BMC Genomics 2009, 10(Suppl 3):S19 http://www.biomedcentral.com/1471-2164/10/S3/S19 Figure 2 Domain architecture (DA) of the three PGIP molecules. A, B & C show the DA of PvPGIP1, PvPGIP2 and GmPGIP3 respectively. Domains in all the three proteins are arranged as one LRR_NT2 domain followed by nine leucine-rich repeats (R1-R9). The domains are shown by rectangular boxes. Out of the nine LRRs, four have been marked as plant-specific (PS) LRRs (R3-R5, R9). The vertical bars in A and C denote the sequence variations with PvPGIP2 and the numbers stand for the residue number. The types of vertical bars change with the position of the varying residue, an information obtained from the multiple sequence alignments shown in Figure 3. Plain vertical bars stand for changes that are found in the LRR_NT2 region, the black and grey bars signify residue positions belonging to the conserved region and the variable region of LRRs respectively, while the hatched bars are for those in the non-LRR region. the proteins. Two (R5 and R9) out of the four PS-LRRs and the first (R1) and the sixth (R6) repeat harbour these four variations mentioned above. The 34 variations between PvPGIP2 and GmPGIP3 on the other hand, are divided amongst all domains including LRRNT_2 and all the plant specific LRRs (Figure 2C). Distribution of the variations in the domains Out of the 34 residues that differ in GmPGIP3 from PvPGIP2 only two changes (Position 297 and 311 in Figure 1) are common with the 8 differing residues between PvPGIP1 and PvPGIP2 leaving the rest 32 variations to be at unique positions. 27 out of these 34 fall in the LRR regions and 2 in the LRRNT_2 region leaving altogether 5 positions to remain scattered in the intervening non-LRR regions. The sequence variation that fall in the LRR region in PvPGIP1(4) and GmPGIP3 (27) with PvPGIP2 could be distributed amongst the conserved portion of the repeat or the variable portion of it. It becomes an important task to determine this, as there are positions in the repeats where sequence variation is accepted without an associated change in structure. To account for the distribution of these variations with respect to different regions in the repeats, we constructed individual multiple sequence alignments. Figure 3 shows the multiple sequence alignment of nine repeats each from PvPGIP1, PvPGIP2 and GmPGIP3. The conserved region of the repeats are marked by the conserved pattern of LRRs (written below each align- ment) while the rest of the repeat signify its variable region. Considering an insertion of a residue (G) in R2 for PvPGIP1 and PvPGIP2 and an insertion of P in R2 of GmPGIP3 at another position, the variations (marked by black rectangles for those between PvPGIP2 and PvPGIP1 and grey rectangles for those between PvPGIP2 and GmPGIP3) can be rightly explained to be concentrated in positions (mostly X or variable region) where the motif itself has the provision for changes. The details of the distribution of the variations (8 for PvPGIP1 and 34 for GmPGIP3) in the LRR (conserved (c) and variable (v) region) and the non-LRR regions with reference to the residue type is tabulated in the Additional file 1. Depending on whether the variation is in the conserved Page 4 of 12 (page number not for citation purposes)