TABLE 2.

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

Annotation category	No. of genes in:
	H. pylori J99	H. pylori 26695	Both strainsa
Functionally classified	877	898
Conserved with no known function	275	290
H. pylori specific	343	364
Total	1,495	1,552
Amino acid biosynthesis	44	44	44
Biosynthesis of cofactors, etc.	60b	59	59
Cell envelope	160	164	156cde
Cellular processes	96	113	92cde
DNA replication	23	23	21ce
DNA restriction-modification, etc.	66	68	51cde
Energy metabolism	104	104	102cde
Fatty acid and phospholipid metabolism	28	29	28e
Purine and pyrimidine biosynthesis	34	34	34
Regulatory functions	32	32	31df
Transcription	13	13	13
Translation	128	128	128
Transport and binding proteins	88g	87	87
Conserved with no known function	275	290	267cde
H. pylori specific	343	364	288cde
Total	1,495	1,552	1,401h

^aUsing J99 genes as the basis for counting. 

^bIncludes the partial duplication of folE (JHP862). 

^cCategories which include H. pylori J99-specific genes (see the text for details). 

^dThese 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. pylori specific. 

^eCategories which include H. pylori 26695-specific genes. 

^fDoes not include the duplication of the response regulator (JHP1283 and JHP1443). 

^gIncludes the partial duplication of proX (JHP754). 

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