Table 2.

Phylogenetic profiles link proteins in EcoCyc classes

EcoCyc class	No. proteins	No. neighbors in EcoCyc class	No. neighbors in random group
Carbon compounds	88	798	60
Anaerobic respiration	66	275	30
Aerobic respiration	28	39	6
Electron transport	26	91	5
Purine biosynthesis	21	11	3
Salvage nucleosides	15	10	1
Fermentation	19	17	3
Tricarboxylic acid cycle	16	6	1
Glycolysis	14	5	1
Peptidoglycan biosynthesis	12	10	1

Proteins grouped according to metabolic function on the basis of EcoCyc classes have more similar phylogenetic profiles than random proteins. Column 2 gives the number of proteins in the EcoCyc class. Column 3 gives the number of protein pairs in the EcoCyc class with profiles that differ by less than 3 bits. These pairs are called neighbors. Column 4 lists the number of neighbors found on average for a random group of proteins of the same size as the keyword group.