MetaCyc

MetaCyc is a comprehensive metabolic pathway database that provides curated information on metabolic pathways and enzymes from all domains of life. It is a valuable resource for researchers in the fields of biochemistry, molecular biology, and systems biology.

Overview

MetaCyc is designed to serve as a reference database for metabolic pathways and enzymes. It contains detailed information about individual pathways, including the reactions involved, the enzymes that catalyze these reactions, and the genes that encode these enzymes. MetaCyc is used for a variety of purposes, including the annotation of genomes, the study of metabolic networks, and the development of metabolic models.

History

MetaCyc was originally developed as part of the EcoCyc project, which focused on the metabolism of Escherichia coli. Over time, MetaCyc expanded to include pathways from a wide range of organisms, making it a universal resource for metabolic pathway information. The database is continuously updated and curated by experts in the field.

Content

MetaCyc contains information on over 2,500 metabolic pathways, 13,000 reactions, and 11,000 enzymes. The database includes pathways from bacteria, archaea, eukaryotes, and plants. Each pathway entry in MetaCyc provides detailed information, including:

• A description of the pathway and its biological significance.
• The list of reactions that comprise the pathway.
• The enzymes that catalyze each reaction, along with their EC numbers.
• The genes that encode the enzymes, when known.
• References to the scientific literature.

Applications

MetaCyc is used in a variety of research applications, including:

• Genome Annotation: MetaCyc is used to annotate the metabolic pathways present in newly sequenced genomes.
• Metabolic Engineering: Researchers use MetaCyc to identify potential targets for metabolic engineering in order to optimize the production of desired compounds.
• Systems Biology: MetaCyc provides a framework for the construction of metabolic models that can be used to simulate and analyze metabolic networks.

Access and Tools

MetaCyc is freely accessible online and provides a variety of tools for users, including:

• Pathway Tools Software: A suite of software tools for pathway analysis and visualization.
• BioCyc Database Collection: A collection of organism-specific databases that are derived from MetaCyc.
• Web Services: APIs that allow programmatic access to MetaCyc data.

Also see

• EcoCyc
• KEGG
• Reactome
• Biochemical pathway
• Systems biology

References

• Caspi, R., et al. (2018). The MetaCyc database of metabolic pathways and enzymes. Nucleic Acids Research, 46(D1), D633-D639.
• Karp, P.D., et al. (2019). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in Bioinformatics, 20(4), 1085-1093.