Dayhoff table (Schwartz, R. M. and Dayhoff, M. O. [1979] in Atlas of Protein Sequence and Structure, Dayhoff, M. O. Ed, pp. 353-358, National Biomedical Research Foundation, Washington D.C.) rescaled by dividing each value by the sum of its row and column, and normalizing to a mean of 0 and standard deviation of 1.0. The value for FY (Phe-Tyr) = RW =1.425. Perfect matches are set to 1.5 and no matches on any row are better than perfect matches.
NB: This table was derived from an analysis of globular proteins!
A B C D E F G H I K L M N P Q R S T V W Y Z .
1.5 0.2 0.3 0.3 0.3 -0.5 0.7 -0.1 0.0 0.0 -0.1 0.0 0.2 0.5 0.2 -0.3 0.4 0.4 0.2 -0.8 -0.3 0.2 A
1.1 -0.4 1.1 0.7 -0.7 0.6 0.4 -0.2 0.4 -0.5 -0.3 1.1 0.1 0.5 0.1 0.3 0.2 -0.2 -0.7 -0.3 0.6 B
1.5 -0.5 -0.6 -0.1 0.2 -0.1 0.2 -0.6 -0.8 -0.6 -0.3 0.1 -0.6 -0.3 0.7 0.2 0.2 -1.2 1.0 -0.6 C
1.5 1.0 -1.0 0.7 0.4 -0.2 0.3 -0.5 -0.4 0.7 0.1 0.7 0.0 0.2 0.2 -0.2 -1.1 -0.5 0.9 D
1.5 -0.7 0.5 0.4 -0.2 0.3 -0.3 -0.2 0.5 0.1 0.7 0.0 0.2 0.2 -0.2 -1.1 -0.5 1.1 E
1.5 -0.6 -0.1 0.7 -0.7 1.2 0.5 -0.5 -0.7 -0.8 -0.5 -0.3 -0.3 0.2 1.3 1.4 -0.7 F
1.5 -0.2 -0.3 -0.1 -0.5 -0.3 0.4 0.3 0.2 -0.3 0.6 0.4 0.2 -1.0 -0.7 0.3 G
1.5 -0.3 0.1 -0.2 -0.3 0.5 0.2 0.7 0.5 -0.2 -0.1 -0.3 -0.1 0.3 0.5 H
1.5 -0.2 0.8 0.6 -0.3 -0.2 -0.3 -0.3 -0.1 0.2 1.1 -0.5 0.1 -0.2 I
1.5 -0.3 0.2 0.4 0.1 0.4 0.8 0.2 0.2 -0.2 0.1 -0.6 0.4 K
1.5 1.3 -0.4 -0.3 -0.1 -0.4 -0.4 -0.1 0.8 0.5 0.3 -0.2 L
1.5 -0.3 -0.2 0.0 0.2 -0.3 0.0 0.6 -0.3 -0.1 -0.1 M
1.5 0.0 0.4 0.1 0.3 0.2 -0.3 -0.3 -0.1 0.4 N
1.5 0.3 0.3 0.4 0.3 0.1 -0.8 -0.8 0.2 P
1.5 0.4 -0.1 -0.1 -0.2 -0.5 -0.6 1.1 Q
1.5 0.1 -0.1 -0.3 1.4 -0.6 0.2 R
1.5 0.3 -0.1 0.3 -0.4 0.0 S
1.5 0.2 -0.6 -0.3 0.1 T
1.5 -0.8 -0.1 -0.2 V
1.5 1.1 -0.8 W
1.5 -0.6 Y
1.1 Z
NB: This default table will probably be replaced by the BLOSUM62 table in later releases of the GCG package. ($ FETCH BLOSUM62.CMP)
Reference: Henikoff, S. and Henikoff, J. G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89: 10915-10919.
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
To use this table in place of the default for Bestfit or Gap (but beware of the default gap penalties, they may be too low):
$ Bestfit/Data1=genmoredata:blosum62.cmp