Seconder Metabolite Finding

[airbender97]

Hello,

Can we find pathways and other related things for seconder metabolites? Is so, can you please help me?

[jotech]

Hi @airbender97
are you looking for secondary metabolites?
By default, gapseq looks for biosynthesis and degradation pathways of secondary metabolites from metacyc.

[airbender97]

I am looking for pathways, but I don't know how can I run a code for them.

[jotech]

You can check the output files if you already have a gapseq annotation.

library(data.table)
meta <- fread("gapseq/dat/meta_pwy.tbl")
sm.pwy <- meta$id[grep("SECONDARY-METABOLITE-BIOSYNTHESIS", meta$hierarchy)]
eco.gs <- fread("gapseq/toy/myb71-all-Pathways.tbl")
eco.gs[eco.gs$ID %in% sm.pwy]

Alternatively, you can also have a look at sm pathways selectively.

./gapseq find -p "SECONDARY-METABOLITE-BIOSYNTHESIS" toy/ecoli.fna.gz