Prokka annotated gene-protein database

[Lenus-sun]

Hi All,

I have got the Prokka-annotated gene names based on the WGS, then I aim to design primers to target the differentiated gene expressions. While, some gene name cannot be found in NCBI Nucleotide, and then I found the database of Prokka--UniProKB. But seems that

1. I cannot find the gene sequence under specific Bacterium, and
2. I saw some same gene names while could code different Protein? can anyone help to resolve this?