BLAST E-value

Selecting "1e-3" includes only sequences with E-values ≤ 1e-3 (10⁻³)
from each species-specific protein sequence database (see below).

NCBI explanation:
https://www.nlm.nih.gov/ncbi/workshops/2023-08_BLAST_evol/e_value.html

Number of BLAST hits

Selecting “5” allows up to five BLAST hits from each genome per query
to be included in the tree estimation.