Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment

Table 2 Description of the dataset.

	Number of Proteins (in KEGG)		Number of possible functional linkages examined		Number of positives
Pathways	E. coli	Yeast	E. coli	Yeast	E. coli	Yeast
All Pathways	1,347	1,191	708,645	635,628	43,968	35,674
Carbohydrate metabolism	292	241	33,153	26,565	5,450	4,859
Energy metabolism	135	134	8,128	8,001	2,113	3,060
Lipid metabolism	83	100	2,080	4,656	602	1,232
Nucleotide metabolism	108	113	5,050	5,995	3,686	5,082
Amino acid metabolism	237	216	20,100	19,900	3,328	3,620
Metabolism of cofactors and vitamins	146	113	7,875	5,253	1,085	740
Translation	80	185	3,081	15,400	1,761	10,792
Membrane transport	259		24,531		16,834
Folding, sorting, and degradation		82		2,926		809

ISSN: 1471-2105