Table 2 Kinetic model parameter values and sensitivites
From: Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast
Parameter | Description | Experimental reference | Initial value | Optimized value | Sensitivity | Enzyme |
|---|---|---|---|---|---|---|
vmax1 | Vmax for carbamoyl synthetase | [48] | 5.40 × 10−1 | 3.62 | 9.68 × 10−1 | URA2 |
Kutp | UTP binding constant | [48] | 1.40 | 1.41 | 5.49 × 10−3 | URA2 |
Katp | ATP binding constant | [48] | 7.50 | 1.29 | −8.68 × 10−1 | URA2 |
Kq | Km for glutamine | [48] | 7.00 × 10−2 | 5.78 × 10-2 | −9.32 × 10−2 | URA2 |
Kbc | Km for bicarbonate | [48] | 8.00 | 2.37 | −5.96 × 10−1 | URA2 |
vmax2 | Vmax for aspartate | [49] | 1.10 | 2.45 | 2.00 × 10−1 | URA2 |
Kasp | Km for aspartate | [50] | 2.80 × 10−1 | 1.68 × 10−1 | −1.24 × 10−1 | URA2 |
Km2 | Km for aspartate | [49] | 4.00 | 2.00 | −1.77 × 10−1 | URA2 |
vmax3 | Vmax for dihydroorotase |  | 2.47 × 101 | 2.87 × 101 | 1.21 × 10−4 | URA4 |
Km3 | Km for dihydroorotase |  | 7.00 × 10−1 | 1.27 | −1.20 × 10−4 | URA4 |
vmax4 | Vmax for dihydroorotate dehydrogenase | [21] | 9.18 × 101 | 9.18 × 101 | 1.73 × 10−5 | URA1 |
Km4 | Km for dihydroorotate dehydrogenase | [21] | 1.60 × 10−2 | 1.60 × 10−2 | −1.73 × 10−5 | URA1 |
vmax5 | Vmax for orotate phosphoribosyl transferase | [51] | 5.18 × 103 | 5.23 × 103 | 2.10 × 10−5 | URA5 |
Km5 | Km for orotate phosphoribosyl transferase | [51] | 1.97 × 10−2 | 1.95 × 10−2 | −2.10 × 10−5 | URA5 |
vmax6 | Vmax for OMP decarboxylase | [52] | 3.03 × 101 | 3.50 × 101 | 4.63 × 10−2 | URA3 |
Km6 | Km for OMP decarboxylase |  | 3.20 × 101 | 2.03 × 101 | −4.62 × 10−2 | URA3 |
vmax7 | Vmax for nucleoside diphosphate kinase | [53] | 6.48 | 5.83 | −6.92 × 10−5 | YNK1 |
Km7 | Km for nucleoside diphosphate kinase | [53] | 1.50 × 10−1 | 1.66 × 10−1 | 6.79 × 10−5 | YNK1 |
vmax8 | Vmax for CTP synthase | [54] | 5.40 | 1.63 × 10−1 | 2.46 × 10−2 | URA7 |
Km8 | Km for CTP synthase | [54] | 7.40 × 10−4 | 4.36 × 10−3 | −5.22 × 10−3 | URA7 |
vmax10 | Vmax for UMP kinase | [55] | 1.14 | 6.56 | −1.02 | URA6 |
Km10 | Km for UMP kinase | [55] | 1.50 × 10−1 | 2.68 × 10−2 | 1.00 | URA6 |
gpyr | Pyrimidine utilization rate |  | 4.00 × 10−1 | 1.98 × 10−1 | 1.16 × 10−4 |  |
KMp | Km for pyrimidine utilization |  | 5.80 | 5.49 | −1.16 × 10−4 |  |
bc | Intracellular bicarbonate conc. | [39] | 4.51 × 10−1 | 1.52 | 5.96 × 10−1 |  |
glu | Intracellular glutamine conc. | [39] | 4.51 × 10−1 | 5.46 × 10−1 | 9.32 × 10−2 |  |
asp | Intracellular aspartate conc. | [39] | 5.85 × 10−2 | 9.73 × 10−2 | 1.24 × 10−1 |  |
atp | Initial ATP conc. | [39] | 2.59 × 10−2 | 1.51 × 10−1 | 8.68 × 10−1 |  |