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[Bio-software] Re: Which amino acid residue does the letter 'J' mean?

Linlin Yan via bio-soft%40net.bio.net (by yanlinlin82 from gmail.com)
Mon Jun 30 09:45:42 EST 2008

Hi everyone in newsgroup bionet.software,

It's very kind of Hamish, who sent me a very detail explain for single
letter amio-acid codes. I forward the mail to the newsgroup. Hope it
could help someone else.

On Mon, Jun 30, 2008 at 10:22 PM, Hamish McWilliam <hpm from ebi.ac.uk> wrote:
> Hi Linlin,
> A brief description of the meanings of the single letter amino-acid codes
> can be found in the RESID FAQ (http://www.ebi.ac.uk/RESID/faq.html#q01).
> In short 'J' is used for cases where the residue can be leucine ('L') or
> isoleucine ('I') and is a result of the use of mass-spec sequencing where
> the 'L' and 'I' cannot be distinguished. The 'B' (aspartic acid or
> asparagine) and 'Z' (glutamic acid or glutamine) codes have a similar
> function in chemical sequencing.
> Note that 'O' (pyrrolysine) and 'U' (selenocysteine) are now appearing in
> the sequence databases (see http://beta.uniprot.org/news/2008/02/26/release
> and
> http://www.ebi.ac.uk/embl/Documentation/Release_notes/relnotes89/relnotes.html#2.2).
> Currently not enough is known about the substitution rates of these residues
> for them to be included in the scoring matrices, so they are generally
> handled as unknown residues ('X').
> I hope this helps,
> Hamish

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