Figure 4
Sequence complexity/hydrophobicity plot for membrane and signal anchors against functional TM-helices. Figure 4A shows the sequence complexity/hydrophobicity plot of the membrane anchors (blue) against the functional α-helices (green), functional TM-helices (UniProt-derived; red) and low-complexity segments (SEG25/3.0/3.3-detected; gray). The dotted lines are defined by xΦ = μΦ + 1.282σΦ and x c = μ c -1.282σ c where (μΦ,σΦ)and (μ c , σ c ) are the summary statistic calculated from the UniProt-derived functional TM-helix set. This corresponds to a false-negative rate of 10% (at f = 1.282). Based on the plot, there is some overlap between the functional α- and TM-helices which justifies for the extension of the sequence homology concept for these cases. 55.8% (169 out of the 303) of the membrane anchors occupy the upper left quadrant, suggestive of simple TM helices. Figure 4B shows the complexity and hydrophobicity plot of signal anchors (blue) against the functional α-helices (green), functional TM-helices (UniProt-derived; red) and signal peptides (cyan). Similarly, the dotted lines define the boundaries at the false-negative rate of 10%. 30.1% of the signal anchors (531 out of the 1767) occupy the upper left quadrant, suggestive of simple TM helices.