Table 2 |
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|
Vector weights calculated for amino acid substitutions. |
||||||||
|
RR |
Lasso |
PLSR |
SVMR |
|||||
|
|
||||||||
|
Substitution |
M |
σ |
M |
σ |
M |
σ |
M |
σ |
|
|
||||||||
|
S107D |
-0.03 |
0.13 |
0.00 |
0.02 |
-0.70 |
0.26 |
-0.16 |
0.13 |
|
S123A |
-1.00 |
0.13 |
-0.41 |
0.35 |
-1.42 |
0.23 |
-0.93 |
0.14 |
|
I132V |
0.04 |
0.44 |
0.04 |
0.55 |
0.32 |
0.76 |
-0.34 |
0.29 |
|
M145F |
-1.46 |
0.19 |
-2.27 |
0.49 |
-1.98 |
0.32 |
-1.58 |
0.20 |
|
Y151A |
1.18 |
0.23 |
0.91 |
0.23 |
1.66 |
0.37 |
0.91 |
0.15 |
|
V167I |
-0.97 |
0.13 |
-1.09 |
0.15 |
-1.10 |
0.17 |
-0.79 |
0.14 |
|
L180I |
-0.23 |
0.15 |
-0.05 |
0.10 |
-0.35 |
0.19 |
-0.36 |
0.13 |
|
Y194S |
0.27 |
0.20 |
0.00 |
0.01 |
0.94 |
0.73 |
0.01 |
0.14 |
|
A199S |
-1.16 |
0.39 |
-1.09 |
0.46 |
-2.66 |
0.98 |
-0.86 |
0.21 |
|
K208H |
0.28 |
0.15 |
0.07 |
0.12 |
0.52 |
0.18 |
0.36 |
0.17 |
|
R237N |
-0.93 |
0.09 |
-0.91 |
0.13 |
-1.21 |
0.12 |
-0.86 |
0.15 |
|
V267I |
-0.48 |
0.11 |
-0.32 |
0.14 |
-0.68 |
0.13 |
-0.16 |
0.12 |
|
S273T |
0.12 |
0.14 |
0.01 |
0.06 |
0.28 |
0.19 |
-0.05 |
0.17 |
|
G293A |
1.95 |
0.13 |
2.24 |
0.14 |
2.10 |
0.17 |
1.70 |
0.13 |
|
K332R |
0.07 |
0.13 |
-0.01 |
0.05 |
0.02 |
0.14 |
0.09 |
0.15 |
|
S337N |
-0.02 |
0.14 |
0.03 |
0.09 |
-0.20 |
0.15 |
0.03 |
0.14 |
|
P355S |
-1.08 |
0.12 |
-1.20 |
0.15 |
-1.25 |
0.13 |
-1.10 |
0.15 |
|
|
||||||||
|
LPSVMR |
LPBoostR |
MR |
ORMR |
|||||
|
|
||||||||
|
Substitution |
M |
σ |
M |
σ |
M |
σ |
M |
σ |
|
|
||||||||
|
S107D |
-0.01 |
0.20 |
-0.02 |
0.21 |
-0.35 |
0.24 |
-0.35 |
0.24 |
|
S123A |
-0.41 |
0.43 |
-0.40 |
0.41 |
0.52 |
0.93 |
0.52 |
0.93 |
|
I132V |
0.22 |
0.69 |
0.18 |
0.56 |
2.61 |
0.91 |
2.61 |
0.91 |
|
M145F |
-2.39 |
0.53 |
-2.39 |
0.53 |
-5.33 |
1.05 |
-5.33 |
1.05 |
|
Y151A |
0.82 |
0.24 |
0.82 |
0.25 |
0.64 |
0.24 |
0.64 |
0.24 |
|
V167I |
-0.99 |
0.24 |
-0.98 |
0.23 |
-1.63 |
0.24 |
-1.63 |
0.24 |
|
L180I |
-0.20 |
0.16 |
-0.19 |
0.16 |
0.60 |
0.23 |
0.60 |
0.23 |
|
Y194S |
-0.02 |
0.08 |
0.21 |
0.38 |
4.59 |
2.10 |
4.59 |
2.10 |
|
A199S |
-0.49 |
0.33 |
-0.73 |
0.54 |
-4.92 |
2.03 |
-4.92 |
2.03 |
|
K208H |
0.16 |
0.18 |
0.14 |
0.18 |
0.01 |
0.13 |
0.01 |
0.13 |
|
R237N |
-0.96 |
0.29 |
-0.96 |
0.29 |
-1.59 |
0.57 |
-1.59 |
0.57 |
|
V267I |
-0.41 |
0.23 |
-0.41 |
0.23 |
-1.33 |
0.14 |
-1.33 |
0.14 |
|
S273T |
0.19 |
0.33 |
0.15 |
0.28 |
0.96 |
0.58 |
0.96 |
0.58 |
|
G293A |
2.18 |
0.25 |
2.20 |
0.25 |
3.20 |
0.14 |
3.20 |
0.14 |
|
K332R |
0.12 |
0.19 |
0.14 |
0.21 |
-0.33 |
0.13 |
-0.33 |
0.13 |
|
S337N |
0.27 |
0.28 |
0.26 |
0.28 |
0.34 |
0.59 |
0.34 |
0.59 |
|
P355S |
-1.34 |
0.35 |
-1.35 |
0.34 |
-1.95 |
0.57 |
-1.95 |
0.57 |
|
|
||||||||
|
Mean (M) and standard deviation (σ) values are shown for the 19 substitutions for which weights were calculated using machine learning. The values were calculated from 1000 subsamples of the variants with measurable activity from sets 1 and 2, where 5 variant sequences were randomly omitted from each subsample. |
||||||||
|
Liao et al. BMC Biotechnology 2007 7:16 doi:10.1186/1472-6750-7-16 |
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