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Conserved domains on  [gi|1422948395|ref|WP_111963426|]
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MULTISPECIES: YafY family protein [Enterobacter]

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 ...
 2-223 6.45e-74

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


:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 226.50  E-value: 6.45e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395   2 TRRADRLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVPVEGEAGS--GYRLMSGFDLPPLMLTNKESEA 79
Cdd:COG2378     1 MSRLERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395  80 LIVAIRLLKTWGGESLSRELESAQEKVLAILPEESRRKAEQTRIYAPDFCMQSHSRSDFDMIHQAISAQRVLALHYRDEA 159
Cdd:COG2378    81 LLLALRLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPEVDPEVLETLREAIRERRRLRIDYRSGR 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1422948395 160 GQLSKREVQPLGLFFWGERWLLAAWCERRDDYRCFRLDRCLNIVATERRFSESADRSLADFLRK 223
Cdd:COG2378   161 GEPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEYLAE 224
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 2-223 6.45e-74

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 226.50  E-value: 6.45e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395   2 TRRADRLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVPVEGEAGS--GYRLMSGFDLPPLMLTNKESEA 79
Cdd:COG2378     1 MSRLERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395  80 LIVAIRLLKTWGGESLSRELESAQEKVLAILPEESRRKAEQTRIYAPDFCMQSHSRSDFDMIHQAISAQRVLALHYRDEA 159
Cdd:COG2378    81 LLLALRLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPEVDPEVLETLREAIRERRRLRIDYRSGR 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1422948395 160 GQLSKREVQPLGLFFWGERWLLAAWCERRDDYRCFRLDRCLNIVATERRFSESADRSLADFLRK 223
Cdd:COG2378   161 GEPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEYLAE 224
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 138-226 6.07e-19

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: 80.39  E-value: 6.07e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395 138 FDMIHQAISAQRVLALHYRDEAGQLSKREVQPLGLFFWGERWLLAAWCERRDDYRCFRLDRCLNIVATERRFSESaDRSL 217
Cdd:pfam13280   3 LETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDEPFEPP-DFDL 81


                  ....*....
gi 1422948395 218 ADFLRKVKQ 226
Cdd:pfam13280  82 AEYLRRSFG 90
PRK10681 PRK10681
DNA-binding transcriptional repressor DeoR; Provisional
 2-49 6.18e-03

DNA-binding transcriptional repressor DeoR; Provisional


Pssm-ID: 182644 [Multi-domain]  Cd Length: 252  Bit Score: 36.98  E-value: 6.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1422948395   2 TRRADRLFQIVQILRGR---RLTTAAHLadrLGVSERTVYRDIRDLSLSGV 49
Cdd:PRK10681    3 TRRDERIGQLLQALKRSdklHLKDAAAL---LGVSEMTIRRDLNAHSAPVV 50
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 2-223 6.45e-74

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 226.50  E-value: 6.45e-74
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395   2 TRRADRLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVPVEGEAGS--GYRLMSGFDLPPLMLTNKESEA 79
Cdd:COG2378     1 MSRLERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395  80 LIVAIRLLKTWGGESLSRELESAQEKVLAILPEESRRKAEQTRIYAPDFCMQSHSRSDFDMIHQAISAQRVLALHYRDEA 159
Cdd:COG2378    81 LLLALRLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPEVDPEVLETLREAIRERRRLRIDYRSGR 160

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1422948395 160 GQLSKREVQPLGLFFWGERWLLAAWCERRDDYRCFRLDRCLNIVATERRFSESADRSLADFLRK 223
Cdd:COG2378   161 GEPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEYLAE 224
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 138-226 6.07e-19

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: 80.39  E-value: 6.07e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395 138 FDMIHQAISAQRVLALHYRDEAGQLSKREVQPLGLFFWGERWLLAAWCERRDDYRCFRLDRCLNIVATERRFSESaDRSL 217
Cdd:pfam13280   3 LETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDEPFEPP-DFDL 81


                  ....*....
gi 1422948395 218 ADFLRKVKQ 226
Cdd:pfam13280  82 AEYLRRSFG 90
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 9-59 2.46e-13

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: 62.45  E-value: 2.46e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1422948395   9 FQIVQILR-GRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVPVEGEAGSGY 59
Cdd:pfam08279   1 LQILQLLLeARGPISGQELAEKLGVSRRTIRRDIKILEELGVPIEAEPGRGY 52
HTH_PafC pfam19187
PafC helix-turn-helix domain; This entry is an N-terminal HTH domain found in the PafC protein. ...
 7-108 6.70e-05

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: 41.00  E-value: 6.70e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1422948395   7 RLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVP---------VEGEAGSGY-RLMSGFDlPPLMLTNKE 76
Cdd:pfam19187   5 RLLDLVPYLRQHPGVSVAEAAARFGVTPAQLRADLDVLFVCGLPgyypgdlidVDWEEGRVSiTNADGLA-RPLRLTPAE 83

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1422948395  77 SEALIVAIRLLKTWGGESLSRELESAQEKVLA 108
Cdd:pfam19187  84 AAALLLGLRALAALPGLADAEAVDSALAKLRA 115
BglG COG3711
Transcriptional antiterminator [Transcription];
21-61 7.13e-05

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 43.31  E-value: 7.13e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1422948395  21 TTAAHLADRLGVSERTVYRDIRD----LSLSGVPVEGEAGSGYRL 61
Cdd:COG3711    12 VTAKELAKKLNVSERTIRYDIKKinewLKKNGLEIISKKGIGFRL 56
GlpR COG1349
DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, ...
 4-44 1.10e-04

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: 42.04  E-value: 1.10e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1422948395   4 RADRLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDL 44
Cdd:COG1349     3 AEERRQKILELLRERGRVSVEELAERLGVSEETIRRDLAEL 43
BirA COG1654
Biotin operon repressor [Transcription];
6-67 7.42e-04

Biotin operon repressor [Transcription];


Pssm-ID: 441260 [Multi-domain]  Cd Length: 324  Bit Score: 39.97  E-value: 7.42e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1422948395   6 DRLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVPVEGEAGSGYRLMSGFDL 67
Cdd:COG1654     4 STRLKLLRLLADGEFHSGEELAEELGVSRAAVWKHIKALRELGYEIESVPGKGYRLAEPPDL 65
COG3177 COG3177
Fic family protein [Transcription];
3-60 3.52e-03

Fic family protein [Transcription];


Pssm-ID: 442410 [Multi-domain]  Cd Length: 316  Bit Score: 37.74  E-value: 3.52e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1422948395   3 RRADRLFQIVQILRGRRLTTAAHLADRLGVSERTVYRDIRDLSLSGVPVEGEAGSGYR 60
Cdd:COG3177   258 RLNERQRKLLELLFENPVLTASELAELLGVSRRTARRDLKDLVELGILEKVGGGRNTR 315
PRK10681 PRK10681
DNA-binding transcriptional repressor DeoR; Provisional
 2-49 6.18e-03

DNA-binding transcriptional repressor DeoR; Provisional


Pssm-ID: 182644 [Multi-domain]  Cd Length: 252  Bit Score: 36.98  E-value: 6.18e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1422948395   2 TRRADRLFQIVQILRGR---RLTTAAHLadrLGVSERTVYRDIRDLSLSGV 49
Cdd:PRK10681    3 TRRDERIGQLLQALKRSdklHLKDAAAL---LGVSEMTIRRDLNAHSAPVV 50
 
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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