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Table 1 Physiological constraints used in constraints-based flux analysis for simulating metabolism of wild-type and lpdA knockout mutant of E. coli

From: Framework for network modularization and Bayesian network analysis to investigate the perturbed metabolic network

Enzyme

Metabolism

Condition

v13Cor vfmt

(mmol/g dry cell weight/h)

σ

Phosphotransferase system for D-glucose transport

Transport

Wild-type

-3.04

0.01824

  

ΔlpdA mutant

-2.48

0.1488

Cell growth rate

-

Wild-type

0.20

0.0100

  

ΔlpdA mutant

0.22

0.0110

Glucose-6-phosphate isomerase

Glycolysis/Gluconeogenesis

Wild-type

2.39

0.3107

  

ΔlpdA mutant

1.79

0.2327

Pyruvate kinase

Glycolysis/Gluconeogenesis

Wild-type

1.09

0.0109

  

ΔlpdA mutant

0.26

0.0026

Glucose 6-phosphate dehydrogenase

Pentose phosphate pathway

Wild-type

0.61

0.0732

  

ΔlpdA mutant

0.64

0.0768

Phosphogluconate dehydrogenase

Pentose phosphate pathway

Wild-type

0.61

0.0732

  

ΔlpdA mutant

0.32

0.0384

Phosphoenolpyruvate carboxylase

Anaplerotic reactions

Wild-type

0.67

0.0469

  

ΔlpdA mutant

1.61

0.1127

Phosphoenolpyruvate carboxykinase

Anaplerotic reactions

Wild-type

0.07

0.0070

  

ΔlpdA mutant

0.93

0.0930

Pyruvate dehydrogenase

Glycolysis/Gluconeogenesis

Wild-type

3.56

0.2136

  

ΔlpdA mutant

0.00

0.0000

α-ketoglutarate dehydrogenase

Citrate Cycle (TCA)

Wild-type

Not constrained

Not constrained

  

ΔlpdA mutant

0.00

0.0000

glycine cleavage system

Folate Metabolism

Wild-type

Not constrained

Not constrained

  

ΔlpdA mutant

0.00

0.0000

  1. Mean values (v13C or vfmt) of physiological constraints are based on 13C-based metabolic flux and cell culture data for the wild-type and lpdA knockout mutant of E. coli, both grown in continuous culture at dilution rate 0.2 h-1[33]. Standard deviations (σ) were calculated by multiplying these mean values with average error percentage associated with each reaction, taken from [43]. In addition to these, flux values of α-ketoglutarate dehydrogenase and glycine cleavage system were additionally constrained to zero due to the knockout of lpdA gene.