Ellis, L.B., Hershberger, C.D., and Wackett, L.P.. "The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics." Nucleic Acids Res. 27
(1).
1999.
pp. 373-6.
[ .pdf ] [ PubMed ]
The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes.
Keywords: Bacteria_genetics ; Bacteria_*metabolism ; Bacterial Proteins_metabolism ; *Biodegradation ; Biotechnology ; *Catalysis ; *Databases Factual_trends ; Environmental Pollution ; Enzymes_chemistry ; Enzymes_genetics ; Enzymes_metabolism ; Genes ; Bacterial_genetics ; Genes ; Bacterial_physiology ; Human ; Information Storage and Retrieval ; Internet ; Minnesota ; Universities
Karp, P.D., Riley, M., Paley, S.M., Pellegrini-Toole, A., and Krummenacker, M.. "EcoCyc: Encyclopedia of Escherichia coli genes and metabolism." Nucleic Acids Res. 26
(1).
1998.
pp. 50-3.
[ .pdf ] [ PubMed ]
The encyclopedia of Escherichia coli genes and metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of E.coli. The database describes 3030 genes of E.coli , 695 enzymes encoded by a subset of these genes, 595 metabolic reactions that occur in E.coli, and the organization of these reactions into 123 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc can be thought of as an electronic review article because of its copious references to the primary literature, and as a (qualitative) computational model of E.coli metabolism. EcoCyc is available at URL http://ecocyc.PangeaSystems.com/ecocyc/
Keywords: Computer Graphics ; *Databases Factual_trends ; Encyclopedias ; Escherichia coli_*genetics ; Escherichia coli_*metabolism ; *Genes Bacterial ; User-Computer Interface