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Conserved domains on  [gi|446759034|ref|WP_000836290|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Enterobacteriaceae]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 10054599)

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
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 96-152 6.75e-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: 40.39  E-value: 6.75e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446759034  96 RWMSESRDLStQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYELLI 152
Cdd:COG3620   23 RLMRKELGLS-QLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLV 78
Cro super family cl46781
Cro; Members of this family are involved in the repression of transcription by binding as a ...
 22-61 4.66e-03

Cro; Members of this family are involved in the repression of transcription by binding as a homodimer to palindromic DNA operator sites in phage lambda: they repress genes expressed in early phage development and are necessary for the late stage of lytic growth. These proteins have a secondary structure consisting of three alpha-helices and three beta-sheets, and dimerize through interactions between the two antiparallel beta-strands.


The actual alignment was detected with superfamily member COG4197:

Pssm-ID: 481121  Cd Length: 68  Bit Score: 34.50  E-value: 4.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446759034  22 GVQTRMAEKLGTQANLVNRWALGKKVIGDQVARKIEAAAN 61
Cdd:COG4197    9 GSQSALARALGVSQQAVSQWLNGKRRVPAERCLAIERATG 48
 
Name Accession Description Interval E-value
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 96-152 6.75e-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: 40.39  E-value: 6.75e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446759034  96 RWMSESRDLStQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYELLI 152
Cdd:COG3620   23 RLMRKELGLS-QLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLV 78
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 106-150 1.65e-04

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: 38.30  E-value: 1.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446759034 106 TQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYEL 150
Cdd:cd00093   14 TQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 93-144 2.18e-04

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: 37.91  E-value: 2.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446759034   93 NLERWMSEsRDLSTQgKLHRASGVAQVTISRLLNNEV-SVSISTLENVASAFG 144
Cdd:pfam13443   1 KLRKLMAD-RGISKS-DLARATGISRATLSRLRKGKPkRVSLDTLDKICDALG 51
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
106-150 6.48e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.34  E-value: 6.48e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 446759034   106 TQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYEL 150
Cdd:smart00530  12 TQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
22-61 4.66e-03

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 34.50  E-value: 4.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446759034  22 GVQTRMAEKLGTQANLVNRWALGKKVIGDQVARKIEAAAN 61
Cdd:COG4197    9 GSQSALARALGVSQQAVSQWLNGKRRVPAERCLAIERATG 48
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
112-148 6.64e-03

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 36.68  E-value: 6.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 446759034 112 RASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGY 148
Cdd:PRK10401   9 RQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGY 45
 
Name Accession Description Interval E-value
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 96-152 6.75e-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: 40.39  E-value: 6.75e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 446759034  96 RWMSESRDLStQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYELLI 152
Cdd:COG3620   23 RLMRKELGLS-QLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLV 78
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 106-150 1.65e-04

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: 38.30  E-value: 1.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 446759034 106 TQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYEL 150
Cdd:cd00093   14 TQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 93-144 2.18e-04

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: 37.91  E-value: 2.18e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 446759034   93 NLERWMSEsRDLSTQgKLHRASGVAQVTISRLLNNEV-SVSISTLENVASAFG 144
Cdd:pfam13443   1 KLRKLMAD-RGISKS-DLARATGISRATLSRLRKGKPkRVSLDTLDKICDALG 51
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
106-151 2.88e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 38.05  E-value: 2.88e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446759034 106 TQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYELL 151
Cdd:COG1396   22 TQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
106-150 6.48e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 36.34  E-value: 6.48e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*
gi 446759034   106 TQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYEL 150
Cdd:smart00530  12 TQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 106-150 2.64e-03

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: 34.82  E-value: 2.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 446759034  106 TQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYEL 150
Cdd:pfam01381  11 SQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
LacI pfam00356
Bacterial regulatory proteins, lacI family;
112-148 3.86e-03

Bacterial regulatory proteins, lacI family;


Pssm-ID: 306791 [Multi-domain]  Cd Length: 46  Bit Score: 34.15  E-value: 3.86e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 446759034  112 RASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGY 148
Cdd:pfam00356   7 RLAGVSKSTVSRVLNNPGRVSEETRERVEAAMEELNY 43
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
22-61 4.66e-03

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 34.50  E-value: 4.66e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 446759034  22 GVQTRMAEKLGTQANLVNRWALGKKVIGDQVARKIEAAAN 61
Cdd:COG4197    9 GSQSALARALGVSQQAVSQWLNGKRRVPAERCLAIERATG 48
HTH_LACI smart00354
helix_turn _helix lactose operon repressor;
112-148 5.49e-03

helix_turn _helix lactose operon repressor;


Pssm-ID: 197675 [Multi-domain]  Cd Length: 70  Bit Score: 34.10  E-value: 5.49e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 446759034   112 RASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGY 148
Cdd:smart00354   8 RLAGVSKATVSRVLNGKGRVSEETREKVLAAMEELGY 44
PRK10401 PRK10401
HTH-type transcriptional regulator GalS;
112-148 6.64e-03

HTH-type transcriptional regulator GalS;


Pssm-ID: 236681 [Multi-domain]  Cd Length: 346  Bit Score: 36.68  E-value: 6.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 446759034 112 RASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGY 148
Cdd:PRK10401   9 RQAGVSVATVSRVLNNSALVSADTREAVMKAVSELGY 45
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 24-59 7.19e-03

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: 34.14  E-value: 7.19e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446759034  24 QTRMAEKLGTQANLVNRWALGKKVIGDQVARKIEAA 59
Cdd:COG1813   28 QEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKA 63
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
100-151 7.34e-03

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 34.05  E-value: 7.34e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 446759034 100 ESRDLsTQGKLHRASGVAQVTISRLLNNEVSVSISTLENVASAFGRHGYELL 151
Cdd:COG1476   14 KERGL-TQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELF 64
 
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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