Microbial Metabolism Databases of Microbial Metabolism & Degradation

1

Microbial MetabolismDatabases of Microbial Metabolism & Degradation

Ching-Tsan Huang (黃慶璨 ) Office: Agronomy Hall, Room 111Tel: (02) 33664454E-mail: cthuang@ntu.edu.tw

2

http://www.elmhurst.edu/~chm/vchembook/5900verviewmet.html

3

http

://u

mbb

d.ah

c.um

n.e

du/

met

a/m

eta

_ma

p.h

tml

4

http

://w

ww

.gen

ome.

jp/k

egg/

pat

hw

ay/m

ap/

map

011

00.h

tml

5

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

6

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

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

8

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/

9

Microbial biocatalytic reactions and biodegradation pathways primarily for xenobiotic, chemical compounds.

UM-BBD

Guided Tour

http://umbbd.ahc.umn.edu/guide.html

10

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

11

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/

12

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/