Towards an automatic classification of protein structural domains based on structural similarity

Sam, Vichetra; Tai, Chin-Hsien; Garnier, Jean; Gibrat, Jean-Francois; Lee, Byungkook; Munson, Peter J

doi:10.1186/1471-2105-9-74

BMC Bioinformatics

Table 6 Excess Span and Largest Homogeneous Cluster Size for SCOP C Class folds.

From: Towards an automatic classification of protein structural domains based on structural similarity

					Excess Span Size^§				Largest Homog. Cluster (%) ⁺
Row	fold	SCOP fold description	Ndom*	Nfam^#	VAST	SHEBA	DALI	INT◊	VAST	SHEBA	DALI	Nc^$
		CONSISTENT FOLDS
1	c.100	Thiamin pyrophosphokinase, catalytic domain	2	1	0	0	0	0	100	100	100	1
2	c.101	Undecaprenyl diphosphate synthase	2	1	0	0	0	0	100	100	100	1
3	c.106	SurE-like	2	1	0	0	0	0	100	100	100	1
4	c.109	PEP carboxykinase N-terminal domain	4	1	0	0	0	0	100	100	100	1
5	c.114	YchN-like	2	1	0	0	0	0	100	100	100	1
6	c.117	Amidase signature (AS) enzymes	3	1	0	0	0	0	100	100	100	1
7	c.16	Lumazine synthase	3	1	0	0	0	0	100	100	100	1
8	c.17	Caspase-like	3	2	0	0	0	0	100	100	100	1
9	c.22	Ribosomal protein L4	2	1	0	0	0	0	100	100	100	1
10	c.27	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	3	1	0	0	0	0	100	100	100	1
11	c.28	Cryptochrome/photolyase, N-terminal domain	4	1	0	0	0	0	100	100	100	1
12	c.32	Tubulin, GTPase domain	2	1	0	0	0	0	100	100	100	1
13	c.33	Cysteine hydrolase	3	2	0	0	0	0	100	100	100	1
14	c.34	DFP DNA/pantothenate metabolism flavoprotein	2	1	0	0	0	0	100	100	100	1
15	c.36	Thiamin diphosphate-binding fold (THDP-binding)	19	4	0	0	0	0	100	100	100	1
16	c.39	Nicotinate mononucleotide:5,6-dimethylbenzimidazole phosphoribosyltransferase (CobT)	2	1	0	0	0	0	100	100	100	1
17	c.42	Arginase/deacetylase	3	2	0	0	0	0	100	100	100	1
18	c.43	CoA-dependent acyltransferases	7	3	0	0	0	0	100	100	100	1
19	c.5	MurCD N-terminal domain	2	1	0	0	0	0	100	100	100	1
20	c.50	Leucine aminopeptidase (Aminopeptidase A), N-terminal domain	2	1	0	0	0	0	100	100	100	1
21	c.59	MurD-like peptide ligases, peptide-binding domain	5	2	0	0	0	0	100	100	100	1
22	c.6	Cellulases	3	1	0	0	0	0	100	100	100	1
23	c.62	vWA-like	8	2	0	0	0	0	100	100	100	1
24	c.65	Formyltransferase	3	1	0	0	0	0	100	100	100	1
25	c.67	PLP-dependent transferases	35	6	0	0	0	0	100	100	100	1
26	c.68	Nucleotide-diphospho-sugar transferases	15	12	0	0	0	0	100	100	100	1
27	c.7	PFL-like glycyl radical enzymes	4	4	0	0	0	0	100	100	100	1
28	c.70	Nucleoside hydrolase	2	1	0	0	0	0	100	100	100	1
29	c.71	Dihydrofolate reductases	8	1	0	0	0	0	100	100	100	1
30	c.73	Carbamate kinase-like	2	2	0	0	0	0	100	100	100	1
31	c.74	AraD-like aldolase/epimerase	3	1	0	0	0	0	100	100	100	1
32	c.76	Alkaline phosphatase-like	6	3	0	0	0	0	100	100	100	1
33	c.77	Isocitrate/Isopropylmalate dehydrogenases	4	2	0	0	0	0	100	100	100	1
34	c.79	Tryptophan synthase beta subunit-like PLP-dependent enzymes	6	1	0	0	0	0	100	100	100	1
35	c.81	Formate dehydrogenase/DMSO reductase, domains 1–3	5	1	0	0	0	0	100	100	100	1
36	c.83	Aconitase iron-sulfur domain	2	1	0	0	0	0	100	100	100	1
37	c.86	Phosphoglycerate kinase	2	1	0	0	0	0	100	100	100	1
38	c.89	Phosphofructokinase	2	1	0	0	0	0	100	100	100	1
		MODERATELY CONSISTENT FOLDS
39	c.25	Ferredoxin reductase-like, C-terminal NADP-linked domain	12	5	643	0	0	0	92	100	100	1
40	c.61	PRTase-like	17	2	0	0	68	0	100	100	88	1
41	c.82	ALDH-like	7	2	0	954	0	0	100	86	100	1
42	c.87	UDP-Glycosyltransferase/glycogen phosphorylase	6	6	0	937	0	0	100	83	100	1
43	c.116	alpha/beta knot	5	3	3	0	0	0	80	100	100	1
44	c.41	Subtilisin-like	4	2	0	0	1056	0	100	100	75	1
45	c.98	MurF and HprK N-domain-like	4	2	8	0	0	0	75	100	100	1
46	c.46	Rhodanese/Cell cycle control phosphatase	7	3	130	54	0	0	86	86	100	1
47	c.57	Molybdenum cofactor biosynthesis proteins	3	2	1056	0	0	0	67	100	100	1
48	c.93	Periplasmic binding protein-like I	13	1	3	0	0	0	62	100	100	1
49	c.45	(Phosphotyrosine protein) phosphatases II	12	2	0	0	267	0	100	100	58	1
50	c.107	DHH phosphoesterases	2	2	0	0	1058	0	100	100	50	1
51	c.18	DNA glycosylase	2	2	1057	0	0	0	50	100	100	1
52	c.108	HAD-like	11	10	1048	932	0	0	55	91	100	1
53	c.10	Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)	18	10	304	0	0	0	44	100	100	1
54	c.48	TK C-terminal domain-like	5	3	50	0	47	0	60	100	80	1
55	c.14	ClpP/crotonase	11	3	240	335	0	0	73	64	100	1
56	c.24	Methylglyoxal synthase-like	3	3	450	0	27	0	67	100	67	1
57	c.8	The "swivelling" beta/beta/alpha domain	10	8	0	28	4	0	100	80	40	1
58	c.63	CoA transferase	5	2	0	1	1	0	100	60	60	1
59	c.55	Ribonuclease H-like motif	53	19	400	362	0	0	94	21	100	1
60	c.91	PEP carboxykinase-like	4	2	449	0	80	0	50	100	50	1
61	c.95	Thiolase-like	13	2	4	0	4	0	46	100	46	1
		DISPERSED FOLDS
62	c.47	Thioredoxin fold	51	13	1	1	1	0	45	82	82	2
63	c.12	Ribosomal proteins L15p and L18e	2	1	1	3	1	0	50	50	50	2
64	c.31	DHS-like NAD/FAD-binding domain	10	5	4	3	4	3	70	70	70	2
65	c.1	TIM beta/alpha-barrel	182	70	3	1148	1148	3	53	43	62	6
66	c.15	BRCT domain	7	4	130	12	4	2	71	86	86	2
67	c.13	SpoIIaa-like	3	2	10	4	7	3	67	67	67	2
68	c.30	PreATP-grasp domain	11	5	4	6	7	3	64	36	45	3
69	c.51	Anticodon-binding domain-like	13	6	6	35	7	0	54	69	77	2
70	c.3	FAD/NAD(P)-binding domain	46	5	7	1015	1014	7	41	41	41	8
71	c.84	Phosphoglucomutase, first 3 domains	6	1	10	94	266	10	67	67	67	2
72	c.4	Nucleotide-binding domain	7	3	46	18	14	14	57	29	29	3
73	c.9	Barstar-like	2	2	18	413	593	17	50	50	50	2
74	c.19	FabD/lysophospholipase-like	3	2	1056	940	40	40	67	67	67	2
75	c.53	Resolvase-like	9	3	444	44	65	16	44	44	44	3
76	c.97	Cytidine deaminase-like	4	2	45	411	139	28	75	75	75	2
77	c.44	Phosphotyrosine protein phosphatases I-like	3	2	52	57	120	46	67	67	67	2
78	c.58	Aminoacid dehydrogenase-like, N-terminal domain	11	5	72	404	59	32	55	55	55	3
79	c.49	Pyruvate kinase C-terminal domain-like	6	2	237	94	182	61	67	67	67	2
80	c.52	Restriction endonuclease-like	23	21	1036	216	141	128	91	57	91	3
81	c.72	Ribokinase-like	15	7	185	372	165	151	67	67	67	2
82	c.80	SIS domain	6	3	198	420	1054	23	67	67	67	2
83	c.92	Chelatase-like	11	5	311	932	221	200	36	36	36	3
84	c.60	Phosphoglycerate mutase-like	7	4	446	415	280	237	57	57	57	2
85	c.26	Adenine nucleotide alpha hydrolase-like	42	11	1017	913	460	459	29	29	29	7
86	c.94	Periplasmic binding protein-like II	25	2	654	970	592	511	96	84	88	2
87	c.66	S-adenosyl-L-methionine-dependent methyltransferases	35	23	620	908	1025	602	23	80	83	3
88	c.78	ATC-like	12	2	643	931	1048	625	42	33	58	3
89	c.35	Phosphosugar isomerase	3	2	652	940	1057	634	67	67	67	2
90	c.37	P-loop containing nucleotide triphosphate hydrolases	122	20	937	821	938	814	25	40	28	9
91	c.23	Flavodoxin-like	65	31	1045	878	1046	873	14	18	18	18
92	c.56	Phosphorylase/hydrolase-like	24	11	1035	919	1036	912	75	83	75	4
93	c.2	NAD(P)-binding Rossmann-fold domains	99	10	960	928	961	921	24	32	32	9
94	c.69	alpha/beta-Hydrolases	51	26	1059	1064	1060	1059	35	96	35	2

Ward Hierarchical Cluster Tree generated using Nres metric for VAST, SHEBA and DALI.
*Ndom, the number of domains in the fold.
^#Nfam, the number of families in the fold.
^§Excess Span Size is Span less Ndom; Span is the number of domains contained in the smallest cluster containing all domains of the fold.
◊ INT is the size of the intersection of the excess spans for VAST, SHEBA and DALI.
⁺Largest Homog. Cluster is the ratio of the size of the largest homogeneous cluster of the fold to the size of the fold itself, expressed as percent.
^$Nc is the minimum number of homogeneous clusters in the fold, across VAST, SHEBA and DALI.
Table is sorted in ascending order of minimum excess span size, then in the ascending order of INT, and then by the average Largest Homog. Cluster Size value for the three methods in the descending order.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com