Uniref90 Gene Families to Pathways

Microbial community profiling HUMAnN
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Hello,

I’ve created tables for UniRef90 gene families and UniRef Pathways and I’m wondering if there’s a way to link these two. In general I’m looking for some sort of mapping file that says which gene families are part of which pathways.

-Eric

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You’d have to do this as a two-step process. Under the HUMAnN pathway data folder, you’ll find a file that maps gene families (UniRefs) to MetaCyc reactions:

metacyc_reactions_level4ec_only.uniref.bz2

And then there is a separate file that defines pathways according to their component reactions and arrangement:

metacyc_structured_pathways_filtered

You can consider that a gene family contributes to a detected pathway if it maps to a RXN that is included in that pathway’s definition.

The files above can also be found here: