I ran into an unexpected feature of blastn.
After extracting some gene sequences from a genome, creating a blast database and blasting back to the reference, lot of extracted genes are not found in the blast result, while they are certainly there in the genome (as they were extracted from there)
What can be the cause?
Some details (I cannot upload the whole files):

My command is:

    blastn -query GCF_000005845.2_ASM584v2_genomic.fna -db MG1655_genes -outfmt 6

The fasta file is downloaded from https://www.ncbi.nlm.nih.gov/genome/167?genome_assembly_id=161521.

The database is gained from extracting the feature table belonging to the assembly above.

A missing gene from the blast is e.g. `aaaD`. However, if blasting only this gene, it is naturally found.
After doing some research, I found the answer for my question. The value for `max_target_seqs` is 500 by default.
If raising `max_target_seqs` to some irrationally high value, all genes are shown.

Hence I used 

    blastn -query GCF_000005845.2_ASM584v2_genomic.fna -db MG1655_genes -outfmt 6 -max_target_seqs 100000000

to obtain all genes.