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Unbalance reactions about FAD/Oxygen #813

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JHL-452b opened this issue Apr 20, 2024 · 3 comments
Closed

Unbalance reactions about FAD/Oxygen #813

JHL-452b opened this issue Apr 20, 2024 · 3 comments
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@JHL-452b
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There appear to be a few unbalanced reactions which FAD/Oxygen have involved

Current behavior:

ID Reaction Cause of imbalance
MAR08415 2 H+ + 2 O2- --> FAD + FADH2 {'charge': -4, 'H': 62, 'C': 54, 'N': 18, 'O': 26, 'P': 4}
MAR03984 2 FADH2 --> FAD + 2 H2O {'charge': 2, 'H': -31, 'O': -13, 'C': -27, 'N': -9, 'P': -2}
MAR12372 2 CoA + FAD + 2 H2O + 2 NAD+ + 3'-S-hydroxy-pravastatin-CoA --> 2 acetyl-CoA + 2 FADH2 + 2 H+ + 2 NADH + 3'-S-hydroxy-pravastatin-tetranor-CoA {'charge': -2, 'C': 27, 'H': 31, 'N': 9, 'O': 13, 'P': 2}

I traced the modification history of these reactions and found that they were modified in PR670 and resulted in an imbalance. There are obvious imbalance errors in these reactions and may even lead to model inconsistencies.

Proposed changes

Modify the reaction back to its original form.

ID Reaction now Reaction before
MAR08415 2 H+ + 2 O2- --> FAD + FADH2 2 H+ + 2 O2- --> H2O2 + O2
MAR03984 2 FADH2 --> FAD + 2 H2O 2 H2O2 --> 2 H2O + O2
MAR12372 2 CoA + FAD + 2 H2O + 2 NAD+ + 3'-S-hydroxy-pravastatin-CoA --> 2 acetyl-CoA + 2 FADH2 + 2 H+ + 2 NADH + 3'-S-hydroxy-pravastatin-tetranor-CoA 2 CoA + 2 H2O + 2 NAD+ + O2 + 3'-S-hydroxy-pravastatin-CoA --> 2 acetyl-CoA + 2 H+ + 2 H2O2 + 2 NADH + 3'-S-hydroxy-pravastatin-tetranor-CoA
@JHL-452b JHL-452b added the bug label Apr 20, 2024
@feiranl
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feiranl commented Apr 23, 2024

Nice catch! @Devlin-Moyer It would be great if you can double check this. Thanks!

@Devlin-Moyer
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ah yep those reactions are all definitely unbalanced and should be reverted to their earlier forms; sorry for not noticing them back in #670

@feiranl
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feiranl commented Apr 23, 2024

Thanks for checking! @Devlin-Moyer . @JHL-452b go ahead and make the PR.

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