Determining the amino acid composition of every protein in Escherichia coli K-12

Understanding the amino acid composition of every protein in a microorganism may be the first step in gaining an appreciation of the metabolic needs of a species. Specifically, amino acid composition of proteins informs the cellular need for each amino acid, and this in turn, provides a glimpse into the metabolic need of the cell. This may hold implications for how the different biosynthesis pathway for each amino acid are regulated. On the other hand, information on amino acid composition of an organism also guide the formulation of a suitable growth medium for the species in view of enabling it to attain fast growth. But, all these discussions must be taken in light of the fact that not all genes in a genome are expressed at any point in time. Using an in-house MATLAB software, the amino acid composition of every protein in Escherichia coli K-12 was calculated. Raw proteome information of the species was obtained from UniProt (accession number: UP000000625), and processed to yield a database comprising protein name, protein amino acid sequence, and the percentage of each amino acid in the protein sequence. Amino acid composition is presented as percentage of each amino acid, which is identified by their single letter abbreviation. Overall, the presented database should find use in fundamental studies aiming to calculate the total metabolic need of E. coli K-12 with respect to amino acid utilization, as well as assessing the compendium of relatively heavily utilized amino acid that may need supplementation in the growth medium.