TABLE 2.

Breakdown of ortholog pillar structure for each species in the comparison set, where pillars containing 9 orthologs represent loci with an ortholog present in every species and single ortholog pillars represent species-specific singletons relative to the other species in the set^a

No. of genes in pillar	No. or % of genes in:
	E. coli K-12	E. coli O157:H7	E. coli S88	S. boydii	S. enterica	Y. pestis	P. syringae	V. cholerae	X. campestris
9	832	832	832	832	832	832	832	832	832
8	479	479	477	458	473	459	398	374	235
7	629	625	631	589	611	553	217	423	146
6	545	540	543	498	465	375	157	110	97
5	540	558	546	475	447	138	121	90	70
4	449	470	463	293	228	135	129	89	108
3	286	393	346	168	208	186	303	197	238
2	200	469	403	134	343	378	889	409	643
1	185	995	455	689	716	1,111	2,436	1,351	1,812
Total no. of genes in species	4,145	5,361	4,696	4,136	4,323	4,167	5,482	3,875	4,181
% of genes in pillars containing 5+ orthologs	73	57	65	69	65	57	32	47	33
No. of candidate genes predicted per species	270	203	170	480	233	86	90	36	114

^aFor example, E. coli K-12 has 185 singletons and 832 genes with orthologs in all species. Species with a greater percentage of genes in higher-number pillars are mapped more successfully against the species set. This is reflected in the identification of more candidate ORFs in species with few singletons (E. coli, Shigella) as opposed to species in which a large percentage of the genome lacks identifiable orthologs (Xanthomonas, Pseudomonas, Vibrio).