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Metabolic Modeling Tutorial
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BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
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MetaCyc Compound: L-alanine

Abbrev Name: ala

Synonyms: alanine, L-α-alanine, ala, A

Superclasses: an amino acid or its derivative an amino acid a neutral amino acid
an amino acid or its derivative an amino acid a non-polar amino acid
an amino acid or its derivative an amino acid an alpha amino acid a standard alpha amino acid
an amino acid or its derivative an amino acid an L-amino acid

Component of: AlaS-L-alanine

Chemical Formula: C3H7NO2

Molecular Weight: 89.094 Daltons

Monoisotopic Molecular Weight: 89.0476784741 Daltons

SMILES: CC([N+])C([O-])=O

InChI: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1

InChIKey: InChIKey=QNAYBMKLOCPYGJ-REOHCLBHSA-N

Unification Links: CAS:56-41-7 , ChEBI:57972 , HMDB:HMDB00161 , IAF1260:33629 , KEGG:C00041 , MetaboLights:MTBLC57972 , PubChem:7311724

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -16.772158 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

5-N-acetylardeemin biosynthesis :
anthranilate + L-alanine + L-tryptophan + 3 ATP → ardeemin FQ + 3 AMP + 3 diphosphate + H2O + 2 H+

8-amino-7-oxononanoate biosynthesis I , 8-amino-7-oxononanoate biosynthesis II :
a pimeloyl-[acp] + L-alanine + H+ → 8-amino-7-oxononanoate + CO2 + a holo-[acyl-carrier protein]

8-amino-7-oxononanoate biosynthesis III :
pimeloyl-CoA + L-alanine + H+ → CO2 + 8-amino-7-oxononanoate + coenzyme A

ergotamine biosynthesis :
lysergate + L-alanine + L-phenylalanine + L-proline → ergotamine + 3 H2O + H+

fumiquinazoline D biosynthesis :
fumiquinazoline F-indoline-2,3-diol + L-alanine + ATP → fumiquinazoline A + AMP + diphosphate + H2O + H+
anthranilate + L-tryptophan + L-alanine + 3 ATP → fumiquinazoline F + 3 AMP + 3 diphosphate + H2O + 2 H+

indole-3-acetyl-amide conjugate biosynthesis :
indole-3-acetate + L-alanine + ATP → indole-3-acetyl-alanine + AMP + diphosphate + H+

phosphinothricin tripeptide biosynthesis :
N-acetyl demethylphosphinothricin + 2 L-alanineN-acetyl-demethylphophinothricin tripeptide + 2 H2O

pyruvate fermentation to opines :
alanopine + NAD+ + H2O ← pyruvate + L-alanine + NADH + H+

tRNA charging :
tRNAala + L-alanine + ATP + H+ → L-alanyl-tRNAala + AMP + diphosphate

UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-DAP-containing) , UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing) :
L-alanine + UDP-N-α-D-acetylmuramate + ATP → UDP-N-acetylmuramoyl-L-alanine + ADP + phosphate + H+

γ-glutamyl cycle :
glutathione + a standard α amino acid → L-cysteinyl-glycine + an (γ-L-glutamyl)-L-amino acid

leukotriene biosynthesis :
leukotriene-C4 + a standard α amino acid → an (γ-L-glutamyl)-L-amino acid + leukotriene-D4

methanofuran biosynthesis :
2-furaldehyde phosphate + a standard α amino acid → 2-methylamine-furan phosphate + a 2-oxo carboxylate

Not in pathways:
a standard α amino acid + oxygen + H2O → ammonium + hydrogen peroxide + a 2-oxo carboxylate

prodigiosin biosynthesis :
(S)-3-acetyloctanal + an L-amino acid → 2-methyl-3-n-amyl-dihydropyrrole + a 2-oxo acid + H2O

rhizocticin A and B biosynthesis :
2-keto-5-phosphono-3-cis-pentenoate + an L-amino acidL-2-amino-5-phosphono-3-cis-pentenoate + a 2-oxo carboxylate
2-keto-4-hydroxy-5-phosphonopentanoate + an L-amino acid → 2-amino-4-hydroxy-5-phosphonopentanoate + a 2-oxo carboxylate


ATP + 2 an L-amino acid → ADP + a dipeptide + phosphate + H+

Reactions known to produce the compound:

alanine biosynthesis III , molybdenum cofactor biosynthesis , thiazole biosynthesis I (E. coli) , thiazole biosynthesis II (Bacillus) :
an [L-cysteine desulfurase]-L-cysteine + L-cysteine → an [L-cysteine desulfurase] L-cysteine persulfide + L-alanine

indole-3-acetate activation I :
indole-3-acetyl-alanine + H2O → indole-3-acetate + L-alanine

isopropylamine degradation :
L-2-aminopropionaldehyde + NAD(P)+ + H2O → L-alanine + NAD(P)H + 2 H+

lupanine biosynthesis :
3 cadaverine + 4 pyruvate → 17-oxosparteine + 4 L-alanine + H+ + 3 H2O

muropeptide degradation :
L-alanyl-L-glutamate + H2O → L-alanine + L-glutamate

thiazole biosynthesis III (eukaryotes) :
glycine + L-cysteine + NAD+ → 2-carboxylate-4-methyl-5-beta-(ethyl adenosine 5-diphosphate) thiazole + nicotinamide + L-alanine + 3 H2O

thio-molybdenum cofactor biosynthesis :
MoO2-molybdopterin cofactor + L-cysteine + 2 H+ → thio-molybdenum cofactor + L-alanine + H2O

tryptophan degradation I (via anthranilate) :
L-kynurenine + H2O → L-alanine + anthranilate + H+

tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde :
3-hydroxy-L-kynurenine + H2O → 3-hydroxyanthranilate + L-alanine + H+

tryptophan degradation XI (mammalian, via kynurenine) :
3-hydroxy-L-kynurenine + H2O → 3-hydroxyanthranilate + L-alanine + H+
L-kynurenine + H2O → L-alanine + anthranilate + H+

[2Fe-2S] iron-sulfur cluster biosynthesis :
a [cysteine desulfurase]-S-sulfanyl-[disordered-form scaffold protein] complex + L-cysteine → an S-sulfanyl-[cysteine desulfurase]-S-sulfanyl-[disordered-form scaffold protein] complex + L-alanine
an [L-cysteine desulfurase] + L-cysteine → an S-sulfanyl-[L-cysteine desulfurase] + L-alanine

Not in pathways:
L-alanyl-L-aspartate + H2O → L-alanine + L-aspartate
L-alanyl-L-glutamine + H2O → L-alanine + L-glutamine
L-alanyl-glycine + H2O → L-alanine + glycine
L-alanyl-L-histidine + H2O → L-alanine + L-histidine
L-alanyl-L-leucine + H2O → L-alanine + L-leucine
L-alanyl-L-threonine + H2O → L-alanine + L-threonine
L-methionyl-L-alanine dipeptide + H2O → L-methionine + L-alanine
a C-terminal [protein]-L-alanine + H2O → L-alanine + a peptide
L-cysteine + an unsulfurated [sulfur carrier] → L-alanine + a sulfurated [sulfur carrier]

dimethylsulfoniopropionate biosynthesis I (Wollastonia) :
S-methyl-L-methionine + a 2-oxo carboxylate + H+ → 3-dimethylsulfoniopropionaldehyde + CO2 + a standard α amino acid

seed germination protein turnover , wound-induced proteolysis I :
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)


a dipeptide + H2O → 2 amino acids
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
β-aspartyl dipeptide + H2O → L-aspartate + a standard α amino acid
amino acids(n) + H2O → amino acids(n-1) + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a dipeptide + H2O → 2 a standard α amino acid
a peptide + H2O → a standard α amino acid + a peptide
a peptide + H2O → a peptide + a standard α amino acid
a peptide + H2O → a peptide + a standard α amino acid
an oligopeptide + H2O → a peptide + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a protein + H2O → a peptide + a standard α amino acid
a protein + H2O → a standard α amino acid + a peptide
a peptide + H2O → a standard α amino acid + a peptide
a protein + H2O → a standard α amino acid + a peptide
a tripeptide + H2O → a dipeptide + a standard α amino acid
a dipetide with L-aspartate at the N-terminal + H2O → L-aspartate + a standard α amino acid
a dipetide with L-histidine at the C-terminal + H2O → a standard α amino acid + L-histidine
a dipeptide with L-methionine at the N-terminal + H2O → a standard α amino acid + L-methionine
a dipeptide with proline at the C-terminal + H2O → L-proline + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
a dipeptide + H2O → a standard α amino acid + a standard α amino acid
amino acids(n) + H2O → a standard α amino acid + amino acids(n-1)


an ester of hydrophobic-amino acids + H2O → a non-polar amino acid + a non-polar amino acid

γ-glutamyl cycle :
an (γ-L-glutamyl)-L-amino acid → an L-amino acid + 5-oxoproline


a peptide + H2O → an L-amino acid + a peptide
a peptide + H2O → a peptide + an L-amino acid
a N-methyl L-amino acid + oxygen + H2O → an L-amino acid + formaldehyde + hydrogen peroxide
a polypeptide + H2O → a polypeptide + an L-amino acid


amino acids(n) + H2O → amino acids(n-1) + an α amino acid
an α amino acid ester + H2O → an alcohol + an α amino acid + H+
a protein + H2O → a protein + an α amino acid

Reactions known to both consume and produce the compound:

2-aminoethylphosphonate degradation I , 2-aminoethylphosphonate degradation II :
pyruvate + (2-aminoethyl)phosphonate ↔ L-alanine + phosphonoacetaldehyde

4-aminobutyrate degradation IV , glutamate degradation IV :
4-aminobutanoate + pyruvate ↔ succinate semialdehyde + L-alanine

alanine biosynthesis I :
pyruvate + L-valine ↔ L-alanine + 3-methyl-2-oxobutanoate
L-alanine ↔ D-alanine

alanine biosynthesis II , alanine degradation II (to D-lactate) , alanine degradation III :
2-oxoglutarate + L-alanine ↔ L-glutamate + pyruvate

alanine degradation I :
L-alanine ↔ D-alanine

alanine degradation IV :
L-alanine + NAD+ + H2O ↔ ammonium + pyruvate + NADH + H+

anaerobic energy metabolism (invertebrates, cytosol) :
2-oxoglutarate + L-alanine ↔ L-glutamate + pyruvate
L-alanine ↔ D-alanine

arginine degradation IX (arginine:pyruvate transaminase pathway) :
L-arginine + pyruvate ↔ 2-ketoarginine + L-alanine

β-alanine biosynthesis II , β-alanine degradation II :
malonate semialdehyde + L-alanine ↔ β-alanine + pyruvate

C4 photosynthetic carbon assimilation cycle, NAD-ME type :
2-oxoglutarate + L-alanine ↔ L-glutamate + pyruvate
2-oxoglutarate + L-alanine ↔ L-glutamate + pyruvate

C4 photosynthetic carbon assimilation cycle, PEPCK type :
2-oxoglutarate + L-alanine ↔ L-glutamate + pyruvate
2-oxoglutarate + L-alanine ↔ L-glutamate + pyruvate

γ-coniciene and coniine biosynthesis :
L-alanine + 5-oxooctanal ↔ 8-aminooctan-4-one + pyruvate

glycine biosynthesis III :
glyoxylate + L-alanine ↔ glycine + pyruvate

histidine degradation V :
L-histidine + pyruvate ↔ imidazole-pyruvate + L-alanine

hypoglycin biosynthesis :
beta-methylenecyclopropyl pyruvate + L-alanine ↔ hypoglycin A + pyruvate

hypotaurine degradation :
pyruvate + hypotaurine ↔ L-alanine + 2-sulfinoacetaldehyde

indole-3-acetate biosynthesis I , indole-3-acetate biosynthesis II :
L-tryptophan + pyruvate ↔ L-alanine + indole-3-pyruvate

L-homophenylalanine biosynthesis :
L-phenylalanine + pyruvate ↔ 2-oxo-3-phenylpropanoate + L-alanine
L-homophenylalanine + pyruvate ↔ 2-oxo-4-phenylbutanoate + L-alanine

lysine degradation IX :
pyruvate + L-lysine ↔ L-alanine + (S)-2-amino-6-oxohexanoate

phenylalanine degradation III :
L-phenylalanine + pyruvate ↔ 2-oxo-3-phenylpropanoate + L-alanine

putrescine degradation V :
putrescine + pyruvate ↔ 4-aminobutanal + L-alanine

serinol biosynthesis :
L-alanine + dihydroxyacetone phosphate ↔ serinol phosphate + pyruvate

streptomycin biosynthesis :
pyruvate + D-1-guanidino-3-amino-1,3-dideoxy-scyllo-inositol ↔ L-alanine + D-1-guanidino-1-deoxy-3-dehydro-scyllo-inositol

taurine degradation I :
pyruvate + taurine ↔ L-alanine + sulfoacetaldehyde

tyrosine degradation III :
L-tyrosine + pyruvate ↔ 4-hydroxyphenylpyruvate + L-alanine

vitamin B6 degradation :
pyruvate + pyridoxamine ↔ L-alanine + pyridoxal

Not in pathways:
pyruvate + 5-aminolevulinate ↔ L-alanine + 4,5-dioxopentanoate
pyruvate + L-2,4-diaminobutanoate ↔ L-aspartate-semialdehyde + L-alanine
pyruvate + D-methionine ↔ L-alanine + 2-oxo-4-methylthiobutanoate
pyruvate + (R)-3-amino-2-methylpropanoate ↔ L-alanine + (S)-methylmalonate-semialdehyde
pyruvate + L-serine ↔ L-alanine + hydroxypyruvate
L-glutamine + pyruvate ↔ 2-oxoglutaramate + L-alanine
(S)-methylmalonate-semialdehyde + L-alanine ↔ (S)-3-amino-2-methylpropanoate + pyruvate
isobutanal + L-alanine ↔ 2-methylpropanamine + pyruvate
oxomalonate + L-alanine ↔ aminomalonate + pyruvate
L-alanine + a 2-oxo carboxylate ↔ pyruvate + an L-amino acid

asparagine degradation II :
a 2-oxo carboxylate + L-asparagine ↔ 2-oxosuccinamate + a standard α amino acid

dimethylsulfoniopropionate biosynthesis III (algae) , ethylene biosynthesis III (microbes) :
L-methionine + a 2-oxo carboxylate ↔ 2-oxo-4-methylthiobutanoate + a standard α amino acid

glucosinolate biosynthesis from dihomomethionine :
2-oxo-6-methylthiohexanoate + a standard α amino acid ↔ L-dihomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from hexahomomethionine :
2-oxo-10-methylthiodecanoate + a standard α amino acid ↔ hexahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from pentahomomethionine :
2-oxo-9-methylthiononanoate + a standard α amino acid ↔ pentahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from tetrahomomethionine :
2-oxo-8-methylthiooctanoate + a standard α amino acid ↔ tetrahomomethionine + a 2-oxo carboxylate

glucosinolate biosynthesis from trihomomethionine :
2-oxo-7-methylthioheptanoate + a standard α amino acid ↔ trihomomethionine + a 2-oxo carboxylate

homomethionine biosynthesis :
2-oxo-5-methylthiopentanoate + a standard α amino acid ↔ L-homomethionine + a 2-oxo carboxylate
L-methionine + a 2-oxo carboxylate ↔ 2-oxo-4-methylthiobutanoate + a standard α amino acid


L-ornithine + a 2-oxo carboxylate ↔ a standard α amino acid + L-glutamate-5-semialdehyde

In Reactions of unknown directionality:

Not in pathways:
L-aspartate + H+ = CO2 + L-alanine
2,2-dialkylglycine + pyruvate + H+ = dialkyl ketone + L-alanine + CO2
aminopentol + pyruvate = (3S,5R,10S,12R,14R,15S,16S)-3,5,10,14,15-pentahydroxy-12,16-dimethylicosan-2-one + L-alanine
N-acetylmuramoyl-L-alaninate + H2O = N-acetylmuramate + L-alanine
a ThiI sulfur-carrier protein + L-cysteine = an S-sulfanyl-[ThiI sulfur-carrier protein] + L-alanine
3-sulfinoalanine + H2O = L-alanine + sulfite + H+
L-selenocysteine + a reduced electron acceptor = L-alanine + selenide + an oxidized electron acceptor + 2 H+
2-amino-4-carboxypyrimidine + L-alanine = lathyrine + CO2 + H2O


an L-amino acid = a D-amino acid
an L-amino acid + NAD+ + H2O = a 2-oxo carboxylate + ammonium + NADH + H+
an N-carbamoyl-L-amino acid + H2O + 2 H+ = an L-amino acid + ammonium + CO2
S-ureidoglycine + a 2-oxo carboxylate = oxalurate + an L-amino acid


a 5-L-glutamyl-[peptide] + an amino acid = a 5-L-glutamyl-amino acid + a peptide

In Transport reactions:
2 L-alanine[out] + 2 H+[out] ↔ 2 L-alanine[in] + 2 H+[in] ,
Na+[periplasmic space] + L-alanine[periplasmic space] → Na+[cytosol] + L-alanine[cytosol] ,
L-alanine[periplasmic space] + H+[periplasmic space]L-alanine[cytosol] + H+[cytosol] ,
L-alanine[cytosol]L-alanine[periplasmic space] ,
a non-polar amino acid[extracellular space] + ATP + H2O ↔ a non-polar amino acid[cytosol] + ADP + phosphate ,
an L-amino acid[cytosol]an L-amino acid[periplasmic space]

Enzymes activated by L-alanine, sorted by the type of activation, are:

Activator (Mechanism unknown) of: glutamate dehydrogenase (NAD-dependent) [Bonete96]

Enzymes inhibited by L-alanine, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: glutamine synthetase [Woolfolk67, Bender77, Dahlquist75]

Inhibitor (Allosteric) of: pyruvate kinase [Holwerda73]

Inhibitor (Mechanism unknown) of: 2-dehydro-3-deoxyphosphoheptonate aldolase , serine acetyltransferase [Hindson03] , L-proline:H+ symporter [MacMillan99] , 2-amino-4-oxopentanoate thiolase [Jeng74, Comment 1]


References

Bender77: Bender RA, Janssen KA, Resnick AD, Blumenberg M, Foor F, Magasanik B (1977). "Biochemical parameters of glutamine synthetase from Klebsiella aerogenes." J Bacteriol 129(2);1001-9. PMID: 14104

Bonete96: Bonete MJ, Perez-Pomares F, Ferrer J, Camacho ML (1996). "NAD-glutamate dehydrogenase from Halobacterium halobium: inhibition and activation by TCA intermediates and amino acids." Biochim Biophys Acta 1996;1289(1);14-24. PMID: 8605224

Dahlquist75: Dahlquist FW, Purich DL (1975). "Regulation of Escherichia coli glutamine synthetase. Evidence for the action of some feedback modifiers at the active site of the unadenylylated enzyme." Biochemistry 14(9);1980-9. PMID: 235974

Hindson03: Hindson VJ, Shaw WV (2003). "Random-order ternary complex reaction mechanism of serine acetyltransferase from Escherichia coli." Biochemistry 42(10);3113-9. PMID: 12627979

Holwerda73: Holwerda DA, de Zwaan A (1973). "Kinetic and molecular characteristics of allosteric pyruvate kinase from muscle tissue of the sea mussel Mytilus edulis L." Biochim Biophys Acta 309(2);296-306. PMID: 4354457

Jeng74: Jeng IM, Somack R, Barker HA (1974). "Ornithine degradation in Clostridium sticklandii; pyridoxal phosphate and coenzyme A dependent thiolytic cleavage of 2-amino-4-ketopentanoate to alanine and acetyl coenzyme A." Biochemistry 1974;13(14);2898-903. PMID: 4407783

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

MacMillan99: MacMillan SV, Alexander DA, Culham DE, Kunte HJ, Marshall EV, Rochon D, Wood JM (1999). "The ion coupling and organic substrate specificities of osmoregulatory transporter ProP in Escherichia coli." Biochim Biophys Acta 1420(1-2);30-44. PMID: 10446288

Woolfolk67: Woolfolk CA, Stadtman ER (1967). "Regulation of glutamine synthetase. 3. Cumulative feedback inhibition of glutamine synthetase from Escherichia coli." Arch Biochem Biophys 118(3);736-55. PMID: 4860415


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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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