Problems with annotations

[manalcric]

Hello,
I am trying to annotate several Pseudomonas aeruginosa curated genomes with my customized database but I have found that something is not running well because of several genes are not being annotated with the name supplied by this database. I have checked this because I downloaded a .gbk file from a reference genome, I created the customized database and then I have annotated the .fasta file of the same reference genome to check if the output .gbk is the same or not, but a lot of genes were annotated diferent. This the command lines that I have used:

prokka-genbank_to_fasta_db /home/administrador/Genomics/Databases/Pseudomonas_aeruginosa_PAO1_107.gbk > /home/administrador/Genomics/Databases/Pseudomonas_aeruginosa_PAO1_107.faa
prokka --cpus 40 --proteins /home/administrador/Genomics/Databases/Pseudomonas_aeruginosa_PAO1_107.faa --outdir /home/administrador/Genomics/Users/Manuel/PAEs/New_Results/Prokka_PAO1_PAO1_107_db/PAO1 --prefix PAO1 Pseudomonas_aeruginosa_PAO1_107.fna

The bigger problem is that prokka is annotating the alleles mexA, mexC, mexD, etc. like mexA_1, mexA_2, mexA_3, etc... I have found that there exists a problem with the generation of the customized database, since some annotations were lost (i.e.: mexC, mexD are not found).
Could I use the option "--rawproduct" together with prokka-genbank_to_fasta_db? Someone could help me to solve this problem?
Thanks in advance.