There are many thousands of proteins in a plant cell. The subcellular locations of proteins determine where the proteins play their biological roles. Prediction and curation of protein subcellular locations are essential for protein functional annotation. We evaluated a number of prediction tools and developed an accurate protocol for predicting protein subcellular locations in plants, and then using the protocol we constructed he Plant Secretome and Subcellular Proteome KnowledgeBase (PlantSecKB) for the plant research community to access and curate plant protein subcellular locations. The database is constructed with all the available plant protein data retrieved from the UniProtKB database and plant protein sequences predicted from EST data assembled by the PlantGDB project. The categories of subcellular locations include secretome, mitochondria, chloroplast, cytosol, cytoskeleton, endoplasmic reticulum, Golgi apparatus, lysosome, peroxisome, nucleus, vacuole, and plasma membrane. The data can be searched by using UniProt accession number or ID, GenBank GI or RefSeq accession number, gene name, and keywords. Species specific secretome and subcellular proteomes can be searched and downloaded into a FASTA file. BLAST is available to allow users to search the database based on protein sequences. Community curation for subcellular locations of plant proteins is also supported. This database aims to facilitate plant protein research and is available at http://bioinformatics.ysu.edu/secretomes/plant/index.php
Take Away Notes:
• The audience will learn how to predict the subcellular locations of their proteins.
• The audience will learn how to use the PlantSecKB database to search for their protein subcellular locations.
• The audience will be able to use the system to deposit the subcellular locations of their proteins into the database for public access.
• The database contains 1.4 millions of proteins with predicted subcellular locations and can be a good resource for research and teaching.