Hi I'm using Blast2Go to annotate and compare the core genome and the whole genome of a species of bacteria (Pseudomonas fluorescens). For the approximately 6000 genes only about 500 of them have GO terms, and 400 of them are in the core genome (which is approx 2000 genes). I was just wondering if anyone knew why this might be? I had heard before that Blast2Go was originally developed for use on prokaryotic genomes. Could this be affecting it?