Table 2.

Comparative analysis of the GPCRtm performance regarding general-purpose substitution matrices in BLASTP searches of one hundred GPCR protein queries against the PDB database

Test matrix	No. of queries GPCRtm better	No. of queries GPCRtm worst	No. of queries GPCRtm the same	p-value
JTTtm	21	0	79	<0.001**
PHAT	8	0	92	0.008*
BLOSUM62	9	1	90	0.021*
BLOSUM45	12	1	87	0.003*

p-values were calculated by McNemar’s test (* significant differences at α = 0.05, ** significant differences at α = 0.001)