Computational protocol: The Candida albicans stress response gene Stomatin-Like Protein 3 is implicated in ROS-induced apoptotic-like death of yeast phase cells

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Protocol publication

[…] CGD (http://www.candidagenome.org/) was utilized to search for all SPFH family members in C. albicans. The Aspergillus Genome Database (AspGD, http://www.aspgd.org/) was used to retrieve SPFH sequences from A. nidulans. Sequences for human, mouse, and nematode SPFH family members were retrieved from UniProt and NCBI: HsSTOM (accession: P27105), HsSTOML1 (accession: Q9UBI4), HsSTOML2 (accession: Q9UJZ1), HsSTOML3 (accession: Q8TAV4), HsPodocin (accession: Q9NP85), MmStoml3 (accession: Q6PE84), CeStomatin2 (accession: NP_001257021.1). Sequences were aligned using T-Coffee [] with default parameters and then formatted using Boxshade (http://www.ch.embnet.org/software/BOX_form.html). Sequence identities and similarities between Slp3p and other SPFH family members were determined using Protein BLAST with default parameters. Post-translational modification and organelle targeting predictions were made using the bioinformatics resource portal ExPASy (https://www.expasy.org/). Protein schematics were constructed using Illustrator for Biological Sequences, version 1.0 []. […]

Pipeline specifications

Software tools T-Coffee, BoxShade, DELTA-BLAST
Databases AspGD ExPASy
Applications Amino acid sequence alignment, Proteome data visualization
Organisms Candida albicans, Saccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans