BLOSUM80: more related proteins
BLOSUM62: midrange
BLOSUM45: distantly related proteins
An article in Nature Biotechnology revealed that the BLOSUM62 used for so many years as a standard is not exactly accurate according to the algorithm described by Henikoff and Henikoff. Surprisingly, the miscalculated BLOSUM62 improves search performance.
The BLOSUM62 matrix with the amino acids in the table grouped according to the chemistry of the side chain, as in (a). Each value in the matrix is calculated by dividing the frequency of occurrence of the amino acid pair in the BLOCKS database, clustered at the 62% level, divided by the probability that the same two amino acids might align by chance. The ratio is then converted to a logarithm and expressed as a log odds score, as for PAM. BLOSUM matrices are usually scaled in half-bit units. A score of zero indicates that the frequency with which a given two amino acids were found aligned in the database was as expected by chance, while a positive score indicates that the alignment was found more often than by chance, and negative score indicates that the alignment was found less often than by chance.