Reactions

Reactions in Genopsis represent the chemical conversion of one or more compounds to one or more compounds. Compounds participating in a reaction can be modified and seen in the 'Equation' section, and seen in the 'Related pages' section.

Reactions are associated with Enzymes. One enzyme can be associated with multiple reactions AND one reactions can be associated with multiple enzymes, seen in the 'Related pages' section of the page.

Adding a new reaction

1. First search to ensure the reaction does not yet exist in Genopsis. If it does not exist, go to the appropriate Enzyme's page. If you need to add a non-heterlogous enzyme first, see the 'Enzyme' help page for instructions.
2. Scroll to the 'Reactions' section. Select 'Add': type a new unique reaction name. Hit 'Save'.
3. Fill out the form. In the 'Equation' section, search for existing compounds by their name (capitalization matters). Choose to add to the left or right side, and adjust the stoichiometry.
   1. If a compound does not yet exist in Genopsis, type a unique name and hit 'Add to Left/Right'. It will then prompt you to provide the compound information in line. To cancel adding a new compound hit 'Cancel'. Otherwise hit 'Save'. You may need to hit 'cancel' between each new compound.
   2. Adding a compound will automatically associate it with the reaction in the 'Related pages' section.
4. If known, adjust flux bounds. Otherwise leave as defaults.
5. If you know EC number and RHEA identifier, please provide.
6. If you need to associate another enzyme with the reactions, see instructions below.

Add heterologous reactions

Note: heterologous reactions will not end with an associated enzyme.

1. Go to Enzyme for testing purposes
2. Follow steps 2-5 above.
3. On the Enzyme for testing purposes page, delete the reaction from the 'Reactions' section which removes the relationship, not the reaction.

Associate existing reaction to an additional enzyme

1. Go to the enzyme's page. scroll to Reactions box. 'Add': type the name or abbreviated name of the reaction to associate.
2. Hit 'Save'.