Structure Topology Prediction of Discriminative Sequence Motifs in Membrane Proteins with Domains of Unknown Functions
Figure 2
WebLogos [31] of the LG5 motif in the order of three topology states “TM” (a), “nTM” (b), and “trans” (c). However, the symbol height in each logo reflect only the relative occurrence of the corresponding amino acid. Additionally, background amino-acid-specific frequencies are not taken into account which decreases the sensitivity of this method. Compared to the heat map generated from LOPs (see Figure 3), less information can be gained. By applying WebLogo, residue propensities, with regard to the topology states, cannot be derived or identified. For instance, the leucine amino acid in “TM” (WebLogo A) cannot be observed as more frequently at the third variable position as at other positions.
