Table 1: Set of reactions included in the model.

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

phosphoglucomutase (cPGM) 5.4.2.2 Glyc c G1P c⇔ G6P c e [1–3] e [4–7]

phosphoglucose isomerase (cPGI) 5.3.1.9 Glyc c F6P c⇔ G6P c [2,3] e [6,8,9]

6-phosphofructokinase (cPFK) 2.7.1.11 Glyc c ATP c + F6P c⇒ ADP c + F1,6P c e [10] e [11–13]

diphosphate-fructose-6-phosphate 1-phosphotrans-

ferase

2.7.1.90 Glyc c F6P c + PP c⇔ P c + F1,6P c e [14–17] e [6, 9, 11, 18,

19]

fructose-bisphosphate aldolase (cALD) 4.1.2.13 Glyc c F1,6P c⇔ DHAP c + GAP c e [1,10] e [6,9,12,19] [20–22]

triose phosphate isomerase (cTIM) 5.3.1.1 Glyc c DHAP c⇔ GAP c e [1,17,23] e [4–6,6,19,24]

glyceraldehyde-3-phosphate dehydrogenase (phospho-

rylating)

1.2.1.12 Glyc c P c + GAP c + NAD+ c⇔ NADH c + 1,3BPG c f [25,26] e [4,6,19,27]

phosphoglycerate kinase (cPGlyK) 2.7.2.3 Glyc c ADP c + 1,3BPG c⇔ ATP c + 3PG c e [1,10,25] e [4–6,19];

phosphoglycerate mutase (cPGlyM) 5.4.2.1 Glyc c 3PG c⇔ 2PG c f [25,26] e [4,6,28–30]

phosphopyruvate hydratase (cENOLASE) 4.2.1.11 Glyc c 2PG c⇔ PEP c f [25,26] e [4,4,6,19,31]

pyruvate kinase (cPK) 2.7.1.40 Glyc c ADP c + PEP c⇒ ATP c + Pyr c [10,25] e [6,12]

fructose-1,6-bisphosphatase (cFBPAse) 3.1.3.11 Glyc c F1,6P c⇒ P c + F6P c [32,33] [21,34]

pyruvate, phosphate dikinase (cPPDK) 2.7.9.1 Glyc c ATP c + P c + Pyr c⇔ PP c + PEP c + AMP c [35] e [4, 6, 19, 35,

35–40]

sucrose synthase 2.4.1.13 Suc c sucrose c + UDP c⇔ UDPGlc c + Frc c e [1–3,41] e [4, 6, 9, 19,

42–47]

[21]

invertase 3.2.1.26 Suc c sucrose c⇒ Glc c + Frc c e [48] [49]

sucrose phosphate phosphatase 3.1.3.24 Suc c S6P c⇒ sucrose c + P c [50–52] e [52] [53]

sucrose phosphate synthase 2.4.1.14 Suc c F6P c + UDPGlc c⇔ UDP c + S6P c e [1] e [?, 54–58]

hexokinase 2.7.1.1 Suc c ATP c + Glc c⇒ ADP c + G6P c e [1–3] e [6, 12, 59, 60,

60,61]

fructokinase 2.7.1.4 Suc c ATP c + Frc c⇒ ADP c + F6P c e [1–3,26] e [4, 6, 19, 61,

62]

UDPglucose pyrophosphorylase 2.7.7.9 Suc c G1P c + UTP c⇔ PP c + UDPGlc c e [2,3,63]; [25] e [1,6,19,64]

ADPglucose pyrophosphorylase (cAGPase) 2.7.7.27 Suc c ATP c + G1P c⇔ PP c + ADPglc c e [2, 3, 14, 16,

65,66]

e [6,67–71,71–

78]

nucleoside-diphosphate kinase (cNDPkin: UDP) 2.7.4.6 Pur c ATP c + UDP c⇔ ADP c + UTP c e [25,79] e [19]

pyruvate decarboxylase 4.1.1.1 Ferm c Pyr c⇒ CO2 c + AcAl c e [79] [6,80,81]

alcohol dehydrogenase 1.1.1.1 Ferm c NAD+ c + Eth c⇔ NADH c + AcAl c e [1,14,25] e [4,82]

lactate dehydrogenase 1.1.1.27 Ferm c NAD+ c + Lac c⇔ NADH c + Pyr c e [79] [6]

aldehyde dehydrogenase (NAD+) (cALDH) 1.2.1.3 Ace c NAD+ c + AcAl c⇒ NADH c + AcA c e [1]

aspartate transaminase (cAAT) 2.6.1.1 Glu c 2OG c + Asp c⇔ OAA c + Glu c [25,83] [6,19,84,85]

glutamate-ammonia ligase (cGS, GSI) 6.3.1.2 GG c ATP c + Glu c + NH3 c⇒ ADP c + P c + Gln c [25,86] [6]

asparagine synthase (glutamine-hydrolysing) 6.3.5.4 Asp c ATP c + Gln c + Asp c⇒ PP c + Glu c + AMP c

+ Asn c

[87] e [88]

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

asparaginase 3.5.1.1 Asp c Asn c⇒ Asp c + NH3 c [89] [89]

alanine transaminase 2.6.1.2 Ala c 2OG c + Ala c⇔ Pyr c + Glu c [25] e [4,6,19]

adenylate kinase (cAdK) 2.7.4.3 Pur c ATP c + AMP c⇔ 2 ADP c [90] [6]

aconitate hydratase (cACO) 4.2.1.3 Icit c Cit c⇔ Icit c [1,25] e [4,6,19]

isocitrate dehydrogenase (NADP+) (cICDH) 1.1.1.42 Icit c NADP+ c + Icit c ⇔ NADPH c + 2OG c +

CO2 c

e [25,91] e [4]

malate dehydrogenase (cMalDH) 1.1.1.37 Glyc c NAD+ c + Mal c⇔ NADH c + OAA c [1,17,92] e [4, 6, 19, 24,

93]

phosphoenolpyruvate carboxylase 4.1.1.31 Ana c PEP c + CO2 c⇒ P c + OAA c e [1,94,95] [6,96]

phosphoenolpyruvate carboxykinase (ATP) 4.1.1.49 Ana c ATP c + OAA c⇒ ADP c + PEP c + CO2 c [97] [6]

glyceraldehyde-3-phosphate dehydrogenase (NADP) 1.2.1.9 Glyc c GAP c + NADP+ c⇒ 3PG c + NADPH c e [98,99]

argininosuccinate synthase 6.3.4.5 Arg c ATP c + Asp c + Citru c ⇔ PP c + AMP c +

ArgSucc c

[90] e [6,19,100]

argininosuccinate lyase 4.3.2.1 Arg c ArgSucc c⇔ Fum c + Arg c [90] e [6,100]

glutamate decarboxylase 4.1.1.15 GABA c Glu c⇒ CO2 c + Gaba c [101]

glucan synthase complex / Car c UDPGlc c⇒ UDP c + B-glucan c [102]

UDP-glucose 6-dehydrogenase 1.1.1.22 Car c UDPGlc c + 2 NAD+ c ⇒ 2 NADH c +

UDPGlu c

[90] [103]

UDP-glucuronate decarboxylase 4.1.1.35 Car c UDPGlu c⇒ CO2 c + UDPXyl c [104,105]

UDP-arabinose 4-epimerase 5.1.3.5 Car c UDPAra c⇔ UDPXyl c [106]

arabinoxylan biosynthesis (simpl.) / Car c 3 UDPXyl c + 2 UDPAra c ⇒ 5 UDP c + 5

AraXyl c

[107]

cellulose synthase (UDP-forming) 2.4.1.12 Car c UDPGlc c⇒ UDP c + Cel c [102]

formate-tetrahydrofolate ligase 6.3.4.3 Fol c ATP c + THF c + For c ⇔ ADP c + P c +

FTHF c

[90] e [6,19] [108]

methenyltetrahydrofolate cyclohydrolase 3.5.4.9 Fol c METHF c⇔ FTHF c [109] [109]

methylenetetrahydrofolate dehydrogenase (NADP+) 1.5.1.5 Fol c NADP+ c + METTHF c ⇔ NADPH c +

METHF c

[90] [110]

methylenetetrahydrofolate reductase (NAD(P)H) 1.5.1.20 Fol c NADH c + METTHF c⇒ NAD+ c + MTHF c [90] [4,111]

isocitrate lyase 4.1.3.1 For c Icit c⇒ Succ c + Glx c [112]

glyoxylate oxidase 1.2.3.5 For c Glx c + O2 c⇒ Oxl c [6]

oxalate decarboxylase 4.1.1.2 For c Oxl c⇒ CO2 c + For c [90]

biomassbiosynthesis / BM c see Table S4

methionine adenosyltransferase 2.5.1.6 Met c ATP c + Met c⇒ P c + PP c + SAM c [113] e [4,6,19]

adenosylhomocysteinase 3.3.1.1 Met c SAH c⇔ HOMO-Cys c + ADN c [114] [6]

adenosine kinase 2.7.4.3 Pur c ATP c + ADN c⇒ ADP c + AMP c [90] [6] [115]

homocysteine S-methyltransferase 2.1.1.10 Met c HOMO-Cys c + SAM c⇒ Met c + SAH c [90] [6]

methionine synthase (cMS) 2.1.1.13 Met c MTHF c + HOMO-Cys c⇒ THF c + Met c [113] [19]

glucose-6-phosphate dehydrogenase (c-G6PDH) 1.1.1.49 PPP c G6P c + NADP+ c⇔ NADPH c + GL6P c f [26] [116,117] [6,118]

6-phosphogluconolactonase 3.1.1.31 PPP c GL6P c⇒ 6PG c f [26] [6] [119]

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

phosphogluconate dehydrogenase (decarboxylating) 1.1.1.44 PPP c NADP+ c + 6PG c ⇒ NADPH c + CO2 c +

Ru5P c

[6,19,24,120]

ribulose-phosphate 3-epimerase (cRuPepimerase) 5.1.3.1 PPP c Ru5P c⇔ X5P c f [26] [6] [121]

glycine hydroxymethyltransferase (cSHMT) 2.1.2.1 Fol c METTHF c + Gly c⇔ THF c + Ser c [90] [6] [122]

pyruvate dehydrogenase complex (mPyrDH) 1.2.4.1 TCA m NAD+ m + Pyr m + CoA m⇒ NADH m + Ac-

CoA m + CO2 m

e [1] e [4,6]

citrate synthase 2.3.3.1 TCA m AcCoA m + OAA m⇒ Cit m + CoA m e [1] [6,24,123]

aconitate hydratase (mACO) 4.2.1.3 TCA m Cit m⇔ Icit m e [1] e [4,6,19]

isocitrate dehydrogenase (NADP+) (mICDH) 1.1.1.42 TCA m NADP+ m + Icit m ⇔ NADPH m + 2OG m +

CO2 m

e [25,91] [4,124]

isocitrate dehydrogenase (NAD+) (mICDH) 1.1.1.41 TCA m NAD+ m + Icit m ⇔ NADH m + 2OG m +

CO2 m

[90] e [19,125]

oxoglutarate dehydrogenase (succinyl-transferring) 1.2.4.2 TCA m NAD+ m + CoA m + 2OG m ⇒ NADH m +

SuccCoA m + CO2 m

[126]

succinate-CoA ligase (ADP-forming) 6.2.1.5 TCA m ATP m + CoA m + Succ m⇔ ADP m + P m +

SuccCoA m

[90] e [6,12]

succinate dehydrogenase (ubiquinone) 1.3.5.1 TCA m Succ m + Q m⇔ QH2 m + Fum m [90] e [6,12]

fumarate hydratase 4.2.1.2 TCA m Mal m⇔ Fum m e [1,92] [6]

malate dehydrogenase (mMalDH) 1.1.1.37 TCA m NAD+ m + Mal m⇔ NADH m + OAA m e [1,17,25,92] e [4,6,19,93]

glutamate dehydrogenase 1.4.1.2 Ana m NAD+ m + Glu m ⇔ NADH m + 2OG m +

NH3 m

[127] [128]

aspartate transaminase (mAAT) 2.6.1.1 Ana m 2OG m + Asp m⇔ OAA m + Glu m [25,83] [?, 6,19,84]

malate dehydrogenase (decarboxylating) 1.1.1.39 Ana m NAD+ m + Mal m ⇒ NADH m + Pyr m +

CO2 m

[129]

4-aminobutyrate transaminase 2.6.1.19 GABA m 2OG m + Gaba m⇔ Glu m + SuccSAl m [130] [131]

succinate-semialdehyde dehydrogenase (NAD(P)+) 1.2.1.16 GABA m NADP+ m + SuccSAl m ⇒ NADPH m +

Succ m

[90] [131]

NADH dehydrogenase (ubiquinone) 1.6.5.3 oxP m NADH m + Q m⇒NAD+ m + QH2 m + 2 H ext [132]

cytochrome-c oxidase 1.9.3.1 oxP m QH2 m + 0.5 O2 m⇒ Q m + 2 H ext [90] [6]

H+-exporting ATPase 3.6.3.6 oxP m ADP m + P m + 3 H ext⇔ ATP m [90]

glycine decarboxylase system / Fol m NADH m + Gly m + THF m ⇔ NAD+ m +

CO2 m + NH3 m + METTHF m

glycine hydroxymethyltransferase (mSHMT) 2.1.2.1 Fol m Gly m + METTHF m⇔ Ser m + THF m [90] [6]

phosphoglucomutase (pPGM) 5.4.2.2 Glyc p G1P p⇔ G6P p e [1–3] e [4–6, 9, 19,

100,133]

phosphoglucose isomerase (pPGI) 5.3.1.9 Glyc p F6P p⇔ G6P p [2,3] [134] e [6,9,100,135]

6-phosphofructokinase (pPFK) 2.7.1.11 Glyc p ATP p + F6P p⇒ ADP p + F1,6P p [10] [134] e [?, 9,12] [22]

fructose-bisphosphate aldolase (pALD) 4.1.2.13 Glyc p F1,6P p⇔ DHAP p + GAP p [134] e [6, 9, 12, 19,

100]

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

triose phosphate isomerase (pTIM) 5.3.1.1 Glyc p DHAP p⇔ GAP p [23] [134] e [4, 5, 5, 6, 19,

24,100]

glyceraldehyde-3-phosphate dehydrogenase (NADP+)

(phosphorylating)

1.2.1.13 Glyc p P p + GAP p + NADP+ p ⇔ 1,3BPG p +

NADPH p

[92] [134] e

phosphoglycerate kinase (pPGlyK) 2.7.2.3 Glyc p ADP p + 1,3BPG p⇔ ATP p + 3PG p [10] [136] e [4–6, 19, 100,

137,138]

phosphoglycerate mutase (pPGlyM) 5.4.2.1 Glyc p 3PG p⇔ 2PG p [25,26] [134] e [4, 6, 28–30,

100,137]

phosphopyruvate hydratase (pENOLASE) 4.2.1.11 Glyc p 2PG p⇔ PEP p f [25,26] e [4–6, 19, 31,

100,137]

pyruvate kinase (pPK) 2.7.1.40 Glyc p ADP p + PEP p⇒ ATP p + Pyr p [1,10] [134] e [6, 12, 100,

137]

fructose-1,6-bisphosphatase (pFBPase) 3.1.3.11 Glyc p F1,6P p⇒ P p + F6P p [33] [6] [139]

inorganic diphosphatase 3.6.1.1 Suc p PP p⇒ 2 P p e [2, 3, 14, 16,

26,140]

e [4,100]

ADPglucose pyrophosphorylase (pAGPase) 2.7.7.27 Suc p ATP p + G1P p⇔ PP p + ADPglc p e [2,3,3,14,16,

65]

e [?,19,67,69–

78,141]

starch synthase (simpl.) 2.4.1.21 Suc p ADPglc p⇒ ADP p + starch p e [2, 3, 14, 16,

142]

e [6, 100, 143–

150]

alpha-amylase 3.2.1.1 Str p 3 starch p⇒ Glc p + Malt p e [1] e [6,151]

beta-amylase 3.2.1.2 Str p 2 starch p⇒ Malt p e [1,152] e [6,19]

alpha-glucosidase 3.2.1.20 Str p Malt p⇒ 2 Glc p [152] [153,154]

adenylate kinase (pAdK) 2.7.4.3 En p ATP p + AMP p⇔ 2 ADP p [90] e [6,100]

glucose-6-phosphate dehydrogenase (p2-G6PDH) 1.1.1.49 PPP p G6P p + NADP+ p⇔ NADPH p + GL6P p [26] [116] e [6,100,118]

6-phosphogluconolactonase 3.1.1.31 PPP p GL6P p⇒ 6PG p f [26] [6] [119] [121]

phosphogluconate dehydrogenase (decarboxylating) 1.1.1.44 PPP p NADP+ p + 6PG p ⇒ NADPH p + CO2 p +

Ru5P p

[6,19,24] [155]

ribulose-phosphate 3-epimerase (pRuPepimerase) 5.1.3.1 PPP p Ru5P p⇔ X5P p f [26] [6,19] [155]

ribose-5-phosphate isomerase (pR5P isomerase) 5.3.1.6 PPP p R5P p⇔ Ru5P p [90] e [100]

transketolase (sedoheptulose 7-P - ribose 5-P) 2.2.1.1 PPP p GAP p + S7P p⇔ X5P p + R5P p e [10] e [4,6,100]

transketolase (fructose 6-P - erythrose 4-P) 2.2.1.1 PPP p F6P p + GAP p⇔ X5P p + E4P p e [10] e [4,6,100]

transaldolase 2.2.1.2 PPP p GAP p + S7P p⇔ F6P p + E4P p e [1,10] e [6,100]

phosphoribulokinase 2.7.1.19 Rub p ATP p + Ru5P p⇒ ADP p + Ru1,5P p [156] [157]

ribulose-bisphosphate carboxylase 4.1.1.39 Rub p CO2 p + Ru1,5P p⇒ 2 3PG p e [1] e [158]

3-deoxy-7-phosphoheptulonate synthase 2.5.1.54 Sh p PEP p + E4P p⇒ P p + DAH7P p [90]

3-dehydroquinate synthase 4.2.3.4 Sh p DAH7P p⇒ P p + 3DHQ p [159] e [100]

3-dehydroquinate dehydratase 4.2.1.10 Sh p 3DHQ p⇔ 3DSh p e [100]

shikimate dehydrogenase 1.1.1.25 Sh p NADP+ p + Sh p⇔ NADPH p + 3DSh p [160] [161]

shikimate kinase 2.7.1.71 Sh p ATP p + Sh p⇒ ADP p + Sh3P p [90]

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

3-phosphoshikimate 1-carboxyvinyltransferase 2.5.1.19 Sh p PEP p + Sh3P p⇔ P p + EPSP p [90] e [100]

chorismate synthase 4.2.3.5 Sh EPSP p⇒ P p + Ch p [90] e [4,6]

chorismate mutase 5.4.99.5 Tyr p Ch p⇒ PRE p [162] [6]

aromatic-amino-acid transaminase 2.6.1.57 Tyr p 2OG p + Agn p⇔ Glu p + PRE p [163]

arogenate dehydrogenase 1.3.1.43 Tyr p NAD+ p + Agn p⇒ NADH p + CO2 p + Tyr p [163]

arogenate dehydratase 4.2.1.91 Phe p Agn p⇒ CO2 p + Phe p [164]

ribose-phosphate diphosphokinase (pPRPPS) 2.7.6.1 His p ATP p + R5P p⇔ AMP p + PRPP p [90] [165]

ATP phosphoribosyltransferase 2.4.2.17 His p ATP p + PRPP p⇒ PP p + PR-ATP p [166] e [100,167]

phosphoribosyl-ATP diphosphatase 3.6.1.31 His p PR-ATP p⇒ PP p + PR-AMP p [90]

phosphoribosyl-AMP cyclohydrolase 3.5.4.19 His p PR-AMP p⇒ PR-AICARP p [90] [168]

1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)-

methylideneamino)imidazole-4-carboxamide isomerase

5.3.1.16 His p PR-AICARP p⇒ PRu-AICARP p e [100]

imidazoleglycerol-phosphate synthase 2.4.2.- His p Gln p + PRu-AICARP p ⇒ Glu p + IGP p +

AICAR p

[90] e [100]

imidazoleglycerol-phosphate dehydratase 4.2.1.19 His p IGP p⇒ IAP p [169] [169]

histidinol-phosphate transaminase 2.6.1.9 His p Glu p + IAP p⇒ 2OG p + HolP p [90]

histidinol-phosphatase 3.1.3.15 His p HolP p⇒ P p + Hol p [166]

histidinol dehydrogenase 1.1.1.23 His c 2 NAD+ p + Hol p⇒ 2 NADH p + His p e [100,170]

glutamate dehydrogenase (NAD(P)) 1.4.1.3 GG p NADP+ p + Glu p ⇔ NADPH p + 2OG p +

NH3 p

e [83] [6]

pyrroline-5-carboxylate synthase 2.7.2.11/1.2.1.41 Pro p ATP p + NADPH p + Glu p ⇒ ADP p + P p +

NADP+ p + GluSA p

[171]

Proline biosynthesis: spontaneous reaction / Pro p GluSA p⇒ PyrrC p

pyrroline-5-carboxylate reductase 1.5.1.2 Pro p NADH p + PyrrC p⇔ NAD+ p + Pro p [172] [173]

ornithine-oxo-acid transaminase 1.5.1.12 Arg p 2OG p + Or p⇔ Glu p + GluSA p [174]

amino-acid N-acetyltransferase 2.3.1.1 Arg p AcCoA p + Glu p⇒ CoA p + AcGlu p [90]

acetylglutamate kinase 2.7.2.8 Arg p ATP p + AcGlu p⇒ ADP p + AcGluP p [90] e [100]

N-acetyl-gamma-glutamyl-phosphate reductase 1.2.1.38 Arg p P p + NADP+ p + AcGluSA p ⇔ NADPH p +

AcGluP p

[90] e [6,100]

acetylornithine transaminase 2.6.1.11 Arg p 2OG p + AcOr p⇔ Glu p + AcGluSA p [90] e [100]

aminoacylase 3.5.1.14 Arg p AcOr p⇒ AcA p + Or p [90] [6]

ornithine carbamoyltransferase 2.1.3.3 Arg p Or p + CP p⇔ P p + Citru p [90] e [6,100]

carbamoyl-phosphate synthase 6.3.5.5 Arg p 2 ATP p + CO2 p + Gln p⇒ 2 ADP p + P p +

Glu p + CP p

e [4,6,19]

aspartate kinase 2.7.2.4 Thr p ATP p + Asp p⇔ ADP p + PAsp p [113, 122,

175]

e [176,177]

aspartate-semialdehyde dehydrogenase 1.2.1.11 Thr p P p + NADP+ p + AspSA p ⇔ NADPH p +

PAsp p

[113] e [100]

homoserine dehydrogenase 1.1.1.3 Thr p NAD+ p + HOMO-Ser p⇔ NADH p + AspSA p [178] [179]

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

homoserine kinase 2.7.1.39 Thr p ATP p + HOMO-Ser p ⇒ ADP p + P-HOMO-

Ser p

[113, 175,

180]

[181]

threonine synthase 4.2.3.1 Thr p P-HOMO-Ser p⇒ P p + Thr p [113,175] e [4,100]

cystathionine gamma-synthase 2.5.1.48 Met p Cys p + P-HOMO-Ser p⇒ P p + CysTh p [113] [6,182]

cystathionine beta-lyase 4.4.1.8 Met p CysTh p⇒ Pyr p + NH3 p + HOMO-Cys p [113]

methionine synthase (pMS) 2.1.1.13 Met p HOMO-Cys p + MTHF p⇒ THF p + Met p [175] e [19] [183]

succinate-CoA ligase (ADP-forming) 6.2.1.5 Lys p ATP p + CoA p + Succ p⇔ ADP p + P p + Suc-

cCoA p

[90] e [6,12]

dihydrodipicolinate synthase 4.2.1.52 Lys p Pyr p + AspSA p⇒ DPA p [113] e [100,184]

dihydrodipicolinate reductase 1.3.1.26 Lys p NADP+ p + THDPA p⇔ NADPH p + DPA p e [100,185]

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate 2.3.1.117 Lys p SuccCoA p + THDPA p⇒ CoA p + SuccAH p [186]

N-succinyltransferase

succinyldiaminopimelate transaminase 2.6.1.17 Lys p 2OG p + SuccDAH p⇔ Glu p + SuccAH p [90]

succinyl-diaminopimelate desuccinylase 3.5.1.18 Lys p SuccDAH p⇒ Succ p + DAH p [90] e [100] [90]

Diaminopimelate epimerase 5.1.1.7 Lys p DAH p⇔ mDAH p [90] e [6,100]

Diaminopimelate decarboxylase 4.1.1.20 Lys p mDAH p⇒ CO2 p + Lys p [113] e [100,187]

threonine ammonia-lyase 4.3.1.19 Iso Thr p⇒ NH3 p + 2OB p [90]

acetolactate synthase (iso. syn.) 2.2.1.6 Iso p Pyr p + 2OB p⇒ CO2 p + 2AHB p [188] e [4,19,100]

ketol-acid reductoisomerase(iso. syn.) 1.1.1.86 Iso p NADPH p + 2AHB p⇒ NADP+ p + DMV p [189] e [4,6,19,100]

dihydroxy-acid dehydratase(iso. syn.) 4.2.1.9 Iso p DMV p⇒ OMV p [90] e [6,100]

branched-chain-amino-acid transaminase (iso syn.) 2.6.1.42 Iso p 2OG p + Ile p⇔ Glu p + OMV p [190] e [100]

acetolactate synthase (valin syn.) 2.2.1.6 Val p 2 Pyr p⇒ CO2 p + AcLac p [188] e [4,19,100]

ketol-acid reductoisomerase (valin syn.) 1.1.1.86 Val p NADPH p + AcLac p⇒ NADP+ p + DIV p [189] e [4,6,19,100]

dihydroxy-acid dehydratase (valin syn.) 4.2.1.9 Val p DIV p⇒ OIV p [90] e [6,100]

branched-chain-amino-acid transaminase (val. syn.) 2.6.1.42 Val p 2OG p + Val p⇔ Glu p + OIV p [190] e [100]

2-isopropylmalate synthase 2.3.3.13 Leu p AcCoA p + OIV p⇒ CoA p + 2IPM p [90] e [6,19,100]

3-isopropylmalate dehydratase 4.2.1.33 Leu p 3IPM p⇔ 2IPM p [90] e [100]

Leucine biosynthesis: spontaneous rct / Leu p IPO p⇒ CO2 p + OIC p

3-isopropylmalate dehydrogenase 1.1.1.85 Leu p NAD+ p + 3IPM p⇒ NADH p + IPO p [90] e [6,100]

branched-chain-amino-acid transaminase (leu. syn.) 2.6.1.42 Leu p 2OG p + Leu p⇔ Glu p + OIC p [190] e [100]

phosphoglycerate dehydrogenase 1.1.1.95 Ser p NAD+ p + 3PG p⇒ NADH p + PHPyr p [90] e [6,191]

phosphoserine transaminase 2.6.1.52 Ser p PHPyr p + Glu p⇒ 2OG p + Pser p [25] [6]

phosphoserine phosphatase 3.1.3.3 Ser p Pser p⇒ P p + Ser p [90]

glycine hydroxymethyltransferase (pSHMT) 2.1.2.1 Gly p METTHF p + Gly p⇔ Ser p + THF p [90] e [6,100]

serine O-acetyltransferase 2.3.1.30 Cys p AcCoA p + Ser p⇒ CoA p + AcSer p [192] [193]

cysteine synthase 2.5.1.47 Cys p AcSer p + H2S p⇒ Cys p + AcA p [90] e [24,100]

aspartate transaminase (pAAT) 2.6.1.1 Asp p 2OG p + Asp p⇔ Glu p + OAA p [25,83] e [?,6,19]

phosphoribosylaminoimidazolecarboxamide 2.1.2.3 Pur p AICAR p + FTHF p⇔ THF p + PRFICA p e [100]

formyltransferase

IMP cyclohydrolase 3.5.4.10 Pur p IMP p⇔ PRFICA p [90]

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

adenylosuccinate synthase 6.3.4.4 Pur p Asp p + GTP p + IMP p ⇒ P p + GDP p +

Asuc p

[90] e [100,194]

adenylosuccinate lyase (AMP) 4.3.2.2 Pur p Asuc p⇔ Fum p + AMP p [90] [6,194]

nucleoside-diphosphate kinase (cNDPkin: GDP) 2.7.4.6 Pur p ATP p + GDP p⇔ ADP p + GTP p e [25,79] e [4,19,100]

malate dehydrogenase (oxaloacetate-decarboxylating)

(NADP+)

1.1.1.40 Pur p NADP+ p + Mal p ⇒ Pyr p + NADPH p +

CO2 p

[25] e [6,195,196]

acetate-CoA ligase 6.2.1.1 TAG p ATP p + CoA p + AcA p⇒ PP p + AcCoA p +

AMP p

[90] [197]

glutamate synthase (NADH) 1.4.1.14 GG p NADH p + 2OG p + Gln p⇒ NAD+ p + 2 Glu p e [10]

ATP citrate synthase 2.3.3.8 TAG p ATP p + CoA p + Cit p ⇒ ADP p + P p + Ac-

CoA p + OAA p

[90] [6] [198]

sucrose transporter / Up cm sucrose ex + H ext⇒ sucrose c e [199] e [200] [201,202]

AA transporter (asparagine) / Up cm Asn ex + H ext⇒ Asn c [201–203]

AA transporter (glutamine) / Up cm Gln ex + H ext⇒ Gln c [201–203]

O2-diffusion / Up cm O2 ex⇒ O2 c [204]

H2S diffusion (cm) / Up cm H2S ex⇒ H2S c

ethanol export / Ex cm Eth c⇒ Eth ex

lactate export / Ex cm Lac c⇒ Lac ex

CO2export / Ex cm CO2 c⇒

biomass export / Ex cm biomass⇒

pyruvate transporter (m) / Int m Pyr c⇔ Pyr m [205]

glutamate/aspartate transporter / Int m Glu c + Asp m⇔ Glu m + Asp c [206]

OAA/malate transporter / Int m OAA c + Mal m⇔ OAA m + Mal c [206]

OAA/2OG transporter / Int m OAA c + 2OG m⇔ OAA m + 2OG c [207]

OAA/succinate transporter / Int m OAA c + Succ m⇔ OAA m + Succ c [207]

OAA/citrate transporter / Int m OAA c + Cit m⇔ OAA m + Cit c [207]

OAA/aspartate transporter / Int m OAA c + Asp m⇔ OAA m + Asp c [207]

succinate/P transporter / Int m P c + Succ m⇔ P m + Succ c [208]

succinate/malate transporter / Int m Succ c + Mal m⇔ Succ m + Mal c [208]

malate/P transporter / Int m P c + Mal m⇔ P m + Mal c [208]

2OG/citrate transporter / Int m Cit c + 2OG m⇔ Cit m + 2OG c [209]

2OG/succinate transporter / Int m 2OG c + Succ m⇔ 2OG m + Succ c [209]

malate/citrate transporter / Int m Cit c + Mal m⇔ Cit m + Mal c [209]

succinate/citrate transporter / Int m Cit c + Succ m⇔ Cit m + Succ c [209]

phosphate transporter / Int m P c⇔ P m [210,211] [212]

ATP/ADP transporter / Int m ATP c + ADP m⇔ ATP m + ADP c [213]

GABA/glutamate transporter / Int m Glu c + Gaba m⇔ Glu m + Gaba c [203, 214,

215]

CO2-diffusion / Int m CO2 c⇔ CO2 m

O2-diffusion / Int m O2 c⇔ O2 m

H. vulgare T. aestivum, O. sativa, Z. mays dicotyledone species

reaction name EC path co equation t seed non-seed

tissue

t seed non-seed

tissue

seed non-seed

tissue

NH3-diffusion / Int m NH3 c⇔ NH3 m

malate/2OG transporter / Int m 2OG m + Mal c⇔ 2OG c + Mal m [209,216]

succinate/fumarate transporter / Int m Succ c + Fum m⇔ Succ m + Fum c [216]

AA transporter m (serine) / Int m Ser p⇔ Ser c [214]

AA transporter m (glycine) / Int m Gly c⇔ Gly m [214]

AA transporter(methionine) / Int p Met p⇔ Met c [214]

mal/succTransporter(plastid) / Int p Succ p + Mal c⇔ Succ c + Mal p [217]

malate/citrateTransporter / Int p Mal c + Cit p⇔ Cit c + Mal p [217]

malate/OAAtransporter / Int p Mal c + OAA p⇔ OAA c + Mal p [217] [218]

pyruvate transporter (p) / Int p Pyr c⇔ Pyr p [21,22]

AA transporter p (serine) / Int p Ser c⇔ Ser m [214]

AA transporter p (gly) / Int p Gly p⇔ Gly c [214]

mal Transporter / Int p Mal p⇔Mal c

X5P/P transporter / Int p X5P c + P p⇔ X5P p + P c [219]

ADP-glucose transporter (AMP) / Int p ADPglc c + AMP p⇔ ADPglc p + AMP c e [3] e [220]

G1Ptransporter / Int p P c + G1P p⇔ P p + G1P c e [3] e [221]

phosphate transporter / Int p P c⇔ P p [210,211] [222]

ATP/ADP transporter / Int p ATP c + ADP p⇔ ATP p + ADP c e [?, 223]

glucose transporter / Int p Glc c⇔ Glc p [224]

triosephosphat/P translocator (TPT1 GAP) / Int p P c + GAP p⇔ P p + GAP c e [31,224]

triosephosphat/P translocator (TPT2 DHAP) / Int p P c + DHAP p⇔ P p + DHAP c e [31,224]

triosephosphat/P translocator (TPT3 3-PGA) / Int p P c + 3PG p⇔ P p + 3PG c e [31,224]

phosphoenolpyruvat/phosphat transporter / Int p P c + PEP p⇔ P p + PEP c e [31,224]

malate/2OG transporter / Int p 2OG c + Mal p⇔ 2OG p + Mal c [217] [225]

malate/fumarate transporter / Int p Mal c + Fum p⇔ Mal p + Fum c

malate/glutamate transporter / Int p Mal c + Glu p⇔ Mal p + Glu c [217]

malate/aspartate transporter / Int p Mal c + Asp p⇔ Mal p + Asp c [217]

AA transporter (glutamine) / Int p Gln c⇔ Gln p [214]

AA transporter (citrulline) / Int p Citru c⇔ Citru p [214]

acetate diffusion / Int p AcA c⇔ AcA p

NH3S-diffusion / Int p NH3 c⇔ NH3 p

CO2-diffusion / Int p CO2 c⇔ CO2 p

H2S diffusion (p) / Int p H2S c⇒ H2S p

folate trasporter (THF) / Int p THF c⇔ THF p [226]

folate trasporter (MTHF) / Int p MTHF c⇔ MTHF p [226]

folate trasporter (METTHF) / Int p METTHF c⇔ METTHF p [226]

folate trasporter (FTHF) / Int p FTHF c⇔ FTHF p [226]

Set of reactions included in the reconstructed network. The references supporting each reaction are given for Hordeum vulgare

(barley), Triticum aestivum (wheat), Oryza sativa (rice), and Zea mays (maize). In case, no information on monocotyledone

species was available, information on dicotyledone species was included. With respect to seed-specific information, further

information on the tissue-level are given whenever available with e and f indicating that some of the references listed con-

tain endosperm- or filial tissue-specific information, respectively. Abbreviations: co: compartment; path: pathway; t: tissue.

Pathways: Glyc: Glycolysis/Gluconeogenesis; Suc: Sucrose-to-starch pathway; Ferm: Fermentation; Ace: Acetate biosyn-

thesis; Glu: Glutamate/Glutamine metabolism; Asp: Aspartate/Asparagine metabolism; Ala: Alanine biosynthesis; Ana: Ana-

/Cataplerosis; Arg: Arginine biosynthesis; GABA: GABA biosynthesis/degradation; Car: Carbohydrates biosynthesis; Fol:

Folate metabolism; oxP: Oxidative phosphorylatoion; For: Formate biosynthesis; BM: biomass biosynthesis/export; Met: Me-

thionine metabolism; Pur: Purine metabolism; PPP: Pentose phosphate pathway; Str: Starch degradation; TCA: Citrate cycle;

Rub: Rubisco bypass; Sh: Shikimate biosynthesis; Tyr: Tyrosine biosynthesis; Phe: Phenylalanine biosynthesis; GG: GS-

GoGAT; His: Histidine biosynthesis; Icit: Isocitrate metabolism; Pro: Proline biosynthesis; Thr: Threonine biosynthesis; Lys:

Lysine biosynthesis; Iso: Isoleucine biosynthesis; Val: Valine biosynthesis; Leu: Leucine biosynthesis; Ser: Serine biosynthe-

sis; Gly: Glycine biosynthesis; Cys: Cysteine biosynthesis; Pur: Purine biosynthesis; TAG: triacylglycerol biosynthesis; Up:

uptake; Ex: export; Int: Internal transport.

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