Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

Wong, Wing-Cheong; Maurer-Stroh, Sebastian; Eisenhaber, Frank

doi:10.1186/1745-6150-6-57

Table 2 False-positive and false-negative rates of membrane/signal anchors versus SCOP/UniProt-derived functional TM-helix sets

From: Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

Section	Description of comparisons	window size	f = 0.84		f = 1.0		f = 1.282		f = 1.645		f = 1.98
			FPR	FNR	FPR	FNR	FPR	FNR	FPR	FNR	FPR	FNR
A	membrane anchors versus functional TMs (SCOP-derived) based on IVL group	10	15.51	24.10	18.15	16.87	25.41	9.64	36.96	2.41	48.84	0.00
		12	14.85	21.69	18.15	16.87	24.75	9.64	38.28	2.41	47.52	1.20
		15	15.84	20.48	18.81	14.46	26.73	9.64	39.93	3.61	49.50	1.20
		18	16.50	18.07	19.47	15.66	29.04	10.84	40.92	3.61	48.84	1.20
B	membrane anchors versus functional TMs (UniProt-derived) based on IVL group	10	16.17	25.04	19.80	19.13	27.06	9.82	41.91	3.96	51.49	1.44
		12	17.16	24.30	19.80	18.84	27.39	9.65	42.57	3.73	51.49	1.49
		15	18.15	23.55	21.45	19.13	29.04	9.94	42.57	4.19	51.49	1.67
		18	19.14	23.26	22.11	19.18	33.99	10.45	44.55	4.19	53.14	1.72
C	signal anchors versus functional TMs (SCOP-derived) based on IVL group	10	23.71	24.10	31.01	16.87	43.52	9.64	59.59	2.41	72.16	0.00
		12	23.77	21.69	30.39	16.87	44.60	9.64	59.54	2.41	72.33	1.20
		15	22.52	20.48	30.56	14.46	43.92	9.64	60.05	3.61	72.72	1.20
		18	22.24	18.07	29.71	15.66	42.39	10.84	58.18	3.61	70.51	1.20
D	signal anchors versus functional TMs (UniProt-derived) based on IVL group	10	27.39	25.04	35.77	19.13	48.10	9.82	63.89	3.96	76.23	1.44
		12	26.26	24.30	34.47	18.84	47.71	9.65	63.38	3.73	75.66	1.49
		15	26.49	23.55	35.37	19.13	47.82	9.94	63.89	4.19	76.85	1.67
		18	28.35	23.26	35.99	19.18	48.84	10.45	64.86	4.19	77.42	1.72
E	membrane anchors versus functional TMs (SCOP-derived)	10	14.52	22.89	18.81	16.87	30.03	9.64	44.22	3.61	54.79	1.21
		12	15.51	20.48	19.14	14.46	30.36	10.84	44.55	4.82	55.12	2.41
		15	15.51	20.48	20.13	13.25	32.34	9.64	45.55	4.82	57.10	2.41
		18	16.17	18.07	20.79	14.46	33.00	10.84	44.88	4.82	57.10	1.21
F	membrane anchors versus functional TMs (UniProt-derived)	10	14.52	25.39	19.14	20.68	30.36	11.26	44.55	4.71	54.13	1.67
		12	14.85	25.16	18.81	20.74	31.35	11.55	43.23	4.42	54.13	1.55
		15	15.84	25.22	19.80	21.02	32.01	12.00	45.21	3.79	56.77	1.49
		18	18.15	24.87	23.10	20.97	34.98	11.20	48.19	4.19	58.42	1.67
G	signal anchors versus functional TMs (SCOP-derived)	10	25.24	22.89	32.26	16.87	46.07	9.64	62.93	3.62	75.21	1.21
		12	24.90	20.48	32.15	14.46	45.95	10.84	62.99	4.82	75.04	2.41
		15	24.39	20.48	31.64	13.25	45.84	9.64	63.50	4.82	74.99	2.41
		18	24.17	18.07	31.18	14.46	44.71	10.84	61.57	4.82	74.42	1.21
H	signal anchors versus functional TMs (UniProt-derived)	10	26.77	25.39	33.16	20.68	46.86	11.26	62.88	4.71	74.36	1.67
		12	25.24	25.16	32.54	20.74	45.73	11.55	61.74	4.42	73.91	1.55
		15	25.18	25.22	32.54	21.02	45.95	12.01	63.10	3.79	74.02	1.49
		18	26.83	24.87	33.73	20.97	48.22	11.20	64.35	4.19	76.51	1.67

Table 2 (section A-D) shows the data generated with collapse of aliphatic hydrophobic residues IVL into one residue group (to suppress sequence variability just among hydrophobic residues). Table 2 (section E-H) presents the data without collapse of IVL into one group for comparison. The error rates of the membrane and signal anchors versus the functional TM-helix sets are given in sections A & B (E & G) and in sections C & D (G & H) respectively. Column 1 gives the subsections (A to H) of the table. Column 2 describes the comparison of the respective datasets. Column 3 gives the window size of the sequence complexity measure. The window size for the hydrophobicity measure was fixed at 19. Column pairs (4,5), (6,7), (8,9), (10,11) and (12,13) give the false-positive rates (FPR) and false-negative rates (FNR) for the z-score thresholds at f = 0.84, 1.0, 1.282, 1.645 and 1.98 (corresponding to the theoretical false-negative rates of 20%, 16%, 10%, 5% and 2.5%) respectively.

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ISSN: 1745-6150

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