Annotated, Hypothetical, and Unannotated classification result of the query

[BinhongLiu]

Hi,
I'm not sure if the annotation_results/.faa.annot file only includes the Annotated proteins, or all three types (also include Hypothetical and Unannotated proteins)? Could you also output the classification results (add one column indicating the A, H, and U) in the annotation_results/.faa.annot file?
Also, I'm a little confused about two columns indicating the best match, protein_id and product. I found that some proteins were annotated by kofam and did not have the specific terms (‘hypothetical,’ ‘uncharacterized,’ ‘domain of unknown function,’ or ‘protein of unknown function’) in the ko_product. But the two best match columns of these proteins were NA. How should I interpret these annotations?
Thanks!