The number limitation of blast

Question

[horsedog]

Hi, I'm trying blastp in terminal to get similar sequences for my database, I set the evalue as 1e-6 and I have 7000 sequences; but the unique results I got are only 4000, so I'm thinking maybe blast has the number limitation of output. Does anyone know how to get all the results? My code like this .

blastp -db refseq_protein -query protein.fasta -out protein_1e-6 -evalue 1e-6 -outfmt '6 sseqid staxid evalue slen'

[GenoMax]

That description is not very clear. How many sequences are in the query and how many did you get in search? There is a default upper limit for blastp. Those are

num_descriptions    integer 500 Show one-line descriptions for this number of database sequences.
num_alignments  integer 250 Show alignments for this number of database sequences.

[Jean-Karim Heriche]

Your e-value threshold is probably too low. The e-value of an alignment represents the probability of seeing this alignment by chance given the database size or put another way, it represents the number of similar hits you would see by chance in your database.