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fix: remove LDHAL6A from MAR11479 for GPR consistency with MAR11476#1038

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fix/mar11479-ldhal6a
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fix: remove LDHAL6A from MAR11479 for GPR consistency with MAR11476#1038
edkerk wants to merge 2 commits into
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fix/mar11479-ldhal6a

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@edkerk edkerk commented Jul 11, 2026

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Main improvements in this PR:

Found while reviewing #528. MAR11476 and MAR11479 are the same promiscuous lactate dehydrogenase side-reaction on adjacent branched-chain 2-oxo acids. The GPR curation in #847 / #885 removed LDHAL6A (ENSG00000166800) from MAR11476 as not relevant to the reaction, but left it on the identical MAR11479.

  • Remove LDHAL6A (ENSG00000166800) from the GPR of MAR11479, so it matches MAR11476 (LDHB, LDHA, LDHC, LDHD, LDHAL6B).

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

…528)

MAR11476 and MAR11479 are the same promiscuous lactate dehydrogenase
side-reaction on adjacent branched-chain 2-oxo acids. The GPR curation in
#847 / #885 removed LDHAL6A (ENSG00000166800) from MAR11476 as not
relevant to the reaction, but left it on MAR11479, leaving the two
inconsistent. Remove LDHAL6A from MAR11479 as well so both carry the same
five-gene rule (LDHB, LDHA, LDHC, LDHD, LDHAL6B).
@edkerk edkerk added this to the 2.1.0 milestone Jul 11, 2026
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This PR has been automatically tested with GH Actions. Here is the output of the MACAW test:

Starting dead-end test...
- Found 1384 dead-end metabolites.
- Found 1141 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- Found 1369 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
Starting duplicate test...
- Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.
- Found 377 reactions that were some type of duplicate:
- 0 were completely identical to at least one other reaction.
- 13 involve the same metabolites but go in the opposite direction or have the opposite reversibility as at least one other reaction.
- 377 involve the same metabolites but with different coefficients as at least one other reaction.

This and a more detailed output from MACAW are also committed to data/testResults/.

Note: In the case of multiple test runs, this post will be edited.

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