Regions containing all of these factors (i.e., viral-like proteins clustered and in a specific orientation, and flanked by a tRNA/integrase on one end and an exact repeat of at least 10 bp of the tRNA on the other end) were considered putative prophage. Regions containing many of these characteristics but lacking one or more, usually an integrase or repeat sequence, were considered prophage-like. BAY 80-6946 in vivo Some att sites are less than 10 bp and are difficult to spot so it is possible that some of the prophage-like elements may actually be true prophages. Prophage and prophage-like

regions so inferred have been designated “”PI-strain-1″”, “”PI-strain-2″”, etc. (PI for Prophage Island), and are listed in Table 1B. Four of the B. pseudomallei strains Selleck BAY 11-7082 represent two paired isolates from two separate patients, one strain isolated from an initial infection and the paired isolate from a re-emergent infection in the same patient. Three of the 16 OTX015 ic50 genomic islands previously identified in B. pseudomallei K96243 were included in the analysis, including ϕK96243

(GI2) and the putative prophages GI3 and GI15 [3]. Three prophage-like islands identified in B. thailandensis E264, GI1, GI12, and GI13, were also included in the analysis (Table 1B) [24]. Additionally, the published genome sequences of ϕ1026b from B. pseudomallei 1026b [6], ϕE125 from B. thailandensis E125 [21], BcepMu from B. cenocepacia J2315 [29], Bcep22 from B. cepacia, and Bcep781 from B. cepacia [30], all of which are classified as dsDNA phages, were included for comparison (Table 1C). Comparative genome sequence analysis and phylogenetic tree construction The program Dotter [31] was used to align nucleotide sequences of all isolated and putative prophage and prophage-like sequences and to identify initial groupings. To refine clusters, distance measures were calculated between all pairs of each of the 30 prophage

and PI sequences. Reciprocal BLASTP comparisons Farnesyltransferase of the translated protein sets were performed for each prophage/PI against all others. BLASTP distances between each pair were calculated according to the formula: 1-(number of significant hits between both genomes/total number of genes in both genomes) [32]. Distances were calculated using E value cutoffs of 1 × E-01, 1 × E-05, and 1 × E-10. FITCH with the global and jumble options was used to generate a phylogenetic tree from each of the three distance matrices derived from the BLASTP distances [33]. Calculation of local collinear blocks (LCB or synteny blocks) was done using progressive Mauve alignment [34] with default settings. Initial identification of morons was conducted in the Mauve alignments by searching for ORFs that disrupted the collinearity in LCBs. Confirmation of morons was done by (i) comparing % GC content of each ORF against the mean % GC of phage-specific genes (i.e., involved in structure, replication, and host lysis); (ii) promoter and terminator prediction analysis with BPROM http://​www.