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
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
Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M.. "KEGG: Kyoto Encyclopedia of Genes and Genomes." Nucleic Acids Res. 27
(1).
1999.
pp. 29-34.
[ .pdf ] [ PubMed ]
Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).
Keywords: Computational Biology ; *Databases Factual ; Gene Expression ; *Genes ; *Genome ; Ligands ; Metabolism ; Sequence Homology