Table 2.

Annotation and classification of genes from H. pylori J99 and 26695

Annotation categoryNo. of genes in:
H. pyloriJ99H. pylori 26695Both strainsa
Functionally classified877898
Conserved with no known function275290
H. pylori specific343364
Total1,4951,552
Amino acid biosynthesis4444 44
Biosynthesis of cofactors, etc.60b59 59
Cell envelope160164 156c, d, e
Cellular processes96113 92c, d, e
DNA replication2323 21c, e
DNA restriction-modification, etc.6668 51c, d, e
Energy metabolism104104 102c, d, e
Fatty acid and phospholipid metabolism2829 28e
Purine and pyrimidine biosynthesis3434 34
Regulatory functions3232 31d, f
Transcription1313 13
Translation128128 128
Transport and binding proteins88g87 87
Conserved with no known function275290 267c, d, e
H. pylorispecific343364 288c, d, e
Total1,4951,5521,401h
  • a Using J99 genes as the basis for counting.

  • b Includes the partial duplication offolE (JHP862).

  • c Categories which include H. pyloriJ99-specific genes (see the text for details).

  • d These numbers include the “split” genes based on the H. pylori J99 definition. There are 6 J99 genes which constitute 12 26695 genes in the cell envelope; 2 J99 genes which constitute 4 26695 genes in cellular processes; 1 J99 gene which constitutes 2 26695 genes in each of DNA restriction-modification, energy metabolism, and Regulatory functions; 5 J99 genes which constitute 7 26695 genes in conserved with no known function; and 24 J99 genes which constitute 33 26695 genes in H. pylorispecific.

  • e Categories which include H. pylori26695-specific genes.

  • f Does not include the duplication of the response regulator (JHP1283 and JHP1443).

  • g Includes the partial duplication ofproX (JHP754).

  • h The remaining 94 genes represent the 89 J99-specific genes, tnpA/B from IS606, and the partial or complete duplications of three genes.