NCBI Blastp was run with the following parameters 

blastp -db $2 -query $1 -evalue 1E-6 -num_threads 60 -outfmt 11

Output was converted to XML format by blast_formatter

BLASTP 2.6.0+

Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.

Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.

Database: Non-redundant UniProtKB/SwissProt sequences
           465,919 sequences; 175,264,251 total letters