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# BLASTP default substitution scores.
# For the default gap scores, as used for BLASTP on NCBI Web
# BLAST, The BLAST documentation shows gap costs a = 11 for opening
# a gap, and b = 1 for each letter in the gap, and defines the
# total score of a gap of k residues as -(a + b*k). In contrast,
# Biopython follows the definition given in "Biological Sequence
# Analysis" (Durbin et al., 1998), for which the total score of a
# gap of k residues is -d - e * (k - 1), where d is the gap-open
# penalty and e is the gap-extend penalty. Biopython uses -d as
# the gap open score and -e as the gap extend penalty:
# gap open score: -12
# gap extend score: -1
# with the substitution matrix below, as the BLASTP score parameters.
# The substitution matrix is identical to BLOSUM62, except for some
# values of the ambiguous amino acids B, Z, and X; the values for
# the ambiguous amino acids U, O, and J are not included in BLOSUM62.
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z *
A 4 -2 0 -2 -1 -2 0 -2 -1 -1 -1 -1 -1 -2 -1 -1 -1 -1 1 0 0 0 -3 -1 -2 -1 -4
B -2 4 -3 4 1 -3 -1 0 -3 -3 0 -4 -3 4 -1 -2 0 -1 0 -1 -3 -3 -4 -1 -3 0 -4
C 0 -3 9 -3 -4 -2 -3 -3 -1 -1 -3 -1 -1 -3 -1 -3 -3 -3 -1 -1 9 -1 -2 -1 -2 -3 -4
D -2 4 -3 6 2 -3 -1 -1 -3 -3 -1 -4 -3 1 -1 -1 0 -2 0 -1 -3 -3 -4 -1 -3 1 -4
E -1 1 -4 2 5 -3 -2 0 -3 -3 1 -3 -2 0 -1 -1 2 0 0 -1 -4 -2 -3 -1 -2 4 -4
F -2 -3 -2 -3 -3 6 -3 -1 0 0 -3 0 0 -3 -1 -4 -3 -3 -2 -2 -2 -1 1 -1 3 -3 -4
G 0 -1 -3 -1 -2 -3 6 -2 -4 -4 -2 -4 -3 0 -1 -2 -2 -2 0 -2 -3 -3 -2 -1 -3 -2 -4
H -2 0 -3 -1 0 -1 -2 8 -3 -3 -1 -3 -2 1 -1 -2 0 0 -1 -2 -3 -3 -2 -1 2 0 -4
I -1 -3 -1 -3 -3 0 -4 -3 4 3 -3 2 1 -3 -1 -3 -3 -3 -2 -1 -1 3 -3 -1 -1 -3 -4
J -1 -3 -1 -3 -3 0 -4 -3 3 3 -3 3 2 -3 -1 -3 -2 -2 -2 -1 -1 2 -2 -1 -1 -3 -4
K -1 0 -3 -1 1 -3 -2 -1 -3 -3 5 -2 -1 0 -1 -1 1 2 0 -1 -3 -2 -3 -1 -2 1 -4
L -1 -4 -1 -4 -3 0 -4 -3 2 3 -2 4 2 -3 -1 -3 -2 -2 -2 -1 -1 1 -2 -1 -1 -3 -4
M -1 -3 -1 -3 -2 0 -3 -2 1 2 -1 2 5 -2 -1 -2 0 -1 -1 -1 -1 1 -1 -1 -1 -1 -4
N -2 4 -3 1 0 -3 0 1 -3 -3 0 -3 -2 6 -1 -2 0 0 1 0 -3 -3 -4 -1 -2 0 -4
O -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
P -1 -2 -3 -1 -1 -4 -2 -2 -3 -3 -1 -3 -2 -2 -1 7 -1 -2 -1 -1 -3 -2 -4 -1 -3 -1 -4
Q -1 0 -3 0 2 -3 -2 0 -3 -2 1 -2 0 0 -1 -1 5 1 0 -1 -3 -2 -2 -1 -1 4 -4
R -1 -1 -3 -2 0 -3 -2 0 -3 -2 2 -2 -1 0 -1 -2 1 5 -1 -1 -3 -3 -3 -1 -2 0 -4
S 1 0 -1 0 0 -2 0 -1 -2 -2 0 -2 -1 1 -1 -1 0 -1 4 1 -1 -2 -3 -1 -2 0 -4
T 0 -1 -1 -1 -1 -2 -2 -2 -1 -1 -1 -1 -1 0 -1 -1 -1 -1 1 5 -1 0 -2 -1 -2 -1 -4
U 0 -3 9 -3 -4 -2 -3 -3 -1 -1 -3 -1 -1 -3 -1 -3 -3 -3 -1 -1 9 -1 -2 -1 -2 -3 -4
V 0 -3 -1 -3 -2 -1 -3 -3 3 2 -2 1 1 -3 -1 -2 -2 -3 -2 0 -1 4 -3 -1 -1 -2 -4
W -3 -4 -2 -4 -3 1 -2 -2 -3 -2 -3 -2 -1 -4 -1 -4 -2 -3 -3 -2 -2 -3 11 -1 2 -2 -4
X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -4
Y -2 -3 -2 -3 -2 3 -3 2 -1 -1 -2 -1 -1 -2 -1 -3 -1 -2 -2 -2 -2 -1 2 -1 7 -2 -4
Z -1 0 -3 1 4 -3 -2 0 -3 -3 1 -3 -1 0 -1 -1 4 0 0 -1 -3 -2 -2 -1 -2 4 -4
* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
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