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
Amino acid biosynthesis4444 44
Biosynthesis of cofactors, etc.60b 59 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 proteins88g 87 87
Conserved with no known function275290 267c,d,e
H. pylorispecific343364 288c,d,e
  • 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.