Table 1 Comparison of MicrobesFlux and other web-based fluxomics software

Model generation

Database

KEGG

KEGG

RAST

iJR904

None

Number of organisms

1,194

~780

~5,000

1

NA

Embedded functions for model reconstruction ¹

Inflow/outflow introduction

●

●

●

Biomass production implementation

●

●

●

●

Automated generation of biomass composition²

○

Heterologous pathways

●

●

●

Knock out pathways

●

●

●

Reactant/product Modification

●

●

Automated mass balance

●

●

●

●

●

Automated compound charging and charge balance

●

Transport reactions with coupling to ATP and proton translocation³

○

○

○

Prediction of reaction directionality/reversibility based on thermodynamics⁴

Gap-fill⁵

○

○

○

Gene-Protein-Reaction associations

●

●

Reaction compartments

●

●

Flux analysis

FBA

●

●

●

●

●

FBA with customized objective function

●

●

Dynamic FBA

●

Flux Variability Analysis

●

Output

Pathway visualization

●

●

●

●

●

SBML output

●

●

●

●

●