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Suspected duplicates in the galactose pathway #400

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Description

@johan-gson

Description of the issue:

There are two metabolites in the model called
galactose-1-phosphate[c]
alpha-D-galactose-1-phosphate[c]

According to https://pubchem.ncbi.nlm.nih.gov/compound/alpha-D-Galactose-1-phosphate, these are synonyms
These are then duplicates (interestingly, they have slightly different GPRs, but the same MNX id (I'm not sure how these work exactly though) )
MAR04130 ATP[c] + galactose[c] => ADP[c] + alpha-D-galactose-1-phosphate[c] + H+[c]
MAR04414 ATP[c] + galactose[c] => ADP[c] + galactose-1-phosphate[c] + H+[c]

Also these, although one of them is unidirectional, unclear which it should be. They have the same GPR and same kegg id:
MAR04131 glucose-1-phosphate[c] + UDP-galactose[c] <=> alpha-D-galactose-1-phosphate[c] + UDP-glucose[c]
MAR04132 galactose-1-phosphate[c] + UDP-glucose[c] => glucose-1-phosphate[c] + UDP-galactose[c]
kegg.reaction/R00955

This is the fifth reaction that is concerned (no duplicate found):
MAR08767 alpha-D-galactose-1-phosphate[c] + H+[c] + UTP[c] => PPi[c] + UDP-galactose[c]

Galactose metabolism in kegg:
https://www.genome.jp/pathway/rn00052+R00955

Expected feature/value/output:

Not sure which to remove, what to do with the GPR (I assume keep the largest one), or what to do with the one that is rev/irrev

Current feature/value/output:

Reproducing these results:

I hereby confirm that I have:

  • Tested my code on my own computer for running the model
  • Done this analysis in the main branch of the repository
  • Checked that a similar issue does not exist already

Activity

  1. haowang-bioinfo commented on May 25, 2023

    @haowang-bioinfo
    Contributor

    @johan-gson do you have plan to fix this?

  2. johan-gson commented on May 25, 2023

    @johan-gson
    CollaboratorAuthor

    Not in the near future, I'm not sure exactly what to do and just got a heavy revision :)

  3. added
    wipA pull request for this issue is open
    fixed in developMerged into develop, will be in the next release
    and removed
    wipA pull request for this issue is open
    on Sep 25, 2026
  4. edkerk commented on Sep 28, 2026

    @edkerk
    Member

    Follow-up to #1089, in #1105 (open): The merges are recorded on the kept entities (MAM01322c, MAR04130, MAR04131); GALK1 and GALT get the references UniProt uses; UGP2 on MAR08767 gets human evidence (PMID:12626383) and a note that it is a minor side activity. Details and evidence are in the comment on #1089.

  5. added
    wipA pull request for this issue is open
    and removed
    wipA pull request for this issue is open
    on Sep 28, 2026
  6. added this to the 2.1.0 milestone on Sep 28, 2026
  7. edkerk commented on Oct 5, 2026

    @edkerk
    Member

    Fixed in Human 2.1.0.

  8. removed
    fixed in developMerged into develop, will be in the next release
    on Oct 14, 2026
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