Skip to main content

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

From: 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

Reaction name Gene name EC Equation kcat [s−1] [E] [mmol/gDW] Organism of kcat data Refs. for kcat 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]
  1. For each reaction reported in the table, encoding gene, equation, kcat and concentration of catalyzing enzyme ([E]) are reported. Moreover, the organism for which the kcat 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