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UniProt release 12.8

Published February 5, 2008

Headlines

Over 20,000 fungal proteins manually annotated in UniProtKB/Swiss-Prot

Almost exactly one year after the integration of the complete proteome of Saccharomyces cerevisiae into UniProtKB/Swiss-Prot (see news), we have increased the number of manually annotated fungal entries to more than 20 000.

The fungal kingdom includes very diverse organisms, from unicellular to multicellular, from microscopic to macroscopic. Fungi have essential roles in many ecological processes. They are required for nutrient cycling within ecosystems, since they recycle dead organic matter into useful nutrients. Many plants would not survive without symbiotic fungi called mycorrhizae, which live in their roots and supply essential nutrients. They are also economically important as they provide numerous drugs (such as penicillin), food (such as mushrooms) and are used for their ability to ferment different sugars to produce bread, wine, beer and even soy sauce.

Fungi are also responsible for a great number of severe plant and animal diseases. Fungal infections, also called mycotic infections, may affect the skin or the internal organs of the body. Severe mycotic infections, such as histoplasmosis and candidiasis, are potentially life-threatening. Fungal diseases are very difficult to treat since fungi are eukaryotic organisms that share many properties with animal or human cells. Plant diseases caused by fungi include rusts and smuts, as well as leaf, root, and stem rot. They can cause severe damage to crop production.

Moreover, many fungi are important model organisms for studying the genetics and molecular biology of eukaryotes.

It is therefore not surprising that many fungi were targeted for the complete genome sequencing. No less that 32 complete fungal genomes have been submitted to public sequence databases to date. Using the S. cerevisiae and Schizosaccharomyces pombe fully annotated proteomes as templates, we are progressively annotating orthologous proteins in these newcomers, in order to provide our users with a high-quality fungal protein dataset that will better reflect the diversity of this kingdom.

UniProtKB News

Cross-references to World-2DPAGE

Cross-references have been added to the public repository of 2D-gel data World-2DPAGE. All 2D gel data to be published in the journal Proteomics needs to be available on the web. The World-2DPAGE repository hosts the data for resources who cannot build and maintain a web interface. There are currently two data sources submitted to World-2DPAGE, which are numbered consecutively:

  • 0001: CGL14067-2DPAGE, Corynebacterium glutamicum entries
  • 0002: NIBR 2D-PAGE, Staphylococcus aureus Mu50 entries

The format of the explicit links in the flat file is:

Resource abbreviation World-2DPAGE
Resource identifier Database name and database accession number (usually from UniProtKB), separated by a colon.
Examples
P61108:
DR   World-2DPAGE; 0002:P61108; -.

P77845:
DR   World-2DPAGE; 0001:P77845; -.

Cornea-2DPAGE, DOSAC-COBS-2DPAGE, HSC-2DPAGE, REPRODUCTION-2DPAGE, SWISS-2DPAGE

In cross-references to Cornea-2DPAGE, DOSAC-COBS-2DPAGE, HSC-2DPAGE, REPRODUCTION-2DPAGE and SWISS-2DPAGE, the optional information field 1 used to be the species origin. The species information has become obsolete/redundant since UniProtKB/Swiss-Prot no longer contains entries describing the same protein from different species (see Release 6.7). We have therefore replaced the species information by "-".

Examples:

Previous format:

DR   SWISS-2DPAGE; P04217; HUMAN.
DR   Cornea-2DPAGE; P04217; HUMAN.
DR   DOSAC-COBS-2DPAGE; P04217; HUMAN.
DR   REPRODUCTION-2DPAGE; P04217; HUMAN.

New format:

DR   SWISS-2DPAGE; P04217; -.
DR   Cornea-2DPAGE; P04217; -.
DR   DOSAC-COBS-2DPAGE; P04217; -.
DR   REPRODUCTION-2DPAGE; P04217; -.

New document on human and mouse protein kinases.

The document pkinfam.txt, available by ftp and on the Web site, provides the classification of human and mouse protein kinases into subfamilies or subgroups, as developed by Gerard Manning. The classification from Diego Miranda-Saavedra has also been taken into account.

This document contains all UniProtKB/Swiss-Prot human and mouse protein kinase entries, subdivided into 10 subfamilies or subgroups. Each gene name is followed by the corresponding human and/or mouse UniProtKB/Swiss-Prot entry name (and accession number).

Changes concerning keywords

New keyword: