Peptide-based functional annotation of carbohydrate-active enzymes by conserved unique peptide patterns (CUPP)

Table 4 F-score of CUPP prediction in relation to dbCAN2 CAZy family annotation tools including both CAZome and non-CAZome proteins

Species of genome origin	F-score of CUPP		F-score of dbCAN2 tools				Relevant proteins in CAZome	Proteins in genome (NCBI)
Species of genome origin	CUPP fast-filtering	CUPP full-filtering	Predicted by ≥ 2 tools	dbCAN-HMM	dbCAN-Hotpep	dbCAN-Diamond	Relevant proteins in CAZome	Proteins in genome (NCBI)
Botrytis cinerea B05.10	95.77	95.44	96.7	95.59	87.5	94.18	341	13,703
Malassezia restricta KCTC 27527	95.33	95.38	96.1	92.56	84.89	95.23	80	4406
Vigna angularis Jingnong6	97.73	97.81	98.38	95.82	96.71	95.78	1133	37,769
Average for eukaryote genomes	96.28	96.21	97.06	94.66	89.7	95.06
Bifidobacterium bifidum NCTC13001	97.36	96.48	95.11	90.19	93.2	82.99	59	1736
Caulobacter segnis ATCC 21756	97.94	97.09	97.26	96.21	91.89	97.97	115	4102
Xanthomonas campestris ATCC 33913	98.38	98.18	97.75	96.3	93.95	95.95	153	4179
Average for bacterial genomes	97.89	97.25	96.71	94.23	93.01	92.3
Average of genomes	97.09	96.73	96.89	94.45	91.36	93.68
Complete runtime of genomes [s]	785	808	6503	3375	2152	976

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