search

PNNL-CompBio / CONCERTO

Continuous integration and validation for genome-scale metabolic model consortia
Apache License 2.0
3 stars 3 forks source link

metabolite consumption test #6

Open djinnome opened 1 year ago

djinnome commented 1 year ago

Carsten Zengler confirmed consumption of metabolites in S. elongatus. We can use this to confirm nonzero uptake flux (but not growth).

JamesPino commented 1 year ago

Would this be as simple as checking for nonzero flux for a species, after running FBA? I would think adding importers would be straight forward, but should the metabolites also need to be incorporated into the rest of the metabolic network? There seems to be a lot of orphan metabolites. Should the network view not present a single graph? (general question about MM)

djinnome commented 1 year ago

That is right, adding an importer is a necessary, but not sufficient step in ensuring that you can get a nonzero flux for a metabolite. It should be incorporated into the rest of the metabolic network.

There are indeed both orphan metabolites (no producing or consuming reactions) and blocked metabolites (no consuming reactions) in most published genome-scale metabolic models. This can be due to insufficient testing (not everyone runs memote before publishing) or incomplete knowledge (no one knows which enzyme consumes the metabolite). There are also metabolites that can have internal consuming reactions, but no producing reactions. Those would be the easiest to add an import reaction to, if there is evidence that the external metabolite can be consumed.

djinnome commented 1 year ago

I say ignore "consumed metabolites" for milestone 2. Just focus on metabolites that enable growth.