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Metabolic network information


A metabolic network is the complete set of metabolic and physical processes that determine the physiological and biochemical properties of a cell. As such, these networks comprise the chemical reactions of metabolism, the metabolic pathways, as well as the regulatory interactions that guide these reactions.

With the sequencing of complete genomes, it is now possible to reconstruct the network of biochemical reactions in many organisms, from bacteria to human. Several of these networks are available online: Kyoto Encyclopedia of Genes and Genomes (KEGG),[1] EcoCyc,[2] BioCyc[3] and metaTIGER.[4] Metabolic networks are powerful tools for studying and modelling metabolism.


Metro-style map of major metabolic pathways
Carbon
fixation
Photo-
respiration
Pentose
phosphate
pathway
Citric
acid cycle
Glyoxylate
cycle
Urea
cycle
Fatty
acid
synthesis
Fatty
acid
elongation
Beta
oxidation
Peroxisomal
beta
oxidation


Glyco-
genolysis
Glyco-
genesis
Glyco-
lysis
Gluconeo-
genesis
Pyruvate
decarb-
oxylation
Fermentation
Keto-
lysis
Keto-
genesis
feeders to
gluconeo-
genesis
Direct / C4 / CAM
carbon intake
Light reaction
Oxidative
phosphorylation
Amino acid
deamination
Citrate
shuttle
Lipogenesis
Lipolysis
Steroidogenesis
MVA pathway
MEP pathway
Shikimate
pathway
Transcription &
replication
Translation
Proteolysis
Glycosyl-
ation


Sugar
acids
Double/multiple
sugars & glycans
Simple
sugars
Inositol-P
Amino sugars
& sialic acids
Nucleotide sugars
Hexose-P
Triose-P
Glycerol
P-glycerates
Pentose-P
Tetrose-P
Propionyl
-CoA
Succinate
Acetyl
-CoA
Pentose-P
P-glycerates
Glyoxylate
Photosystems
Pyruvate
Lactate
Acetyl
-CoA
Citrate
Oxalo-
acetate
Malate
Succinyl
-CoA
α-Keto-
glutarate
Ketone
bodies
Respiratory
chain
Serine group
Alanine
Branched-chain
amino acids
Aspartate
group
Homoserine
group
& lysine
Glutamate
group
& proline
Arginine
Creatine
& polyamines
Ketogenic &
glucogenic
amino acids
Amino acids
Shikimate
Aromatic amino
acids & histidine
Ascorbate
(vitamin C)
δ-ALA
Bile
pigments
Hemes
Cobalamins (vitamin B12)
Various
vitamin Bs
Calciferols
(vitamin D)
Retinoids
(vitamin A)
Quinones (vitamin K)
& tocopherols (vitamin E)
Cofactors
Vitamins
& minerals
Antioxidants
PRPP
Nucleotides
Nucleic
acids
Proteins
Glycoproteins
& proteoglycans
Chlorophylls
MEP
MVA
Acetyl
-CoA
Polyketides
Terpenoid
backbones
Terpenoids
& carotenoids (vitamin A)
Cholesterol
Bile acids
Glycero-
phospholipids
Glycerolipids
Acyl-CoA
Fatty
acids
Glyco-
sphingolipids
Sphingolipids
Waxes
Polyunsaturated
fatty acids
Neurotransmitters
& thyroid hormones
Steroids
Endo-
cannabinoids
Eicosanoids
The image above contains clickable links
Major metabolic pathways in metro-style map. Click any text (name of pathway or metabolites) to link to the corresponding article.
Single lines: pathways common to most lifeforms. Double lines: pathways not in humans (occurs in e.g. plants, fungi, prokaryotes). Orange nodes: carbohydrate metabolism. Violet nodes: photosynthesis. Red nodes: cellular respiration. Pink nodes: cell signaling. Blue nodes: amino acid metabolism. Grey nodes: vitamin and cofactor metabolism. Brown nodes: nucleotide and protein metabolism. Green nodes: lipid metabolism.
  1. ^ "GenomeNet". www.genome.ad.jp. Archived from the original on 2009-02-24. Retrieved 2020-04-01.
  2. ^ "EcoCyc: Encyclopedia of E. coli Genes and Metabolic Pathways". www.ecocyc.org.
  3. ^ "BioCyc Pathway/Genome Database Collection". biocyc.org.
  4. ^ "metaTIGER - Home". www.bioinformatics.leeds.ac.uk. Archived from the original on 2012-03-04. Retrieved 2010-06-09.

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the identification of bottleneck enzymes in metabolic networks for metabolic engineering efforts. Metabolic flux analysis may use 13C-labeled isotope tracers...

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predicting this complex behavior. Metabolic flux refers to the rate of metabolite conversion in a metabolic network. For a reaction this rate is a function...

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informative in analyzing its pathogenesis. Extensive study of the metabolic network of this organism has led to the identification of biomarkers that...

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the study of the molecular and biochemical underpinninngs for i) the metabolic regulation of immune function, and ii) the regulation of metabolism by...

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Zhuo (2012). "Systematic Comparison of C3 and C4 Plants Based on Metabolic Network Analysis". BMC Systems Biology. 6 (59): S9. doi:10.1186/1752-0509-6-S2-S9...

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considering only the number of incoming edges (in-degree) of a node in the metabolic network. The reason for this is that some already known, important protein...

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an integrative model that comprises the QS gene regulatory network and the metabolic network of P. aeruginosa, providing a detailed view of how the production...

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production of a metabolite product or to increase the efficiency of a metabolic network. The use of engineering single celled organisms to create lucrative...

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Cytosol

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Vasu D. Appanna (2007). "The Tricarboxylic Acid Cycle, an Ancient Metabolic Network with a Novel Twist". PLOS ONE. 2 (8): e690. Bibcode:2007PLoSO...2...

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