I remember that, earlier, enzymes in the SEED classification often were found in multiple subsystems. This is at least true for how it was in the M5NR database around five years ago and I believe it was the case in MEGAN 5. This made sense, because an enzyme can of course participate in multiple metabolic pathways.
When we now work with data exported from MEGAN/SEED (readname to SEED hierarchy from the GUI), there are no duplicate entries for the last level of the hierarchy. I’m just curious to know if something changed in MEGAN or in the SEED classification (perhaps you can’t answer that last part).