Table 1. Family-based analysis using functional similarity and sequence identity.

	Biological Process		Molecular Function
	Paralog has higher functional similarity	Ortholog has higher functional similarity	Paralog has higher functional similarity	Ortholog has higher functional similarity
Paralog has higher sequence identity	17.4±0.2	3.6±0.1	17.7±0.2	7.2±0.1
Ortholog has higher sequence identity	442.4±0.8	221.6±0.8	346.8±0.9	339.3±0.9

Each field shows the average number of protein families (±standard error), out of 100 runs with randomly selected target proteins, in which the row and column conditions were satisfied.