Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

BMC Bioinformatics

Table 2 Estimated parameter values and confidence intervals

	Parameter	Value	95% Confidence	Units
PTS	k_cat	20.7	±9.1	mmol/mg protein/hr
PGI	k_cat	40.2	±9.5	mmol/mg protein/hr
	K_eq	1.23	±0.29	Dimensionless
PFK	k_cat	26	±35	mmol/mg protein/mM/hr
ALDO	k_cat	3.965	±0.010	mmol/mg protein/mM/hr
	K_eq	0.18	±0.17	mM
	K_fdp	0.0074	±0.0036	mM
TPI	k_cat	10000	±14000	mmol/mg protein/hr
	K_eq	0.11400	±0.00031	Dimensionless
GAPD	k_cat	10000	±4100	mmol/mg protein/mM²/hr
	K_eq	1.21	±0.14	Dimensionless
PGM	k_cat	9995	±40	mmol/mg protein/hr
	K_eq	0.53570	±0.00063	Dimensionless
PGK	k_cat	54.3	±2.9	mmol/mg protein/hr
	K_eq	5512.1	±1.2	Dimensionless
ENO	k_cat	2	±45	mmol/mg protein/mM/hr
	K_eq	1.4	±4.1	Dimensionless
PYK	k_cat	40	±49	mmol/mg protein/hr
PDH	K_cat	10.4	±4.6	mmol/mg protein/hr
	K_pyr	0.000020	±0.000029	mM⁴
PPC	k_cat	2.15	±1.80	mmol/mg protein/hr
	K_fdp	2.5	±6.5	mM
	K_pep	0.10	±0.16	mM
G6PDH	k_cat	859.6	±1.1	mmol/mg protein/mM²/hr
GND	k_cat	18.5	±10.8	mmol*mM/mg protein/hr
	K_6pg	0.021	±0.012	mM
RPI	k_cat	549.46	±0.69	mmol/mg protein/mM/hr
	K_eq	1.40000	±0.00019	Dimensionless
RPE	k_cat	10000	±13000	mmol/mg protein/mM/hr
	K_eq	0.4900	±0.0044	Dimensionless
TKT1	k_cat	10000	±7800	mmol/mg protein/mM²/hr
	K_eq	1.99	±0.012	Dimensionless
TKT2	k_cat	10000	±5800	mmol/mg protein/mM²/hr
	K_eq	3.500	±0.013	Dimensionless
TALA	k_cat	10000	±2300	mmol/mg protein/mM²/hr
	K_eq	0.3675	±0.0021	Dimensionless

Binding coefficient parameters have units of mM, except for K_pyr in PDH, which has units of mM⁴. Equilibrium constants (K_eq) are dimensionless, except for ALDO, which has units of mM. Values for k_cat have units such that fluxes have units of mmol/gDW/h. Global upper and lower bounds for binding and enzyme activity were 10⁴ and 10^-6, respectively. Bounds on equilibrium constants were 0.35K_eq^o and 2.85K_eq^o, where K_eq^o is the measured equilibrium constant.

ISSN: 1471-2105