A kingdom-specific protein domain HMM library for improved annotation of fungal genomes

BMC Genomics

Table 4 Category-A and B instances for FPfam and Pfam domains in 30 original and five test genomes

Domain	Description		Total	Category B (f)		Category B (p)		Category A
		B^ffrac	B^f: B^p:A	FPfam30	FPfam5	Pfam30	Pfam5	FP:Pf30	FP:Pf5
DUF229	Protein of unknown function (DUF229)	87.5	7:0:1	6	1	0	0	1	0
LicD	LICD Protein Family	73.91	51:2:16	51	0	2	0	9	7
Neugrin	Neugrin	71.43	45:0:18	41	4	0	0	11	7
Copper-bind	Copper binding proteins, plastocyanin/az	70.59	36:1:14	32	4	1	0	12	2
DUF946	Plant protein of unknown function (DUF94	68.33	41:3:16	35	6	1	2	12	4
DUF143	Domain of unknown function DUF143	67.44	29:0:14	27	2	0	0	8	6
Laminin_B	Laminin B (Domain IV)	66.67	2:0:1	2	0	0	0	1	0
Ribosomal_S6	Ribosomal protein S6	66.67	26:0:13	26	0	0	0	6	7
Fascin	Fascin domain	66.67	6:0:3	6	0	0	0	2	1
Fungal_ODC_AZ	Fungal ornithine decarboxylase antizyme	66.67	8:0:4	6	2	0	0	4	0
Chitin_bind_3	Chitin-binding domain	65.04	80:5:38	80	0	3	2	35	3
DUF1279	Protein of unknown function (DUF1279)	64.81	35:0:19	34	1	0	0	11	8
GCC2_GCC3	GCC2 and GCC3	64.29	27:0:15	26	1	0	0	15	0
TRI5	Trichodiene synthase (TRI5)	64	16:0:9	14	2	0	0	5	4
Hormone_1	Somatotropin hormone family	63.64	14:0:8	13	1	0	0	5	3
Sulfotransfer_1	Sulphotransferase domain	63.64	7:1:3	7	0	1	0	3	0
Far-17a_AIG1	FAR-17a/AIG1-like protein.	62.5	40:0:24	36	4	0	0	18	6
UPF0139	Uncharacterised protein family (UPF0139)	61.9	13:0:8	12	1	0	0	5	3
ATP-synt_E	ATP synthase E chain	61.7	29:0:18	26	3	0	0	15	3
LRRNT	Leucine-rich repeat N-terminal domain	61.54	8:1:4	7	1	1	0	4	0

ISSN: 1471-2164