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Conserved domains on  [gi|503994167|ref|WP_014228161|]
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MULTISPECIES: YafY family protein [Klebsiella]

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 ...
 3-223 5.85e-71

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


:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 219.18  E-value: 5.85e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167   3 RRADRLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGVPVEGEAGS--GYRLLAGYDLPPLMLTTQESEAL 80
Cdd:COG2378    2 SRLERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALAL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167  81 MAAIRLLQTWGGASLSQALESAQEKVLAILPAESRRKAEQSRVFAPDFGAQGYSKDQFDIVHRAVSAQQALGLRYRDEAG 160
Cdd:COG2378   82 LLALRLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPEVDPEVLETLREAIRERRRLRIDYRSGRG 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503994167 161 NVSQRDVLPLGLFFWGERWLLVTWCELREDYRCFRLDRCLEISATGRHFSERADRSLSDFLRK 223
Cdd:COG2378  162 EPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEYLAE 224
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 3-223 5.85e-71

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 219.18  E-value: 5.85e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167   3 RRADRLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGVPVEGEAGS--GYRLLAGYDLPPLMLTTQESEAL 80
Cdd:COG2378    2 SRLERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALAL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167  81 MAAIRLLQTWGGASLSQALESAQEKVLAILPAESRRKAEQSRVFAPDFGAQGYSKDQFDIVHRAVSAQQALGLRYRDEAG 160
Cdd:COG2378   82 LLALRLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPEVDPEVLETLREAIRERRRLRIDYRSGRG 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503994167 161 NVSQRDVLPLGLFFWGERWLLVTWCELREDYRCFRLDRCLEISATGRHFSERADRSLSDFLRK 223
Cdd:COG2378  162 EPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEYLAE 224
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 138-223 5.11e-16

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: 72.69  E-value: 5.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167  138 FDIVHRAVSAQQALGLRYRDEAGNVSQRDVLPLGLFFWGERWLLVTWCELREDYRCFRLDRCLEISATGRHFsERADRSL 217
Cdd:pfam13280   3 LETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDEPF-EPPDFDL 81


                  ....*.
gi 503994167  218 SDFLRK 223
Cdd:pfam13280  82 AEYLRR 87
HTH_DEOR smart00420
helix_turn_helix, Deoxyribose operon repressor;
7-49 9.33e-03

helix_turn_helix, Deoxyribose operon repressor;


Pssm-ID: 197714 [Multi-domain]  Cd Length: 53  Bit Score: 33.35  E-value: 9.33e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 503994167     7 RLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGV 49
Cdd:smart00420   1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGL 43
 
Name Accession Description Interval E-value
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 3-223 5.85e-71

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 219.18  E-value: 5.85e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167   3 RRADRLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGVPVEGEAGS--GYRLLAGYDLPPLMLTTQESEAL 80
Cdd:COG2378    2 SRLERLLALLQLLQSRRGVTAAELAERLEVSERTIYRDIDALRELGVPIEAERGRggGYRLRDGYRLPPLMLTEEEALAL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167  81 MAAIRLLQTWGGASLSQALESAQEKVLAILPAESRRKAEQSRVFAPDFGAQGYSKDQFDIVHRAVSAQQALGLRYRDEAG 160
Cdd:COG2378   82 LLALRLLAALGGAPLAEAAASALAKLEAVLPERLRERLEALAERVGVDPPPEVDPEVLETLREAIRERRRLRIDYRSGRG 161

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 503994167 161 NVSQRDVLPLGLFFWGERWLLVTWCELREDYRCFRLDRCLEISATGRHFSERADRSLSDFLRK 223
Cdd:COG2378  162 EPTERTVEPYGLVFYGGRWYLVAWCELRDDIRTFRLDRIRSLELTDERFEPPPDFDLAEYLAE 224
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 138-223 5.11e-16

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: 72.69  E-value: 5.11e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167  138 FDIVHRAVSAQQALGLRYRDEAGNVSQRDVLPLGLFFWGERWLLVTWCELREDYRCFRLDRCLEISATGRHFsERADRSL 217
Cdd:pfam13280   3 LETLREAILERRRVRFRYRSPRGEGTERTVEPYGLVYKDGRWYLVAYCRLRDDIRTFRLDRIESVEVLDEPF-EPPDFDL 81


                  ....*.
gi 503994167  218 SDFLRK 223
Cdd:pfam13280  82 AEYLRR 87
HTH_11 pfam08279
HTH domain; This family includes helix-turn-helix domains in a wide variety of proteins.
 9-59 6.78e-14

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: 63.99  E-value: 6.78e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 503994167    9 FQIVQILR-GRRLTTAGLLAERLGVSERTIYRDIRDLSLSGVPVEGEAGSGY 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 2.16e-06

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: 45.24  E-value: 2.16e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 503994167    7 RLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGVP---------VEGEAGSGYRLLAGYDLPPLMLTTQES 77
Cdd:pfam19187   5 RLLDLVPYLRQHPGVSVAEAAARFGVTPAQLRADLDVLFVCGLPgyypgdlidVDWEEGRVSITNADGLARPLRLTPAEA 84

                          90       100       110
                  ....*....|....*....|....*....|.
gi 503994167   78 EALMAAIRLLQTWGGASLSQALESAQEKVLA 108
Cdd:pfam19187  85 AALLLGLRALAALPGLADAEAVDSALAKLRA 115
GlpR COG1349
DNA-binding transcriptional regulator of sugar metabolism, DeoR/GlpR family [Transcription, ...
 4-44 2.43e-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: 40.89  E-value: 2.43e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 503994167   4 RADRLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDL 44
Cdd:COG1349    3 AEERRQKILELLRERGRVSVEELAERLGVSEETIRRDLAEL 43
BglG COG3711
Transcriptional antiterminator [Transcription];
11-61 2.72e-04

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 41.38  E-value: 2.72e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 503994167  11 IVQILRGRR-LTTAGLLAERLGVSERTIYRDIRD----LSLSGVPVEGEAGSGYRL 61
Cdd:COG3711    1 ILKILLKNNnVVTAKELAKKLNVSERTIRYDIKKinewLKKNGLEIISKKGIGFRL 56
COG3177 COG3177
Fic family protein [Transcription];
2-60 3.30e-03

Fic family protein [Transcription];


Pssm-ID: 442410 [Multi-domain]  Cd Length: 316  Bit Score: 37.74  E-value: 3.30e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 503994167   2 SRRADRLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGVPVEGEAGSGYR 60
Cdd:COG3177  257 GRLNERQRKLLELLFENPVLTASELAELLGVSRRTARRDLKDLVELGILEKVGGGRNTR 315
HTH_DeoR pfam08220
DeoR-like helix-turn-helix domain;
7-49 3.41e-03

DeoR-like helix-turn-helix domain;


Pssm-ID: 285436 [Multi-domain]  Cd Length: 57  Bit Score: 34.93  E-value: 3.41e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 503994167    7 RLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGV 49
Cdd:pfam08220   1 RIQQILELLKQQGTLSVEELAELLGVSEMTIRRDLNELEEQGL 43
HTH_DEOR smart00420
helix_turn_helix, Deoxyribose operon repressor;
7-49 9.33e-03

helix_turn_helix, Deoxyribose operon repressor;


Pssm-ID: 197714 [Multi-domain]  Cd Length: 53  Bit Score: 33.35  E-value: 9.33e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 503994167     7 RLFQIVQILRGRRLTTAGLLAERLGVSERTIYRDIRDLSLSGV 49
Cdd:smart00420   1 RQQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGL 43
 
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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