ArticleBMC bioinformatics2013
A systematic comparison of the MetaCyc and KEGG pathway databases.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
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- The effect of high-fat diet on serum metabolites in rats with heart failure: a non-targeted metabolomics approach.BMC cardiovascular disorders · 2025Article
- Evaluation of extended-spectrumFrontiers in microbiology · 2025Article
- Advances in functional analysis of the microbiome: Integrating metabolic modeling, metabolite prediction, and pathway inference with Next-Generation Sequencing data.Journal of microbiology (Seoul, Korea) · 2025Review
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- Current approaches and outstanding challenges of functional annotation of metabolites: a comprehensive review.Briefings in bioinformatics · 2024Review
- Techniques, Databases and Software Used for Studying Polar Metabolites and Lipids of Gastrointestinal Parasites.Animals : an open access journal from MDPI · 2024Review
- Biodegradation of DDT using multi-species mixtures: From genome-mining prediction to practical assessment.Microbial biotechnology · 2024Article
- md_harmonize: A Python Package for Atom-Level Harmonization of Public Metabolic Databases.Metabolites · 2023Article
- Metabolomics of early blight (Alternaria solani) susceptible tomato (Solanum lycopersicum) unfolds key biomarker metabolites and involved metabolic pathways.Scientific reports · 2023Article
- Enzyme Databases in the Era of Omics and Artificial Intelligence.International journal of molecular sciences · 2023Review
- Flux balance analysis-based metabolic modeling of microbial secondary metabolism: Current status and outlook.PLoS computational biology · 2023Review
- Chronic kidney disease and gut microbiota.Heliyon · 2023Review
24 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
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Abstract
backgroundThe MetaCyc and KEGG projects have developed large metabolic pathway databases that are used for a variety of applications including genome analysis and metabolic engineering. We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope. To assess their overlap, we must know the correspondences between compounds, reactions, and pathways in MetaCyc, and those in KEGG. We devoted significant effort to computational and manual matching of these entities, and we evaluated the accuracy of the correspondences.
resultsKEGG contains 179 module pathways versus 1,846 base pathways in MetaCyc; KEGG contains 237 map pathways versus 296 super pathways in MetaCyc. KEGG pathways contain 3.3 times as many reactions on average as do MetaCyc pathways, and the databases employ different conceptualizations of metabolic pathways. KEGG contains 8,692 reactions versus 10,262 for MetaCyc. 6,174 KEGG reactions are components of KEGG pathways versus 6,348 for MetaCyc. KEGG contains 16,586 compounds versus 11,991 for MetaCyc. 6,912 KEGG compounds act as substrates in KEGG reactions versus 8,891 for MetaCyc. MetaCyc contains a broader set of database attributes than does KEGG, such as relationships from a compound to enzymes that it regulates, identification of spontaneous reactions, and the expected taxonomic range of metabolic pathways. MetaCyc contains many pathways not found in KEGG, from plants, fungi, metazoa, and actinobacteria; KEGG contains pathways not found in MetaCyc, for xenobiotic degradation, glycan metabolism, and metabolism of terpenoids and polyketides. MetaCyc contains fewer unbalanced reactions, which facilitates metabolic modeling such as using flux-balance analysis. MetaCyc includes generic reactions that may be instantiated computationally.
conclusionsKEGG contains significantly more compounds than does MetaCyc, whereas MetaCyc contains significantly more reactions and pathways than does KEGG, in particular KEGG modules are quite incomplete. The number of reactions occurring in pathways in the two DBs are quite similar.
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