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Conserved domains on  [gi|2440757020|ref|WP_272492255|]
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MULTISPECIES: YafY family protein [unclassified Alteromonas]

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 ...
 12-226 2.65e-51

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


:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 169.10  E-value: 2.65e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020  12 RQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIDSDRGRGGGIRLVGRWGLGRLQMSSTEVISLLLAL 91
Cdd:COG2378     6 RLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRGGGYRLRDGYRLPPLMLTEEEALALLLAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020  92 IVAEQLKSPILMENLSSIRNRIASAFPSEQQIKINELRARILVGSKASqnvsqtytmPDETILPAISQGFIDLKKIKIKY 171
Cdd:COG2378    86 RLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPE---------VDPEVLETLREAIRERRRLRIDY 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2440757020 172 ESEDNVITHRLIEPQFMLLNWPIWYLVAWDNLREDVRVFRIDRVKHAVLQRDDFR 226
Cdd:COG2378   157 RSGRGEPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFE 211
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-226 2.65e-51

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 169.10  E-value: 2.65e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020  12 RQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIDSDRGRGGGIRLVGRWGLGRLQMSSTEVISLLLAL 91
Cdd:COG2378     6 RLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRGGGYRLRDGYRLPPLMLTEEEALALLLAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020  92 IVAEQLKSPILMENLSSIRNRIASAFPSEQQIKINELRARILVGSKASqnvsqtytmPDETILPAISQGFIDLKKIKIKY 171
Cdd:COG2378    86 RLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPE---------VDPEVLETLREAIRERRRLRIDY 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2440757020 172 ESEDNVITHRLIEPQFMLLNWPIWYLVAWDNLREDVRVFRIDRVKHAVLQRDDFR 226
Cdd:COG2378   157 RSGRGEPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFE 211
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 153-245 4.66e-13

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: 64.98  E-value: 4.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020 153 ILPAISQGFIDLKKIKIKYESEDNVITHRLIEPQFMLLNWPIWYLVAWDNLREDVRVFRIDRVKHAVLQRDDFRLKsrkl 232
Cdd:pfam13280   2 VLETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDEPFEPP---- 77

                          90
                  ....*....|...
gi 2440757020 233 liGDELDPYFNRL 245
Cdd:pfam13280  78 --DFDLAEYLRRS 88
HTH_DEOR smart00420
helix_turn_helix, Deoxyribose operon repressor;
12-64 3.78e-04

helix_turn_helix, Deoxyribose operon repressor;


Pssm-ID: 197714 [Multi-domain]  Cd Length: 53  Bit Score: 37.59  E-value: 3.78e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2440757020   12 RQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIdsdRGRGG 64
Cdd:smart00420   1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT---RVHGG 50
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 12-226 2.65e-51

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 169.10  E-value: 2.65e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020  12 RQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIDSDRGRGGGIRLVGRWGLGRLQMSSTEVISLLLAL 91
Cdd:COG2378     6 RLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRGGGYRLRDGYRLPPLMLTEEEALALLLAL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020  92 IVAEQLKSPILMENLSSIRNRIASAFPSEQQIKINELRARILVGSKASqnvsqtytmPDETILPAISQGFIDLKKIKIKY 171
Cdd:COG2378    86 RLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPE---------VDPEVLETLREAIRERRRLRIDY 156

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2440757020 172 ESEDNVITHRLIEPQFMLLNWPIWYLVAWDNLREDVRVFRIDRVKHAVLQRDDFR 226
Cdd:COG2378   157 RSGRGEPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFE 211
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 153-245 4.66e-13

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: 64.98  E-value: 4.66e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2440757020 153 ILPAISQGFIDLKKIKIKYESEDNVITHRLIEPQFMLLNWPIWYLVAWDNLREDVRVFRIDRVKHAVLQRDDFRLKsrkl 232
Cdd:pfam13280   2 VLETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDEPFEPP---- 77

                          90
                  ....*....|...
gi 2440757020 233 liGDELDPYFNRL 245
Cdd:pfam13280  78 --DFDLAEYLRRS 88
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 20-63 3.26e-06

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: 43.19  E-value: 3.26e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 2440757020  20 LRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIDSDRGRG 63
Cdd:pfam08279   8 LEARGPISGQELAEKLGVSRRTIRRDIKILEELGVPIEAEPGRG 51
HTH_DeoR pfam08220
DeoR-like helix-turn-helix domain;
12-64 6.72e-05

DeoR-like helix-turn-helix domain;


Pssm-ID: 285436 [Multi-domain]  Cd Length: 57  Bit Score: 39.55  E-value: 6.72e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2440757020  12 RQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIdsdRGRGG 64
Cdd:pfam08220   1 RIQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNELEEQGLLT---RTHGG 50
HTH_DEOR smart00420
helix_turn_helix, Deoxyribose operon repressor;
12-64 3.78e-04

helix_turn_helix, Deoxyribose operon repressor;


Pssm-ID: 197714 [Multi-domain]  Cd Length: 53  Bit Score: 37.59  E-value: 3.78e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 2440757020   12 RQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMGIPIdsdRGRGG 64
Cdd:smart00420   1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLT---RVHGG 50
IscR COG1959
DNA-binding transcriptional regulator, IscR family [Transcription];
27-68 2.19e-03

DNA-binding transcriptional regulator, IscR family [Transcription];


Pssm-ID: 441562  Cd Length: 141  Bit Score: 37.51  E-value: 2.19e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2440757020  27 TTVDLCNQVGTSLRTLRRDLVELKEMGIpIDSDRGRGGGIRL 68
Cdd:COG1959    26 TSKEIAERQGISPSYLEKILQKLRKAGL-VESVRGPGGGYRL 66
GlpR COG1349
DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, ...
 8-53 5.84e-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: 37.04  E-value: 5.84e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 2440757020   8 NKKLRQDEIVSCLRSRSYWTTVDLCNQVGTSLRTLRRDLVELKEMG 53
Cdd:COG1349     2 LAEERRQKILELLRERGRVSVEELAERLGVSEETIRRDLAELEEQG 47
 
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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