Table 1.

Scoring matrix used to define domain boundaries and calculate dos score, representing likelihood for a given amino acid to be found in GW domain

Amino acid	Score [half-bits]	Score [bits]	Ratio	Frequency	Count
W	2.666	1.333	2.520	0.063:0.025	743:1062
G	2.068	1.034	2.048	0.213:0.104	2490:4447
N	1.510	0.755	1.688	0.081:0.048	949:2051
S	1.236	0.618	1.535	0.152:0.099	1774:4213
A	0.280	0.140	1.102	0.065:0.059	762:2537
D	0.184	0.092	1.066	0.081:0.076	950:3254
T	0.000	0.000	1.000	0.040:0.040	467:1718
Q	−0.076	−0.038	0.974	0.038:0.039	440:1686
K	−0.120	−0.060	0.959	0.070:0.073	821:3136
R	−0.590	−0.295	0.815	0.044:0.054	518:2319
P	−0.644	−0.322	0.800	0.032:0.040	373:1726
E	−1.288	−0.644	0.640	0.048:0.075	560:3219
V	−2.408	−1.204	0.434	0.023:0.053	274:2260
F	−2.558	−1.279	0.412	0.014:0.034	169:1443
H	−3.324	−1.662	0.316	0.006:0.019	76:796
C	−3.398	−1.699	0.308	0.004:0.013	43:568
Y	−4.792	−2.396	0.190	0.004:0.021	50:890
M	−5.012	−2.506	0.176	0.003:0.017	39:743
I	−5.030	−2.515	0.175	0.007:0.040	79:1705
L	−5.252	−2.626	0.162	0.011:0.068	132:2925

The amino acids are sorted by the score value, from highest to lowest. The second and third columns were used in domain identification calculations. The last two colums contain counts and frequencies of a given amino acid found in the whole protein sequence versus the domain (format–domain: entire protein).