Table 4.

The total numbers of proteins and the EFs of three de novo (SVM, KNN and PNN) identified by two similarity-based (BLAST and HMMER) and the deep learning (CNN) methods proposed in this study based on the training and testing data sets (for all 20 studied GO families) of the lowest similarity. Each GO family was indicated by its GO ID, and its corresponding GO term was provided in Table 1

GO ID	No. of proteins identified by each method						EF
	CNN	SVM	KNN	PNN	BLAST	PHMM	CNN	SVM	KNN	PNN	BLAST	PHMM
GO:0009975	56	235	657	1416	1594	1347	53.61	0	2.28	3.18	8.48	11.14
GO:0097472	202	434	619	561	1598	923	44.59	14.65	8.56	13.22	8.29	14.92
GO:0004721	352	712	1824	1402	2403	1844	32.73	12.36	5.17	7.17	6.28	8.41
GO:0003712	637	1403	2648	3114	4408	3541	10.79	3.38	2.19	2.40	2.80	3.65
GO:0051347	725	1689	3873	1421	5858	4521	9.15	3.37	1.22	4.17	2.43	3.22
GO:0043086	1087	2291	3822	528	5911	4888	7.75	2.63	1.92	9.37	2.14	2.67
GO:0016746	924	2173	3878	401	2076	1604	12.61	3.51	2.51	17.44	7.76	10.44
GO:0019787	1954	2339	3822	3921	3328	2499	7.72	4.79	2.67	3.06	5.02	6.62
GO:0016757	881	1265	4146	2352	1770	1451	11.20	6.05	2.56	3.88	8.36	10.20
GO:0003735	520	750	965	1564	1207	1029	33.03	21.22	17.8	10.98	14.58	17.10
GO:0051336	1436	4334	6885	6693	7187	5887	3.76	1.10	0.81	1.26	1.81	2.28
GO:0043085	2152	4710	8846	8082	7984	6470	4.27	1.78	1.23	1.53	1.83	2.29
GO:0044093	3458	5172	9417	2664	8654	7048	2.65	1.61	1.10	2.79	1.69	2.07
GO:0008233	2850	3842	8106	5906	5409	4327	3.52	1.85	1.18	1.50	2.24	2.77
GO:0003700	3877	6586	6861	6604	6537	5167	4.07	1.87	1.66	1.84	2.58	3.27
GO:0016788	3975	4867	9351	7019	5338	4414	2.45	1.75	1.18	1.52	2.72	3.33
GO:0004672	2904	5918	8287	4895	6621	4633	3.87	1.40	1.35	2.05	2.21	2.96
GO:0016817	2207	5443	10 649	8903	6531	5053	5.15	1.89	1.24	1.48	2.43	3.13
GO:0038023	4230	5919	7314	6684	5616	3573	3.06	1.93	1.79	2.03	2.60	3.48
GO:1902494	4133	6900	10 017	8399	6466	4991	2.45	1.31	1.04	1.35	2.16	2.84