'oops... Something Went Wrong' Error for 1,3-beta-Glucan

[Scott McCain]

Hi!

Thanks for putting all these resources in one place on your website! I've found it extremely helpful and informative.

I'm trying to get Gibbs Free Energies of reactions for some reactions in Yeast8 Genome-Scale Flux Balance Analysis model, but running into some challenges. I don't know if it's because the reaction deltaG can't be computed, or if I'm putting the reaction equation incorrectly into the search bar. For example, I'm interested in the the reaction done by 1,3-beta-glucan synthase. When I search for reactions with 1,3-beta-glucan, and try to click on this, there is the 'error' and the 'oops' link. I also haven't been able to successfully search for the reaction I'm looking for as well (specifically, "UDP-glucose + 1,3-beta-Glucan = 1,3-beta-Glucan + UDP", but I've tried other variations as well).

Here are some screen shots of what I'm getting!

Any help is appreciated,

Scott

[Robert Giessmann]

Dear Scott,

sorry for the long delay to follow-up on your question. I wanted to notify you asap that you have probably run in a difficult problem, but wasn't completely sure, and wanted to check myself... So here we go:

What you are looking for is a chain of carbohydrates, and you will find e.g. this representation in KEGG: https://www.genome.jp/entry/C00965

The reaction you are looking for is here in KEGG: https://www.genome.jp/entry/R03118

Please correct me here if I got it wrong.

Assuming it is correct, the problem is that eQuilibrator does not know what to do with C00965, because it is not chemically defined -- it doesn't know how many units of glucose it should consider.

Your assumption might be that, starting from a specific chain length, it does not matter much whether n=20 or n=21. Right?

What you can do (respectively, I could do for you), is to explicitly provide a chemically defined reaction; say "UDP-glucose + 1,3-Glucose_(20) = UDP + 1,3-Glucose_(21)". Maybe it's better to take n=2->3 and n=3->4, but you know what I mean?

Do you know of any experimental measurements for that reaction? This might be very interesting! In the data used to train eQuilibrator, I did not find any (one-step) polymerisation reactions like this.

Hope this helps a bit -- happy to discuss further! Best,

   Robert

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