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Conserved domains on  [gi|1382636107|gb|PUY23442|]
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YafY family transcriptional regulator [Cronobacter sakazakii]

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 ...
 18-219 1.15e-61

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


:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 195.30  E-value: 1.15e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  18 RYPVTAMTLAERLNISVRSIYRDIETLKTQGVDIEGSAGI--GYVLQSDYHLPPLMFDAHEVDALILGLHWVMRHTDPQL 95
Cdd:COG2378    17 RRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALALLLALRLLAALGGAPL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  96 EAAARNAVAKIHAILPENLAQQINSPSLMVAPTGN-EGSLRFLTDIRSAIHQRRKLELVYTDKDGTASSRLVWPIALGFF 174
Cdd:COG2378    97 AEAAASALAKLEAVLPERLRERLEALAERVGVDPPpEVDPEVLETLREAIRERRRLRIDYRSGRGEPTERTVEPYGLVFY 176

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1382636107 175 DAVRVLACWCELRQAFRHFRIDRMQQVAISEQLCPQSRYKLLKEW 219
Cdd:COG2378   177 GGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEY 221
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 18-219 1.15e-61

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 195.30  E-value: 1.15e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  18 RYPVTAMTLAERLNISVRSIYRDIETLKTQGVDIEGSAGI--GYVLQSDYHLPPLMFDAHEVDALILGLHWVMRHTDPQL 95
Cdd:COG2378    17 RRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALALLLALRLLAALGGAPL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  96 EAAARNAVAKIHAILPENLAQQINSPSLMVAPTGN-EGSLRFLTDIRSAIHQRRKLELVYTDKDGTASSRLVWPIALGFF 174
Cdd:COG2378    97 AEAAASALAKLEAVLPERLRERLEALAERVGVDPPpEVDPEVLETLREAIRERRRLRIDYRSGRGEPTERTVEPYGLVFY 176

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1382636107 175 DAVRVLACWCELRQAFRHFRIDRMQQVAISEQLCPQSRYKLLKEW 219
Cdd:COG2378   177 GGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEY 221
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 135-206 3.19e-14

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: 68.06  E-value: 3.19e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1382636107 135 RFLTDIRSAIHQRRKLELVYTDKDGTASSRLVWPIALGFFDAVRVLACWCELRQAFRHFRIDRMQQVAISEQ 206
Cdd:pfam13280   1 EVLETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDE 72
PRK11886 PRK11886
bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;
26-61 5.21e-03

bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;


Pssm-ID: 237010 [Multi-domain]  Cd Length: 319  Bit Score: 37.07  E-value: 5.21e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1382636107  26 LAERLNISVRSIYRDIETLKTQGVDIEGSAGIGYVL 61
Cdd:PRK11886   24 LGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYRL 59
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 18-219 1.15e-61

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 195.30  E-value: 1.15e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  18 RYPVTAMTLAERLNISVRSIYRDIETLKTQGVDIEGSAGI--GYVLQSDYHLPPLMFDAHEVDALILGLHWVMRHTDPQL 95
Cdd:COG2378    17 RRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALALLLALRLLAALGGAPL 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  96 EAAARNAVAKIHAILPENLAQQINSPSLMVAPTGN-EGSLRFLTDIRSAIHQRRKLELVYTDKDGTASSRLVWPIALGFF 174
Cdd:COG2378    97 AEAAASALAKLEAVLPERLRERLEALAERVGVDPPpEVDPEVLETLREAIRERRRLRIDYRSGRGEPTERTVEPYGLVFY 176

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 1382636107 175 DAVRVLACWCELRQAFRHFRIDRMQQVAISEQLCPQSRYKLLKEW 219
Cdd:COG2378   177 GGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEY 221
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 135-206 3.19e-14

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: 68.06  E-value: 3.19e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1382636107 135 RFLTDIRSAIHQRRKLELVYTDKDGTASSRLVWPIALGFFDAVRVLACWCELRQAFRHFRIDRMQQVAISEQ 206
Cdd:pfam13280   1 EVLETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDE 72
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 18-59 3.68e-12

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: 59.37  E-value: 3.68e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1382636107  18 RYPVTAMTLAERLNISVRSIYRDIETLKTQGVDIEGSAGIGY 59
Cdd:pfam08279  11 RGPISGQELAEKLGVSRRTIRRDIKILEELGVPIEAEPGRGY 52
BglG COG3711
Transcriptional antiterminator [Transcription];
20-64 1.53e-05

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 45.24  E-value: 1.53e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1382636107  20 PVTAMTLAERLNISVRSIYRDI----ETLKTQGVDIEGSAGIGYVLQSD 64
Cdd:COG3711    11 VVTAKELAKKLNVSERTIRYDIkkinEWLKKNGLEIISKKGIGFRLDID 59
BirA COG1654
Biotin operon repressor [Transcription];
26-81 3.62e-04

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 40.74  E-value: 3.62e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1382636107  26 LAERLNISvRS-IYRDIETLKTQGVDIEGSAGIGYVLQSdyhlPPLMFDAHEVDALI 81
Cdd:COG1654    24 LAEELGVS-RAaVWKHIKALRELGYEIESVPGKGYRLAE----PPDLLDPEEIRAGL 75
HTH_PafC pfam19187
PafC helix-turn-helix domain; This entry is an N-terminal HTH domain found in the PafC protein. ...
 21-106 2.51e-03

PafC helix-turn-helix domain; This entry is an N-terminal HTH domain found in the PafC protein. Transcriptional activator PafBC is responsible for upregulating the majority of genes induced by DNA damage.


Pssm-ID: 465990 [Multi-domain]  Cd Length: 115  Bit Score: 36.77  E-value: 2.51e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1382636107  21 VTAMTLAERLNISVRSIYRDIETLKTQGV---------DIEGSAGIGYVLQSDYHLPPLMFDAHEVDALILGLHWVMRHT 91
Cdd:pfam19187  19 VSVAEAAARFGVTPAQLRADLDVLFVCGLpgyypgdliDVDWEEGRVSITNADGLARPLRLTPAEAAALLLGLRALAALP 98

                          90
                  ....*....|....*
gi 1382636107  92 DPQLEAAARNAVAKI 106
Cdd:pfam19187  99 GLADAEAVDSALAKL 113
PRK11886 PRK11886
bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;
26-61 5.21e-03

bifunctional biotin--[acetyl-CoA-carboxylase] ligase/biotin operon repressor BirA;


Pssm-ID: 237010 [Multi-domain]  Cd Length: 319  Bit Score: 37.07  E-value: 5.21e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1382636107  26 LAERLNISVRSIYRDIETLKTQGVDIEGSAGIGYVL 61
Cdd:PRK11886   24 LGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYRL 59
 
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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