. 2014 Sep 19;13:128. doi: 10.1186/s12934-014-0128-x

Table 1.

List of selected reactions contained in the RN and GN model and associated reaction IDs that will be used when discussing results of CASOP and cut set analysis

Reaction ID	Reaction
(enzyme/name)
R1 (NDH1)	NADPH + 5 H ⁺ + PQ ⇒ NADP ⁺ + PQH ₂ + 4 H $_{tll}^{+}$
R2 (NDH1)	NADPH + 4 H ⁺ + PQ + H ₂O + CO ₂ ⇒ NADP ⁺ + PQH ₂ + 4 H $_{tll}^{+}$ + HCO3 ⁻
R3 (Cox)	4 Reduced plastocyanin + O ₂ + 8 H ⁺ ⇒ 4Oxidized plastocyanin + 4 H $_{tll}^{+}$ + 2 H ₂O
R4 (Cyd)	2 PQH ₂ + O ₂ + 4 H ⁺ ⇒ 2 PQ + 4 H $_{tll}^{+}$ + 2 H ₂O
R5 (Mehler)	O ₂ + Reduced ferredoxin ⇒ Oxidized ferredoxin + O $_{2}^{-}$
R6	2 O $_{2}^{-}$ + 2 H ⁺ ⇒ H ₂ O ₂ + O ₂
R7 (FQR)	PQ + 2 Reduced ferredoxin + 2 H ⁺ ⇒ 2 Oxidized ferredoxin + PQH ₂
R8	D-Ribulose 1,5-bisphosphate + O ₂ ⇒ 3-Phospho-D-glycerate + 2-Phosphoglycolate
R9	O ₂⇒ O _2cax
R10	2-Phosphoglycolate + H ₂O ⇒ Glycolate + Orthophosphate
R11	2-Phosphoglycolate _cax⇒ 2-Phosphoglycolate
R12	NADPH + NAD ⁺ ⇔ NADP ⁺ + NADH
R13	ATP + Acetate ⇔ ADP + Acetyl-phosphate
R14	sn-Glycerol 3-phosphate + NAD ⁺ ⇔Glycerone-phosphate + NADH + H ⁺
R15	ATP + Glycerol ⇒ ADP + sn-Glycerol3-phosphate
R16	Glycerol + NADP ⁺ ⇔ D-Glyceraldehyde + NADPH + H ⁺
R17	D-Glyceraldehyde + NAD ⁺ + H ₂O ⇔D-Glycerate + NADH + H ⁺
R18	5,10-Methylenetetrahydrofolate + Glycine + H ₂O ⇔ Tetrahydrofolate + L-Serine
R19	Glycine + Tetrahydrofolate + NAD ⁺ ⇒5,10-Methylenetetrahydrofolate + NH3 + CO2 + NADH + H ⁺
R20	D-Glycerate + NADP ⁺ ⇔ Hydroxypyruvate + NADPH + H ⁺
R21	L-Serine + Glyoxylate ⇔ Hydroxypyruvate + Glycine
R22	Glycine + 2-Oxoglutarate ⇔ Glyoxylate +L-Glutamate
R23	3-Phospho-D-glycerate + NAD ⁺ ⇔3-Phosphonooxypyruvate + NADH + H ⁺
R24	O-Phospho-L-serine + 2-Oxoglutarate ⇔3-Phosphonooxypyruvate + L-Glutamate
R25	O-Phospho-L-serine + H ₂O ⇒ L-Serine +Orthophosphate
R26	(S)-Malate + NAD ⁺ ⇔ Oxaloacetate + NADH + H ⁺
R27	D-Fructose-6-phosphate + Orthophosphate ⇒ Acetyl-phosphate + D-Erythrose-4-phosphate + H ₂O
R28	D-Xylulose-5-phosphate + Orthophosphate ⇒ Acetyl-phosphate + D-Glyceraldehyde-3-phosphate + H ₂O
R29	Ethanol ⇒ Ethanol _ex
R30	Acetaldehyde + NADPH + H ⁺⇒ Ethanol + NADP ⁺
R31	Pyruvate ⇒ CO ₂ + Acetaldehyde
R32	ADP + Phosphoenolpyruvate ⇒ ATP + Pyruvate
R33	CO ₂ ⇒ CO _2ext
R34	ATP + D-Fructose-6-phosphate ⇒ ADP + D-Fructose-1,6-bisphosphate
R35 (ATPm)	1 ATP + H ₂O ⇒ 1 ADP + Orthophosphate
R36	Cyanophycine + 2 H ₂O ⇒ 1 L-Aspartate + 1 L-Arginine + Cyanophycin-polymer
R37	1 L-Aspartate + 1 L-Arginine + 2 ATP + Cyanophycin-polymer ⇒ Cyanophycin + 2 Orthophosphate + 2 ADP
R38	ATP + Sedoheptulose-7-phosphate ⇒ ADP + Sedoheptulose-1,7-bisphosphate

Some specific reaction (or enzyme) names used in this study (e.g., in Figure 1) are also given. The corresponding reaction IDs used in the model of Knoop et al. [39] can be found in Additional file 1: Table S1.