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  October 5, 2019

The MetaCyc Database of Metabolic Pathways and Enzymes – A 2019 Update

SRI Authors Wai Kit Ong, Peter Karp

Citation

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Ron Caspi, Richard Billington, Ingrid M. Keseler, Anamika Kothari, Marcus Krummenacker, Peter E. Midford, Suzanne Paley, Pallavi Subhraveti. Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D445-D453, https://doi.org/10.1093/nar/gkz862

 

Abstract

MetaCyc (MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains 2749 pathways derived from more than 60 000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc are evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in BioCyc.org and other genomic portals. This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1. Some of the topics that received intensive curation during this period include cobamides biosynthesis, sterol metabolism, fatty acid biosynthesis, lipid metabolism, carotenoid metabolism, protein glycosylation, antibiotics and cytotoxins biosynthesis, siderophore biosynthesis, bioluminescence, vitamin K metabolism, brominated compound metabolism, plant secondary metabolism and human metabolism. Other additions include modifications to the GlycanBuilder software that enable displaying glycans using symbolic representation, improved graphics and fonts for web displays, improvements in the PathoLogic component of Pathway Tools, and the optional addition of regulatory information to pathway diagrams.

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