The MetaCyc database is one of the largest

metabolic pathways In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a sequence of chemical re ...

and

enzymes Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different molecule ...

databases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. The data have been curated from more than 58,000 publications. MetaCyc has been designed for multiple types of uses. It is often used as an extensive online encyclopedia of metabolism. In addition, MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in the

BioCyc Database Collection The BioCyc database collection is an assortment of organism specific Pathway/Genome Databases (PGDBs) that provide reference to genome and metabolic pathway information for thousands of organisms. As of June 2021, there were over 17,800 databases w ...

. MetaCyc is also used in

metabolic engineering Metabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cell's production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enzy ...

and

metabolomics Metabolomics is the scientific study of chemical processes involving metabolites, the small molecule substrates, intermediates, and products of cell metabolism. Specifically, metabolomics is the "systematic study of the unique chemical fingerprin ...

research. MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. It also provides extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, and, when available, kinetic constants. MetaCyc data on

metabolites In biochemistry, a metabolite is an intermediate or end product of metabolism. The term is usually used for small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, c ...

includes chemical structures, predicted Standard energy of formation, and links to external databases. Reactions in MetaCyc are presented in a visual display that includes the structures of all components. The reactions are balanced and include EC numbers, reaction direction, predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds, and computed

Gibbs free energy In thermodynamics, the Gibbs free energy (or Gibbs energy; symbol G) is a thermodynamic potential that can be used to calculate the maximum amount of work that may be performed by a thermodynamically closed system at constant temperature and pr ...

. All objects in MetaCyc are clickable and provide easy access to related objects. For example, the page for L-lysine lists all of the reactions in which L-lysine participates, as well as the enzymes that catalyze them and pathways in which these reactions take place.

References

{{reflist Chemical databases Enzyme databases Metabolism