1 Microbial Metabolism Databases of Microbial Metabolism & Degradation Ching-Tsan Huang ( 黃慶璨 ) Office: Agronomy Hall, Room 111 Tel: (02)

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Encyclopedia of Homo sapiens Genes and Metabolism Encyclopedia of E. coli K12 Genes and Metabolism Databases of Metabolism

6 Genome EcoCyc 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.operons Membrane transporters The project is annotating E. coli transport proteins Metabolism EcoCyc 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 structuremetabolic pathways

7 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 metabolism Tend to be more complex than primary compounds. The metabolism of secondary compounds. Examples of secondary compounds include antibiotics, and mycotoxins.

8 Biocatalysis/Biodegradation Database UPATHWAY Kyoto Encyclopedia of Genes and Genomes

9 Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds. UM-BBD Guided Tour

10 Metabolosim Carbohydrates, Energy, Lipids, Nucleotides, Amino acids, Glycans, Polyketides/Nonribosome peptides, Secondary metabolites, Xenobiotics Genetic Information Processing Environmental Information Processing Cellular Processes Human Diseases

11 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..

12 Other Pathway/Genome Databases AraCycArabidopsis thaliana ools/aracyc/ LacPlantCyc Lactobacillus plantarum WCFS1 MjCyc Methanococcus jannaschii MJNRDB2/server.htm PseudoCyc Pseudomonas aeruginosa nas.com:1555/ Yeast Biochemical Pathways Saccharomyces cerevisiae e.org/biocyc/