I am trying to perform a comparative genomics amongst 30 bacterial strains available in NCBI. As I was going through all the genomes , I found that one of the genome is having almost 3730 genes but only 2350 proteins. All the RNAs put together are 45 in number. It was quite unusual compared to other genomes. I tried checking in forum as to what may be the reason behind the genome having large no. of genes and less proteins, but couldn't find any satisfying answer. Can anyone help me to understand why there are 1335 hypothetical proteins ? Why large no. of genes are not annotated?
Thanks in advance.