FIG. 3.

Terminal sequences of ISHp609, ISHp609var, and the orf1-2 remnant and their sites of insertion in H. pylori. ISHp609, ISHp609var, and orf1-2 remnant termini are in uppercase type. Flanking DNA and empty sites in reference strains 26695 and J99 (gene designations beginning with hp and jhp, respectively) are in lowercase type. (A) ISHp609 predominant type. (B) ISHp609var type. Terminal sequences were extrapolated from a comparison with sequences of the predominant ISHp609 type, because its flanking sequences did not have homology with known H. pylori sequences and therefore the site of insertion (empty site) was not known. (C) Predicted left end of the orf1-2 remnant and its flanking sequences. Sites of insertion could not be determined precisely due to local sequence heterogeneity in strains lacking this element (intergenic region between jhp959 and jhp962) (see Fig. S2 in the supplemental material). (D) Predicted right end of the orf1-2 remnant compared to the corresponding region of orfA in the ISHp609 sequence.