The BLOSUM matrices: Henikoff & Henikoff (Henikoff, S. & Henikoff J.G. (1992) PNAS 89:10915-10919) .
-Use blocks of sequence fragments from different
protein families which can be aligned without the introduction of gaps.
Amino acid pair frequencies can be compiled from these
blocks
Different evolutionary distances are incorporated into this scheme with a clustering procedure: two sequences that are identical to each other for more than a certain threshold of positions are clustered.
More sequences are added to the cluster if they are identical to any sequence already in the cluster at the same level.
All sequences within a cluster are then simply averaged.
(A consequence of this clustering is that the contribution of closely related sequences to the frequency table is reduced, if the identity requirement is reduced. )
This leads to a series of matrices, analogous to the PAM
series of matrices. BLOSUM80: derived at the 80% identity level.
BLOSUM62 amino acid substitution matrix. Reference: Henikoff, S. and Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89: 10915-10919. April 20, 1993 11:49 A B C D E F G H I K L M N P Q R S T V W X Y Z 4.0 -2.0 0.0 -2.0 -1.0 -2.0 0.0 -2.0 -1.0 -1.0 -1.0 -1.0 -2.0 -1.0 -1.0 -1.0 1.0 0.0 0.0 -3.0 -1.0 -2.0 -1.0 A 6.0 -3.0 6.0 2.0 -3.0 -1.0 -1.0 -3.0 -1.0 -4.0 -3.0 1.0 -1.0 0.0 -2.0 0.0 -1.0 -3.0 -4.0 -1.0 -3.0 2.0 B 9.0 -3.0 -4.0 -2.0 -3.0 -3.0 -1.0 -3.0 -1.0 -1.0 -3.0 -3.0 -3.0 -3.0 -1.0 -1.0 -1.0 -2.0 -1.0 -2.0 -4.0 C 6.0 2.0 -3.0 -1.0 -1.0 -3.0 -1.0 -4.0 -3.0 1.0 -1.0 0.0 -2.0 0.0 -1.0 -3.0 -4.0 -1.0 -3.0 2.0 D 5.0 -3.0 -2.0 0.0 -3.0 1.0 -3.0 -2.0 0.0 -1.0 2.0 0.0 0.0 -1.0 -2.0 -3.0 -1.0 -2.0 5.0 E 6.0 -3.0 -1.0 0.0 -3.0 0.0 0.0 -3.0 -4.0 -3.0 -3.0 -2.0 -2.0 -1.0 1.0 -1.0 3.0 -3.0 F 6.0 -2.0 -4.0 -2.0 -4.0 -3.0 0.0 -2.0 -2.0 -2.0 0.0 -2.0 -3.0 -2.0 -1.0 -3.0 -2.0 G 8.0 -3.0 -1.0 -3.0 -2.0 1.0 -2.0 0.0 0.0 -1.0 -2.0 -3.0 -2.0 -1.0 2.0 0.0 H 4.0 -3.0 2.0 1.0 -3.0 -3.0 -3.0 -3.0 -2.0 -1.0 3.0 -3.0 -1.0 -1.0 -3.0 I 5.0 -2.0 -1.0 0.0 -1.0 1.0 2.0 0.0 -1.0 -2.0 -3.0 -1.0 -2.0 1.0 K 4.0 2.0 -3.0 -3.0 -2.0 -2.0 -2.0 -1.0 1.0 -2.0 -1.0 -1.0 -3.0 L 5.0 -2.0 -2.0 0.0 -1.0 -1.0 -1.0 1.0 -1.0 -1.0 -1.0 -2.0 M< 6.0 -2.0 0.0 0.0 1.0 0.0 -3.0 -4.0 -1.0 -2.0 0.0 N 7.0 -1.0 -2.0 -1.0 -1.0 -2.0 -4.0 -1.0 -3.0 -1.0 P 5.0 1.0 0.0 -1.0 -2.0 -2.0 -1.0 -1.0 2.0 Q 5.0 -1.0 -1.0 -3.0 -3.0 -1.0 -2.0 0.0 R 4.0 1.0 -2.0 -3.0 -1.0 -2.0 0.0 S 5.0 0.0 -2.0 -1.0 -2.0 -1.0 T 4.0 -3.0 -1.0 -1.0 -2.0 V 11.0 -1.0 2.0 -3.0 W -1.0 -1.0 -1.0 X 7.0 -2.0 Y 5.0 Z