Table 1.

Test clusters for evaluating functional coherence

PROSITE pattern	min # proteins	max # proteins
COPPER_BLUE	6	61
PROTEIN_KINASE_ST	9	1303
ADH_SHORT	10	262
4FE4S_FERREDOXIN	11	169
TRYPSIN_SER	13	399
EF_HAND	19	1248

We tested the functional coherence measure using clusters associated with six functional motifs from PROSITE. The minimum number of proteins is the smallest cluster size we used for that particular PROSITE pattern, derived from training sets from existing FEATURE models. The maximum number is the total number of proteins in Swiss-Prot annotated to that pattern.