Summary: GLEYA domain
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GLEYA domain Provide feedback
The GLEYA domain is related to lectin-like binding domains found in the S. cerevisiae Flo proteins and the C. glabrata Epa proteins . It is a carbohydrate-binding domain that is found in fungal adhesins (also referred to as agglutinins or flocculins) . Adhesins with a GLEYA domain possess a typical N-terminal signal peptide and a domain of conserved sequence repeats, but lack glycosylphosphatidylinositol (GPI) anchor attachment signals . They contain a conserved motif G(M/L)(E/A/N/Q)YA, hence the name GLEYA. Based on sequence homology, it is suggested that the GLEYA domain would predominantly contain beta sheets . The GLEYA domain is also found in S. pombe protein Q92344 thought to be a kinetochore portein (Sim4 complex subunit), however no direct evidence for kinetochore association has been found . Furthermore, a global protein localisation study in S. pombe identified it as a secreted protein localized to the Golgi complex .
Linder T, Gustafsson CM; , Fungal Genet Biol. 2007; [Epub ahead of print]: Molecular phylogenetics of ascomycotal adhesins-A novel family of putative cell-surface adhesive proteins in fission yeasts. PUBMED:17870620 EPMC:17870620
Andersson KM, Meerupati T, Levander F, Friman E, Ahren D, Tunlid A;, Appl Environ Microbiol. 2013;79:4993-5004.: Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum. PUBMED:23770896 EPMC:23770896
Liu MC, Yang CS, Yeh FL, Wei CH, Jane WN, Chung MC, Wang CS;, J Exp Bot. 2014;65:2023-2037.: A novel lily anther-specific gene encodes adhesin-like proteins associated with exine formation during anther development. PUBMED:24591055 EPMC:24591055
Liu X, McLeod I, Anderson S, Yates JR 3rd, He X; , EMBO J. 2005;24:2919-2930.: Molecular analysis of kinetochore architecture in fission yeast. PUBMED:16079914 EPMC:16079914
Sideri T, Rallis C, Bitton DA, Lages BM, Suo F, Rodriguez-Lopez M, Du LL, Bahler J;, G3 (Bethesda). 2014;5:145-155.: Parallel profiling of fission yeast deletion mutants for proliferation and for lifespan during long-term quiescence. PUBMED:25452419 EPMC:25452419
Internal database links
|Similarity to PfamA using HHSearch:||PA14|
This tab holds annotation information from the InterPro database.
InterPro entry IPR018871
The GLEYA domain is related to lectin-like binding domains found in the Saccharomyces cerevisiae Flo proteins and the Candida glabrata Epa proteins [ PUBMED:17870620 ]. It is a carbohydrate-binding domain that is found in fungal adhesins (also referred to as agglutinins or flocculins) [ PUBMED:23770896 ]. Adhesins with a GLEYA domain possess a typical N-terminal signal peptide and a domain of conserved sequence repeats, but lack glycosylphosphatidylinositol (GPI) anchor attachment signals [ PUBMED:24591055 ]. They contain a conserved motif G(M/L)(E/A/N/Q)YA, hence the name GLEYA. Based on sequence homology, it is suggested that the GLEYA domain would predominantly contain beta sheets [ PUBMED:17870620 ]. The GLEYA domain is also found in Schizosaccharomyces pombe protein SWISSPROT , thought to be a kinetochore protein (Sim4 complex subunit), however no direct evidence for kinetochore association has been found [ PUBMED:16079914 ]. Furthermore, a global protein localisation study in S. pombe identified it as a secreted protein localized to the Golgi complex [ PUBMED:25452419 ].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
The graphic that is shown by default represents the longest sequence with a given architecture. Each row contains the following information:
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a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
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We make a range of alignments for each Pfam-A family:
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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.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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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.
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|Seed source:||Linder T|
|Author:||Linder T , Bateman A|
|Number in seed:||180|
|Number in full:||930|
|Average length of the domain:||93.9 aa|
|Average identity of full alignment:||25 %|
|Average coverage of the sequence by the domain:||11.42 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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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...
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
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For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
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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 GLEYA domain has been found. There are 27 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|
|A0A175VNJ8||View 3D Structure||Click here|
|P0CU04||View 3D Structure||Click here|
|P0CU05||View 3D Structure||Click here|
|Q7Z9I1||View 3D Structure||Click here|
|Q92344||View 3D Structure||Click here|
|Q9C0Y2||View 3D Structure||Click here|