Table 2.

Phylogenetic analysis of 46cagA sequencesa

Sequence comparedDistancebHomologycTransitions (Ts)dTransversions (Tv)eTs:TvKsfKagKa/Ks ratio
cagA1 (n = 20)0.032 ± 0.01296.2 ± 2.5 (94.2 ± 2.3)0.024 ± 0.0090.008 ± 0.0063.00.060 ± 0.0240.023 ± 0.0110.38
cagA2 (n = 19)0.027 ± 0.01195.9 ± 1.8 (94.8 ± 2.7)0.020 ± 0.0060.007 ± 0.0032.90.064 ± 0.0260.018 ± 0.0070.28
cagA1 + cagA2 (n = 39)0.068 ± 0.03993.6 ± 3.5 (90.5 ± 5.6)0.045 ± 0.0230.024 ± 0.0161.90.110 ± 0.0520.053 ± 0.0330.48
All cagA sequences (n = 46)0.077 ± 0.03792.8 ± 3.3 (83.1 ± 5.5)0.053 ± 0.0250.025 ± 0.0142.10.121 ± 0.0510.060 ± 0.0320.50
  • a Based on the 5′ 462 bp from thecagA ORF in each of the 46 H. pylori strains.

  • b Average substitution rates (corrected with the Jukes and Cantor parameters) ± standard deviation.

  • c Average percentage similarity ± standard deviation based on pairwise comparisons of sequences of the corresponding subtypes. Homologies are based on nucleotide sequences; values in parentheses are based on deduced amino acid sequences.

  • d Transitions are nucleotide replacements of one purine by another purine.

  • e Transversions are nucleotide replacements of a purine by a pyrimidine or vice versa.

  • f Synonymous substitutions do not result in an amino acid change in the encoded open reading frame.

  • g Nonsynonymous substitutions result in an amino acid change.