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Microbial MetabolismDatabases of Microbial Metabolism & Degradation
Ching-Tsan Huang (黃慶璨 ) Office: Agronomy Hall, Room 111Tel: (02) 33664454E-mail: [email protected]
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http://www.elmhurst.edu/~chm/vchembook/5900verviewmet.html
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http://metacyc.org/index.shtml
http://ecocyc.org/
http://biocyc.org/
http://humancyc.org/
Encyclopedia of Homo sapiens Genes and Metabolism
Encyclopedia of E. coli K12 Genes and Metabolism
Databases of Metabolism
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GenomeEcoCyc contains the complete genome sequence of E. coli, and describes the nucleotide position and function of every E. coli gene.
Transcriptional regulation
EcoCyc describes E. coli operons, promoters, transcription factors, and transcription-factor binding sites.
Membrane transporters
The project is annotating E. coli transport proteins
MetabolismEcoCyc describes all known metabolic pathways and signal-transduction pathways of E. coli. It describes each metabolic enzyme of E. coli, including its cofactors, activators, inhibitors, and subunit structure
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Primary metabolism (including photosynthesis) Reactions involving those compounds which are formed as a part of the normal anabolic and catabolic processes which result in assimilation, respiration, transport, and differentiation. Primary metabolism is simply defined as the metabolism of primary compounds. Common examples of primary compounds are sugars, amino acids, nucleotides etc.
Secondary metabolismTend to be more complex than primary compounds. The metabolism of secondary compounds.Examples of secondary compounds include antibiotics, and mycotoxins.
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Biocatalysis/Biodegradation Database
UPATHWAYKyoto Encyclopedia of Genes and Genomes
http://www.genome.ad.jp/kegg/ http://www.ebi.ac.uk/
http://umbbd.ahc.umn.edu/
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Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds.
UM-BBD
Guided Tour
http://umbbd.ahc.umn.edu/guide.html
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http://www.genome.jp/kegg/pathway.html
MetabolosimCarbohydrates, Energy, Lipids, Nucleotides, Amino acids, Glycans, Polyketides/Nonribosome peptides, Secondary metabolites, Xenobiotics
Genetic Information Processing Environmental Information Processing Cellular Processes Human Diseases
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http://www.gwu.edu/~mpb/index.html
EMP (Enzymes and Metabolic Pathways) , the largest publicly available database of Enzymes and Metabolic Pathways in the world. EMP covers all aspects of enzymologyand metabolism and represents the whole factual content of an original journal publication in a structured, indexed, and searchable form..
http://emp.mcs.anl.gov/
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Other Pathway/Genome Databases
AraCyc Arabidopsis thaliana http://www.arabidopsis.org/tools/aracyc/
LacPlantCycLactobacillus plantarum WCFS1
http://www.lacplantcyc.nl/
MjCycMethanococcus jannaschii
http://maine.ebi.ac.uk:1555/MJNRDB2/server.htm
PseudoCycPseudomonas aeruginosa
http://pseudocyc.pseudomonas.com:1555/
Yeast Biochemical Pathways
Saccharomyces cerevisiae
http://pathway.yeastgenome.org/biocyc/