Peptide-based functional annotation of carbohydrate-active enzymes by conserved unique peptide patterns (CUPP)

Background Insight into the function of carbohydrate-active enzymes is required to understand their biological role and industrial potential. There is a need for better use of the ample genomic data in order to enable selection of the most interesting proteins for further studies. The basis for elaborating a new approach to sequence analysis is the hypothesis that when using conserved peptide patterns to determine the similarities between proteins, the exact spacing between conserved adjacent amino acids in the proteins plays a prominent functional role. Thus, the objective of developing the method of conserved unique peptide patterns (CUPP) is to construct a peptide-based grouping and validate the method to provide evidence that CUPP captures function-related features of the individual carbohydrate-active enzymes (as defined by CAZy families). This approach facilitates grouping of enzymes at a level lower than protein families and/or subfamilies. A standardized, efficient, and robust approach to functional annotation of carbohydrate-active enzymes would support improved molecular insight into enzyme–substrate interaction.