Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Carnitine synthesis (R-HSA-71262) #291

Open
3 of 7 tasks
ukemi opened this issue Oct 6, 2023 · 0 comments
Open
3 of 7 tasks

Carnitine synthesis (R-HSA-71262) #291

ukemi opened this issue Oct 6, 2023 · 0 comments
Assignees

Comments

@ukemi
Copy link

ukemi commented Oct 6, 2023

  • make mouse model: gomodel:6516135700000632
  • direction of transport in the GO-CAM for R-HSA-8949413 is backwards, but it is fixed on Noctua dev.
  • periodically check for the publication of https://europepmc.org/article/ppr/ppr727037
  • request RHEA reaction for "SHMT1 tetramer cleaves HTMLYS to yield TEABL and Gly" (R-HSA-71249) based on Figure 3 of https://europepmc.org/article/ppr/ppr727037. All other catalyzed Reactome reactions are charge- and mass-balanced and have RHEA reaction counterparts.
  • explicitly specify gene product activeUnits for all catalyzed reactions in Reactome.
  • "Unknown carnitine exporter transports CAR from the cytosol to the extracellular space" R-HSA-164967 - Is the transporter SLC22A4 as annotated in Reactome R-HSA-549297 (see also PMID: 10215651? is there evidence for the mouse ortholog? Should we edit the existing reaction to add OCT2 as transporter, with Na+ co-transport (RHEA:72091)?
  • (copied from heme Heme biosynthesis (R-HSA-189451) #290) PMID: 20306513 suggests that THA1 may be the mouse enzyme that catalyzes this reaction, not SHMT1. https://europepmc.org/article/ppr/ppr727037 But in humans it is a pseudogene! I blasted it against the Candida one and it was not a significant hit. Curoiuser and curiouser.
    Human THA1, unlike mouse, IS a pseudogene - see https://europepmc.org/article/ppr/ppr727037 for argument that human SHMT1 has the role in carnitine biosynthesis that Tha1 has for mice (don't think they checked for other functions of SHMT1 / Tha1 aside from carnetine biosynthesis - recent evolutionary divergence to add to our list along with purine catabolism and vitamin C synthesis.)
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Development

No branches or pull requests

2 participants