The strain 26695 carried a sabA gene at both the sabA and sabB loci, Metabolism inhibitor whereas the strain P12 carried a sabB gene at both the loci. The strain B8 carried a sabA gene at the sabA locus and a hopQ gene at the sabB locus, along with another hopQ gene at the hopQ locus. Some of these genes (oipA, babA and babB) and homAB genes were previously reported to diverge between the East Asian and Western strains [13, 14, 17]. Difference in the number of copies of homAB genes between East Asian and Western strains was reported [17]. For hopMN, two gene types (hopM and hopN) have been recognized [26, 27]. Phylogenetic network

analysis revealed two variable regions within the hopMN family (region II and IV; Figure 2). Combining the two types of two variable regions defined four main gene types, of which two corresponded to hopM and hopN. The EPZ015666 research buy two types in region II were designated m1 and m2 (m for mid). The types in region IV were designated c1 and c2 (c for C-terminus); c3 was another variant type in region IV, composed of parts of c1 and c2. In this designation, previous hopM and hopN genes correspond to hopMNm1-c1

and hopMNm2-c1, respectively. All hpEastAsia strains except the strains 52 and PeCan4 (9/11) carry sequence type c2 at region IV. The c3 variant is observed in J99, PeCan4 and SJM180 (Figure 2A and 2F). Figure 2 East Asia-specific sequence at the C-terminus buy SB525334 of the putative product of hopMN. (A) Four types of hopMN genes. Type c3 of m1-c3 and m2-c3 is composed of parts of c1 and c2. The c1-m1 and c2-m1 types correspond to hopM and hopN, respectively. (B) Phylogenetic network

of whole region of proteins. Types m1-c3 and m2-c3 cannot be clearly distinguished Vildagliptin from m1-c1 and m2-c1 in this figure. (C)-(F) Phylogenetic networks for the four domains. Scale bar indicates substitutions per amino acid residue (change/amino-acid site). Positions are for HP0227 of strain 26695. Three vacA paralogs and vacA itself were found in 26695 [28]. Those paralogs share the auto-transporter domain at the C-terminus with vacA [28]. A large deletion in vacA-2 (HP0289) (approximately 2400 amino acids) was found in all the hspEAsia strains except the strain 51 (5/6) (Table 2 and Additional file 2 (= Table S1)). It was described earlier that horA OMP locus in 26695 is composed of two open reading frames (ORFs) (HP0078/HP0079) whereas that in J99 is composed of one ORF (jhp0073) [27]. The horA locus in all the hspEAsia strains shows apparent gene decay by fragmentation through various mutations (Figure 3). Whether the genes in the other strains are functional is not known. Figure 3 Fragmentation of horA OMP gene through various mutations in the hspEAsia strains. Genes homologous to horA in J99 (jhp0073) are classified by the number of ORFs. Numbers indicate coordinates on the genome sequence. Nucleotide similarity between each pair of strains is indicated by gray parallelogram. The state in strain 98-10 is: two ORFs.