Thank you so much for the file you provided. We've checked and effectively both accessions mapped by our contig are included in the reference file.
contig-3000000 ref|YP_002004542.1| 31.4 175 108 5 1454 942 164 330 5.7e-18 94.7
contig-3000000 ref|YP_008060116.1| 35.6 87 52 1 5162 4902 345 427 2.7e-04 49.3
But, we still do not understand why MEGAN6 does not assign any taxa to this contig, even more when the accession hit with blastx is included in the reference file. Do you have any idea about what's going on here? Could it be something related to the .tree or .map files MEGAN6 uploads when it opens?
Thank you so much for your help!