HHBLITS_AA_TO_ID

Use the hhblits convention to map amino acids to corresponding numbers. Map some undefined single-letter symbols to definite values, such that B can be expressed as aspartic acid or aspartic acid. It is specified that B has the same number as D for aspartic acid (ASP), while J and O have the same number as X for unknown amino acid. U has the same number as C for cysteine (CYS). Z has the same number as E for glutamic acid (GLU), and ‘-’ represents the missing amino acid. Except B, J, O, U, and Z, other letters are numbered in sequence, and their meanings correspond to those in restype_1to3 .

key	value
A	0
B	2
C	1
D	2
E	3
F	4
G	5
H	6
I	7
J	20
K	8
L	9
M	10
N	11
O	20
P	12
Q	13
R	14
S	15
T	16
U	1
V	17
W	18
X	20
Y	19
Z	3
-	21