Table 1.

Phylogenetic profiles link protein with similar keywords

Keyword	No. proteins	No. neighbors in keyword group	No. neighbors in random group
Ribosome	60	197	27
Transcription	36	17	10
tRNA synthase and ligase	26	11	5
Membrane proteins*	25	89	5
Flagellar	21	89	3
Iron, ferric, and ferritin	19	31	2
Galactose metabolism	18	31	2
Molybdoterin and Molybdenum, and molybdoterin	12	6	1
Hypothetical†	1,084	108,226	8,440

Proteins grouped on the basis of similar keywords in SwissProt have more similar phylogenetic profiles than random proteins. Column 2 gives the number of nonhomologous proteins in the keyword group. Column 3 gives the number of protein pairs in the keyword group 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. 

^*Only membrane proteins without uniformly zero phylogenetic profiles were included. 

^†Unlike the other rows of the table, the hypothetical proteins do contain homologous pairs.