Hello! I am trying to make a custom pathway database for Humann3 to study lactose degradation. I found 3 lactose degradation pathways on MetaCyc, but it seems that only one of them (LACTOSECAT-PWY) is in the default pathway database for Humann3. Below is the file I made after reading the Humann3 manual. I am not sure what exactly I should put in for “gene families” column.
LACTOSECAT-PWY lacG ( LacA + LacB ) ( pfkB , pfkA , lacC ) ( gatY , lacD , ( kbaY + kbaZ ) , kbaY )
LACTOSEUTIL-PWY ( LacC + LacA ) klhA
BGALACT-PWY ( lacA , LacZ , bga1 , ( LacM + LacL ) )
Any help would be appreciated. Thank you!
HUMAnN only bundles pathways from MetaCyc with 4+ quantifiable reactions, so maybe the other two pathways were too small OR included enzymes that didn’t have any associated UniProt sequences?
The general workflow is that HUMAnN maps reads to sequences that have been annotated with sequence identifiers (default, UniRef90). These sequence identifiers are then assigned to reactions that they mediate (default, MetaCyc reactions). Reactions are then organized into pathways using syntax like you examples above.
Hi franzosa,
Thank you very much for your explanation! You are def right that the other two pathways are too small (1-2 reactions).
Glad that explanation panned out!