Figure 4

N. meningitidis FrpB protein variability zone detection (a) Topology model of the FrpB protein of N. meningitidis strain H44/76. Topology of the β-barrel. Surface-exposed loops (L) and β-strands are numbered. Residues are framed according to their predicted secondary structure: Amino acid residues in β-strands are depicted by diamonds. Amino acid residues present in exposed loops and periplasmic turns are depicted by circles (reproduced from Kortekaas et al., 2007) [20]. (b)-(c) Variability zone detection by the hit region identification Q′-tγpe functions, achieved without prior knowledge of invasive taxa (case b), and Q″-type functions, using this prior knowledge along with the ARI coefficient (case c). Functions and are depicted by a dashed line and functions and are depicted by a continuous line. A non-overlapping sliding window of size 9 nucleotides was used during the scan of the gene FrpB MSA. The abscissa axis represents the window position along the nucleotide MSA. 11 gray zones correspond to extracellular loops. Annotations start at the solid vertical line (near the 400 abscissa mark).