The comparison result of the amino acid sequences of native protein and mutant was showed in Fig. 2A, where 27 mutation positions were highlighted.
Sixty-six mutation positions were identified, including five mutation hotspots: U25A, C26A, G54A, U193C and U281A.
Similarly, from HpSVd-grapevine maintained in five hops, 116 cDNA clones (5 from the inoculum and 111 from the progeny) were sequenced and 25 mutation positions were identified.
From the original HpSVd-hop isolate maintained in five hop plants, 22 mutation positions were identified in 67 cDNA clones (5 from the inoculum and 62 from the progeny).
Mutation positions are given with respect to the rat GC-D cDNA sequence (L37203), e.g. 1958del44 indicates a 44-bp deletion beginning at position 1958 1859_TAAA indicates that a stop codon has been created beginning at position 1859, and 924insTG indicates that the sequence TG has been inserted after position 924.
Mutation positions were assigned according to the following human mRNA reference sequences: NM_006244 (PPP2R5B), NM_001161725 (PPP2R5C) and NM_006245 (PPP2R5D).
For the interacting pairs, 55% of the motif positions was overlapped by at least one correlated mutation position, and 39% of the correlated mutation positions was covered by a motif, whereas for the non-interacting pairs, 42% of the motif positions was overlapped by at least one correlated mutation position, and 32% of the correlated mutation positions was covered by a motif.
Because these interaction motifs are grouped into pairs of complementary motifs, correlated mutation positions were compared both to individual motifs and to pairs of complementary motifs.
The variations observed between the two types of fusion curves obtained depend on whether the base at the mutation positions was complementary to the probes [ 14].
We thus analysed whether or not the missense mutation positions were located in the molecular interaction sites based on the quaternary protein structures available from the PDB.
