Any tutorial to graph a metabolic pathway from a metabolic model ?

Question

[v.berriosfarias]

Hello!, I'm new to systems biology, and I was asked to graph the metabolic pathway that is underneath the production of certain a metabolite from a bacterial taxon.

I have a fasta file corresponding to the complete genome of this microorganism so I used gapseq to predict the full metabolic network of this genome. Now I want to know if is there any tool/tutorial that you can recommend for me to extract the specific pathway related to my metabolite of interest and graph it in R or Python.

By far, I have gapseq outputs that corresponds to tables of predicted pathways (.tbl file) and the final emtabolic network saved in a xml file.

Answer 1

[VineethVenumadhavan]

I am not sure how helpful my response will be as I am in same situation like yours, but..

Did you already try using BigMec - Biosynthetic Gene cluster Metabolic pathway Constructor with antiSMASH output and visualise pathway json file using tools like Escher or Cytoscape ?

Escher maps have options to load JSON and pathway models but unfortunately didn't work in my case.