Table 1.

Predicted protein-protein interaction pairs using different sets of reference genomes.

Reference genome	No. clusters >2	No. Co-Conserved predicted pairs	No. Co-Conserved proteins
Aerobic	112	3,825	1,410
All	143	6,987	1,700
All (Inverse homology)	146	6,694	1,770
High GC Gram positive	33	7,932	1,389
Low GC Gram negative	43	56,659	1,667
Motile	110	16,905	1,990
Proteobacteria	111	24,047	2,072
Selected	133	7,408	1,361

Pearson correlation coefficient with confidence 0.8 and E-value of 10^-5 were used on binary profile vectors unless noted.