Figure 4

Mapping between the sensor kinase and the response regulator families of the Ntr-type two-component system. In the pairs of confronted trees, the tree on the left corresponds to the response regulators and the one on the right to the sensor kinases. The representations of the trees were generated with MEGA [21]. a) Schematic representation of the predicted pairings between KOs. Within each of the trees, the colour of the leaves corresponds to the 6 KO (12 in the two trees). The inter-tree lines represent the predicted KO pairings, derived from the individual pairings between proteins. These KO pairings are in full agreement with the KO-KO interactions based on the original 14 pairs of interacting proteins (see Materials and Methods). b and c) Detailed view of interactions #4 and #7 in panel a and the corresponding sub-trees. In these panels, the inter-tree black lines represent the potentially incorrect protein pairings predicted by the method. In these two examples, it can be seen that all these potentially incorrect pairings are possibly due to wrong KO assignments (see Results). The two green lines represent correct pairings even though the KO assignments look incorrect. Figure S2 (supplementary material) shows all the pairs in the predicted mapping, and Table S2 contains the whole list of protein pairs within that mapping indicating whether they are correct or not.