Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
Figure 3
Proof of principle: Gap filling highly-likely reactions in B. subtilis.
B. subtilis synthesizes lipids via the non-mevalonate pathway (blue) [37]. We removed this pathway from the B. subtilis genome-scale model and then tried to fill the gap using both the likelihood and parsimony-based approaches. The parsimony-based gap filling approach instead filled the gap with the mevalonate pathway (red), which is shorter but not supported by genetic evidence. The likelihood-based approach filled the gap with the correct pathway. Black indicates reactions that were not knocked out (there was no explicit link to literature evidence in the B. subtilis model). The numeric labels are the computed likelihoods of gap filling reactions.