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Phospho.ELM: a database of phosphorylation sites--update 2008.

Diella F, Gould CM, Chica C, Via A, Gibson TJ - Nucleic Acids Res. (2007)

Bottom Line: The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites.The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references.The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

ABSTRACT
Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets. The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites. The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references. The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING. A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query (by sequence or UniProt accession) to search against the curated data set of phosphorylated peptides. Phospho.ELM is available on line at: http://phospho.elm.eu.org.

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Output example of a PhosphoBLAST Search using as query the Danio rerio Aurora A kinase sequence. The summary graphic shows the phospho-hits on the query sequence and features from SMART. Details about the matches are shown below in the results table. Clicking on the ‘subject name’ the users can retrieve additional information about the matched Phospho.ELM phosphorylated sites, including the flanking sequence, the PubMed reference, the kinase responsible for the phosphorylation (where known) and links to additional information for the substrate and other relevant databases.
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Figure 2: Output example of a PhosphoBLAST Search using as query the Danio rerio Aurora A kinase sequence. The summary graphic shows the phospho-hits on the query sequence and features from SMART. Details about the matches are shown below in the results table. Clicking on the ‘subject name’ the users can retrieve additional information about the matched Phospho.ELM phosphorylated sites, including the flanking sequence, the PubMed reference, the kinase responsible for the phosphorylation (where known) and links to additional information for the substrate and other relevant databases.

Mentions: A BLAST search has been implemented which is complementary to the retrieval by keyword or UniProt accession/identifier. This tool identifies phospho-peptides contained in the query sequence that match those stored in Phospho.ELM (Figure 2). It consists of a two-step process: a BLAST (20) search and a parsing of the BLAST output. The BLAST program performs a sequence-similarity search against the Phospho.ELM data set of peptides (16 471), which have been experimentally proven to contain phospho-residues. It returns a set of local gapped alignments between the query sequence peptides and the phospho-peptides. In the parsing stage, those matches that present more than 70% sequence similarity and that conserve the phospho-residue in the same position as the corresponding phospho-peptide are selected. The final output shows the list of chosen matches, with their alignments and links to database records.Figure 2.


Phospho.ELM: a database of phosphorylation sites--update 2008.

Diella F, Gould CM, Chica C, Via A, Gibson TJ - Nucleic Acids Res. (2007)

Output example of a PhosphoBLAST Search using as query the Danio rerio Aurora A kinase sequence. The summary graphic shows the phospho-hits on the query sequence and features from SMART. Details about the matches are shown below in the results table. Clicking on the ‘subject name’ the users can retrieve additional information about the matched Phospho.ELM phosphorylated sites, including the flanking sequence, the PubMed reference, the kinase responsible for the phosphorylation (where known) and links to additional information for the substrate and other relevant databases.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238828&req=5

Figure 2: Output example of a PhosphoBLAST Search using as query the Danio rerio Aurora A kinase sequence. The summary graphic shows the phospho-hits on the query sequence and features from SMART. Details about the matches are shown below in the results table. Clicking on the ‘subject name’ the users can retrieve additional information about the matched Phospho.ELM phosphorylated sites, including the flanking sequence, the PubMed reference, the kinase responsible for the phosphorylation (where known) and links to additional information for the substrate and other relevant databases.
Mentions: A BLAST search has been implemented which is complementary to the retrieval by keyword or UniProt accession/identifier. This tool identifies phospho-peptides contained in the query sequence that match those stored in Phospho.ELM (Figure 2). It consists of a two-step process: a BLAST (20) search and a parsing of the BLAST output. The BLAST program performs a sequence-similarity search against the Phospho.ELM data set of peptides (16 471), which have been experimentally proven to contain phospho-residues. It returns a set of local gapped alignments between the query sequence peptides and the phospho-peptides. In the parsing stage, those matches that present more than 70% sequence similarity and that conserve the phospho-residue in the same position as the corresponding phospho-peptide are selected. The final output shows the list of chosen matches, with their alignments and links to database records.Figure 2.

Bottom Line: The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites.The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references.The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.

ABSTRACT
Phospho.ELM is a manually curated database of eukaryotic phosphorylation sites. The resource includes data collected from published literature as well as high-throughput data sets. The current release of Phospho.ELM (version 7.0, July 2007) contains 4078 phospho-protein sequences covering 12 025 phospho-serine, 2362 phospho-threonine and 2083 phospho-tyrosine sites. The entries provide information about the phosphorylated proteins and the exact position of known phosphorylated instances, the kinases responsible for the modification (where known) and links to bibliographic references. The database entries have hyperlinks to easily access further information from UniProt, PubMed, SMART, ELM, MSD as well as links to the protein interaction databases MINT and STRING. A new BLAST search tool, complementary to retrieval by keyword and UniProt accession number, allows users to submit a protein query (by sequence or UniProt accession) to search against the curated data set of phosphorylated peptides. Phospho.ELM is available on line at: http://phospho.elm.eu.org.

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