Figure 3

Distinguishing between secreted and N-anchored proteins. Tjalsma et al. [41] have identified 33 N-anchored and 36 secreted proteins from Bacillus subtilis (by 2D gel electrophoresis) which have a putative SPI-cleavage site motif in the C-region that follows the transmembrane helix H-region (see Fig. 1B). (A): A sequence composition chart, made using WebLogo [47], based on multiple-sequence alignment of the H- and C-regions (see Fig. 1B) of the N-anchored and secreted protein sets. The red arrow indicates the cleavage position of true SPI-site motifs (see Figure 1B), and the green dashed arrow represents the corresponding position in N-anchored proteins that is not cleaved. (B): The specificity of HMMs of different lengths containing the putative cleavage site A* = the Alanine after which cleavage takes place. Mod1: residues -9 to A*; Mod2: residues -11 to A*; Mod3: residues -14 to A*; Mod4: residues -8 to +3 of A*; Mod5: residues -13 to +10 of A*; Mod6: residues -8 to +17 of A*; Mod7: residues -3 to +10 of A*; Mod8: residues -3 to +17 of A*; Mod9: residues +1 to +25.