Plant Metabolic Pathways in MetaCyc and SolCyc

Abstract

AbstractMetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations. The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes, 4748 genes, 7234 chemical compounds, curated from 17916 citations. The MetaCyc database is the reference database on which the pathways are predicted from annotated genomes by PathoLogic called Pathway/genome Databases (PGDB's). The Biocyc Database ("biocyc.org":http://biocyc.org) has a collection over 300 PGDB's. Each BioCyc Database describes the genome and predicted metabolic pathways of a single organism, which are then taken up by interested groups for curation. SolCyc is one such PGDB, developed for the clade oriented Solanceae Genomics Network (SGN) database. It has predicted metabolic pathway databases of significant species belonging to Solanaceae and includes Lycocyc(tomato), Solacyc (eggplant), Nicotianacyc (tobacco),Petuniacyc (Petunia), Capcyc (Capsicum) , Potatocyc (potato). An interactive webinterface has been developed for the seamless flow of information from the SGN phenotype and locus database with SolCyc. This facilitates researchers with the capacity to search for underlying metabolic pathway information of genes and phenotypes that has been curated into the SolCyc database.