Here are references for the methods accessed here:
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.
Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.
The default options are used, along with the "NR" (non-redundant) database. If you want to use other options or databases, please run BLAST yourself, save the results to a file (HTML is OK, if you save a copy of the web page returned by the NCBI server), and load it in from the "load proteins" dialog.
For regular BLAST, Pred2ary runs blastall, and for PSI-BLAST, Pred2ary runs blastpgp. Please be sure the right program is in your path, and working (this involves setting up a ~/.ncbirc file on UNIX machines). Be sure they work with the NR database; i.e. a command like "blastall -p blastp -d nr -i some.seq" works.