PHOSIDA: Difference between revisions
| Line 74: | Line 74: | ||
===Searching=== | ===Searching=== | ||
For each protein, the user is presented with general features such as isoelectric point (pI), molecular weight, sequence, and description at the protein level in addition to corresponding GO accession numbers, which are directly hyperlinked to the detailed description of the annotation at the Gene Ontology website. In addition, a hyperlink to the Reactome database is provided, if the specified protein is annotated in Reactome (www.reactome.org).<br /> | For each protein, the user is presented with general features such as isoelectric point (pI), molecular weight, sequence, and description at the protein level in addition to corresponding GO accession numbers, which are directly hyperlinked to the detailed description of the annotation at the Gene Ontology website. In addition, a hyperlink to the Reactome database is provided, if the specified protein is annotated in Reactome (www.reactome.org).<br /> | ||
[[Image:Example.jpg]] | [[Image:Example.jpg]]<br /><br /> | ||
Furthermore, annotated protein features such as active sites, binding sites, domains, and signal sequences are derived from the Swissprot database and illustrated for eukaryotic phosphoproteins, when clicking the ‘motifs/domains’ button. In the case of human, protein assignments were based on the IPI database, which is cross-referenced with the Swissprot database by PHOSIDA. Entries of both databases that correspond to the same proteins were aligned to derive the exact positions of these protein features. Already annotated phosphosites derived from Swissprot are transferred to the IPI sequences in the same way and listed when clicking the ‘sites (other sources)’ button. The aligned regions can be visualized via ‘check alignment’ buttons. Furthermore, corresponding literature is also provided.<br /> | |||
[[Image:Proteinfeatures.jpg]] | |||
===Usage examples=== | ===Usage examples=== | ||
Revision as of 20:32, 17 March 2008
You can help EcoliWiki by editing the content of this page. For information about becoming a registered user and obtaining editing privileges, see Help:Accounts.
| Link/URL: | |
|---|---|
| What: |
Phosida - Phosphorylation Site Database |
| Who: |
Florian Gnad and Matthias Mann |
| Updates: |
Genome Annotation Section |
| Upcoming events: |
Inclusion of additional phosphoproteomes of various organisms |
| Web Services: | |
| edit table | |
See Help:Database_table for how to add or edit information in this section of EcoliWiki.
About PHOSIDA
Add general information here
PHOSIDA, the phosphorylation site database, integrates thousands of high-confidence in-vivo phosphosites identified by mass spectrometry-based proteomics in various species. It includes phosphoproteomes of organisms, which cover the entire phylogenetic tree representatively, ranging from bacteria such as Escherichia coli and Bacillus subtilis to eukaryotes such as yeast and human. It contains 81 phosphorylation sites on 79 E.coli proteins, for example.
E.coli results are described in Macek and Gnad et al.[1].
Content
PHOSIDA contains phosphoproteomes of the following prokaryotes:
|
Escherichia coli (79 phosphoproteins, 81 phosphosites) |
|
Bacillus subtilis (78 phosphoproteins, 78 phosphosites) |
| edit table |
Using PHOSIDA
Browsing
The web user is able to search for any protein of interest within a specified organism. In the case of human, it is possible to search via IPI accession number, Swissprot identifier, gene symbol, protein name, peptide sequence, protein sequence or any substring that matches with the description of a given protein, for example.
Searching
For each protein, the user is presented with general features such as isoelectric point (pI), molecular weight, sequence, and description at the protein level in addition to corresponding GO accession numbers, which are directly hyperlinked to the detailed description of the annotation at the Gene Ontology website. In addition, a hyperlink to the Reactome database is provided, if the specified protein is annotated in Reactome (www.reactome.org).
Furthermore, annotated protein features such as active sites, binding sites, domains, and signal sequences are derived from the Swissprot database and illustrated for eukaryotic phosphoproteins, when clicking the ‘motifs/domains’ button. In the case of human, protein assignments were based on the IPI database, which is cross-referenced with the Swissprot database by PHOSIDA. Entries of both databases that correspond to the same proteins were aligned to derive the exact positions of these protein features. Already annotated phosphosites derived from Swissprot are transferred to the IPI sequences in the same way and listed when clicking the ‘sites (other sources)’ button. The aligned regions can be visualized via ‘check alignment’ buttons. Furthermore, corresponding literature is also provided.
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
Discussion
References
External Links
PHOSIDA (Phosphorylation Site Database): http://www.phosida.com
MAPU (Max-Planck Unified Proteome Database): http://www.mapuproteome.com