BioCyc Support for Synthetic Biology and Metabolic Engineering

Accelerate Your SynBio Workflow

BioCyc supports the data and analytical needs of the synbio community across the synbio project life cycle:

• Integrated Chassis Data: High-fidelity databases for genomes, metabolic pathways, and regulation.
• Visual Exploration: Intuitive genome and pathway browsers for seamless navigation.
• Pathway Discovery: MetaCyc drives rapid expansive metabolic route searches.
• Strain Analytics: Powerful omics tools to characterize and optimize strain performance.

Curated Chassis Genome Databases: BioCyc provides high-quality curated databases for major synthetic biology chassis organisms listed below. Each database combines the sequenced genome with the organism's metabolic pathways, reactions, enzymes, and metabolites, and with additional organism-specific data such as protein features, genetic regulatory networks, and essential genes.

• EcoCyc -- Escherichia coli K-12 MG1655 -- curated from 45,000 publications
• BsubCyc -- Bacillus subtilis 168
• Pseudomonas putida KT2440
• Cupriavidus necator H16
• Vibrio natriegens ATCC 14048
• Synechococcus elongatus PCC 7942
• YeastCyc -- Saccharomyces cerevisiae S288c
• [uncurated] Yarrowia lipolytica CLIB122 and CLIB89(W29)
• [uncurated] Komagataella phaffii GS115

Other less commonly utilized chassis are among BioCyc's 20,000 databases.

Benefits for SynBio Researchers: Better Science, Faster.

Bad annotations in the public genome databases can undermine your experiments, publications, and grant proposals.

• BioCyc curators typically revise several hundred functional annotations for each organism we curate, giving an accurate foundation for decision making
• BioCyc performs a vast data integration to put diverse data at your fingertips
• Curators author mini-reviews that distill the literature on genes and pathways -- a huge time saver

MetaCyc Universal Pathway Database: MetaCyc contains 3,280 metabolic pathways from all domains of life, as well as 20,200 metabolic reactions (7,450 more than KEGG in 2025) and 15,000 enzymes. Curated from 81,000 publications, MetaCyc is a comprehensive metabolic parts catalog, listing metabolic enzymes that can be engineered into other organisms. MetaCyc enzyme data includes subunit composition, cofactors, activators, inhibitors, and kinetic parameters.

Software Tools for Pathway Design and More: BioCyc provides more than 60 software tools, ranging from a genome browser to a metabolic network browser to unique tools for comparative analysis and omics data analysis. Key tools for synthetic biology:

• The RouteSearch tool designs novel metabolic pathways -- given a starting metabolite and an ending metabolite, RouteSearch finds a minimal-cost path from the starting to the ending metabolite.

• Multiple tools enable exploration of metabolic networks, such as finding all reactions that produce or consume a specified metabolite, and graphically exploring a local region of the metabolic network.

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