Single gene essentiality test

Use this tool to predict essentiality of a particular gene for synthesis of particular metabolite. The program will inactivate all reactions that require the gene and compute the maximal flux towards selected metabolite. If the maximal growth rate is close to 0 (cutoff 1e-3) or the system is declared infeasible, the gene is predicted to be essential for growth.

The output contains maximal theoretical growth rate, status of the optimisation and essentiality prediction.

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.

Select the gene to be inactivated. Only genes present in the model are shown on the list. Wild-type (WT strain) means that no genes are inactivated. The genes on the list are ordered by SCO numbers.