The codon-based Z-test bootstrap

analysis confirmed that a vast majority (98.86%) of the nucleotide sequences had a high probability (p < 0.01) of being under purifying selection. Table 1 depicts the results of the test for positive selection in PAML. The two models that allowed positive selection, M2 and M8, fit our data better than the models, M1 and M7, that did not. The LRT showed that the M8 model best fit these data. This model estimated that fourteen sites (4.63%) were under positive selection (Table 2), with ω = 1.55 and 85.83% were signaling pathway under purifying selection, with ω < 0.2. The M2 model estimated that 92.12% of the sites were under purifying selection, while 1.46% was positively selected. PAML estimated κ ≈ 4 for M2 and M8. Table 1 Likelihood ratio test for model selection Model lnL LRT χ2 distribution M1 −12515.96 47.04 >9 with 2 d.o.f. P < 0.01 M2 −12492.44     M7 −12521.64 83.94 >9 with 2 d.o.f. Selleckchem CT99021 P < 0.01 M8 −12479.67     Nested models with and without positive selection (M1 vs. M2 and M7 vs. M8) were compared in PAML. The χ2 distribution column shows the minimum likelihood ratio (=2ΔlnL) necessary for

the more complex of two models to be significantly better (p < 0.01). Table 2 Positively-selected sites in pldA of Helicobacter pylori Site Residue Probability ω >1 Posterior probability 5 W 0.955* 1.48 ± 0.20 6 L 0.996** 1.52 ± 0.15 21 S 0.830 1.37 ± 0.33 27 I 1.000** 1.52 ± 0.14 34 R 0.576 1.15 ± 0.42 40 I 0.999** 1.52 ± 0.14 50 A 0.989* 1.51 ± 0.15 59 P 0.858 1.39 ± 0.29 137 D 1.000** 1.52 ± 0.14 144 D 0.760 1.32 ± 0.33 153 M 1.000** 1.52 ± 0.14 209 P 0.851 1.39 ± 0.31 211 G 0.836 1.38

± 0.30 278 V 0.962* 1.48 ± 0.15 PAML predicted that 14 sites were under positive selection (ω >1) using Bayes empirical Bayes analysis for the M8 model. check details One asterisk (*) signifies a probability >95% that ω >1, while two asterisks (**) signify a probability greater than 99%. The best ancestral reconstruction is indicated by the highest value in the final posterior probability column. LDN-193189 cell line Discussion Brok et al. compared OMPLA protein orthologs from eleven different species and concluded that OMPLA contained 30 highly-conserved residues. The fact that OMPLA is present in a wide range of species, including H. pylori, and that the sequence is conserved across those species, strongly indicates that its physiological role is significant [23]. This study aimed to better understand the significance of pldA, the gene coding for OMPLA, in H. pylori; an important gut bacterium in humans. The H. pylori pldA gene had a low degree of variability and, thus, a conserved OMPLA protein sequence alignment. Housekeeping genes are essential for bacterial survival, and are thus highly conserved. The seven HK genes, atpA, efp, ppa, tphC, ureI, trpC, and mutY, and the pldA gene are among the core genes that are found in all H. pylori genomes sequenced to date [10].