Table 3.

Highly divergent alleles in strain J99

Gene number (J99)	Gene number (26695)	Description	% aa identity (J99)a	% aa identity (non-J99)b	% unique sitesc
jhp0028	HP0032	Hypothetical	68	91	24
jhp0080	HP0087d	Hypothetical	89	96	8
jhp0173	HP0185d	Hypothetical	88	93	7
jhp0395	HP1029d	Hypothetical	88	95	7

^a The sequences of the indicated gene products in strain J99 were compared with corresponding sequences in each of the other 4 strains (26695, HPAG1, B128, and 98-10), and mean % amino acid identities were calculated.

^b The sequences of the indicated gene products in each strain were compared in all permutations, except that comparisons involving strain J99 were excluded from analysis. Mean % amino acid identities were calculated.

^cPercentage of aligned sites in which the protein from strain J99 contained an amino acid different from the corresponding amino acids in proteins from 4 other strains.

^d Reported to be a constituent of the H. pylori core genome, based on at least one array analysis [18-20].