Metabolic pathway

In biochemistry, a metabolic pathway is a linked series of chemical reactions occurring within a cell. The
reactants, products, and intermediates of an enzymatic reaction are known as metabolites, which are modified by a
sequence of chemical reactions catalyzed by enzymes.[1]: 26  In most cases of a metabolic pathway, the product of one
enzyme acts as the substrate for the next. However, side products are considered waste and removed from the
cell.[2] These enzymes often require dietary minerals, vitamins, and other cofactors to function.

Different metabolic pathways function based on the position within a eukaryotic cell and the significance of the
pathway in the given compartment of the cell.[3] For instance, the, electron transport chain, and oxidative
phosphorylation all take place in the mitochondrial membrane.[4]: 73, 74 & 109  In contrast, glycolysis, pentose
phosphate pathway, and fatty acid biosynthesis all occur in the cytosol of a cell.[5]: 441–442 

There are two types of metabolic pathways that are characterized by their ability to either synthesize molecules with
the utilization of energy (anabolic pathway), or break down complex molecules and release energy in the process
(catabolic pathway).[6] The two pathways complement each other in that the energy released from one is used up by
the other. The degradative process of a catabolic pathway provides the energy required to conduct the biosynthesis
of an anabolic pathway.[6] In addition to the two distinct metabolic pathways is the amphibolic pathway, which can
be either catabolic or anabolic based on the need for or the availability of energy.[7]

Pathways are required for the maintenance of homeostasis within an organism and the flux of metabolites through
a pathway is regulated depending on the needs of the cell and the availability of the substrate. The end product of a
pathway may be used immediately, initiate another metabolic pathway or be stored for later use. The metabolism of
a cell consists of an elaborate network of interconnected pathways that enable the synthesis and breakdown of
molecules (anabolism and catabolism).

Contents
Overview
Major metabolic pathways
Catabolic pathway (catabolism)
Cellular respiration
Anabolic pathway (anabolism)
Amphibolic pathway
Regulation
Clinical Applications in Targeting Metabolic Pathways
Targeting Oxidative Phosphorylation
Targeting Heme
Targeting the Tricarboxylic acid cycle and Glutaminolysis
See also
References
External links

Overview
Each metabolic pathway consists of a series of biochemical reactions that are connected by their intermediates: the
products of one reaction are the substrates for subsequent reactions, and so on. Metabolic pathways are often
considered to flow in one direction. Although all chemical reactions are technically reversible, conditions in the cell
are often such that
it is

Net reactions of common metabolic pathways

thermodynamically more favorable for flux to proceed in one direction of a reaction.[8] For example, one pathway
may be responsible for the synthesis of a particular amino acid, but the breakdown of that amino acid may occur via
a separate and distinct pathway. One example of an exception to this "rule" is the metabolism of glucose. Glycolysis
results in the breakdown of glucose, but several reactions in the glycolysis pathway are reversible and participate in
the re-synthesis of glucose (gluconeogenesis).

Glycolysis was the first metabolic pathway discovered:

1. As glucose enters a cell, it is immediately phosphorylated by ATP to glucose 6-phosphate in the irreversible first
step.
2. In times of excess lipid or protein energy sources, certain reactions in the glycolysis pathway may run in
reverse to produce glucose 6-phosphate, which is then used for storage as glycogen or starch.
Metabolic pathways are often regulated by feedback inhibition.
Some metabolic pathways flow in a 'cycle' wherein each component of the cycle is a substrate for the
subsequent reaction in the cycle, such as in the Krebs Cycle (see below).
Anabolic and catabolic pathways in eukaryotes often occur independently of each other, separated either
physically by compartmentalization within organelles or separated biochemically by the requirement of different
enzymes and co-factors.

Major metabolic pathways

Ascorbate
Sugar
Double/multiple
Simple

(vitamin C) acids sugars & glycans Glyco-

sugars Inositol-P Various
Neurotransmitters

genolysis vitamin Bs & thyroid hormones Glycosyl-

Proteolysis
ation
Glyco- Amino acids Translation
Amino sugars
Proteins Glycoproteins

genesis & proteoglycans

& sialic acids
Hexose-P Transcription &

Pentose-P
Nucleotide sugars replication

PRPP Nucleotides Nucleic

Cofactors Vitamins

Light reaction Pentose

acids & minerals
Photosystems Pentose-P Carbon
Gluconeo-
Glyco- phosphate

Shikimate

Aromatic amino

pathway
Glyoxylate
fixation genesis
Triose-P
lysis
pathway
acids & histidine
Antioxidants
Photo-
Tetrose-P Shikimate Quinones (vitamin K)

& carotenoids (vitamin E)

respiration P-glycerates MEP pathway

Direct / C4 / CAM
Terpenoid

MEP MVA pathway Terpenoids

Retinoids

backbones
carbon intake Glycerol MVA & carotenoids (vitamin A) (vitamin A)
Homoserine

group
P-glycerates Acetyl
Steroidogenesis
& lysine
Aspartate

Serine group -CoA Fatty

group
Citrate Alanine
acid
Cholesterol Bile acids
Oxalo-

acetate
shuttle
Lactate
synthesis Calciferols
(vitamin D)
Steroids
Malate Pyruvate

Polyketides Endo-
Glycero-

Pyruvate
Fermentation
Citric decarb-
Acetyl
Branched-chain
Fatty
cannabinoids phospholipids
Glyco-

Oxidative

Respiratory
phosphorylation acid cycle
oxylation -CoA amino acids
acid
sphingolipids
chain
Citrate elongation
Ketogenic &

glucogenic
Glycerolipids Sphingolipids
Urea
Succinyl
α-Keto-
amino acids
Amino acid
-CoA glutarate Lipogenesis
cycle
deamination Keto- Keto-

Propionyl

Beta
Acyl-CoA
Waxes
lysis genesis
Glutamate

group
Ketone

-CoA oxidation Lipolysis

Creatine
Arginine & proline bodies Eicosanoids
& polyamines feeders to
gluconeo-

δ-ALA
genesis Succinate
Peroxisomal Fatty
Polyunsaturated

fatty acids
Bile

pigments Hemes Chlorophylls

Glyoxylate
beta

acids

cycle Acetyl

 -CoA
oxidation

Cobalamins (vitamin B12)

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.

Catabolic pathway (catabolism)

A catabolic pathway is a series of reactions that bring about a net release of energy in the form of a high energy
phosphate bond formed with the energy carriers adenosine diphosphate (ADP) and guanosine diphosphate (GDP)
to produce adenosine triphosphate (ATP) and guanosine triphosphate (GTP), respectively.[4]: 91–93  The net reaction
is, therefore, thermodynamically favorable, for it results in a lower free energy for the final products.[9]: 578–579  A
catabolic pathway is an exergonic system that produces chemical energy in the form of ATP, GTP, NADH, NADPH,
FADH2, etc. from energy containing sources such as carbohydrates, fats, and proteins. The end products are often
carbon dioxide, water, and ammonia. Coupled with an endergonic reaction of anabolism, the cell can synthesize
new macromolecules using the original precursors of the anabolic pathway.[10] An example of a coupled reaction is
the phosphorylation of fructose-6-phosphate to form the intermediate fructose-1,6-bisphosphate by the enzyme
phosphofructokinase accompanied by the hydrolysis of ATP in the pathway of glycolysis. The resulting chemical
reaction within the metabolic pathway is highly thermodynamically favorable and, as a result, irreversible in the
cell.

Cellular respiration

A core set of energy-producing catabolic pathways occur within all living organisms in some form. These pathways
transfer the energy released by breakdown of nutrients into ATP and other small molecules used for energy (e.g.
GTP, NADPH, FADH). All cells can perform anaerobic respiration by glycolysis. Additionally, most organisms can
perform more efficient aerobic respiration through the citric acid cycle and oxidative phosphorylation. Additionally
plants, algae and cyanobacteria are able to use sunlight to anabolically synthesize compounds from non-living
matter by photosynthesis.

Anabolic pathway (anabolism)

In contrast to catabolic pathways, anabolic pathways require an energy input to construct macromolecules such
as polypeptides, nucleic acids, proteins, polysaccharides, and lipids. The isolated reaction of anabolism is
unfavorable in a cell due to a positive Gibbs Free Energy (+ΔG). Thus, an input of chemical energy through a
coupling with an exergonic reaction is necessary.[1]: 25–27  The coupled reaction of the catabolic pathway affects the
thermodynamics of the reaction by lowering the overall activation energy of an anabolic pathway and allowing the
reaction to take place.[1]: 25  Otherwise, an endergonic reaction is non-spontaneous.

An anabolic pathway is a biosynthetic pathway, meaning that it combines smaller molecules to form larger and
more complex ones.[9]: 570  An example is the reversed pathway of glycolysis, otherwise known as gluconeogenesis,
which occurs in the liver and sometimes in the kidney to maintain proper glucose concentration in the blood and
supply the brain and muscle tissues with adequate amount of glucose. Although gluconeogenesis is similar to the
reverse pathway of glycolysis, it contains three distinct enzymes from glycolysis that allow the pathway to occur
spontaneously.[11] An example of the pathway for gluconeogenesis is illustrated in the image titled
"Gluconeogenesis Mechanism (https://upload.wikimedia.org/wikipedia/commons/d/da/Gluconeogenese_Schema
_2.png)".
Amphibolic pathway

An amphibolic pathway is one that can be either

catabolic or anabolic based on the availability of or
the need for energy.[9]: 570  The currency of energy in
a biological cell is adenosine triphosphate (ATP),
which stores its energy in the phosphoanhydride
bonds. The energy is utilized to conduct
biosynthesis, facilitate movement, and regulate
active transport inside of the cell.[9]: 571  Examples of
amphibolic pathways are the citric acid cycle and the
glyoxylate cycle. These sets of chemical reactions
contain both energy producing and utilizing
pathways.[5]: 572  To the right is an illustration of the
amphibolic properties of the TCA cycle.

The glyoxylate shunt pathway is an alternative to the

tricarboxylic acid (TCA) cycle, for it redirects the
pathway of TCA to prevent full oxidation of carbon
compounds, and to preserve high energy carbon
sources as future energy sources. This pathway
occurs only in plants and bacteria and transpires in
the absence of glucose molecules.[12]

Regulation
The flux of the entire pathway is regulated by the
rate-determining steps.[1]: 577–578  These are the
slowest steps in a network of reactions. The rate-
limiting step occurs near the beginning of the Gluconeogenesis Mechanism
pathway and is regulated by feedback inhibition,
which ultimately controls the overall rate of the
pathway.[13] The metabolic pathway in the cell is regulated by covalent or non-covalent modifications. A covalent
modification involves an addition or removal of a chemical bond, whereas a non-covalent modification (also known
as allosteric regulation) is the binding of the regulator to the enzyme via hydrogen bonds, electrostatic interactions,
and Van Der Waals forces.[14]

The rate of turnover in a metabolic pathway, also known as the metabolic flux, is regulated based on the
stoichiometric reaction model, the utilization rate of metabolites, and the translocation pace of molecules across the
lipid bilayer.[15] The regulation methods are based on experiments involving 13C-labeling, which is then analyzed
by Nuclear Magnetic Resonance (NMR) or gas chromatography-mass spectrometry (GC-MS)-derived mass
compositions. The aforementioned techniques synthesize a statistical interpretation of mass distribution in
proteinogenic amino acids to the catalytic activities of enzymes in a cell.[15]: 178 

Clinical Applications in Targeting Metabolic Pathways

Targeting Oxidative Phosphorylation

Metabolic pathways can be targeted for clinically therapeutic uses. Within the mitochondrial metabolic network, for
instance, there are various pathways that can be targeted by compounds to prevent cancer cell proliferation.[16] One
such pathway is oxidative phosphorylation (OXPHOS) within the electron transport chain (ETC). Various inhibitors
can downregulate the electrochemical reactions that take place at Complex I, II, III, and IV, thereby preventing the
formation of an electrochemical gradient and downregulating the movement of electrons through the ETC. The
substrate-level phosphorylation that occurs at ATP synthase can also be directly inhibited, preventing the formation
of ATP that is necessary to supply energy for cancer cell
proliferation.[17] Some of these inhibitors, such as
lonidamine and atovaquone,[16] which inhibit Complex II and
Complex III, respectively, are currently undergoing clinical
trials for FDA-approval. Other non-FDA-approved inhibitors
have still shown experimental success in vitro.

Targeting Heme

Heme, an important prosthetic group present in Complexes

I, II, and IV can also be targeted, since heme biosynthesis
and uptake have been correlated with increased cancer
progression.[18] Various molecules can inhibit heme via
different mechanisms. For instance, succinylacetone has
been shown to decrease heme concentrations by inhibiting 6-
aminolevulinic acid in murine erthroleukemia cells. [19]The
primary structure of heme-sequestering peptides, such as
HSP1 and HSP2, can be modified to downregulate heme
concentrations and reduce proliferation of non-small lung
cancer cells.[20]

Targeting the Tricarboxylic acid cycle and

Glutaminolysis

The tricarboxylic acid cycle (TCA) and glutaminolysis can

also be targeted for cancer treatment, since they are essential Amphibolic Properties of the Citric Acid Cycle
for the survival and proliferation of cancer cells. Ivosidenib
and Enasidenib, two FDA-approved cancer treatments, can
arrest the TCA cycle of cancer cells by inhibiting isocitrate dehydrogenase-1
(IDH1) and isocitrate dehydrogenase-2 (IDH2), respectively.[16] Ivosidenib is
specific to acute myeloma leukemia (AML) and cholangiocarcinoma, whereas
Enasidenib is specific to just acute myeloma leukemia (AML).

In a clinical trial consisting of 185 adult patients with cholangiocarcinoma and

an IDH-1 mutation, there was a statistically significant improvement
(p<0.0001; HR: 0.37) in patients randomized to Ivosidenib. Still, some of the
adverse side effects in these patients included fatigue, nausea, diarrhea, Various therapies that can inhibit
decreased appetite, ascites, and anemia. [21] In a clinical trial consisting of 199 key reactions within oxidative
adult patients with AML and an IDH2 mutation, 23% of patients experienced phosphorylation to prevent cancer
complete response (CR) or complete response with partial hematologic recovery proliferation[16]
(CRh) lasting a median of 8.2 months while on Enasidenib. Of the 157 patients
who required transfusion at the beginning of the trial, 34% no longer required
transfusions during the 56-day time period on Enasidenib. Of the 42% of patients who did not require transfusions
at the beginning of the trial, 76% still did not require a transfusion by the end of the trial. Side effects of Enasidenib
included nausea, diarrhea, elevated bilirubin and most notably, differentiation syndrome.[22]

Glutaminase (GLS), the enzyme responsible for converting glutamine to glutamate via hydrolytic deamidation
during the first reaction of glutaminolysis, can also be targeted. In recent years, many small molecules, such as
azaserine, acivicin, and CB-839 have been shown to inhibit glutaminase, thus reducing cancer cell viability and
inducing apoptosis in cancer cells.[23] Due to its effective antitumor ability in several cancer types such as ovarian,
breast and lung cancers, CB-839 is the only GLS inhibitor currently undergoing clinical studies for FDA-approval.

See also
Metabolism
 Metabolic network
Metabolic network modelling
Metabolic engineering

Various therapies that can inhibit

pathways within the TCA and
glutaminolysis to prevent cancer
proliferation[16]

References
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Elliott, Daphne C. (Fifth ed.). Oxford. ISBN 9780199609499. OCLC 862091499 (https://www.worldcat.org/oclc/8
62091499).
3. Nicholson, Donald E. (March 1971). An Introduction to Metabolic Pathways by S. DAGLEY (Vol. 59, No. 2 ed.).
Sigma Xi, The Scientific Research Society. p. 266.
4. Harvey, Richard A (2011). Biochemistry (5th ed.). Baltimore, MD 21201: Wolters Kluwer. ISBN 978-1-60831-
412-6.
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Level (4th ed.). Hoboken, NJ: Wiley. ISBN 978-0470-54784-7.
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00reec/page/143) (9th ed.). Boston: Benjamin Cummings. pp. 143 (https://archive.org/details/campbellbiologyj0
0reec/page/143). ISBN 978-0-321-55823-7.
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York: W.H. Freeman. p. 429. ISBN 978-1429229364.
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irreversible?" (http://academic.sun.ac.za/natural/biochem/btk/book/cornish-bowden.pdf) (PDF). Animating the
Cellular Map: 65–71.
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pp. 100–106. ISBN 978-1-4292-1961-7.
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York: W.H. Freeman. pp. 480–482. ISBN 9781429229364.
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systems biology workshop summary. Washington, D.C.: National Academies Press. p. 135. ISBN 978-0-309-
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in plants : [proceedings of an international conference held on 9 - 11 January 1997 at St Hugh's College, Oxford
under the auspices of the Phytochemical Society of Europe]. Dordrecht [u.a.]: Kluwer. p. 258.
ISBN 079235494X.
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p. 133. ISBN 0-19-508439-X.
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ISBN 1597452440.
16. Frattaruolo, Luca (2020). "Targeting the Mitochondrial Metabolic Network: A Promising Strategy in Cancer
Treatment" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503725). International Journal of Molecular
Sciences. 21 (17): 2–11. doi:10.3390/ijms21176014 (https://doi.org/10.3390%2Fijms21176014). PMC 7503725
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7503725). PMID 32825551 (https://pubmed.ncbi.nlm.nih.gov/32
825551).
17. Yadav, N.; Kumar, S.; Marlowe, T.; Chaudhary, A.; Kumar, R.; Wang, J.; O'Malley, J.; Boland, P.; Jaynathi, S.;
Kumar, T.; Yadava, N.; Chandra, D. (2015). "Oxidative phosphorylation-dependent regulation of cancer cell
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18. Hooda, Jagmohan; Cadinu, Daniela; Alam, Md; Shah, Ajit; Cao, Thai; Sullivan, Laura; Brekken, Rolf; Zhang, Li
(2013). "Enhanced heme function and mitochondrial respiration promote the progression of lung cancer cells"
(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3660535). PLOS ONE. 8 (5): e63402.
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effect on cell growth, heme content and delta-aminolevulinic acid dehydratase activity of malignant murine
erythroleukemia cells". Biochem Biophys Res Commun. 88 (4): 1382–1390. doi:10.1016/0006-291x(79)91133-1
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External links
Full map of metabolic pathways (http://biochemical-pathways.com/#/map/1)
Biochemical pathways, Gerhard Michal (http://www.astrojan.nhely.hu/protein/bohr1.htm)
Overview Map from BRENDA (https://www.brenda-enzymes.org/pathway_index.php)
BioCyc: Metabolic network models for thousands of sequenced organisms (http://www.biocyc.org/)
KEGG: Kyoto Encyclopedia of Genes and Genomes (http://www.genome.jp/kegg/)
Reactome, a database of reactions, pathways and biological processes (http://www.reactome.org/)
MetaCyc: A database of experimentally elucidated metabolic pathways (2,200+ pathways from more than 2,500
organisms). (http://metacyc.org/)
MetaboMAPS: A platform for pathway sharing and data visualization on metabolic pathways (https://metaboma
ps.brenda-enzymes.org)
The Pathway Localization database (PathLocdb) (https://web.archive.org/web/20131016111652/http://pathloc.c
bi.pku.edu.cn/)
DAVID: Visualize genes on pathway maps (http://david.abcc.ncifcrf.gov/)
 Wikipathways: pathways for the people (http://www.wikipathways.org/)
ConsensusPathDB (http://cpdb.molgen.mpg.de/)
metpath: Integrated interactive metabolic chart (http://www.metabolicpathways.teithe.gr/)
Metabolic pathway diagram

Purine biosynthesis

Glucuronate metabolism Pentose interconversion

Histidine metabolism
Aspartate amino acid

group synthesis

Other sugar
Aromatic amino

metabolism acid synthesis Porphyrins and

corrinoids

metabolism
Inositol metabolism
Pentose phosphate pathway

Citric acid cycle

Cellulose and sucrose
Pyruvate

metabolism decarboxylation
Glycolysis and Gluconeogenesis Fermentation
Glutamate amino

acid group

synthesis
Starch and glycogen

metabolism Amino sugars metabolism

Small amino acid synthesis Urea cycle Pyrimidine biosynthesis

Fatty acid

Branched amino acid

metabolism
synthesis

All pathway labels on this image are links, simply click to access the article.

A high resolution labeled version of this image is available here.

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