1. Unbalanced Reactions by
Markus Krummenacker
Q4 2013

2. FBA needs balanced reactions
If an FBA model contains unbalanced reactions, it can cause infinite sources of material
Thus, reactions have to balance all the atoms on the left with the atoms on the right
Including H+ . Our convention is pH7.3
Reaction balance checker filters away reactions that are unbalanced or undetermined

3. .log file lists unbalanced reactions
Lists unbalanced reactions for the current PGDB (but not for MetaCyc)
4 sections of problematic reactions:
In pathways
Standalone small-molecule reactions
In signalling-pathways (which contain non-metabolic protein metabolites). (Should be empty these days, because of an earlier filtering step.)
All other problematic reactions. Usually, macromolecule metabolites. Usually, not involved in core metabolism.

4. Common sources of problems (1)
SRI has ongoing curation efforts to fix erroneous reactions. By now, most straight forward errors in compound structures or reaction equations have been fixed.
Sometimes, in old PGDBs, reactions are wrong, which no longer exist in MetaCyc, and so they can’t be updated automatically.
Some reactions describe fairly unknown biochemistry. Lack of knowledge is indicated by the CANNOT-BALANCE? flag (in Reaction Editor).

5. Common sources of problems (2)
H+ unbalanced, with metabolite classes.
Protonation by Marvin can not handle structures with R groups. Thus generic reactions have not been automatically proton-balanced.
Have to be manually balanced by using Marvin to edit structure (by educated guess)
Class metabolites without structures.
Macromolecule metabolites, like redox proteins
Tricky class metabolites for extremely generic classes. Example: SUGAR-PHOSPHATASE-RXN

6. Remedies Add/Edit metabolite structures with Marvin
Edit reaction with Reaction Editor
Balance checker in editor, shows residual
Special cases of the balance checker:
Structure with R groups: R, R1, R2, R3, R4, R5
MOLECULAR-WEIGHT slot set (by Frame Editor) to less than 0.01 (e.g. E- , light)
Frame pairs, where one is a modified form of the other. Structure of modified form has to use unmodified frame as an “atom”. Only 1 such reference supported currently. Example: NAD(P)+ / NAD(P)H

7. Consistency Checker
Under Manual Tasks, “Generate reaction balance report”
Independent of FBA. But a good idea in any case.
Right-click on listed reaction, to show or fix

8. Compartments of Transporters
For FBA modelling core metabolism, a few transport reactions are essential: ATP synthase, some ETRs like cytochrome oxidase, NADH:ubiquinone oxidoreductase
Pathologic inference for a PGDB may not yet infer the correct compartments. RXN-LOCATIONS slot will be cleared, and so defaults are “in” and “out”
Reaction Editor can be used to manually fix compartment assignments