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.

Pan Proteomes
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The current pan proteome sequences are derived from the reference proteome
clusters (75% proteome similarity for Fungus and 55% proteome similarity for
Archaea and Bacteria). A reference proteome cluster is also known as a
representative proteome group (RPG) (Chen et al., 2011). A RPG contains similar
proteomes calculated based on their co-membership in UniRef50 clusters. For each
non-singleton reference proteome cluster, a pan proteome is a set of sequences
consisting of all the sequences in the reference proteome, plus the addition of
unique protein sequences that are found in other species or strains of the
cluster but not in the reference proteome. These additional sequences are
identified using UniRef50 membership. See http://pir.georgetown.edu/rps/pp.shtml 
for more information.

This directory 'databases/uniprot/current_release/knowledgebase/pan_proteomes'
contains the Pan Proteome data files which are updated in conjunction with the
UniProt Knowledgebase (UniProtKB).

1. PPMembership.txt
This is a tab-delimited two columns file with header. Column 1 are the UPIds of
Pan Proteomes. Column 2 are the UPIds of Pan Proteome members.

2. Compressed sequence files in Fasta format.
File is named as UPxxxxxxxxx.fasta.gz, where UPxxxxxxxxx is the UPId of the Pan
Proteome.

The decription line of each Fasta record is the standard UniProt Fasta plus
UP Id and Pan Proteome ID.

Example:

>sp|Q9RGZ4|MRPB_BACPE Na(+)/H(+) antiporter subunit B OS=Bacillus pseudofirmus (strain OF4) GN=mrpB PE=1 SV=1 UPId=UP000001544 PPId=UP000001544
MKNLKSNDVLLHTLTRVVTFIILAFSVYLFFAGHNNPGGGFIGGLMTASALLLMYLGFDM
RSIKKAIPFDFTKMIAFGLLIAIFTGFGGLLVGDPYLTQYFEYYQIPILGETELTTALPF
DLGIYLVVIGIALTIILTIAEDDM


3. README
This file

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