Figure 2

Multiple alignments of the 10 repeats of 1BK5A (1bk5-1 to 1bk5-10) and the 8 repeats of mesothelin model (msln-1 to msln-8). The three double-headed arrows at the top of the Figure indicate the boundaries of the three helical regions of the 7th repeat of 1BK5A. The first two form the outer helices and the third the inner helix. The helix boundaries of other repeats do not always agree with those of the 1BK5A 7^th repeat. The residues in the 7^th repeat of 1BK5A are shown in the next line in uppercase letters. The residues in all other repeats that follow are in upper or lower case letters depending on whether they align with residues of the 7^th repeat of 1BK5A or not, respectively. The columns labelled 10, 13, 16 and 17 at the bottom are the key positions in the outer helix that are hydrophobic in many ARM/HEAT repeats [40]. Similarly LxxxAxxxL at the bottom indicates the conserved LEU and ALA positions in the inner helix, x being any residue. The hydrophobic residues (A, V, I, L, M, F, Y, W) in these 7 columns are highlighted.