Special symbols

A few special symbols deserve a particular treatment when computing MNXref or mapping models

Special symbols for chemical:

• BIOMASS - used to tag growth reaction.
• MNXM01 or PMF (Proton Motive Force) - used to distinguish protons that are transported across a membrane from those that are introduced to balance chemical equations (MNXM1).
• WATER

Special symbols for compartments:

• BOUNDARY - used to tag "external" exchange reactions. As a consequence, reaction with an empty side are forbidden here.

Special symbols for reaction:

• EMPTY - designates reactions that have no-reactants after being mapped to MNXref, typically these correspond to acid-base or some tautomerization reactions.

Special symbols for peptides/genes:

• SPONTANEOUS - used to tag spontaneous reactions. Reactions with no enzymes nor this tag have an unknow or unspecified catalyst.