PlantSecKB: the Plant Secretome and Subcellular Proteome KnowledgeBase

Gengkon Lum, John Meinken, Jessica Orr, Stephanie Frazier, Xiang Min
2014 Computational Molecular Biology  
Prediction and curation of protein subcellular locations is essential for protein functional annotation. We developed the Plant Secretome and Subcellular Proteome KnowledgeBase (PlantSecKB) for the plant research community to access and curate plant protein subcellular locations, with a focus on secreted proteins. 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
more » ... B project. The database contains information collected from three sources: (1) subcellular locations that were curated or computationally predicted in the UniProtKB; (2) subcellular locations and features predicted by eight computational tools; (3) secreted proteins that were curated from recent literature. 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. A primary analysis revealed that monocots and dicots had a similar proportion of secretomes, and monocots had a significantly higher proportion of proteins distributed to mitochondria (both membrane and non-membrane) and chloroplast membrane, while dicots had significantly more proteins distributed to cytosol and nucleus. This database aims to facilitate plant protein research and is available at
doi:10.5376/cmb.2014.04.0001 fatcat:y2ag2yovf5cwljf3rpkl3evahm