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Objective Comprehensive analysis on CagM amino acid sequences in Helicobacter pylori by using bioinformatics method, to deduce its structure and function and to explore its role in the pathogenesis of Helicobacter pylori. Method Helicobacter pylori NCTC11637 as a template, primers were designed, using polymerase chain reaction (PCR) to amplify target fragment; amino acids then were sequenced after TA cloning; the sequencing results were fully analyzed by the application of a variety of biological software and database; all results were used to predict its structure and function. Results cagM gene sequencing results showed that its full length was 1131bp, with the sequencing homology of 96% to 98%, amino acid homology of 98% to 99% compared to other Hp strains in GenBank. The protein contained 376 amino acid, and its molecular weight was 43.7kD, isoelectric point was 9.3, N-terminal 20 amino acids were signal peptide, In its secondary structure a-helix were more than 60% with several hydrophobic regions and epitopes and multiple phosphorylation sites. It is a multi-kinase substrate, may be located in the periplasmic space, may have function of assembling proteins in type IV secretion system and regulating CagA transportation Conclusion The cagM genes in Helicobacter pylori cag pathogenicity island was successfully cloned, a preliminary analysis showed CagM was an important protein in cag pathogenicity island, it was in the periplasmic space and its function was possibily to help other proteins assemble and transport toxic factors like CagA.