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Conserved domains on  [gi|851937116|ref|WP_048225434|]
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MULTISPECIES: YafY family protein [Enterobacterales]

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 ...
 12-196 9.05e-15

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


:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 71.65  E-value: 9.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  12 ASRLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLrERLR----YIDTE-YIDGHVSLRDARGPFRTN---------S 77
Cdd:COG2378    4 LERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDI-DALRelgvPIEAErGRGGGYRLRDGYRLPPLMlteeealalL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  78 DIIRFAQITRVAHYFPALDP---KLLSVLLDNGQD-----SPCIIWNAPPRQAPALfggFQVIIQAIISNRRIHFLHHGH 149
Cdd:COG2378   83 LALRLLAALGGAPLAEAAASalaKLEAVLPERLRErlealAERVGVDPPPEVDPEV---LETLREAIRERRRLRIDYRSG 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 851937116 150 HQSA----VAPYRLICLEGEWYLTA--VTGERIQVFTLSAITDVVMTIGGFTR 196
Cdd:COG2378  160 RGEPtertVEPYGLVFYGGRWYLVAwcELRDDIRTFRLDRIRSLELTDERFEP 212
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-196 9.05e-15

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 71.65  E-value: 9.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  12 ASRLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLrERLR----YIDTE-YIDGHVSLRDARGPFRTN---------S 77
Cdd:COG2378    4 LERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDI-DALRelgvPIEAErGRGGGYRLRDGYRLPPLMlteeealalL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  78 DIIRFAQITRVAHYFPALDP---KLLSVLLDNGQD-----SPCIIWNAPPRQAPALfggFQVIIQAIISNRRIHFLHHGH 149
Cdd:COG2378   83 LALRLLAALGGAPLAEAAASalaKLEAVLPERLRErlealAERVGVDPPPEVDPEV---LETLREAIRERRRLRIDYRSG 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 851937116 150 HQSA----VAPYRLICLEGEWYLTA--VTGERIQVFTLSAITDVVMTIGGFTR 196
Cdd:COG2378  160 RGEPtertVEPYGLVFYGGRWYLVAwcELRDDIRTFRLDRIRSLELTDERFEP 212
SpoIIID pfam12116
Stage III sporulation protein D; This stage III sporulation protein is a small DNA-binding ...
 16-58 4.33e-06

Stage III sporulation protein D; This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.


Pssm-ID: 403367  Cd Length: 82  Bit Score: 43.51  E-value: 4.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 851937116   16 AILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRERLRYIDTE 58
Cdd:pfam12116   8 VIEIAKYIVESKATVRQTAKVFGVSKSTVHKDVTERLPKINPQ 50
HTH_DEOR smart00420
helix_turn_helix, Deoxyribose operon repressor;
14-50 3.90e-03

helix_turn_helix, Deoxyribose operon repressor;


Pssm-ID: 197714 [Multi-domain]  Cd Length: 53  Bit Score: 34.51  E-value: 3.90e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 851937116    14 RLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRE 50
Cdd:smart00420   1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNK 37
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 6-49 8.57e-03

RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 36.14  E-value: 8.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 851937116    6 QRYDRLASRLAILVS-RLFMGetLSIRQLAQEFGVSERTVQRDLR 49
Cdd:TIGR02999 130 DKLAQVDPRQAEVVElRFFAG--LTVEEIAELLGVSVRTVERDWR 172
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-196 9.05e-15

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 71.65  E-value: 9.05e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  12 ASRLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLrERLR----YIDTE-YIDGHVSLRDARGPFRTN---------S 77
Cdd:COG2378    4 LERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDI-DALRelgvPIEAErGRGGGYRLRDGYRLPPLMlteeealalL 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  78 DIIRFAQITRVAHYFPALDP---KLLSVLLDNGQD-----SPCIIWNAPPRQAPALfggFQVIIQAIISNRRIHFLHHGH 149
Cdd:COG2378   83 LALRLLAALGGAPLAEAAASalaKLEAVLPERLRErlealAERVGVDPPPEVDPEV---LETLREAIRERRRLRIDYRSG 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 851937116 150 HQSA----VAPYRLICLEGEWYLTA--VTGERIQVFTLSAITDVVMTIGGFTR 196
Cdd:COG2378  160 RGEPtertVEPYGLVFYGGRWYLVAwcELRDDIRTFRLDRIRSLELTDERFEP 212
SpoIIID pfam12116
Stage III sporulation protein D; This stage III sporulation protein is a small DNA-binding ...
 16-58 4.33e-06

Stage III sporulation protein D; This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.


Pssm-ID: 403367  Cd Length: 82  Bit Score: 43.51  E-value: 4.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 851937116   16 AILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRERLRYIDTE 58
Cdd:pfam12116   8 VIEIAKYIVESKATVRQTAKVFGVSKSTVHKDVTERLPKINPQ 50
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 129-208 1.06e-05

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: 44.18  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 851937116  129 FQVIIQAIISNRRIHFLHHGHHQSA----VAPYRLICLEGEWYLTAVTGER--IQVFTLSAITDVVMTIGGFTR-----S 197
Cdd:pfam13280   3 LETLREAILERRRVRFRYRSPRGEGtertVEPYGLVYKDGRWYLVAYCRLRddIRTFRLDRIESVEVLDEPFEPpdfdlA 82

                          90
                  ....*....|.
gi 851937116  198 SHIRRIFEDPR 208
Cdd:pfam13280  83 EYLRRSFGVFP 93
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 26-58 7.02e-04

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: 36.64  E-value: 7.02e-04
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 851937116   26 ETLSIRQLAQEFGVSERTVQRD---LRERLRYIDTE 58
Cdd:pfam08279  12 GPISGQELAEKLGVSRRTIRRDikiLEELGVPIEAE 47
COG3177 COG3177
Fic family protein [Transcription];
3-50 3.12e-03

Fic family protein [Transcription];


Pssm-ID: 442410 [Multi-domain]  Cd Length: 316  Bit Score: 37.74  E-value: 3.12e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 851937116   3 EQEQRYDRLASRLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRE 50
Cdd:COG3177  251 LLELARGRLNERQRKLLELLFENPVLTASELAELLGVSRRTARRDLKD 298
HTH_DeoR pfam08220
DeoR-like helix-turn-helix domain;
14-50 3.62e-03

DeoR-like helix-turn-helix domain;


Pssm-ID: 285436 [Multi-domain]  Cd Length: 57  Bit Score: 34.54  E-value: 3.62e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 851937116   14 RLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRE 50
Cdd:pfam08220   1 RIQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNE 37
HTH_DEOR smart00420
helix_turn_helix, Deoxyribose operon repressor;
14-50 3.90e-03

helix_turn_helix, Deoxyribose operon repressor;


Pssm-ID: 197714 [Multi-domain]  Cd Length: 53  Bit Score: 34.51  E-value: 3.90e-03
                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 851937116    14 RLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRE 50
Cdd:smart00420   1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNK 37
HTH_PafC pfam19187
PafC helix-turn-helix domain; This entry is an N-terminal HTH domain found in the PafC protein. ...
 9-71 6.97e-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: 35.23  E-value: 6.97e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 851937116    9 DRLAsRLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLrERLRY-----------IDTEYIDGHVSLRDARG 71
Cdd:pfam19187   1 DRLA-RLLDLVPYLRQHPGVSVAEAAARFGVTPAQLRADL-DVLFVcglpgyypgdlIDVDWEEGRVSITNADG 72
Sig-70_X6 TIGR02999
RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the ...
 6-49 8.57e-03

RNA polymerase sigma factor, TIGR02999 family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.


Pssm-ID: 132044 [Multi-domain]  Cd Length: 183  Bit Score: 36.14  E-value: 8.57e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 851937116    6 QRYDRLASRLAILVS-RLFMGetLSIRQLAQEFGVSERTVQRDLR 49
Cdd:TIGR02999 130 DKLAQVDPRQAEVVElRFFAG--LTVEEIAELLGVSVRTVERDWR 172
BglG COG3711
Transcriptional antiterminator [Transcription];
14-50 8.65e-03

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 36.76  E-value: 8.65e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 851937116  14 RLAILVSRLFM-GETLSIRQLAQEFGVSERTVQRDLRE 50
Cdd:COG3711   82 RVAYILLRLLLaGDPISLDDLAEELFVSRSTILNDLKK 119
GlpR COG1349
DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, ...
 14-50 9.49e-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: 36.27  E-value: 9.49e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 851937116  14 RLAILVSRLFMGETLSIRQLAQEFGVSERTVQRDLRE 50
Cdd:COG1349    6 RRQKILELLRERGRVSVEELAERLGVSEETIRRDLAE 42
 
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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