I strongly disagree with what says @Joe!!!
translation can actually occur from pretty much any initial codon but the first AA attached is a Methione
First I was highly surprised that such thing (Non methione at the N-terminus) would havn't reach my hear while it is going against the dogma everyone learn at school.
Then I was septical, how NCBI and EBI (Two eminent infrastructure in the field) could not be aware of it and dealing wrongly with the first AA in their records.
I read-up the publication suggested by @Joe I realised that what you say @Joe is not written in this publication. Below the most important part of the publication looking at the AA attached at the N-terminus
In the Result part:
We used proteolytic digestion and mass spectrometry to determine if
translation began at modified start codons for five selected codons
(AUC, ACG, CAU, GGA and CGC, please see ‘Materials and Methods’
section). We cloned a 6x-His tag into the C-terminus of these five
genes and, following expression and purification, recovered
significant amounts of protein. Little to no protein was recovered
from the CGC culture, as expected. We digested proteins with AspN and
analyzed the mixture via mass spectrometry. Each expressed protein
released peptides of intact N-termini that included an N-terminal
methionine. [...] In cultures with ACG as the start codon a small
fraction of spectra (1 of 8) indicated that the N-terminal peptide
might be the cognate amino acid, threonine (Mr = 119), with a mass
shift of −30 Da relative to methionine (Mr = 149) (Supplementary
Tables S8 and 11). Other researchers have also observed methionine
in the N-terminal position of proteins whose translation initiates
from GUG or UUG start codons.
In the Discussion part:
We observed evidence of translation initiation with N-terminal
methionine from four codons (AUC, ACG, CAU and GGA), and with the
N-terminal cognate amino acid in one spectrum from one codon (ACG)
(Supplementary Tables S7–11). In the spectra in which we observed
N-terminal methionine, it is likely that tRNAfMet is the initiating
tRNA. We did not perform comprehensive mass spectrometry experiments
to identify the N-terminal amino acid from the remaining codons, so we
cannot be certain from which codon, with which tRNA and with which
amino acid, translation is initiating.
Almost all E. coli genes with non-AUG start codons initiate with
methionine as the N-terminal amino acid (4,6,7,65,66,87,88), and such
events are not considered to be errors in translation initiation. By
this same logic, we argue that translation initiation of genes with
other non-AUG codons, in which methionine is observed as the
N-terminal amino acid, should also not be considered an error.
To conclude, the paper shows that AUC (originally Ile), ACG (originally Thr), CAU (originally His), GGA (originally Gly) and CGC (originally Arg) codons attach a N-terminal methionine and they say that other papers show the same for GUG (originally Val) or UUG (originally Leu).
=> Non-methionine codons usually code for their corresponding AA, but when they act as START codons they are substituted by a Methionine.
=> EBI and NCBI are correct
=> @bioinfo2345 your GTG (V) is correct to be a M when recorded in EBI/NCBI DB. But when using a translation tool, the tool doesn't know if your sequence is complete or not (That the first codon is really a start codon). Thus by default it will just translate the corresponding AA. This is the case for most of the tool and you see the same in bioperl and biopython.
=> The only thing I might agree with @Joe is that it seems methionine isn’t required 100%. In the publication they say that for ACG as start codon, a small portion of spectra (1 of 8) indicated that the N-terminal peptide might be the cognate amino acid, threonine. As everything in biology, it is never 100%. But it is shown only for Threonine.