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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

From: Cyanobacterial biofuels: new insights and strain design strategies revealed by computational modeling

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 + 4 Oxidized 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 2e x t
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
  1. 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.