search

microbialphenotypes / OMP-ontology

This repository contains the editors's working copy of OMP and public release files.
8 stars 2 forks source link

fix annotations for the alternate serine pathway (Tut cycle) #256

Closed dsiegele closed 5 years ago

dsiegele commented 5 years ago

There is an alternate pathway (Tut cycle) that can make serine from threonine. In E. coli, tdh, gcv, and glyA are essential for the Tut cycle (PMID:3108237). Ser- auxotrophs can grow on minimal medium containing 240 mg/liter each of leucine, arginine, lysine, threonine, and methionine).

EcoliWiki has GO annotations for tdh linked to serine biosynthesis, but there aren't annotations for glyA or gcv.

One of the tdh annotations is missing an entry in the with/from field. Also need to expand entry in notes field to better explain the phenoype. For example, "tdh serC double mutants are unable to synthesize serine by the alternate pathway and cannot grow on LRKTM:240 medium (minimal medium containing 240 mg/liter of leucine, arginine, lysine, threonine, and methionine)"

dsiegele commented 5 years ago

This is an issue for GO annotations at Ecoliwiki. Close issue here and open new issue at HuLab/ecoliwiki