Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs

BMC Bioinformatics

Table 4 Correspondence between extreme ubiquitous words and small structural motifs

	Statistics in the initial data set			Comparison with known motifs
Word	Occurrence	Lp _max	nb _sf* */ nb* _sf ^a	Known motif	Match ^b	Precision (%)
				β-turn comparison
PZCD	903	34.82	25/211	β-turn	902	100
HBDS	1588	21.97	22/285	β-turn	1588	100
ZCDS	1112	27.55	22/246	β-turn	996	88
UFQK	449	27.77	15/134	β-turn	441	98
GYUQ	278	14.40	11/96	β-turn	278	100
YBDS	391	20.60	9/136	β-turn	391	100
FQLG	242	25.37	8/77	β-turn	236	98
YZDS	397	10.30	7/130	β-turn	394	99
GUDO	43	27.55	6/11	β-turn	43	100
FFFI	265	21.62	6/80	β-turn	206	78
FQKG	237	32.77	5/71	β-turn	223	94
				Motivated Proteins comparison^c
SLGI	258	15.60	8/114	β-turn end	11 (13)	85
QLGI	185	15.16	7/89	β-turn end	4 (4)	100
DRPI	232	14.95	14/94	Nest	9 (10)	90
DSPI	541	27.15	9/158	Nest	14 (15)	93
DSGI	387	32.45	7/115	Nest	20 (20)	100
DSKG	346	23.16	9/145	Nest	9 (9)	100
DSKH	411	20.46	7/145	Nest	10 (10)	100
DOIP	219	63.30	7/82	Nest	10 (10)	100
OIPI	201	69.81	8/71	Nest	11 (11)	100
HBBQ	616	23.29	10/219	Niche	23 (23)	100
BQGI	337	21.06	9/130	Niche	18 (19)	95
SKGI	34	18.93	12/127	-	NA
DGPI	56	15.77	5/32	-	NA

^a: nb_sfdenote the number of SCOP superfamilies in which a structural word occurs. ^b: match denotes the number of fragments containing a known motif. ^c: comparison with Motivated Proteins motifs is restricted to the set of proteins common to our database and the Motivated Proteins database. In this case, the number between brackets denotes the number of fragments involved in the comparison.

ISSN: 1471-2105