Equation not balanced

[MathySmith]

Description of the issue

A proton is missing on the right side; here is the correction:

ATP + H2O + L-Arabinose[e] <=> ADP + L-Arabinose[c] + 2 H+ + Phosphate [C10H12N5O13P3(4-) + H2O + C5H10O5 <=> C10H12N5O10P2(3-) + C5H10O5 + 2 H(+) + PO4(3-)]

Page

http://bigg.ucsd.edu/universal/reactions/ARBabc

Browser

Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/55.0.2883.87 Safari/537.36

[zakandrewking]

Hi @MathySmith-

We check for mass balance during database loading, and I just double checked a few of the cases you mention, and they look OK. A couple things to note:

1. BiGG keeps track of metabolite formulae for each model separately. Therefore, a reaction like ARBabc might be balanced in one model and not in another.

2. There are known issues with metabolites balance. For instance, I just checked the model iJR904 for unbalanced reactions and found ~ 20. However, all of these were unbalanced in the published model as well. We strive to maintain exactly the same mathematical representation of these models that was published originally, so we do not try to fix these unbalanced reactions.

3. This strategy could potentially change for a future version of BiGG Models, so we are always interested in getting more feedback.

I am going to close these issues for now, but feel free to ask more questions here.

Best,

zak

[MathySmith]

Hi Mr King,

What an honor for me to be contacted by you in person! Sorry for this sharp introduction, but it really means something to me, as I've read several of your publications and estimate a lot your work and Mr Palsson's work as well...

Thank you very much for your explanations by the way, I've understood what you said. I am currently checking the reactions for a metabolic model of a gut bacteria and BiGG is very useful to help me check all metabolites and enzymes involved in each reaction.

Thanks again for your feedback, if I have any further questions I'll let you know.

Best regards,

Mathias BONAL Research Associate Fellow KU Leuven Guest Student

mathias.bonal@student.kuleuven.be mathias.bonal@ulb.ac.be

Rega Institute Laboratory of Molecular Bacteriology Department of Microbiology and Immunology KU Leuven, Campus Gasthuisberg Heretsraat 49, postbus 1028 3000 Leuven Belgium

Interuniversity Institute of Bioinformatics in Brussels Vrije Universiteit Brussel La Plaine Campus, Triomflaan, BC Building, 6th floor 1050 Brussels Belgium

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De : Zachary A. King notifications@github.com Envoyé : mercredi 1 février 2017 19:24 À : SBRG/bigg_models Cc : MathySmith; Author Objet : Re: [SBRG/bigg_models] Equation not balanced (#242)

Hi @MathySmith-

We check for mass balance during database loading, and I just double checked a few of the cases you mention, and they look OK. A couple things to note:

1. BiGG keeps track of metabolite formulae for each model separately. Therefore, a reaction like ARBabc might be balanced in one model and not in another.

2. There are known issues with metabolites balance. For instance, I just checked the model iJR904 for unbalanced reactions and found ~ 20. However, all of these were unbalanced in the published model as well. We strive to maintain exactly the same mathematical representation of these models that was published originally, so we do not try to fix these unbalanced reactions.

3. This strategy could potentially change for a future version of BiGG Models, so we are always interested in getting more feedback.

I am going to close these issues for now, but feel free to ask more questions here.

Best,

zak

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