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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GNU General Public License v3.0
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Question about gap-filling medium #80

Closed altaiii closed 3 years ago

altaiii commented 3 years ago

Hello,

I'm trying to use gapfill with my custom-made medium. I've seen that file format for medium was like (compounds,name,maxFlux). May I ask how I can get maxFlux numbers?

Thank you in advance.

for bug reports and errors please report the output of: ./gapseq test

Waschina commented 3 years ago

Hi,

the maxFlux values correspond to the (potential) maximum uptake rates of the nutrient by the organism. The unit is mmol/hr/gDW (mmol per hour and per gram dry weight).

As an example: The maximum uptake rate of Glucose by Salmonella typhimurium ranges from 7.6 to 21.6 mmol/hr/dDW (link).

Hope this helps

altaiii commented 3 years ago

@Waschina Thank you for your explanation. It’s definitely helpful. However, what if a maxflux is unknown for my target metabolites or organisms? In that case, what can I do?

altaiii commented 3 years ago

@Waschina Can I also ask one more thing? How the compound composition of media gets determined when it's not provided in KOMODO (DB for known media)?

Waschina commented 3 years ago

Hi @altaiii ,

maxFlux values if no experimental information is available for the organism-compound-combination

This is unfortunately usually the case. I think (please everyone correct me if I am wrong) that the metabolic modelling community does not follow a standardized way to deal with this lack of knowledge. However, what is commonly done is that experimental data on maximum uptake rates from a few model organisms is propagated to non-model organisms. Simply said, since the maximum uptake rate of Glucose in the Escherichia-Shigella genus has been estimated to range between 6 and 18.5 mmol/gDW/hr, many researchers use this also as maxFlux for Glucose or other potential main Carbon+Energy sources in their in-silico growth/gapfill media formulations. Another common 'reference point' is the maximum uptake rate of oxygen, which has experimentally been estimated to ~27 mmol/gDW/hr.

That said, the definition of maxFlux (or better: lower bounds for the exchange reactions) is one crucial source of uncertainty in genome-scale metabolic modelling. I highly recommend this recent article by Bernstein, Sulheim, Almaas and Segrè in Genome Biology; where this and other sources of uncertainty are discussed.

Concerning your second question: You may find this article by @maringos helpful, which exactly addresses this question.

Best wishes Silvio

Midnighter commented 3 years ago

Depending on your use-case, you can also set the uptake rate of your carbon source to 1 mmol / gCDW / h. The optimal growth or production rate is then directly the flux yield. So if you are not interested in replicating experimental replication but rather metabolic engineering this may be just as or even more informative.