I am doing functional prediction of bacteria, to do that I have a list of selected KO that are involved in the target functionality for example nitrogen fixation, phosphorous solubilization etc. First I obtain the KOs of my bacterial proteomes and do search for the KOs involved in the target function, then if the KOs are present I classified the bacteria as potential to do that function. This candidates are further validated experimentally

Some of my proteins are not assigned to a specific KO, however if I open the tabular kfamscan output some of the not assigned proteins seems to have good Evalues and domain scores, thus I am confused about how kfamscan assign a KO to a protein

Kfamscan does not assign a KO to this proteins but in the list there some possible KO that seems to have a good score value