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Conserved domains on  [gi|2419103985|gb|WBF77102|]
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hypothetical protein [Lacticaseibacillus phage R9.2]

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];
13-69 6.96e-09

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


:

Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 47.54  E-value: 6.96e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSIIFLPK 69
Cdd:COG1476   12 LRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
13-69 6.96e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 47.54  E-value: 6.96e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSIIFLPK 69
Cdd:COG1476   12 LRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-64 2.94e-07

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: 42.93  E-value: 2.94e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSI 64
Cdd:cd00093    7 LRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-62 4.97e-06

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: 39.83  E-value: 4.97e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFD 62
Cdd:pfam01381  4 LREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-62 2.00e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.27  E-value: 2.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2419103985  13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFD 62
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 14-59 8.72e-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: 32.60  E-value: 8.72e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2419103985  14 RNNLHFSQKEVAEALGMSTKTYADYEkyRKVLRTDKAFEfaKLVKL 59
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYE--RGEVRPSKALD--KLLRL 115
 
Name Accession Description Interval E-value
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
13-69 6.96e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 47.54  E-value: 6.96e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSIIFLPK 69
Cdd:COG1476   12 LRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLEE 68
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 13-64 2.94e-07

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: 42.93  E-value: 2.94e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSI 64
Cdd:cd00093    7 LRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-65 4.20e-06

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 40.75  E-value: 4.20e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2419103985  1 MTEIEPAF--TLEGARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSII 65
Cdd:COG1396    1 MSTLKKALgeRLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELL 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 13-62 4.97e-06

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: 39.83  E-value: 4.97e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFD 62
Cdd:pfam01381  4 LREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLD 53
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
13-62 2.00e-05

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 38.27  E-value: 2.00e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2419103985  13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFD 62
Cdd:smart00530  5 LREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLD 54
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 3-82 5.15e-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: 38.08  E-value: 5.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2419103985  3 EIEPAFTLEGA----RNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSIIFLPKDYETFVVGK 78
Cdd:COG3620   11 TVSPDDTLGEAlrlmRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGKLVGIITR 90


                 ....
gi 2419103985 79 KDLL 82
Cdd:COG3620   91 RDLL 94
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 10-62 4.25e-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: 35.30  E-value: 4.25e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 2419103985 10 LEGARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFD 62
Cdd:COG1813   17 IREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLA 69
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
13-40 4.58e-04

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 34.91  E-value: 4.58e-04
                         10        20
                 ....*....|....*....|....*...
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEK 40
Cdd:COG2944   14 LRERLGLSQAEFAALLGVSVSTVRRWEQ 41
HTH_CRP cd00092
helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic ...
 11-59 1.26e-03

helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.


Pssm-ID: 238044 [Multi-domain]  Cd Length: 67  Bit Score: 34.18  E-value: 1.26e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 2419103985 11 EGARNNLHFSQKEVAEALGMSTKTyadyekyrkVLRTDKAFEFAKLVKL 59
Cdd:cd00092   18 AGDLVQLPLTRQEIADYLGLTRET---------VSRTLKELEEEGLISR 57
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 13-65 2.69e-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: 33.03  E-value: 2.69e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 2419103985 13 ARNNLHFSQKEVAEALGMSTKTYADYEKYRKVLRTDKAFEFAKLVKLPFDSII 65
Cdd:pfam12844  7 AREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLL 59
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 14-59 8.72e-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: 32.60  E-value: 8.72e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2419103985  14 RNNLHFSQKEVAEALGMSTKTYADYEkyRKVLRTDKAFEfaKLVKL 59
Cdd:TIGR03830  74 RKKLGLSQREAAELLGGGVNAFSRYE--RGEVRPSKALD--KLLRL 115
 
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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