BLAST is used to generate the ACT comparison file (for more details see the ACT manual) one of the sequences needs to be made the database sequence and indexed with formatdb:
formatdb -i NC_004314.fasta -p 'F'
The other sequence is the query and you can then search for matches between these:
blastall -p tblastx -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_tblastx -m 8
or
blastall -p blastn -d NC_004314.fasta -i NC_011907.fasta -o NC_004314_v_NC_011907_blastn -m 8 -e 0.1
Use the '-m 8' option to provide the tabular output that ACT uses.
An alternative to this is to use WebACT or Double ACT to generate the comparison file.