I have been using carveme to generate metabolic reconstructions of bacterial isolates and testing them with memote. In the "Charge Balance" test, memote is routinely flagging ~200 reactions with unbalanced charge.
After checking some reactions, it seems that some metabolite species are indeed defined with incorrect charges in the reconstructions, and the root cause for this seems to lie in the pre-generated universe .xml files. For example, M_6pgg_c is listed correctly with charge 0 on the pre-built "bigg_universe.xml" file, but with -2 charge in "universe_bacterial.xml".
How straightforward is it to generate the specific bacteria/gram+/- universal models from scratch? If I understood correctly, the "BiGG" universal model is easy to generate automatically but the bacteria ones require more manual curation?
Please let me know if you would like more information and examples to reproduce, and I am also happy to contribute to the fix and test.
Hi,
I have been using carveme to generate metabolic reconstructions of bacterial isolates and testing them with memote. In the "Charge Balance" test, memote is routinely flagging ~200 reactions with unbalanced charge.
After checking some reactions, it seems that some metabolite species are indeed defined with incorrect charges in the reconstructions, and the root cause for this seems to lie in the pre-generated universe .xml files. For example, M_6pgg_c is listed correctly with charge 0 on the pre-built "bigg_universe.xml" file, but with -2 charge in "universe_bacterial.xml".
How straightforward is it to generate the specific bacteria/gram+/- universal models from scratch? If I understood correctly, the "BiGG" universal model is easy to generate automatically but the bacteria ones require more manual curation?
Please let me know if you would like more information and examples to reproduce, and I am also happy to contribute to the fix and test.
Best Wishes, Gonçalo