In MetaboAnalyst, the KEGG pathways were obtained based on the KEGG REST APIs followed by manual curations. For some pathways, there may be a discrepancy in the number of compounds listed from KEGG directly compared to MetaboAnalyst (the compounds are primarily based on HMDB). This is because a KEGG pathway can contain compounds that have not been verified for that species or a generic compound, and there is no corresponding compound in HMDB. In most cases, these discrepancies should not affect data interpretation as we cannot measure those compounds anyway.