Codes for amino acids
It is known that amino acids or nucleotide acids can be represented as codes of either triple letters or single letter. When I was learning pairwise alignment algorithm a few days ago, I found that there is a letter ‘J’, a single letter for amino acid that I had never seen before, in NCBI’s scoring matrix. I posted the question in the newsgroup and got the answer in the next day. Thank Hamish McWilliam of EBI, who mailed me with a very detail explanation. Following are the codes for amino acids (from http://www.ebi.ac.uk/RESID/faq.html#q01).
| Standard Encoded Amino Acids | |||||
|---|---|---|---|---|---|
| A | Ala | alanine | M | Met | methionine |
| C | Cys | cysteine | N | Asn | asparagine (“asparagiNe”, “aspartic-NH2″) |
| D | Asp | aspartic acid (“asparDic acid”) | P | Pro | proline |
| E | Glu | glutamic acid (“gluEtamic acid”) | Q | Gln | glutamine (“Qutamine”) |
| F | Phe | phenylalanine (“Fenylalanine”) | R | Arg | arginine (“aRginine”) |
| G | Gly | glycine | S | Ser | serine |
| H | His | histidine | T | Thr | threonine |
| I | Ile | isoleucine | V | Val | valine |
| K | Lys | lysine (“K” next to “L”) | W | Trp | tryptophan (“tWiptophan”, or double-ring) |
| L | Leu | leucine | Y | Tyr | tyrosine (“tYrosine”) |
| Amino Acid Ambiguities | |||||
| B | Asx | aspartic acid or asparagine (“B” near “D”, uncertain result of hydrolysis) | |||
| J | Xle | leucine or isoleucine (“J” between “I” and “L”, uncertain result of mass-spec) | |||
| X | Xaa | unknown or unspecified amino acid (“Unk” is sometimes used as an abbreviation) | |||
| Z | Glx | glutamic acid or glutamine (“Z” near “X”, uncertain result of hydrolysis) | |||
| Special Encoded Amino Acids | |||||
| U | Sec | selenocysteine (the UniProt Knowledgebase uses “C” and a feature rather than “U”) | |||
| O | Pyl | pyrrolysine (“pyrrOlysine”, the UniProt Knowledgebase uses “K” and a feature rather than “O”) | |||