search

C-CoMP-STC / GEM-mit1002

Creative Commons Attribution 4.0 International
0 stars 0 forks source link

Make model using new gene calls #47

Closed hgscott closed 11 months ago

hgscott commented 1 year ago

Zac sent me a new gff file with slightly different gene calls to use for the model. We want to use the new gene calls so that we match Michelle and Zac's work in anvio.

hgscott commented 1 year ago

I uploaded the genome from Zac to KBase as a GFF/FASTA genome: Image

Then, I reannotated with RASTtk and built the model.

hgscott commented 1 year ago

The new model had the same ATP-generating cycle: Image

hgscott commented 1 year ago

The new model has 1 more reaction and a slightly higher metabolic coverage.

Here's the MEMOTE report for the old model. Image

And here's the report for the new model. Image

hgscott commented 1 year ago

The reaction that the newer model has that was not in the old model was 'rxn05206_c0', which was the reaction I removed to fix the ATP-generating cycle.

hgscott commented 1 year ago

I used the "Edit Metabolic Model" app to remove just that reaction in KBase so that I didn't have to edit the SBML file and reupload it before gap filling.

Image Image