Metabolism

Biocatalysis/Biodegradation: Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical
compounds. Includes compounds such as hexachlorocyclohexane, toluene, and xylene.

Biochemical Compounds Data Base-Klotho:  A comprehensive list of about 450 biochemical compounds including classics such as ATP and glucose. The molecules can be viewed statically and dynamically.

Chemical Information Site Index: A comprehensive site containing information on a wide variety of chemicals and biochemicals. Entering farnesyl diphosphate, for example, yields a list of synonyms, molecular mass, structure, and relevant metabolic pathways. Also, there are hyperlinks to enzymes that use the compound as substrate or product. The site also contains hyperlinks to a variety of chemical, drug, and toxicology sites.

Chromosomal Location of Human Genes:  This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information. The database contains textual information, pictures, and reference information. It also contains copious links to NCBI's Entrez database of MEDLINE
articles and sequence information.

Encyclopedia of E. coli Genes and Metabolism: Site provides information on (a) 4390 E. coli genes, (b) 629 enzymes encoded by these genes, (c) 946 metabolic reactions, (d)159 metabolic pathways, (e)1868 chemical compounds (f) 13 transporters involved in E. coli metabolism, (f) 79 tRNAs, (g) 60 two-component signal transduction proteins, and (h)1944 citations to the primary literature. Registration is required for some parts of the data base, but there is no fee for educational and non-profit institutions.

ENZYME Database: Each entry is a single reaction, and these are linked to the SWISS-PROT sequences for enzymes that canalyze the reaction.

Enzyme Commission Database: Hyperlinks to OMIM, or Online Mendelain Inheritance in Man, and SWISSPROT, or Swiss Protein Database.

Enzymes Information from a University of Michigan web site: Includes classes of enzymes, nomenclature, and links to enzyme structure.

KEGG: This Japanese site links genes to biochemical pathways. It holds molecular and gene catalogs for all known compounds in living cells along with some 100 maps of metabolic and regulatory pathways. KEGG links into gene databases such as SWISS-PROT and GenBank. Searching for "alcohol dehydrogenase" pulls up maps showing the enzyme's position in five metabolic processes, or its gene's sequence in the rat genome. By right clicking on a pathway, the image can be saved on a hard drive. The image can be loaded in Corel Photo House or equivalent program, and the diagram can be printed. One can feed in several genes or enzymes and determine what pathways connect them.

National Institute of Standards and Technology Online References and Databases: Free information on chemicals from melting points to half-lives maintained by the US government. It contains the Thermodynamics of Enzyme-Catalyzed Reactions listed below.

Protein Kinases: Everything that you want to know about protein-serine/threonine and protein-tyrosine kinases at a UC-San Diego site.

Soybean Metabolism: Clickable diagrams of metabolic pathways covering 524 enzymes and 640 metabolites that are operative in soybeans.

"If there is any doubt, write the term out. Otherwise, your reader may be in the position of the farmer who shot a crow and read the tag on his leg that said 'Wash. Biol. Surv.' The farmer remarked that he washed the crow, boiled it, and served it, but it still tasted awful. If there is any doubt, write the term out."   Deborah C. Andrews & Margaret D. Blickle