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fix: sedoheptulose kinase/phosphatase reactions - #551

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haowang-bioinfo merged 5 commits into
SysBioChalmers:developfrom
Devlin-Moyer:develop
May 6, 2023
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fix: sedoheptulose kinase/phosphatase reactions#551
haowang-bioinfo merged 5 commits into
SysBioChalmers:developfrom
Devlin-Moyer:develop

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@Devlin-Moyer

@Devlin-Moyer Devlin-Moyer commented May 5, 2023

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Main improvements in this PR:

Make changes proposed in #547:

  • Remove MAR04568, since it doesn't appear to actually occur in humans
  • Make MAR04567 irreversible in the direction of ATP consumption (and switch products and reactants so it can't only have negative fluxes)
  • Add new reaction MAR20070 to represent the corresponding phosphatase reaction: MAM02883c + MAM02040c -> MAM02884c + MAM02751c

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Selected develop as a target branch
  • Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

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ah you made it!

very good - welcome to feedback anything unclear and should be instructed with tutorial

Comment thread data/deprecatedIdentifiers/deprecatedReactions.tsv Outdated
Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
@Devlin-Moyer

Devlin-Moyer commented May 5, 2023

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The tutorial covered everything I needed to know and, imo, was clearly written

@haowang-bioinfo
haowang-bioinfo merged commit 757585f into SysBioChalmers:develop May 6, 2023
@haowang-bioinfo haowang-bioinfo mentioned this pull request May 7, 2023
edkerk added a commit that referenced this pull request Jul 11, 2026
…1003) (#1032)

MAR20070 had its subsystem set to "Pentose Phosphate Pathway" (title
case) when it was added in #551, while the other 25 reactions of that
pathway use "Pentose phosphate pathway". This made the pentose phosphate
pathway appear as two subsystems, one containing only MAR20070. Correct
MAR20070 to "Pentose phosphate pathway" so the two merge into one.
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3 participants