The MetaCyc Metabolic Pathway Database

Sri International, Menlo Park CA

Investigators

Linked publications & trials

Abstract

[unreadable] DESCRIPTION (provided by applicant): SRI International (SRI) and The Carnegie Institution of Washington (Carnegie) propose to expand the MetaCyc database (DB) and the Pathway Tools software used to visualize, query, and edit MetaCyc. MetaCyc describes metabolic pathways in a wide variety of microorganisms and plants. The DB contains extensive information about pathways (including their reactions, substrates, comments, and literature citations) and about enzymes (including their activators, inhibitors, cofactors, subunit composition, and substrate specificity). MetaCyc is a resource for several applications. As a reference DB of pathways and enzymes, MetaCyc can be used in conjunction with SRI's PathoLogic program to predict the metabolic pathway complements of organisms from their annotated genomes. MetaCyc also serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research and education, metabolic engineering, and systems biology. We propose to expand MetaCyc and to make it more comprehensive to increase its value to all these applications. [unreadable] [unreadable] This project involves the continued curation of new and existing pathways in MetaCyc. MetaCyc already describes most of the well-established pathways that are ubiquitous to microorganisms and to plants. The goal of this project is to add more breadth to MetaCyc by adding newly discovered pathways and pathways that are diverse among microorganisms, and plants, such as secondary metabolism. As part of this project, SRI also proposes to further develop the Pathways Tools software by enhancing (1) visual displays and internal representations of pathways and chemical compounds, (2) user querying capabilities, and (3) software editing capabilities. [unreadable] [unreadable]