Here is another way to write that, less typing, fixed to dereference properly ( references quick reference ) , and filtered through perltidy -csc -otr -opr -ce -nibc -i=4

sub Flag {
    my ( $Subj_id, $proph_prots, $euk_prots, $vir_prots ) = @_;
    return "Proph", "Phage" if exists $$proph_prots{$Subj_id};
    return "Euk",   "Euk"   if exists $$euk_prots{$Subj_id};
    return "Vir",   "Phage" if exists $$vir_prots{$Subj_id};
    return "Bact",  "Bact";
} ## end sub Flag
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