Table 2.

Genes under inferred positive selection from the pairwise genome comparisons of four H.pylori strains isolated from Japan

35a (Kyoto, PUD)	83 (Kyoto, PUD)	F16 (Fukui, Ga)	F57 (Fukui, GC)
Flagellar exodeoxyribonuclease hook-associated protein 2, fliD (YP_005769952.1) (P value: 0.0001)	Lipid A 1-phosphatase (YP_005769383.1) (P value: 1.10E−05)	Urease-enhancing factor (YP_005779079) (P value: 1.15E−06)	Thioredoxin (BAJ55951.1) (P value: 0.001)
Probable outer membrane protein (ADU41365.1) (P value: 0.001)	DNA-directed RNA polymerase subunit omega (YP_005769931.1) (P value: 3.67E−05)	50S ribosomal protein L9 (BAJ55437.1) (P value: 3.94E−07)	Outer membrane protein, HorA (YP_005776806.1) (P value: 0.002)
Dethiobiotin synthetase (YP_005770624.1) (P value: 0.0001)	6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase beta chain) (YP_005769366.1) (P value: 0.001)	30s ribosomal protein S6 (BAJ55777.1) (P value: 0.00)	Conserved hypothetical ATP-binding protein (BAJ54919.1) (P value: 0.00)
Neuraminyllactose-binding hemagglutinin (YP_005769912.1) (P value: 0.00)	ATP-binding protein (YP_005770583.1) (P value: 0.0008)	50S ribosomal protein L3 (BAJ55847.1) (P value: 0.00)	Putative secretion/efflux ABC transporter ATP-binding protein (YP_006227497.1) (P value: 0.001)
Urease-enhancing factor (YP_005770181) (P value: 0.00)	Phosphonate metabolism protein PhnI (YP_005769292.1) (P value: 0.0002)	ABC transporter permease (BAJ55515.1) (P value: 0.00)	CMP-N-acetylneuraminic acid synthetase (BAJ54930.1) (P value: 0.001)
Periplasmic competence protein (YP_005769282.1) (P value: 0.00)	Type II methylase protein (YP_005769308.1) (P value: 1.03E−05)	Sialidase A (YP_003728769.1) (P value: 0.001)	Putative endonuclease (YP_005776737.1) (P value: 0.002)
gfo/Idh/MocA family oxidoreductase (YP_005770018.1) (P value: 0.0001)	Methyl-accepting chemotaxis protein (YP_005769452.1) (P value: 6.64E−05)	Type II modification enzyme (BAJ55149.1) (P value: 0.002)	D-Amino acid dehydrogenase (BAJ55519.1) (P value: 0.002)
Pseudouridine synthase D (YP_005769708.1) (P value: 0.0002)	Lipopolysaccharide ABC superfamily ATP binding cassette transporter permease protein (YP_005769347.1) (P value: 3.92E−15)	Adenine-specific DNA methyltransferase (BAJ54643.1) (P value: 0.001)	RNA-binding protein (BAJ55130.1) (P value: 0.001)
Ribosomal protein L11 methyltransferase (YP_005769743.1) (P value: 0.001)	Shikimate kinase (YP_005769533.1) (P value: 4.29E−06)	cag pathogenicity island protein (CagG) (BAJ55413.1) (P value: 0.002)	Putative lipopolysaccharide biosynthesis protein (BAJ55644.1) (P value: 0.00)
50S ribosomal protein L22 (YP_005770576.1) (P value: 0.00)	UDP-sugar diphosphatase (YP_005770185.1) (P value: 0.002)	flgM protein (BAJ55661.1) (P value: 0.001)	ABC transporter ATP-binding protein (YP_005777218.1) (P value: 0.001)
Holliday junction resolvase family protein (YP_005769700.1) (P value: 0.00)	NADH-quinone oxidoreductase subunit A (YP_005770524.1) (P value: 0.0004)	7-cyano-7-deazaguanine reductase (BAJ55907.1) (P value: 0.001)	cell filamentation protein (BAJ55696.1) (P value: 0.001)
Disulfide interchange protein (YP_005770340.1) (P value: 0.00)	Poly(A) polymerase (YP_005770052.1) (P value: 5.45E−05)	Biotin protein ligase (BAJ55679.1) (P value: 0.001)	Ribose-5-phosphate isomerase B (BAJ55382.1) (P value: 0.00)
Flagellar hook-basal body complex protein FliE (YP_005769337.1) (P value: 0.00)	Proteobacterial sortase system OmpA family protein (YP_005769939.1) (P value: 3.67E−05)	RNA-binding protein (BAJ55130.1) (P value: 0.00)	Peptidase M50 (YP_005770113.1) (P value: 0.00)
Orotate phosphoribosyltransferase (YP_005770521.1) (P value: 0.00)	DASS family divalent anion:sodium (Na+) symporter (YP_005769519.1) (P value: 0.0002)	Type II DNA modification enzyme (BAJ55625.1) (P value: 0.0003)	feoA gene product (YP_005770102.1) (P value: 0.00)
CDP-diacylglycerol-glycerol-3-phosphate, 3-phosphatidyltransferase (YP_005769796.1) (P value: 0.001)	Phosphoserine phosphatase (YP_005770041.1) (P value: 5.61E−05)	Type II restriction endonuclease (BAJ55626.1) (P value: 0.0003)	Riboflavin synthase subunit alpha (YP_005778223.1) (P value: 3.19E−05
Fatty acid/phospholipid synthesis protein PlsX (YP_005769572.1) (P value: 0.00)	Polar flagellin (YP_005769953.1) (P value: 0.0007)	Riboflavin synthase subunit alpha (YP_005779723.1) (P value: 2.14E−4)	Type II restriction endonuclease (YP_005777226.1) (P value: 3.59E−06)
Pyrroline-5-carboxylate reductase (YP_005770419) (P value: 0.00)	Chorismate mutase (YP_005769657.1) (P value: 4.39E−05)	Secreted protein involved in flagellar motility (YP_006219827.1) (P value: 0.003)	Transcription elongation factor GreA (BAJ55095.1) (P value: 0.001)
H. protein HPF30_0649 (ADU41023) (P value: 0.00)	50S ribosomal protein L15 (YP_005770563) (P value: 0.001)	H. protein HPF16_0633 (YP_005778868) (P value: 0.0007)	50S ribosomal protein L10 (YP_005777971.1) (P value: 5.91E−06)
H. protein HPCPY3281_0951 (ADU40935) (P value: 0.00)	Thiamine-phosphate diphosphorylase (YP_005769865) (P value: 5.97E−07)	H. protein HPF16_0710 * (YP_005778945) (P value: 0.0001)	Succinyl-CoA-transferase subunit B (BAJ55301.1) (P value: 0.001)
H. protein HPHPA14_0570 (ADU40948) (P value: 0.00)	HOP family outer membrane porin (YP_005769995) (P value: 2.35E−09)	H. protein HPF16_0214 (YP_005778449) (P value: 6.05E−05)	Biotin sulfoxide reductase BisC fragment (YP_005777721.1) (P value: 0.001)
Conserved hypothetical protein (ADU40534.1) (P value: 0.00)	Integral membrane protein (YP_005769244) (P value: 7.67E−06)	H. protein HPF16_0250 (YP_005778485) (P value: 0.001)	cag pathogenicity island protein (CagU) YP_005777275.1) (P value: 7.47E−06)
H. protein HP9810_881g5 (ADU40463) (P value: 0.002)	Undecaprenyl phosphate N-acetylglucosaminyltransferase (YP_005769359) (P value: 1.52E−08)	H. protein HPF16_0244 (YP_005778479) (P value: 0.002)	H. protein HPF57_1192 (YP_005777906.1) (P value: 0.006)
H. protein HP0385 (ADU41339) (P value: 0.00)	Acyl-phosphate glycerol 3-phosphate acyltransferase (YP_005769268) (P value: 2.25E−05)	H. protein HPF16_1359 * (BAJ55956) (P value: 0.001)	H. protein HPF57_0261 (YP_005776975.1) (P value: 1.88E−05)
H. protein HPCPY6311_1233 (ADU41477.1) (P value: 0.00)	Conserved hypothetical protein * (ADU41024) (P value: 8.6E−05)	H. protein HPF16_0796 (BAJ55393) (P value: 0.001)	H. protein HPF57_0394 (YP_005777108.1) (P value: 5.47E−12)
H. protein HPKB_0158 (ADU40191.1) (P value: 0.00)	Conserved hypothetical protein * (ADU41633) (P value: 0.01)	H. protein HPF16_0423 * (BAJ55020) (P value: 0.001)	H. protein HPF57_0426 (YP_005777140.1) (P value: 8.42E−06)
	Conserved hypothetical protein (ADU40713) (P value: 0.00)	H. protein HPF16_0253 (YP_005778488) (P value: 0.0003)	H. protein HPF57_1344 (YP_005778058.1)* (P value: 0.003)
	H. protein KHP_0683 (ADU41063) (P value: 0.00)	H. protein HPKB_0212 (YP_005761745) (P value: 0.0003)	H. protein HPF57_0789 (YP_005777503.1) (P value: 1.22E−5)
	H. protein HPHPP23_1030 (ADU41054) (P value: 0.00)	H. protein HPF16_1167 (YP_005779402) (P value: 6.26E−21)	H. protein rpmJ (YP_005777967.1) (P value: 5.71E−05)
	H. protein HPKB_1436 (ADU40297) (P value: 0.00)	H. protein HPF16_0878 (YP_005779113 (P value: 2.48E−07)	H. protein HPF57_0703 (YP_005777417.1) (P value: 3.27E−09)
	H. protein HPF30_1072 (ADU40599) (P value: 0.00)	H. protein HPF16_1062 (YP_005779297) (P value: 1.34E−05)	H. protein HPF57_0549 (YP_005777263.1) (P value: 3.94E−07)
			H. protein HPF57_1078 (YP_005777792.1) (P value: 2.39E−06)

The area of Japan from where the strains were isolated, and the disease status of the individuals from whom the H.pylori strains were isolated is indicated in brackets (‘PUD’ signifies peptic ulcer disease, ‘Ga’ gastritis, ‘GC’ gastric cancer). References describing the respective disease status for each strain are as follows: 35a and 83 (Yoshio Yamaoka, Michael E. DeBakey Veterans Affairs Medical Center, Baylor College of Medicine, personal communication), F16 (27) and F57 (27). Those genes that were inferred as being under positive selection, with a value of Ka/Ks > 1, are listed. p values generated by each respective likelihood ratio test are shown; values of P = 0.00 represent the rounding of small values of p by the codeml program. Predicted membrane localized proteins (according to either Psortb or CELLO) are denoted with an asterisk. ‘H. protein’ denotes ‘hypothetical protein’. Genbank accession numbers are in brackets.