Table 2.

Analysis of Strain-Specific Genes of Helicobacter pylori

Gene identifiera	Strain 26695 (HP**)	StrainbJ99 (Jhp**)	Verdictc	Tree analysisd	Nucleotide composition biase	Closest BLAST homologf	E-valueg
HP0315h		-	?	Undecided		Paracoccus alcaliphilus	5e-12
HP0342		-	?	Undecided	•	Streptococcus pneumoniae	6e-05
HP0435	+		✓	HGT	••	Arabidopsis thaliana	6e-07
HP0447	+		✓	HGT		Aquifex aeolicus	2e-21
HP0452	+		✓	HGT	••	Aquifex aeolicus	2e-21
HP0454	+		✓	HGT	••	Mus musculus	1e-12
HP0855		-	✓	Loss	•	Campylobacter jejuni	1e-130
HP1045		-	✓	Loss	••	Campylobacter jejuni	0.0
HP1193		-	✓	Loss	••	Yersinia pestis	2e-88
HP1334	+		✓	NAi	•	Neisseria meningitidis	5e-46
jhp0164	-		?	Undecided	•	Lactococcus lactis	5e-40
jhp0165		+	✓	NAi	•	Bacillus subtilis	5e-12
jhp0540	-		✓	Loss	•	Campylobacter jejuni	4e-25
jhp0928		+	✓	HGT		Rhizobium rhizogenes	1e-119
jhp0932		+	✓	NAi	•	Neisseria meningitidis	2e-50
jhp1297		+	✓	HGT	••	Mycoplasma pulmonis	2e-86

^aGene identifier

^bStrains 26695 and J99 display the gene gain (+) or loss (-) for the corresponding gene as predicted by GeneTRACE

^cVerdict represents that there is agreement (✓) with supporting evidence (13 cases) or the verdict is inconclusive (?) where it has not been possible to delineate the evolutionary history of the corresponding genes, because of very low sequence similarity relationships and lack of relevant information (3 cases)

^dTree analysis lists the most likely scenario using a phylogenetic tree of the corresponding family

^eNucleotide composition bias signifies highly (••) or moderately (•) anomalous nucleotide composition

^fClosest BLAST homolog lists the species name for the best BLAST hit in the nonredundant protein database

^gE-Value is also reported in the last column. The analysis is performed with an HGT penalty of 3

^hGene content tree suggests a gain

ⁱNonapplicable—no tree: insufficient sequence data