for mapping a nucleotide sequence against a protein database

nucleotide sequences are translated automatically by BLAST

blastx -query DNA_gene_sequences.ffn -subject protein_sequences.faa -outfmt 6 -evalue 1e-50

BLASTx options

http://www.ncbi.nlm.nih.gov/books/NBK279675/table/appendices.T.blastx_application_options/