MetaCyc: a multiorganism database of metabolic pathways and enzymes

Abstract

MetaCyc is a database of metabolic pathways and enzymes located at . Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the website. These PGDBs also include predicted operons and pathway hole fillers.

New surveyor tools for charting microbial metabolic maps

“…Metabolite networks have been reconstructed automatically for a large number of microorganisms [5][6][7] . The network reconstructions are primarily accomplished using computational functional transfer from experimental results that have been obtained from a small number of model organisms.…”

Enumerating Precursor Sets of Target Metabolites in a Metabolic Network

“…One interesting thing in these results is that glutamine, threonine, and ion bicarbonate are present in all solutions. Glutamine and ion bicarbonate are involved in reaction 6.3.5.5, which represents an essential step in the arginine biosynthesis pathway, as described in MetaCyc [1]. Threonine as precursor of arginine deserves to be discussed.…”

“…One way to answer this question is to manually inspect the metabolic pathways defined as present in the organism: the presence of any metabolic pathway is determined by comparing the set of reactions of a reconstructed metabolic network with the set of reactions in the reference metabolic pathways contained in metabolic databases such as metacyc from the biocyc database collection [1] or kegg [5]. However, each reference metabolic pathway represents a very small part of the whole network and does not consider what occurs upstream of the pathway, nor whether some alternative organism-specific pathways exist.…”

Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems

“…The set of predicted enzymes in a newly annotated genome allows the reconstruction of metabolic networks that potentially exist in this organism. These reconstructions are based on reference metabolic databases such as KEGG (Kanehisa et al, 2006) and MetaCyc (Caspi et al, 2006) and comparisons of pathways allow the identification of conserved and missing reactions. This information is helpful for inferring functional coupling of genes participating in the same cellular process.…”