A peptide chain has two different ends. One end has a free amino group, called the N-terminus. The other has a free carboxyl group, called the C-terminus. By convention, sequences are always written from the N-terminus on the left to the C-terminus on the right.
Each amino acid has a three-letter code and a one-letter code. The three-letter codes are mostly the first three letters of the name, such as Gly for glycine and Ala for alanine. A few break the pattern, such as Asn for asparagine, Gln for glutamine, Ile for isoleucine and Trp for tryptophan.
The one-letter codes are compact but less obvious. G, A, V, L, I, S, T, C, M, P and H match first letters. Others had to be chosen because letters clashed. F is phenylalanine, W is tryptophan, Y is tyrosine, R is arginine and K is lysine. D is aspartate, E is glutamate, N is asparagine and Q is glutamine. Extra letters cover special cases. U is selenocysteine and O is pyrrolysine. B, Z and X mark uncertain or unknown residues.
Databases store sequences in a simple text format called FASTA. A FASTA record starts with a line beginning with the greater-than sign, which holds the name and description. The lines below hold the sequence in one-letter code.
Public databases such as UniProt use this format, so anyone can look up and compare sequences for free.
References
- Berg JM, Tymoczko JL, Stryer L. Biochemistry, 5th ed., Section 3.2: Primary Structure: Amino Acids Are Linked by Peptide Bonds (2002)
- NCBI, BLAST Topics: Query Input and Database Selection (FASTA format) (n.d.)
- IUPAC-IUB Joint Commission on Biochemical Nomenclature, Nomenclature and Symbolism for Amino Acids and Peptides (1983)
Educational content about laboratory research. Not medical advice. All Orion compounds are for laboratory research use only.
