Table 1. Comparison of Psi-sqaure with and without pseudocounts in numbers of true positive (TP) and sensitivity.

COG	Definition	With pseudocount		Without pseudocount
		TP	Sensitivity	TP	Sensitivity
01298	Flagellar biosynthesis pathway; component FlhA	32	0.78	26	0.63
01317	Flagellar biosynthesis/type III secretory pathway protein	34	0.83	26	0.63
01334	Uncharacterized flagellar protein FlaG	36	0.88	24	0.59
02747	Negative regulator of flagellin synthesis	35	0.85	26	0.63
02882	Flagellar biosynthesis chaperone	32	0.78	25	0.61

The table shows Psi-sqaure search results for the tightly linked group of proteins involved in flagellum structure and biogenesis. Based on our current knowledge, 41 COGs (TP) participate in flagellum structure and biogenesis pathway, including 29 known COGs defined in the pathway, 8 chemotaxis related COGs, and 4 experimentally verified proteins (COG02747, COG03144, COG03190, and COG04787).