Universal Protein Resource (UniProt)
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The Universal Protein Resource (UniProt), a collaboration between the European
Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics, and
the Protein Information Resource (PIR), is comprised of three databases, each
optimized for different uses. The UniProt Knowledgebase (UniProtKB) is the
central access point for extensively curated protein information, including
function, classification and cross-references. The UniProt Reference Clusters
(UniRef) combine closely related sequences into a single record to speed up
sequence similarity searches. The UniProt Archive (UniParc) is a comprehensive
repository of all protein sequences, consisting only of unique identifiers and
sequences.
UniProt Reference Clusters (UniRef)
=================================================
The UniProt Reference Clusters (UniRef) provide clustered sets (UniRef100, UniRef90
and UniRef50 clusters) of sequences from the UniProt Knowledgebase and selected UniParc
records, in order to obtain complete coverage of sequence space at several resolutions
(100%, >90% and >50%) while hiding redundant sequences (but not their descriptions)
from view.
UniRef50
=========
UniRef50 clusters are generated from the UniRef90 seed sequences with a 50% sequence
identity threshold using the MMseqs2 algorithm. The seed sequences are the longest
members of the UniRef90 cluster. However, the longest sequence is not always the
most informative. There is often more biologically relevant information and annotation
(name, function, cross-references) available on other cluster members. All the proteins
in each cluster are ranked to facilitate the selection of a biologically relevant
representative for the cluster. The proteins are ranked as follows:
1. quality of annotation: order of preference is a member from UniProtKB/Swiss-Prot
then UniProtKB/TrEMBL and last is UniParc
2. annotation score: prefer entries that have higher UniProtKB Annotation Score
3. organism: prefer entries from Reference proteomes and Model Organisms
4. sequence length: longest sequence is preferred.
As new proteins are added to UniProtKB and UniParc, UniRef cluster memberships and/or
identifiers might change.
UniRef50 cluster titles and identifiers are derived from the representative UniRef90
entry. The UniRef50 identifier is generated by replacing "UniRef90_" prefix of
the representative with "UniRef50_".
Ftp access
==========
Currently, UniRef50 is available from UniProt FTP site:
ftp.uniprot.org/pub/databases/uniprot/uniref/uniref50
The UniRef50 files and their descriptions are as follows:
File Name File Description
------------- -----------------------------------------------------------
uniref50.fasta This file contains all UniRef50 entries in FASTA format.
The definition line in the FASTA format includes cluster
specific information such as cluster name, number of members and
and common taxonomy and also the ID of the representative protein.
The format is as follows:
>UniqueIdentifier ClusterName n=Members Tax=Taxon RepID=RepresentativeMember
where:
- UniqueIdentifier is the primary accession number of the UniRef cluster.
- ClusterName is the name of the UniRef cluster.
- Members is the number of UniRef cluster members.
- Taxon is the scientific name of the lowest common taxon shared
by all UniRef cluster members.
- RepresentativeMember is the entry name of the representative member
of the UniRef cluster.
For example:
>UniRef50_P99999 Cytochrome c n=33 Tax=Eukaryota RepID=CYC_HUMAN
uniref50.xml This file contains all UniRef50 entries in XML format. Each entry is
identified by the UniRef identifier, and contains:
- cross-reference to representative UniProtKB or UniParc entry and its
sequence
- cluster member that served as the seed sequence is flagged
- cross-references to member UniProtKB and/or UniParc entries
- cross-references to UniRef90 and UniRef100 entries
- member count
- common taxon
Document type definition for uniref50.xml
------------------------------------------
<?xml version="1.0" encoding="ASCII"?>
<!DOCTYPE UniRef50 [
<!ELEMENT UniRef50 (entry+)>
<!ATTLIST UniRef50
xmlns CDATA #FIXED "http://uniprot.org/uniref"
xmlns:xsi CDATA #IMPLIED
xsi:schemaLocation CDATA #IMPLIED
releaseDate CDATA #IMPLIED
version CDATA #IMPLIED
>
<!-- entry: UniRef50 entry -->
<!ELEMENT entry (name,property*,representativeMember,member*)>
<!ATTLIST entry id ID #REQUIRED
updated CDATA #IMPLIED
>
<!-- name: UniRef50 cluster name derived from representative -->
<!-- UniRef100 entry -->
<!ELEMENT name (#PCDATA)>
<!-- representativeMember: information for representative -->
<!-- UniRef100 entry -->
<!ELEMENT representativeMember (dbReference,sequence)>
<!-- memberList: members of UniRef50 cluster other than representative -->
<!ELEMENT member (dbReference)>
<!-- dbReference: cross-reference to member UniRef100 entries -->
<!-- of the UniRef50 cluster -->
<!ELEMENT dbReference (property*)>
<!ATTLIST dbReference
type CDATA #REQUIRED
id CDATA #REQUIRED
>
<!-- property: properties of cross-references -->
<!ELEMENT property EMPTY>
<!ATTLIST property
type CDATA #REQUIRED
value CDATA #REQUIRED
>
<!ELEMENT sequence (#PCDATA ) >
<!ATTLIST sequence
length CDATA #IMPLIED
checksum CDATA #IMPLIED
>
]>
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(https://creativecommons.org/licenses/by/4.0/) to all copyrightable parts of
our databases.
(c) 2002-2022 UniProt Consortium
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Any medical or genetic information is provided for research, educational and
informational purposes only. It is not in any way intended to be used as a
substitute for professional medical advice, diagnosis, treatment or care.