Organism-specific Kegg Pathway: Must all boxes be high-lighted/present for a reaction to occur? I'm new to using Kegg and not sure how to interpret the position of the pathway enzymes in the pathway that I'm looking at. More specifically: If all boxes (of KOs) must be present/colored green or not for a reaction to occur. I'm looking at this pathway: < Looking at the 'help' for Kegg indicates that the KOs represent a protein complex, because the boxes are 'stacked' against each other. Is this correct? Specific reactions that I've been looking at: alpha-D-glucose-6P to beta-D-glucose-6P (One box is there, the other is missing). Or the route from Glyceraldehyde-3P to pyruvate. I'm thinking that these pathways must be present, but in the very first reaction only 1 of 2 boxes are colored. I suppose it's also a possibility that Kegg's database is simply incomplete?

Your interpretation of the pathway map is incorrect.

The boxes do not represent KOs (Kegg Orthologues) and they do not represent a protein complex. They are Enzyme Commission (EC) numbers and where there is more than one box this means that there is more than one enzyme that can catalyse the reaction.

In the case you cite the two enzymes are EC 5.3.1.9, glucose-6-phosphate isomerase, as you can see by clicking the box, and EC 5.1.3.15, glucose-6-phosphate 1-epimerase. Only one is needed to catalyse the reaction.