Carnitine synthesis (R-HSA-71262)

[ukemi]

• 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.)