# Protein Sequence Key: `representation.scientific.protein_sequence` Amino acid sequence in single-letter IUPAC notation (20 standard amino acids plus ambiguity codes). Page: Samples: `MKVLLIVGS`, `ACDEFGHIKLMNPQRSTVWYFL`, `MPKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQAPILSRVG` ## Background ### Origin The IUPAC-IUB Commission on Biochemical Nomenclature published A One-Letter Notation for Amino Acid Sequences in 1968.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) The IUB-IUPAC one-letter recommendations were approved in 1968 on the basis of proposals of a subcommittee of W. E. Cohn, M. O. Dayhoff, R. V. Eck and B. Keil.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) The possibility of using one-letter symbols for amino acids was mentioned by Gamow and Yčas in 1958.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) Šorm and colleagues systematised the idea of one-letter amino acid symbols in 1961.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) Dayhoff and Eck used one-letter symbols derived partly from the code of Šorm and colleagues in their compilations of protein sequences.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) The IUPAC recommendations describe a one-letter code as much more concise than the three-letter system for presenting long protein sequences.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) The IUPAC recommendations name aligning and comparing homologous sequences as one of the uses of the one-letter code.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) Where several amino acids shared an initial letter, the letter went to the most frequently occurring and structurally simplest of them: alanine (A), glycine (G), leucine (L), proline (P) and threonine (T).[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) F for phenylalanine and R for arginine were chosen for their phonetic associations.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) Tryptophan was given W because the double ring of the molecule is associated with the bulky letter.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) The IUPAC note on the choice of symbols says U was avoided because it is easily confused with V in handwritten material.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) The IUPAC note on the choice of symbols says O was avoided because it could be confused with G, Q, C and D in imperfect computer print-outs, and also with zero.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) J was avoided because it is absent from several languages.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) In the IUPAC code, X means that the identity of an amino acid is undetermined, or that the amino acid is atypical.[[1]](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) ### Use The FASTA format originated from the FASTA software package.[[2]](https://en.wikipedia.org/wiki/FASTA_format) A sequence in FASTA format begins with a single-line description, marked by a greater-than symbol, followed by lines of sequence data.[[3]](https://blast.ncbi.nlm.nih.gov/doc/blast-topics/) NCBI recommends that all lines of text in FASTA input be shorter than 80 characters.[[3]](https://blast.ncbi.nlm.nih.gov/doc/blast-topics/) NCBI BLAST expects sequences to be written in the standard IUB/IUPAC amino acid and nucleic acid codes.[[3]](https://blast.ncbi.nlm.nih.gov/doc/blast-topics/) NCBI BLAST accepts lower-case letters and maps them into upper case.[[3]](https://blast.ncbi.nlm.nih.gov/doc/blast-topics/) ### Where you'll meet it UniProt documents the FASTA headers it uses for UniProtKB, UniRef and UniParc.[[4]](https://rest.uniprot.org/help/fasta-headers) UniProtKB's FASTA file for entry P69905, human haemoglobin subunit alpha, gives the sequence in one-letter code beginning MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMF.[[5]](https://rest.uniprot.org/uniprotkb/P69905.fasta) ## Sources 1. [Nomenclature and Symbolism for Amino Acids and Peptides](https://iupac.qmul.ac.uk/AminoAcid/A2021.html) — standard 2. [FASTA format](https://en.wikipedia.org/wiki/FASTA_format) — secondary source 3. [Query Input and database selection — BlastTopics 0.1.1 documentation](https://blast.ncbi.nlm.nih.gov/doc/blast-topics/) — documentation 4. [FASTA headers](https://rest.uniprot.org/help/fasta-headers) — organisation 5. [P69905.fasta](https://rest.uniprot.org/uniprotkb/P69905.fasta) — dataset