Development of PROSITE Pattern and Profiles

Patterns - Small regions with high sequence similarity. Alignment table from a group or family of proteins. Find biologically significant regions or residues such as: Enzyme catalytic sites. Prostethic group attachment sites (heme, pyridoxal-phosphate, biotin, etc). Amino acids involved in binding a metal ion. Cysteines involved in disulfide bonds. Regions involved in binding a molecule (ADP/ATP, GDP/GTP, calcium, DNA, etc.) or another protein. The pattern(s) created at this stage is the 'core' pattern(s). SWISS-PROT knowledgebase is then scanned with these core pattern(s). Example of a pattern entry. Profiles (or weight matrixes) - Protein family or domain over its entire length. A table of position-specific amino acid weights and gap costs (scores) derived from a multiple sequence alignment and a symbol comparison table to convert residue frequency distributions into weights. Scores are used to calculate a similarity score for any alignment between a profile and a sequence. Example of a profile (matrix) entry.