Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Table 1 List of k_cat values and protein quantifications integrated in iYO844 model

Reaction name	Gene name	EC	Equation	k_cat [s⁻¹]	[E] [mmol/g_DW]	Organism of k_cat data	Refs. for k_cat data
PGI	pgi	5.3.1.9	g6p → f6p	126	1.55 × 10⁻⁵	E. coli	[59]
TPI	tpiA	4.1.1.31	dhap → g3p	150	1.28 × 10⁻⁵	E. coli	[60]
GAPD_NAD	gapA	1.2.1.12	g3p + nad +pi → 13dpg + h + nadh	70	5.77 × 10⁻⁵	B. subtilis	[61]
PGK	pgk	2.7.2.3	13dpg + adp → 3pg + atp	329	3.60 × 10⁻⁵	E. coli	[62]
PGM	pgm	5.4.2.12	3pg → 2pg	765.9	8.85 × 10⁻⁶	B. subtilis	[63]
ENO	eno	4.2.1.11	2pg → h2o + pep	130.4	3.17 × 10⁻⁵	B. subtilis	[64]
G6PDH	zwf	1.1.1.49	g6p + nadp → 6pgl + h + nadph	174	8.05 × 10⁻⁶	E. coli	[65]
CS	citZ	2.3.3.16	accoa + h2o + oaa → cit + coa + h	49	2.51 × 10⁻⁵	B. subtilis	[30]
ICDHy	icd	1.1.1.42	icit + nadp → akg + co₂ + nadph	82	1.10 × 10⁻⁴	B. subtilis	[66]
FUM	citG	4.2.1.2	fum + h2o → mal-l	283.3	7.29 × 10⁻⁶	E. coli	[67]
MDH	mdh	1.1.1.37	mal-l + nad → h + nadh + oaa	177.1	1.06 × 10⁻⁴	B. subtilis	[68]
PTAr	pta	2.3.1.8	accoa + pi → actp + coa	651.6	8.49 × 10⁻⁶	B. subtilis	[69]
LDH_L	ldh	1.1.1.27	lac-l + nad → h + nadh + pyr	6416.6	3.60 × 10⁻⁶	B. subtilis	[70]
PGCDr	serA	1.1.1.95	3pg + nad → 3php + h + nadh	14.56	1.90 × 10⁻⁵	B. subtilis	[71]
OXADC	oxdC	4.1.1.2	h + oxa → co₂ + for	59	6.21 × 10⁻⁷	B. subtilis	[72]
MICITL	yqiQ	4.1.3.30	micit → pyr + succ	19	6.80 × 10⁻⁸	E. coli	[73]
OXGDC	menD	4.1.1.71	akg +h → co₂ + sucsal	0.2	6.80 × 10⁻⁸	B. subtilis	[55]

For each reaction reported in the table, encoding gene, equation, k_cat and concentration of catalyzing enzyme ([E]) are reported. Moreover, the organism for which the k_cat value was measured and the reference for this measurement are specified. The reaction names, with the associated gene names and equations, correspond to the annotations used in the iYO844 model

ISSN: 1475-2859