Reaction sides and directions
Content:
Reaction sides
A chemical reaction is usually represented by a chemical equation that consists of two reaction sides that are separated by a symbol. Each side is comprised of a set of reaction participants that are defined by their structures and stoichiometric coefficients.
In Rhea reactions there is no semantic meaning attached to these two sides, i.e. the left side does not necessarily represent substrates and the right side products. When the stoichiometric coefficient is equal to 1, it is not displayed.
Rhea reactions are chemically balanced for mass and charge at pH 7.3 (see details), i.e. the sum of the formulas on the left side is identical to the sum of the formulas on the right side, and likewise for the sum of the charges of the two sides.
Reaction directions
Depending on external conditions, a chemical reaction may have a net flux from the left to the right side, or vice versa, or be at equilibrium. To allow users of Rhea to specify what is known about the direction of a reaction, Rhea organizes them in quartets that have identical reaction sides, but a different direction of net flux:
| Equation symbol | Direction | Meaning |
|---|---|---|
| = | undefined | The net flux of the reaction is undefined. |
| => | left-to-right (aka forward) | There is a net flux from left to right. |
| <= | right-to-left (aka reverse) | There is a net flux from right to left. |
| <=> | bidirectional | The reaction is at equilibrium. |
Each reaction of a Rhea quartet has its own identifier. A mapping of the identifiers of a Rhea quartet can be downloaded from our FTP site.
Not all databases that describe reactions use all these directions. Rhea links to the following resources via the Rhea reactions that have the same direction as the one in the linked record (see links to other resources):
| Resource | undefined | left-to-right | right-to-left | bidirectional |
|---|---|---|---|---|
| UniProtKB | yes | yes | yes | no |
| Enzyme Classification (EC) | yes | no | no | no |
| Gene Ontology (GO) | yes | no | no | no |
| MetaCyc / EcoCyc | yes | yes | yes | yes |
| KEGG | no | no | no | yes |
| Reactome | yes | yes | yes | no |
| M-CSA/MACiE | no | yes | yes | no |