I am wondering why the same protein sequence can appear in multiple orthologous groups _within the same taxonomic level_ in eggNOG?
I have been looking at the orthologous groups (OG) provided for archaea (arNOG) in eggNOG v4.5. When parsing the archaea members file (arNOG.members.tsv.gz), I notice that ~3% of protein sequences are assigned to more than one OG.
For example, the protein sequence MTH548 appears in three OGs: arCOG02392, arCOG02393, and arCOG01386. These OGs have different functional classifications.
I assume I am missing something in my understanding of how OGs are created -- any explanation would be greatly appreciated!