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BioCyc specifications


Unique identifier OMICS_02675
Name BioCyc
Restrictions to use Academic or non-commercial use
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


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  • person_outline Peter D Karp

Additional information

Publication for BioCyc

BioCyc citations


SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases

PMCID: 5946812
PMID: 29762652
DOI: 10.1093/database/bay035

[…] atabase for the computational prediction of species-specific databases for organisms with annotated genomes (). To date, about 9400 such derivative PGDBs have been generated and made available in the BioCyc database collection (, but very few have been curated in a way that would corroborate the predicted metabolic network and integrate experimental information from the publishe […]


Identification of a highly active tannase enzyme from the oral pathogen Fusobacterium nucleatum subsp. polymorphum

Microb Cell Fact
PMCID: 5828091
PMID: 29482557
DOI: 10.1186/s12934-018-0880-4

[…] l bacteria genera using NCBI blastx. Among the hits, a gene from Fusobacterium nucleatum subsp. polymorphum (annotated as a hypothetical protein) showed 44% identity to TanBLp (GMHT-1603-MONOMER from BioCyc database) []. Because of the identity, we annotated the gene as tanBFnp and the protein that it encodes as TanBFnp. In addition, the CDD web tool revealed that TanBFnp presented domains conserv […]


Functional Genomics and Phylogenetic Evidence Suggest Genus Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium

Front Microbiol
PMCID: 5816740
PMID: 29487583
DOI: 10.3389/fmicb.2018.00189

[…] c cobalamin biosynthesis pathway (Helliwell et al., ), these data suggest that B12 biosynthesis and thus overall environmental bioavailability could be influenced by limiting iron. Interestingly, the BioCyc database ( implicates another gene, Tery_4461, as the cobalt reductase while the KEGG database ( implicates isiB (Tery_1666) as above. […]


FunGeneNet: a web tool to estimate enrichment of functional interactions in experimental gene sets

BMC Genomics
PMCID: 5836822
PMID: 29504895
DOI: 10.1186/s12864-018-4474-7

[…] others [–].Around the world, many databases containing molecular genetic networks describing metabolic processes, diseases, phenotypic traits, etc. have been developed – for example, KEGG PATHWAY [], BioCyc [], BioGRID [] and IntAct [].There are systems that allow the reconstruction of gene networks for a given set of genes/proteins including FunCoup [], STRING [], Pathway Studio [], Ingenuity Pat […]


A comprehensive transcriptome analysis of skeletal muscles in two Polish pig breeds differing in fat and meat quality traits

Genet Mol Biol
PMCID: 5901489
PMID: 29658965
DOI: 10.1590/1678-4685-GMB-2016-0101

[…] ysis of DEGs was performed by Panther Gene List software, where the P-value was estimated in overrepresentation tests and Kobas 3.0, which predicts biological pathways based on the KEGG, Reactome and Biocyc databases. […]


Structure based drug discovery for designing leads for the non toxic metabolic targets in multi drug resistant Mycobacterium tuberculosis

J Transl Med
PMCID: 5740895
PMID: 29268770
DOI: 10.1186/s12967-017-1363-9

[…] for their series of biochemical steps. Literature mining was used as a key source to elucidate their metabolic interference and the collected data was verified through the pathways available in KEGG, BioCyc and MetaCyc. Of these 33 targets, 15 with available crystal structures were utilized for the Molecular Docking studies. The GLIDE suite of Schrodinger for the corresponding natural substrate (N […]


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BioCyc institution(s)
SRI International, Menlo Park, CA, USA
BioCyc funding source(s)
Supported by The National Institute of General Medical Sciences of the National Institutes of Health (grant numbers R01GM080746, R01GM75742 and R01GM077678).

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