No growth in draft model from modelseed

[priya dharshini]

Hello Everyone, 

I am currently working with a draft plant model with multiple compartments consisting of 1155 metabolites and 1094 reactions. The draft model generated by modelseed, initially did not show any growth. Through the addition of demand reactions, it was found that precursor biotin was not being synthesized because all reactions preceding it were blocked. When I added a sink reaction for desthiobiotin (involved in biotin synthesis) the model shows some growth value. The flux through the added sink reaction is -0.008481.  The number of blocked reactions reduce from 707 to 404 with no change in the number of dead-end metabolites. 

How can I determine which gaps to fill to make the model grow without the sink reaction? Is there a possible way to trace from which pathway the model takes the flux of - 0.008481?

[Thomas Pfau]

Hi Priya,

You could have a look at the surfNet function, which allows you to navigate the network. Other visualisation methods might also help but can become quite crowded.

Best

Thomas

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[Almut Heinken]

Hi Priya,

is the organism known to synthesize biotin?

best

Almut

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[Ronan M.T. Fleming]

Hi Priya,

these tutorials should help

https://github.com/opencobra/COBRA.tutorials/tree/master/analysis/relaxedFBA

https://github.com/opencobra/COBRA.tutorials/tree/master/reconstruction/recon2FBAmodel

Regards,

Ronan

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[priya dharshini]

Thank you, Thomas !!

[priya dharshini]

Yes Almut, the organism synthesizes biotin.

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