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Conserved domains on  [gi|2094012397|gb|UAL36929|]
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helix-turn-helix domain-containing protein (plasmid) [Klebsiella aerogenes]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 366238)

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

Gene Ontology:  GO:0003677|GO:0006355

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HTH_19 super family cl48150
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 10-54 1.78e-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.


The actual alignment was detected with superfamily member pfam12844:

Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 38.42  E-value: 1.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2094012397 10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVPRTIQLATAALTLK 54
Cdd:pfam12844  8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
 
Name Accession Description Interval E-value
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 10-54 1.78e-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: 38.42  E-value: 1.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2094012397 10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVPRTIQLATAALTLK 54
Cdd:pfam12844  8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
6-42 1.20e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 36.36  E-value: 1.20e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2094012397  6 LILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPR 42
Cdd:COG1476    9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPS 45
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-57 2.51e-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: 35.22  E-value: 2.51e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 2094012397  6 LILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPR--TIQLATAALTLKAEW 57
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSleTLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-53 2.90e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.19  E-value: 2.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2094012397   6 LILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPRTIQLATAALTL 53
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 10-41 5.15e-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: 33.37  E-value: 5.15e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2094012397  10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVP 41
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYERGEVRP 105
 
Name Accession Description Interval E-value
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 10-54 1.78e-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: 38.42  E-value: 1.78e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 2094012397 10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVPRTIQLATAALTLK 54
Cdd:pfam12844  8 REERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLG 52
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
6-42 1.20e-04

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 36.36  E-value: 1.20e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 2094012397  6 LILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPR 42
Cdd:COG1476    9 LKELRKERGLTQEELAELLGVSRQTISAIENGKYNPS 45
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
9-49 1.86e-04

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 36.13  E-value: 1.86e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 2094012397  9 WRRGLNWTQERAAAELGISRTSLVKYEDGEAVPRT---IQLATA 49
Cdd:COG1396   15 LRKARGLTQEELAERLGVSRSTISRIERGRRNPSLetlLKLAKA 58
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 6-57 2.51e-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: 35.22  E-value: 2.51e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 2094012397  6 LILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPR--TIQLATAALTLKAEW 57
Cdd:cd00093    4 LKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSleTLEKLAKALGVSLDE 57
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-53 2.90e-04

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.19  E-value: 2.90e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2094012397   6 LILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPRTIQLATAALTL 53
Cdd:smart00530  2 LKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKAL 49
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 10-42 4.76e-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: 34.91  E-value: 4.76e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 2094012397 10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVPR 42
Cdd:COG1813   21 REARGLSQEELAEKLGVSESTIRRIERGEATPS 53
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 10-57 1.08e-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: 33.67  E-value: 1.08e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2094012397 10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVP--RTIQLATAALTLKAEW 57
Cdd:pfam01381  5 REELGLSQEELAEKLGVSRSTISKIENGKREPslETLKKLAEALGVSLDE 54
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
1-47 1.91e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 33.37  E-value: 1.91e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 2094012397  1 MTGFDLILWRRGLNWTQERAAAELGISRTSLVKYEDGEAVPRTIQLA 47
Cdd:COG2944    6 LTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRKPSGAALK 52
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 10-41 5.15e-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: 33.37  E-value: 5.15e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 2094012397  10 RRGLNWTQERAAAELGISRTSLVKYEDGEAVP 41
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYERGEVRP 105
 
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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