It thus appears GSK461364 that the initial Axxx is more strongly conserved than the terminating xxxA. Just two of the YscL sequences contained repeats with both the initial AxxxG and the terminal GxxxA, and an equal number (4 each) contained only the initial AxxxG or only the terminal GxxxA. Secondary
structure prediction Several secondary structure prediction programs were used to predict the secondary structure of the primary repeat segments of selected FliH and YscL proteins, and the prediction programs consistently and convincingly classified these regions as α-helical for all of the GSK126 proteins tested. The tools used are given in [27–31]. Thus, there is a strong basis for interpreting the sequence this website characteristics of the glycine repeat segments as being important either for helical stability, or for making helix-helix interactions. Multiple alignment of the glycine repeats We have performed a multiple alignment of the glycine repeats in both FliH (Figure 5) and YscL (Figure 6) to illustrate the composition of their repeat segments. The alignment was essentially
carried out by hand and forces both the initial (Axxx or Gxxx) and terminal (xxxA or xxxG) motif to be in the same register. One interesting observation in Figure 5 is that sequences with shorter repeats appear to be more likely to have the initial Axxx and the terminating xxxG than sequences with longer repeats, suggesting that longer repeats may compensate in some way for the absence of the alanine “”caps”". Figure 6 Multiple alignment of the primary repeat segments from the YscL proteins of different organisms. The primary repeat segments in the YscL proteins were aligned by hand. Only sequences that contained a repeat segment appear in this alignment. Calculating the amino acid distribution Fluorometholone Acetate in the primary repeat segments After this initial characterization of the glycine repeats, we then sought to determine the frequency of each amino acid in each position of each repeat type. Figures 7 and 8 give these data for all three repeat types in FliH, and just for GxxxGs
in YscL (the sample size of AxxxGs and GxxxAs in YscL is too small to justify making inferences about the distribution of amino acids in the variable positions). While the frequencies reported in Figures 7 and 8 certainly appear to diverge significantly from what one might consider to be a “”normal”" distribution of amino acids, we confirmed this observation statistically. A χ2 test was used to determine whether the amino acid frequencies in each position – repeat-type combination was significantly different than the amino acid frequencies in the entirety of all the FliH proteins. The x1, x2, and x3 positions in both AxxxGs and GxxxGs all had P-values less than 10-30, while those same positions for GxxxAs had P-values of 1.4 × 10-3, 1.8 × 10-9, and 9.