HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data.
Read more about the tool: http://huttenhower.sph.harvard.edu/humann
This tool unpacks the pathways to show the genes for each.
It adds another level of stratification to the pathway abundance table by including the gene families (or EC) abundances.