Web alert: systems biology relevant to microbial metabolism

MetaCyc is a database of experimentally determined metabolic pathways from over 900 organisms, mostly microorganisms. The KEGG database consists of pathway maps that have hypertext links to further information on compounds, enzymes and genes. It extensively covers metabolism found in diverse organisms. The Biocatalysis/Biodegradation database is a metabolism database that focuses on catabolic pathways found in microorganisms. It is highly curated with links to many other databases. The BioPathways Consortium is designed to promote the development of computational pathways biology. It does this by supporting the development and use of open technologies , standards, and resources for representing and analysing pathway information. The Pathguide is a curated list of approximately 240 online biological pathway resources. A major category is for metabolic pathway resources. The BioModels database stores and provides access to published mathematical models relating to biological processes. Models are linked to relevant data resources, such as publications, databases of compounds and pathways , and controlled vocabularies. The metabolic pathfinding database provides tools for selecting the shortest path in a metabolic network to generate biochemically relevant pathways. The metabolic graph that is used is derived from the reactions and compounds found in the KEGG database. The microbial metabolism prediction system uses metabolic rules to generate metabolites predicted from any starting organic compound entered by the user. The metabolic rules are based largely on reactions found in the Biocatalysis/Biodegradation database.