Infection with strains of Helicobacter pylori that carry the cytotoxin-associated antigen a (cagA) gene is associated with gastric carcinoma. Recent studies have shed light on the mechanism through which the cagA gene product, CagA, elicits pathophysiological actions. Helicobacter pylori infection has an association with histological gastritis, gastric atrophy, gastric cancer, and mucosaassociated lymphoid tissue (MALT) lymphoma in the stomach. There are some strains of H. pylori that are capable of triggering a greater inflammatory response in the stomach of its host. This strain carries the cag pathogenicity island (cag PAI). The research work deals with analysis and prediction of structural motif of cagA protein present in different strains of helicobacter pylori. The variations among the motifs in different strains are analyzed. The significant motif showing highest variability is traced. Through this changes in the conserved region of the motif the variability among different strains were studied.