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feat-curate GPR for cysteine metabolism #560

Merged
merged 5 commits into from
Jun 7, 2023
Merged

feat-curate GPR for cysteine metabolism #560

merged 5 commits into from
Jun 7, 2023

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feiranl
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@feiranl feiranl commented May 9, 2023

Main improvements in this PR:

Fix issues in #552

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

@haowang-bioinfo
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haowang-bioinfo commented May 9, 2023

AHCYL1 (ENSG00000168710) is annotated as Multifaceted cellular regulator and hows no hydrolase activity to SAH, probably should be removed from the model?

Everything else is fine - good work

@feiranl
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feiranl commented May 22, 2023

@haowang-bioinfo it says In spite of its similarity with AHCY, which catalyzes the reversible hydrolysis of S-adenosyl-L-homocysteine to adenosine and homocysteine, recombinant AHCYL1 expressed in bacteria shows no hydrolase activity, nor does it affect the enzyme activity of AHCY, thus, I decided to remove it.

@haowang-bioinfo
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haowang-bioinfo commented May 22, 2023

thus, I decided to remove it.

agree, go ahead to remove it

@feiranl
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feiranl commented Jun 5, 2023

I see your point, you mean not only remove the gene from the rxn, but remove the gene totally from the model. Done!

@haowang-bioinfo haowang-bioinfo merged commit 4520a84 into develop Jun 7, 2023
@haowang-bioinfo haowang-bioinfo deleted the fix-cys branch June 7, 2023 12:11
@haowang-bioinfo haowang-bioinfo mentioned this pull request Jun 17, 2023
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2 participants