Summary: u-PAR/Ly-6 domain
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u-PAR/Ly-6 domain Provide feedback
This extracellular disulphide bond rich domain is related to PF00087.
Internal database links
SCOOP: | PLA2_inh Toxin_TOLIP UPAR_LY6_2 |
Similarity to PfamA using HHSearch: | Toxin_TOLIP QVR |
External database links
PROSITE: | PDOC00756 |
SCOP: | 1erg |
This tab holds annotation information from the InterPro database.
InterPro entry IPR016054
This entry represents a three-fold repeated domain in urokinase-type plasminogen activator receptor (uPAR) that occurs singly in other GPI-linked cell-surface glycoproteins (Ly-6 family, CD59, thymocyte B cell antigen, Sgp-2).
A variety of GPI-linked cell-surface glycoproteins are composed of one or more copies of a conserved domain of about 100 amino-acid residues [PUBMED:1850423, PUBMED:8394346]. Among these proteins, U-PAR contains three tandem copies of the domain, while all the others are made up of a single domain.
As shown in the following schematic, this conserved domain contains 10 cysteine residues involved in five disulphide bonds - in U-PAR, the first copy of the domain lacks the fourth disulphide bond.
+------+ +------------------------+ +---+ | | | | | | xCxxCxxxxxxCxxxxxCxxxxxCxxxxxxxxxxxxxxxxxxCxxxxCxxxxxxxxxxxxxxCCxxxCxxxxxxxx | | | | +---------------------+ +--------------+ 'C': conserved cysteine involved in a disulphide bond.
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 uPAR_Ly6_toxin (CL0117), which has the following description:
This superfamily contains snake toxins as well as extracellular cysteine rich domains.
The clan contains the following 10 members:
Activin_recp BAMBI DUF5746 ecTbetaR2 Ly-6_related PLA2_inh QVR Toxin_TOLIP UPAR_LY6 UPAR_LY6_2Alignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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.
Seed (27) |
Full (3060) |
Representative proteomes | UniProt (5030) |
NCBI (11202) |
Meta (0) |
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RP15 (211) |
RP35 (618) |
RP55 (1541) |
RP75 (2819) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
Seed (27) |
Full (3060) |
Representative proteomes | UniProt (5030) |
NCBI (11202) |
Meta (0) |
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RP15 (211) |
RP35 (618) |
RP55 (1541) |
RP75 (2819) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logo
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...
Trees
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
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Sonnhammer ELL |
Number in seed: | 27 |
Number in full: | 3060 |
Average length of the domain: | 74.40 aa |
Average identity of full alignment: | 22 % |
Average coverage of the sequence by the domain: | 50.79 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 77 | ||||||||||||
Family (HMM) version: | 22 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Selections
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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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Interactions
There are 6 interactions for this family. More...
V-set UPAR_LY6 Somatomedin_B Kringle Kringle Thiol_cytolysinStructures
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 UPAR_LY6 domain has been found. There are 80 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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