The MetaCyc database of metabolic pathways and enzymes - a 2019 update

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.

Figure 1.

A typical MetaCyc pathway. A short pathway was selected for this figure; the average number of metabolites in a MetaCyc pathway is 13, with the largest pathway containing 244 metabolites. The green captions are links to the upstream and downstream pathways that produce the inputs and outputs for this pathway. Enzymes are labeled in ochre, genes are labeled in purple and compounds are labeled in red. When available, EC numbers are shown next to reactions. Each item in a pathway diagram is a clickable hyperlink to a dedicated page for that item. Below each pathway is a summary and additional information such as the pathway’s taxonomic range, some taxa known to possess it, the pathway’s position within the pathway ontology, and potential pathway variants (not shown).

Figure 2.

A section from a pathway that describes the biosynthesis of Lewis-type epitopes by the bacterium Helicobacter pylori. This pathway was drawn using a modified version of the GlycanBuilder software (18). The modifications, introduced by the SRI International, allow the software to display text strings or other, non-glycan, compounds as part of the structure (shown as R in this example). As in non-glycan type pathways, each item in the diagram is a clickable hyperlink to a dedicated page for that item.

Figure 3.

A comparison of the reactions content of MetaCyc and the KEGG database. Data for KEGG are available only since 2008. Since that time the number of reactions in MetaCyc has been growing at about twice the rate of the comparable rate in KEGG. As of 20 August 2019 KEGG contains 11,289 biochemical reactions, as opposed to 16,031 reactions in MetaCyc.