Peter D. Karp, Ron Caspi, SIMB News, January/February/March, 2023, v.73 n1
Abstract
This article describes a coordinated set of bioinformatics databases and software tools designed to solve multiple problems faced by metabolic engineers and microbiologists related to metabolic pathways. Those problems include the following: (1) Answering basic questions about the metabolism of a given organism; that is, what pathways does a given bacterium possess and what enzymes and metabolites participate in a given pathway? (2) Predicting the metabolism of an organism from its genome sequence. (3) Engineering new pathways into an organism. (4) Predicting pathway activation levels from omics datasets. (5) Comparative analyses of metabolism. BioCyc.org provides 20,000 Pathway/Genome databases for sequenced microbes that describe their reconstructed metabolic networks. The MetaCyc DB provides a universal encyclopedia of metabolism across all domains of life. BioCyc computational tools provide search, comparison, and multiple analysis operations, including omics data analysis.