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Conserved domains on  [gi|553864937|ref|WP_023138489|]
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MULTISPECIES: YafY family protein [Salmonella]

Protein Classification

helix-turn-helix transcriptional regulator( domain architecture ID 11457199)

helix-turn-helix (HTH) transcriptional regulator containing DNA-binding HTH and WYL domains, may function in the regulation of DNA damage response and bacterial immunity

Gene Ontology:  GO:0003677|GO:0003700|GO:0006355
PubMed:  24817877|37027901|15808743|10473770|8831795

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-198 7.62e-14

Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription];


:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 69.34  E-value: 7.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  12 ADRLTQIIRRLFAGENLNMRHLAEEFGVSVRTLRRDLRE-RLTGLDLEYNDGHC---RLVTADSAG-----QRERSGLTL 82
Cdd:COG2378    4 LERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDAlRELGVPIEAERGRGggyRLRDGYRLPplmltEEEALALLL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  83 ARQSDMEALFPGLDLRLAGAL------LDETEHSPCCIWPPVALTAGSFT---GIFSHLVTAINRRNRISLLAKGQRCE- 152
Cdd:COG2378   84 ALRLLAALGGAPLAEAAASALakleavLPERLRERLEALAERVGVDPPPEvdpEVLETLREAIRERRRLRIDYRSGRGEp 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 553864937 153 ---CLAPYRLICLDRNWYLTG--ELWNDIAVFPLAEIQNVAVLADTYTRNE 198
Cdd:COG2378  164 terTVEPYGLVFYGGRWYLVAwcELRDDIRTFRLDRIRSLELTDERFEPPP 214
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-198 7.62e-14

Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription];


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 69.34  E-value: 7.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  12 ADRLTQIIRRLFAGENLNMRHLAEEFGVSVRTLRRDLRE-RLTGLDLEYNDGHC---RLVTADSAG-----QRERSGLTL 82
Cdd:COG2378    4 LERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDAlRELGVPIEAERGRGggyRLRDGYRLPplmltEEEALALLL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  83 ARQSDMEALFPGLDLRLAGAL------LDETEHSPCCIWPPVALTAGSFT---GIFSHLVTAINRRNRISLLAKGQRCE- 152
Cdd:COG2378   84 ALRLLAALGGAPLAEAAASALakleavLPERLRERLEALAERVGVDPPPEvdpEVLETLREAIRERRRLRIDYRSGRGEp 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 553864937 153 ---CLAPYRLICLDRNWYLTG--ELWNDIAVFPLAEIQNVAVLADTYTRNE 198
Cdd:COG2378  164 terTVEPYGLVFYGGRWYLVAwcELRDDIRTFRLDRIRSLELTDERFEPPP 214
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 128-233 4.30e-04

WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the WYL-like superfamily, named for three conserved amino acids found in a subset of the superfamily. However, these residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a ligand-binding groove typical of the Sm-like SH3 beta-barrels. A WYL domain protein (sll7009) is a negative regulator of the I-D CRISPR-Cas system in Synechocystis sp. It is predicted to be a ligand-sensing domain that could bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense systems such as the abortive infection AbiG system.


Pssm-ID: 433082  Cd Length: 172  Bit Score: 39.94  E-value: 4.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  128 IFSHLVTAINRRNRISL----LAKGQRCECLAPYRLICLDRNWYLTG--ELWNDIAVFPLAEIQNVAVLADTYTR-NETI 200
Cdd:pfam13280   2 VLETLREAILERRRVRFryrsPRGEGTERTVEPYGLVYKDGRWYLVAycRLRDDIRTFRLDRIESVEVLDEPFEPpDFDL 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 553864937  201 SRLTRHPNFINALPH---YRFIRDLLATFKSGPFPN 233
Cdd:pfam13280  82 AEYLRRSFGVFPGPIevkLRFSPEAARRLRERRFPD 117
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 7-50 2.47e-03

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 35.50  E-value: 2.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 553864937   7 RHERLADRLTQIIR--RLFAGENL-NMRHLAEEFGVSVRTLRRDLRE 50
Cdd:cd07377    2 LYEQIADQLREAILsgELKPGDRLpSERELAEELGVSRTTVREALRE 48
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-198 7.62e-14

Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains [Transcription];


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 69.34  E-value: 7.62e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  12 ADRLTQIIRRLFAGENLNMRHLAEEFGVSVRTLRRDLRE-RLTGLDLEYNDGHC---RLVTADSAG-----QRERSGLTL 82
Cdd:COG2378    4 LERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDAlRELGVPIEAERGRGggyRLRDGYRLPplmltEEEALALLL 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  83 ARQSDMEALFPGLDLRLAGAL------LDETEHSPCCIWPPVALTAGSFT---GIFSHLVTAINRRNRISLLAKGQRCE- 152
Cdd:COG2378   84 ALRLLAALGGAPLAEAAASALakleavLPERLRERLEALAERVGVDPPPEvdpEVLETLREAIRERRRLRIDYRSGRGEp 163

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 553864937 153 ---CLAPYRLICLDRNWYLTG--ELWNDIAVFPLAEIQNVAVLADTYTRNE 198
Cdd:COG2378  164 terTVEPYGLVFYGGRWYLVAwcELRDDIRTFRLDRIRSLELTDERFEPPP 214
BglG COG3711
Transcriptional antiterminator [Transcription];
13-138 2.50e-04

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 41.77  E-value: 2.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  13 DRLTQIIRRLF-AGENLNMRHLAEEFGVSVRTLRRDL---RERLT--GLDLEYNDGHCRLVTADSAGQR--------ERS 78
Cdd:COG3711   81 ERVAYILLRLLlAGDPISLDDLAEELFVSRSTILNDLkkiEKILKkyGLTLERKPNYGIKLEGSELDIRkalaellsELL 160

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  79 GLTLARQSDMEALFPGLDLRLAGALLDETEHSpcciwPPVALTAGSFTGIFSHLVTAINR 138
Cdd:COG3711  161 SENDLLSLLLLKLIPEEDLELIEEIIEEAEKK-----LGIKLSDSIYINLTDHIAIAIKR 215
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 128-233 4.30e-04

WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the WYL-like superfamily, named for three conserved amino acids found in a subset of the superfamily. However, these residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine, which are predicted to line a ligand-binding groove typical of the Sm-like SH3 beta-barrels. A WYL domain protein (sll7009) is a negative regulator of the I-D CRISPR-Cas system in Synechocystis sp. It is predicted to be a ligand-sensing domain that could bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense systems such as the abortive infection AbiG system.


Pssm-ID: 433082  Cd Length: 172  Bit Score: 39.94  E-value: 4.30e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 553864937  128 IFSHLVTAINRRNRISL----LAKGQRCECLAPYRLICLDRNWYLTG--ELWNDIAVFPLAEIQNVAVLADTYTR-NETI 200
Cdd:pfam13280   2 VLETLREAILERRRVRFryrsPRGEGTERTVEPYGLVYKDGRWYLVAycRLRDDIRTFRLDRIESVEVLDEPFEPpDFDL 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 553864937  201 SRLTRHPNFINALPH---YRFIRDLLATFKSGPFPN 233
Cdd:pfam13280  82 AEYLRRSFGVFPGPIevkLRFSPEAARRLRERRFPD 117
GlpR COG1349
DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, ...
 1-50 2.17e-03

DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, Carbohydrate transport and metabolism];


Pssm-ID: 440960 [Multi-domain]  Cd Length: 254  Bit Score: 38.19  E-value: 2.17e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 553864937   1 MPQTERRHerladrltQIIRRLFAGENLNMRHLAEEFGVSVRTLRRDLRE 50
Cdd:COG1349    1 MLAEERRQ--------KILELLRERGRVSVEELAERLGVSEETIRRDLAE 42
Mga pfam05043
Mga helix-turn-helix domain; M regulator protein trans-acting positive regulator (Mga) is a ...
 11-50 2.29e-03

Mga helix-turn-helix domain; M regulator protein trans-acting positive regulator (Mga) is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions. This domain is found in the centre of the Mga proteins. This family also contains a number of bacterial RofA transcriptional regulators that seem to be largely restricted to streptococci. These proteins have been shown to regulate the expression of important bacterial adhesins. This is presumably a DNA-binding domain.


Pssm-ID: 428276 [Multi-domain]  Cd Length: 87  Bit Score: 36.05  E-value: 2.29e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 553864937   11 LADRLT-QIIRRLFAGENLNMRHLAEEFGVSVRTLRRDLRE 50
Cdd:pfam05043  13 LKESLKfQLLKYLFFEEFVSIKSLAQKLYISESTLYRKIKE 53
WHTH_GntR cd07377
Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional ...
 7-50 2.47e-03

Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators; This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is presumed to result in a conformational change that regulates the DNA-binding affinity of the repressor. The GntR-like proteins bind as dimers, where each monomer recognizes a half-site of 2-fold symmetric DNA sequences.


Pssm-ID: 153418 [Multi-domain]  Cd Length: 66  Bit Score: 35.50  E-value: 2.47e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 553864937   7 RHERLADRLTQIIR--RLFAGENL-NMRHLAEEFGVSVRTLRRDLRE 50
Cdd:cd07377    2 LYEQIADQLREAILsgELKPGDRLpSERELAEELGVSRTTVREALRE 48
GntR pfam00392
Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the ...
 9-57 5.22e-03

Bacterial regulatory proteins, gntR family; This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerization domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.


Pssm-ID: 306822 [Multi-domain]  Cd Length: 64  Bit Score: 34.51  E-value: 5.22e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 553864937    9 ERLADRLTQIIR--RLFAGENLN-MRHLAEEFGVSVRTLRRDLReRLTGLDL 57
Cdd:pfam00392   3 EQVYARLREDILsgRLRPGDKLPsERELAAEFGVSRTTVREALR-RLEAEGL 53
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 17-58 5.69e-03

HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.


Pssm-ID: 429896 [Multi-domain]  Cd Length: 52  Bit Score: 33.95  E-value: 5.69e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 553864937   17 QIIRRLF-AGENLNMRHLAEEFGVSVRTLRRDLRE-RLTGLDLE 58
Cdd:pfam08279   2 QILQLLLeARGPISGQELAEKLGVSRRTIRRDIKIlEELGVPIE 45
 
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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