Implicit representation of the phosphate regulatory network reconstructed and graphically displayed in extended Petri net format. a) This Petri net model of the phosphate regulatory network in enteric bacteria  was predefined and used to perform the in silico experiments listed in Table 1 to give the data set compiled into the state vectors of Tables 3 and 4. Phosphorylation sites of the PhoR and PhoB proteins are represented as places (PhoR-S and PhoB-S, respectively). Site-directed deletion of the phosphorylation sites is modeled by removing the token from the respective places to give the initial marking of the Petri net used for simulation of the token flow in the mutants. The net shown in a) was also returned as one result of the reconstruction algorithm. It represents the combination of one controled reaction choosen for each difference vector obtained as shown in Figure 7a. The core of the Petri net as drawn in black is identical in all solutions. However, there are alternatives to the wiring of transitions and places due to the existence of more than one controled reaction for each of the corresponding difference vectors. Transitions with alternative wiring are drawn in red. The alternative controled reactions for each of those difference vectors are shown in panels b) to e). A detailed explanation of these alternatives is given as supplementary material in Additional file 1.