Use of a multi-way method to analyze the amino acid composition of a conserved group of orthologous proteins in prokaryotes

Background: Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between proteins from the same species (related to protein function, expression or subcellular localization, for example). As several factors contribute to the different amino acid usage in proteins, it is difficult both to analyze these differences and to separate the contributions made by each factor. Results: Using a multi-way method called Tucker3, we have analyzed the amino composition of a set of 64 orthologous groups of proteins present in 62 archaea and bacteria. This dataset corresponds to essential proteins such as ribosomal proteins, tRNA synthetases and translational initiation or elongation factors, which are common to all the species analyzed. The Tucker3 model can be used to study the amino acid variability within and between species by taking into consideration t...

• Type: Journal
• Year: 2006
• Where: BMCBI
• Authors: Alberto Pasamontes, Santiago Garcia-Vallvé
• Keywords: Acids, Amino Acids, BMCBI 2006, Proteins