Reaction essentiality scan

Use this tool to find reactions essential for the synthesis of selected metabolite. Flux through each reaction in turn is constrained to 0 and FBA is run. Calculations will take about 10 minutes. Results will be displayed, as calculation progresses.

The output contains the name of the reaction which was removed from the system, its formula, status of FBA (OPTIMAL, UNDEFINED), maximal flux towards selected metabolite and gene annotation linked to ScoDB, ScoCYC and KEGG.

Experimental conditions. The form below shows definition of glucose minimal medium. Media conditions are defined by specifying nutrient transport reactions in the following format: Reaction_name lower_bound upper_bound comment. You can modify experimental conditions by changing their maximal uptake rates. You can also constrain any reaction in the system by stating its name, lower bound and upper bound. See model file and the list of metabolite names.

Optimisation criterion. Optimisation criterion is specified as the name of metabolite. The program computes maximal theoretical flux towards this metabolite. Default optimisation criterion is a BIOMASS. The maximal flux towards BIOMASS represents maximal theoretical growth rate under given media conditions.

Optimisation criterionMedia conditions

The model: The GSMN model file including reaction formulas and gene/reaction associations can be found here. Follow this link for the list of metabolite names.