Table 2.

Functional prediction performance (per gene).

Group	ID	Conf.	Comp.	Incomp.	Conf. Depth	Conf. Dist.	Comp. Depth	Comp. Dist.
E. coli	APEC01	13278	660	485	3.77	0.09	4.9	2.49
	CFT073	13580	145	208	3.8	0.02	4.53	2.32
	H7EDL933	14731	52	66	3.83	0.01	4.65	2.29
	H7Sakai	14694	80	84	3.83	0.01	4.61	2.09
	UTI89Min	13158	118	146	3.8	0.02	4.74	2.31
	W3110Min	13855	60	67	3.84	0.01	4.58	2.6
Pseudo.	aerPAO1	12704	303	420	3.8	0.06	4.15	2.21
	entL48	10616	482	1092	3.77	0.16	4.78	2.39
	fluPf5	14101	201	371	3.8	0.02	4.02	2.03
	fluPfO1	13210	275	441	3.78	0.05	4.44	2.34
	pha1448A	11714	167	312	3.83	0.02	4.65	2.41
	puKT2440	10838	341	330	3.81	0.08	4.65	2.37
	syrB728a	12167	259	254	3.79	0.04	4.51	2.46
	syrDC3000	12002	254	253	3.8	0.05	4.59	2.43
Gamma.	aerPAO1	12631	1344	1913	3.75	0.22	4.52	2.26
	CO92	11742	770	1185	3.85	0.09	4.66	2.25
	KW20	6732	132	321	3.95	0.03	4.66	2.47
	N16961	8165	374	616	3.9	0.08	4.82	2.4
	RSA493	4036	282	335	3.9	0.1	4.77	2.58
	W3110	12913	271	302	3.84	0.03	4.81	2.54

Number of terms for each GO evaluation classifier. Only TP ORFs that have "verifiable" terms can be evaluated. Depth and distance are averaged over all term assignments for each organism.