When using BLASTX take care to define the correct genetic code that will be used to translate the query using the -query_gencode option.
Available genetic codes are

• 1 - Standard (default)
• 2 - Vertebrate Mitochondrial
• 3 - Yeast Mitochondrial
• 4 - Mold Mitochondrial
• 5 - Invertebrate Mitochondrial
• 6 - Ciliate Nuclear
• 9 - Echinoderm Mitochondrial
• 10 - Euplotid Nuclear
• 11 - Bacteria & Archaea
• 12 - Alternative Yeast Nuclear
• 13 - Ascidian Mitochondrial
• 14 - Blepharisma Macronuclear

Essential BLAST Search Options

• -evalue <Real>
    Expectation value (E) threshold for saving hits
    Default = '10'

• -matrix <String>
    Scoring matrix name (normally BLOSUM62)

LCR-handling options

• -comp_based_stats <String>
    Use composition-based statistics for blastp / tblastn:
        D or d: default (equivalent to 2)
        0 or F or f: no composition-based statistics
        1: Composition-based statistics as in NAR 29:2994-3005, 2001
        2 or T or t : Composition-based score adjustment as in
        Bioinformatics 21:902-911, 2005, conditioned on sequence
        properties
        3: Composition-based score adjustment as in Bioinformatics
        21:902-911, 2005, unconditionally
    For programs other than tblastn, must either be absent or be D, F
    or 0
    Default = `2'

• -seg <String>
    Filter query sequence with SEG (Format: 'yes', 'window locut hicut',
    or 'no' to disable)
    Default = `no'

• -soft_masking <Boolean>
    Apply filtering locations as soft masks
    Default = `false'

• -lcase_masking
    Use lower case filtering in query and subject sequence(s)?