SGD Help: Model Organism BLASTP Best Hits

Contents

Description
Accessing the Model Organism BLASTP Best Hits page
BLASTP analysis
Summary table
Other relevant links
Associated glossary terms

Description

SGD's Model Organism BLASTP Best Hits page displays the results of NCBI BLASTP analysis using the protein sequence of each S. cerevisiae open reading frame as the query sequence against the predicted protein sequences of several model organisms. Results are displayed in a table with links to the web pages of the hit proteins in other model organism databases, facilitating access to curated information about proteins of other organisms that have similarity to S. cerevisiae proteins.

Accessing the Model Organism BLASTP Best Hits page

The Model Organism BLASTP Best Hits page is accessed from each SGD Locus page. Its link is an option in the 'Comparison Resources' pull-down menu on the right-hand side of the Locus page.

BLASTP analysis

The BLASTP query sequences are all translated open reading frames in SGD, including those classified as Verified, Uncharacterized, and Dubious. The BLASTP program used is NCBI BLASTP, with the default parameters. The analysis is re-run periodically. The predicted protein sequences against which the BLASTP analysis is run, and the corresponding model organism databases, are from:

Arabidopsis thaliana (TAIR)
Ashbya gossypii (Ashbya Genome Database (AGD))
Caenorhabditis elegans (WormBase)
Drosophila melanogaster (FlyBase)
Homo sapiens (ENSEMBL (HUMAN)
Saccharomyces cerevisiae (SGD)
Candida albicans (CGD)
Schizosaccharomyces pombe (Schizosaccharomyces pombe GeneDB)

The Best-hit is chosen from the set of BLASTP hits with E-value less than or equal to 0.01. For S. cerevisiae, the query protein is excluded from the hits.

Summary table

The columns in the summary table are as follows:

Species: the species in which the hit protein sequence is found.

Database: the model organism database for that species. The database name or abbreviation is linked to its home page.

Hit: the name for the hit protein, as assigned by the model organism database. The name is linked to the curated web page for that protein in the model organism database.

Description: The description of the hit protein from the model organism database.

E-value: Expect threshold, reflecting the number of hits expected to be found by chance. The lower the E-value, the more significant the hit. The hits in the summary table are presented in order of increasing E-value.
% Aligned: the percentage of the length of the query protein over which it aligns with the hit protein.
Source Range: displays the amino acid coordinates of the region of the S. cerevisiae query protein that was aligned.
Target Range: displays the amino acid coordinates of the region of the 'hit' protein that was aligned with the S. cerevisiae query protein.

Associated glossary terms

Return to Saccharomyces Genome Database Send a Message to the SGD Curators