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Conserved domains on  [gi|519034040|ref|WP_020189915|]
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WYL domain-containing protein [Pseudomonas putida]

Protein Classification

WYL domain-containing protein( domain architecture ID 11971429)

WYL domain-containing protein similar to Mycobacterium PafB and PafC, which are involved in resistance to reactive nitrogen intermediates at the level of transcriptional regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 76-173 1.42e-08

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: 51.50  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040   76 PGLSLGEAQQLQPDALAPPTHVVLyaWVDDALARRLEQSPLSvDMQLTPQASGGAALV-ATVDDNRALMGWLLSQAGSIR 154
Cdd:pfam13280  77 PDFDLAEYLRRSFGVFPGPIEVKL--RFSPEAARRLRERRFP-DQQIEEEDDDGSLRVtLPVDDLEELARWLLSFGPDVE 153

                          90
                  ....*....|....*....
gi 519034040  155 IQAPQALRAAMIEQLRQSL 173
Cdd:pfam13280 154 VLEPPELREEVREEAKRLL 172
YobV super family cl28501
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 9-109 3.16e-05

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


The actual alignment was detected with superfamily member COG2378:

Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 43.14  E-value: 3.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040   9 TIARQWQLLKLLpGRHPGMSSTQLQAALTTvghttSKRTVERDLVELAAL-FPLQCNsKGMPYGWYWQPG-------LSL 80
Cdd:COG2378    3 RLERLLALLQLL-QSRRGVTAAELAERLEV-----SERTIYRDIDALRELgVPIEAE-RGRGGGYRLRDGyrlpplmLTE 75

                         90       100       110
                 ....*....|....*....|....*....|.
gi 519034040  81 GEAQQLQ--PDALAPPTHVVLYAWVDDALAR 109
Cdd:COG2378   76 EEALALLlaLRLLAALGGAPLAEAAASALAK 106
 
Name Accession Description Interval E-value
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 76-173 1.42e-08

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: 51.50  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040   76 PGLSLGEAQQLQPDALAPPTHVVLyaWVDDALARRLEQSPLSvDMQLTPQASGGAALV-ATVDDNRALMGWLLSQAGSIR 154
Cdd:pfam13280  77 PDFDLAEYLRRSFGVFPGPIEVKL--RFSPEAARRLRERRFP-DQQIEEEDDDGSLRVtLPVDDLEELARWLLSFGPDVE 153

                          90
                  ....*....|....*....
gi 519034040  155 IQAPQALRAAMIEQLRQSL 173
Cdd:pfam13280 154 VLEPPELREEVREEAKRLL 172
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 93-177 3.07e-08

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 52.00  E-value: 3.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040  93 PPTHVVLyaWVDDALARRLEQspLSVDMQLTPQASGGAALVATVDDNRALMGWLLSQAGSIRIQAPQALRAAMIEQLRQS 172
Cdd:COG2378  234 EPVTVTL--RFSPEAARYLRE--RHPSQEIEELPDGSVRVTLTVADLDELARWLLSFGADVEVLEPEELREAVREEARRL 309


                 ....*
gi 519034040 173 LALHE 177
Cdd:COG2378  310 LARYE 314
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 9-109 3.16e-05

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 43.14  E-value: 3.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040   9 TIARQWQLLKLLpGRHPGMSSTQLQAALTTvghttSKRTVERDLVELAAL-FPLQCNsKGMPYGWYWQPG-------LSL 80
Cdd:COG2378    3 RLERLLALLQLL-QSRRGVTAAELAERLEV-----SERTIYRDIDALRELgVPIEAE-RGRGGGYRLRDGyrlpplmLTE 75

                         90       100       110
                 ....*....|....*....|....*....|.
gi 519034040  81 GEAQQLQ--PDALAPPTHVVLYAWVDDALAR 109
Cdd:COG2378   76 EEALALLlaLRLLAALGGAPLAEAAASALAK 106
 
Name Accession Description Interval E-value
WYL pfam13280
WYL domain; WYL is a Sm-like SH3 beta-barrel fold containing domain. It is a member of the ...
 76-173 1.42e-08

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: 51.50  E-value: 1.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040   76 PGLSLGEAQQLQPDALAPPTHVVLyaWVDDALARRLEQSPLSvDMQLTPQASGGAALV-ATVDDNRALMGWLLSQAGSIR 154
Cdd:pfam13280  77 PDFDLAEYLRRSFGVFPGPIEVKL--RFSPEAARRLRERRFP-DQQIEEEDDDGSLRVtLPVDDLEELARWLLSFGPDVE 153

                          90
                  ....*....|....*....
gi 519034040  155 IQAPQALRAAMIEQLRQSL 173
Cdd:pfam13280 154 VLEPPELREEVREEAKRLL 172
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 93-177 3.07e-08

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 52.00  E-value: 3.07e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040  93 PPTHVVLyaWVDDALARRLEQspLSVDMQLTPQASGGAALVATVDDNRALMGWLLSQAGSIRIQAPQALRAAMIEQLRQS 172
Cdd:COG2378  234 EPVTVTL--RFSPEAARYLRE--RHPSQEIEELPDGSVRVTLTVADLDELARWLLSFGADVEVLEPEELREAVREEARRL 309


                 ....*
gi 519034040 173 LALHE 177
Cdd:COG2378  310 LARYE 314
YobV COG2378
Predicted DNA-binding transcriptional regulator YobV, contains HTH and WYL domains ...
 9-109 3.16e-05

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


Pssm-ID: 441945 [Multi-domain]  Cd Length: 314  Bit Score: 43.14  E-value: 3.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 519034040   9 TIARQWQLLKLLpGRHPGMSSTQLQAALTTvghttSKRTVERDLVELAAL-FPLQCNsKGMPYGWYWQPG-------LSL 80
Cdd:COG2378    3 RLERLLALLQLL-QSRRGVTAAELAERLEV-----SERTIYRDIDALRELgVPIEAE-RGRGGGYRLRDGyrlpplmLTE 75

                         90       100       110
                 ....*....|....*....|....*....|.
gi 519034040  81 GEAQQLQ--PDALAPPTHVVLYAWVDDALAR 109
Cdd:COG2378   76 EEALALLlaLRLLAALGGAPLAEAAASALAK 106
 
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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