The decimal portion of the score represents the quality of alignments between the wBm gene and the other cluster members. Thus, within a group of clusters with the same MST, wBm genes are individually ranked based on the quality of their BLAST alignment to other genes within the cluster (see Materials and Methods). The distribution of GCS scores for the wBm genome is shown in Figure 4 [see also Additional file 1]. Approximately 300 wBm genes cluster with selleck inhibitor orthologs in PD98059 ic50 all or nearly all Rickettsia members in the analysis and have a GCS of approximately 100. The next large group consists of 60 wBm genes that have a GCS of approximately 91 and orthologs in all members except for Pelagibacter ubique, the only

free-living organism in the group. A third group of 60 genes has a GCS of approximately 29, and corresponds to clusters https://www.selleckchem.com/products/bms-345541.html lacking orthologs to Orientia and most of the Rickettsia species. When picking an empirical threshold for prediction of gene essentiality we chose

a GCS of 29 or higher, which includes the three groups described above and contains 544 genes. Though the third group of 60 genes has lost orthologs to most of the Rickettsia, it retains orthologs in the Anaplasma, Ehrlichia, Neorickettsia and the other Wolbachiae. As is illustrated by the distribution along the y-axis of Figure 5, however, there is a large break between groups with a GCS of 91 and 29, and a more conservative estimate could place a threshold significantly higher. From a practical standpoint, however, because the GCS value represents a prediction of the importance of a specific gene, a more useful approach is to sort the genome by GCS rather than picking a threshold. Manually assessing from the top of the ranking allows the identification of highly conserved genes which can be searched for favorable secondary protein properties; in our case, properties useful for ADAMTS5 entry into the rational drug design pipeline. Figure 4 Distribution of GCS in w Bm. The X-axis indicates the 805 protein

coding genes in the wBm genome, ranked by GCS. The Y-axis shows the value of the GCS for each protein. Figure 5 Comparison of the prediction of w Bm gene essentiality by MHS and GCS. The X-axis shows normalized MHS on a log scale, while the Y-axis shows GCS. Grey lines indicate empirically determined thresholds for confidence in prediction of essentiality and are set at 7.3 × 10-3 for the MHS and 29 for the GCS. Therefore, the upper right quadrant contains genes with high confidence by both metrics. The upper left quadrant contains genes identified only by GCS, while the bottom right quadrant contains genes identified only by MHS. The numbers adjacent to the quadrant lines indicate gene counts in each quadrant. Red dots indicate Wolbachia genes which have significant protein sequence similarity to the targets of approved drugs and are predicted to be druggable.