Phylogenetic network analysis of the hopM/N family was carried out using NeighborNet [130] implemented on SpritsTree [131]. Analyses NCT-501 of molybdenum-related genes H. pylori protein sequences were searched against the CDD conserved protein domain database, by RPS-BLAST [132]. Protein families extracted from the search results for Mo-cofactor synthesis or binding domain were: PF03404 (Mo-co_dimer), PF03205 (MobB), PF02738 (Ald_Xan_dh_C2), PF01568 (Molydop_binding), PF02730 (AFOR_N), PF02597

(ThiS), PF03454 (MoeA_C), PF06463 (Mob_synth_C), PF03453 (MoeA_N), PF01315 (Ald_Xan_dh_C), PF01493 (GXGXG), PF02579 (Nitro_FeMo-Co, PF01967 (MoaC), PF03459 (TOBE), PF02391 (MoaE), PF00384 (Molybdopterin), PF04879 (Molybdop_Fe4S4), PF02665 (Nitrate_red_gam), PF00174 (Oxidored_molyb), PF00994 (MoCF_biosynth), PF03473 (MOSC), PF02625 (XdhC_CoxI), PF01314 (AFOR_C), PF01547 (SBP_bac_1) (pfam name in parentheses). Homologs of two molybdoproteins [133] that were not detected in the above protein families were absent in the H. pylori genomes. bisC was the only molybdoenzyme gene in the

20 H. pylori genomes with detected domains PF01568 (Molydop_binding) and PF00384 (Molybdopterin). A multidomain TIGR00509 (bisC_fam) was also detected in bisC. Analyses of horizontally transferred regions GIs were detected by searching for regions that fulfilled the see more conditions of: (i) longer than 5 kb; (ii) continuous ORFs not perfectly conserved in all 20 H. pylori strains; and (iii) whole regions assumed as extrinsic by Alien Hunter [134]. Counterparts of detected GIs in Amerind strains were previously reported as TnPZ [48, 49]. Genes with a large distance between East Asian and European strains OGs diverged between six hspEAsia and seven hpEurope strains were screened based on two values related to their phylogenetic tree. The d a value was the distance between the last common ancestral (LCA) node of hspEAsia and the LCA node of hpEurope. The d b value was the average distance

of hspEAsia from its LCA node. OGs with hspEAsia-diverged genes were screened by introducing the following Rucaparib supplier conditions (with hspAmerind omitted): (i) OGs in which all the hspEAsia genes of the OG formed a sub tree without any hpEurope genes in the phylogenetic tree; (ii) OGs universally conserved (not less than 12 of the 13 genomes; not less than 10 among 11 genomes for comparison of 6 hspEAsia and 5 hpEurope strains in Additional file 7 (= Table S5)); (iii) genes with no domain fusion/fission event among the 13 genomes (within ± 20% of the mean length of the OG, measured in amino acid residues); (iv) d a value greater than twice the d a value of the concatenated well-defined core tree (of Stem Cells inhibitor amino-acid sequences) (denoted as d a *; with the resulting cutoff of d a > 0.02324; 1079 OGs; see “”core genome analysis”" section above).