Further research showed that only five reactions (R2, R3, R4, R5, and R6) involving accumulation of NADPH were significantly altered. When ARA production was increased, three reactions (R4, R5, and R6) underwent flux increases, which corresponded to enhanced enzyme activities due to up-regulation of the genes encoding the enzymes. Of these, malic enzyme (ME, EC 1.1.1.40), which catalyzes the conversion of malate to pyruvate (R4), is considered a key enzyme in lipogenesis in M. alpina. ME expression and enzyme activity are enhanced during ARA production [43], and the minimization of metabolic adjustment (MOMA) method was used to investigate the role of this enzyme. With the biomass and ARA flux maximized by ME deletion using MOMA, 410 (22.11%) reactions showed flux changes (Additional file 6) compared with the wild type model. The ARA exchange reaction flux was lowered from 0.128 mmol gDW−1 h−1 to 0.079 mmol gDW−1 h−1, a decrease of 38.28%. Additionally, all reactions involving NADPH consumption reactions other than R13, R16, R51, and R53 were associated with lipid metabolism. These results indicated that the increase in ARA production was directly correlated with the NADPH consumption rate.