Consider the following sequence:
>sequence GTGACCGGCAGCGCGGCCACGATCCGCCCGGCCAAGGCGGCCGATGCGGTCGCGTGGGCG CAGCTGCGTCTGGGCCTGTGGCCCGATGCCGATGATCCGCTGGAGACGCTGGTGGCGGCG CTGGCCGAGGACGCAGGTGCGGTTTTCCTGGCGTGTGCAGCGGGTGGCCAGGCGATCGGC TTCGCCGAAGTGCGCCTGCGCCATGACTACGT
In this bacterial organism, GTG is an alternative start codon. It means that it can initiate translation via an initiator-tRNA that puts in the amino acid Methionine (M) into the protein. However, if GTG occurs inside the sequence, it gets translated to valine (V) as usual.
However, when using programs that involve translating a nucleotide sequence to a amino acid sequence (such as EBI transeq online, command-line transeq or blastx with this sequence against it's translation starting with V), the above sequence will be translated to an amino acid sequence that begins with V regardless if the codon table is standard code or bacterial. In fact, even using command-line transeq option -methionine does not produce the desired M result.
Why is GTG at the start of this sequence not translated to M when using the bacterial codon table?
What use is the bacterial codon table then, if it does not have a different behavior in this case (since this is the only major difference between standard or bacterial codon table)?