* Kyoto Encyclopedia of Genes and Genomes ([http://www.kegg.jp/ KEGG]): a bioinformatics database containing information on genes, proteins, reactions, and pathways. The ‘KEGG Organisms’ section, which is divided into eukaryotes and prokaryotes, encompasses many organisms for which gene and DNA information can be searched by typing in the enzyme of choice.
* BioCyc, EcoCyc, and MetaCyc: [http://biocyc.org/ BioCyc] Is a collection of 3,000 pathway/genome databases (as of Oct 2013), with each database dedicated to one organism. For example, [http://ecocyc.org/ EcoCyc] is a highly detailed bioinformatics database on the genome and metabolic reconstruction of Escherichia coli, including thorough descriptions of E. coli signaling pathways and regulatory network. The EcoCyc database can serve as a paradigm and model for any reconstruction. Additionally, [http://biocyc.org/metacyc/index.shtml MetaCyc], an encyclopedia of experimentally defined metabolic pathways and enzymes, contains 2,100 metabolic pathways and 11,400 metabolic reactions (Oct 2013).
* [http://enzyme.expasy.org/ ENZYME]: An enzyme nomenclature database (part of the ExPASy proteonomics server of the Swiss Institute of Bioinformatics). After searching for a particular enzyme on the database, this resource gives you the reaction that is catalyzed. ENZYME has direct links to other gene/enzyme/literature databases such as KEGG, BRENDA, and PUBMED.
* [http://www.brenda-enzymes.info/ BRENDA]: A comprehensive enzyme database that allows for an enzyme to be searched by name, EC number, or organism.
* [http://bigg.ucsd.edu/ BiGG]: A knowledge base of biochemically, genetically, and genomically structured genome-scale metabolic network reconstructions.
* [https://web.archive.org/web/20120304065541/http://www.bioinformatics.leeds.ac.uk/metatiger/ metaTIGER]: Is a collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes which provides novel facilities for viewing and comparing the metabolic profiles between organisms.