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4  structures 5223  species 0  interactions 17749  sequences 73  architectures

Family: WYL (PF13280)

Summary: WYL domain

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

WYL domain Provide feedback

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 [1] 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 [2]. 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.

Literature references

  1. Makarova KS, Anantharaman V, Grishin NV, Koonin EV, Aravind L;, Front Genet. 2014;5:102.: CARF and WYL domains: ligand-binding regulators of prokaryotic defense systems. PUBMED:24817877 EPMC:24817877

  2. Hein S, Scholz I, Voss B, Hess WR;, RNA Biol. 2013;10:852-864.: Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. PUBMED:23535141 EPMC:23535141

This tab holds annotation information from the InterPro database.

InterPro entry IPR026881

This presumed domain is often found to the C terminus of a DNA-binding helix-turn-helix domain. This domain may be involved in binding to an as yet unknown ligand that allows a transcriptional regulation response to that molecule. There are a number of proteins that contain two tandem copies of this domain such as SWISSPROT . This suggests that this domain may form a dimeric arrangement.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan WYL (CL0654), which has the following description:

Members of this clan all belong to the WYL-like superfamily, and show structural similarity to the Sm-like SH3 beta-barrel fold. The WYL domain was first named for three conserved amino acids, however this motif was subsequently shown to be found only in a small subset of examples of this clan. The conservation pattern more widely applicable across the clan includes four basic residues and a position often occupied by a cysteine. These residues are predicted to line a ligand-binding groove similar to that found in Sm-like SH3 beta-barrels. WYL domains often occur in two copies in the same protein, or are encoded alongside neighbouring genes that encode multi-WYL domain proteins, and it has been suggested that they form toroidal multimeric assemblies. WYL domains are often associated with various predicted DNA-binding N-terminal wHTH domains, but may also exist as fusions to several enzymatic domains.

The clan contains the following 4 members:



We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Jackhmmer:Q7P457
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Anantharaman V
Number in seed: 384
Number in full: 17749
Average length of the domain: 159.40 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 51.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.8 25.8
Trusted cut-off 25.8 25.8
Noise cut-off 25.7 25.7
Model length: 172
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the WYL domain has been found. There are 4 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
P52133 View 3D Structure Click here
P9WIL9 View 3D Structure Click here
P9WIM1 View 3D Structure Click here