.40e-04

Predicted transcriptional regulator [Transcription];


Pssm-ID: 441005 [Multi-domain]  Cd Length: 313  Bit Score: 37.51  E-value: 6.40e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2788144534   3 PKRLREAREASGLSQGKLAELIGLegvslnSR--LSNYEVGRFTPSFDFVVRVAKVLD 58
Cdd:COG1395   129 GEKLRELREERGLSLGELASELGV------SRrtISKYERGEMDASIEVALKLEEILG 180
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 5-63 6.45e-04

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 37.79  E-value: 6.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2788144534   5 RLREAREASGLSQGKLAELIGLEGVSLN-SRLSNYEVGRFTPSFDFVVRVAKVLDYPECY 63
Cdd:PRK13355    7 RLKQAMKARGLKQEDLVHAAEARGVKLGkSHISQYVSGKTGPRRDVLPFLAAILGVSEDW 66
PRK04140 PRK04140
transcriptional regulator;
4-60 1.28e-03

transcriptional regulator;


Pssm-ID: 235224 [Multi-domain]  Cd Length: 317  Bit Score: 36.76  E-value: 1.28e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2788144534   4 KRLREAREASGLSQGKLAELIgleGVSLNSrLSNYEVGRFTPSFDFVVRVAKVLDYP 60
Cdd:PRK04140  129 DVLREAREELGLSLGELASEL---GVSRRT-ISKYENGGMNASIEVAIKLEEILDVP 181
PRK09943 PRK09943
HTH-type transcriptional regulator PuuR;
4-65 5.05e-03

HTH-type transcriptional regulator PuuR;


Pssm-ID: 182158 [Multi-domain]  Cd Length: 185  Bit Score: 34.77  E-value: 5.05e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2788144534   4 KRLREAREASGLSQGKLAELIGLEgvslNSRLSNYEVGRFTPSFDFVVRVAKVLDYPECYFY 65
Cdd:PRK09943   10 KRLSEIRQQQGLSQRRAAELSGLT----HSAISTIEQDKVSPAISTLQKLLKVYGLSLSEFF 67
 
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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