VPS13 - PFAM28P - GREMLIN Contacts

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VPS13 - Vacuolar sorting-associated protein 13, N-terminal

PFAM:	PF16908	Sequences: FTESLVTKIIDNLQVTIKNIHIRYEDSISNPGHPFAFGITLEELSAVTTDENWKPTFIDSTSKIIHKLLELDSLAVYWNKSLEDLSPEELLEKFKSGIASGDNSPKHQYILKPVSGSAKLTLNKSGETDTPKIDADLELDEIGLVLDDDQYRDILKLLDSFHRFIRRQKYRKYRPKVPVKENPRAWWKYAINAVLEEIRERNRRWSWEYIKERRDDRKRYIELYKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	226 (225)
Sequences:	1185 (886)
Seq/√Len:	59.1
META:	0.291

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_N	107_H	6.141	1.00
21_H	77_Y	5.761	1.00
38_G	77_Y	5.027	1.00
21_H	38_G	4.684	1.00
50_D	54_K	4.087	1.00
78_W	153_D	3.508	1.00
211_K	215_D	3.330	1.00
182_N	185_A	3.215	1.00
41_L	44_L	3.027	1.00
40_T	75_A	2.841	1.00
209_Y	213_R	2.664	1.00
49_T	66_H	2.635	1.00
175_P	186_W	2.600	1.00
214_R	218_K	2.597	1.00
21_H	25_E	2.503	1.00
9_I	12_N	2.442	1.00
23_R	77_Y	2.371	1.00
23_R	36_A	2.291	1.00
53_W	119_K	2.260	1.00
49_T	53_W	2.112	1.00
53_W	68_L	2.074	1.00
217_R	221_I	2.067	1.00
8_K	11_D	2.016	1.00
108_Q	147_D	2.010	1.00
48_T	67_K	1.990	1.00
111_L	114_V	1.961	1.00
182_N	186_W	1.916	1.00
25_E	36_A	1.909	1.00
92_E	96_S	1.884	1.00
39_I	76_V	1.862	1.00
210_I	214_R	1.792	0.99
188_K	192_N	1.776	0.99
68_L	119_K	1.768	0.99
23_R	38_G	1.735	0.99
81_S	84_D	1.715	0.99
179_V	186_W	1.712	0.99
25_E	38_G	1.635	0.99
71_L	116_G	1.619	0.99
41_L	74_L	1.588	0.99
47_V	55_P	1.582	0.99
209_Y	214_R	1.531	0.98
212_E	216_D	1.516	0.98
219_R	222_E	1.496	0.98
12_N	48_T	1.483	0.98
90_L	94_F	1.462	0.98
205_W	210_I	1.460	0.98
203_R	212_E	1.454	0.98
48_T	53_W	1.450	0.97
117_S	136_D	1.441	0.97
30_N	34_P	1.439	0.97
217_R	223_L	1.426	0.97
42_E	72_D	1.419	0.97
20_I	41_L	1.403	0.97
42_E	73_S	1.385	0.97
178_P	186_W	1.384	0.97
219_R	223_L	1.372	0.96
50_D	53_W	1.348	0.96
213_R	216_D	1.341	0.96
110_I	137_L	1.300	0.95
69_L	193_A	1.299	0.95
25_E	77_Y	1.285	0.95
75_A	109_Y	1.280	0.95
167_R	189_Y	1.248	0.94
213_R	218_K	1.246	0.94
26_D	29_S	1.245	0.94
26_D	34_P	1.241	0.94
187_W	191_I	1.215	0.93
198_I	202_N	1.213	0.93
22_I	39_I	1.207	0.93
204_R	209_Y	1.186	0.92
200_E	213_R	1.179	0.92
210_I	215_D	1.170	0.92
94_F	97_G	1.157	0.91
20_I	165_I	1.151	0.91
43_E	72_D	1.136	0.91
40_T	98_I	1.134	0.90
44_L	69_L	1.131	0.90
1_F	4_S	1.127	0.90
186_W	189_Y	1.114	0.90
50_D	56_T	1.113	0.90
78_W	154_I	1.111	0.90
87_P	91_L	1.095	0.89
49_T	119_K	1.094	0.89
151_Y	155_L	1.093	0.89
19_N	159_D	1.090	0.89
38_G	79_N	1.085	0.88
51_E	66_H	1.081	0.88
76_V	110_I	1.074	0.88
123_N	130_T	1.063	0.87
2_T	6_V	1.051	0.87
88_E	93_K	1.043	0.86
37_F	177_V	1.035	0.86
177_V	186_W	1.029	0.86
93_K	96_S	1.028	0.86
82_L	93_K	1.026	0.85
73_S	115_S	1.024	0.85
4_S	132_K	1.018	0.85
208_E	212_E	1.017	0.85
195_L	199_R	1.015	0.85
28_I	157_L	1.013	0.85
169_K	197_E	1.009	0.85
200_E	216_D	0.996	0.84
210_I	222_E	0.995	0.84
113_P	131_P	0.987	0.83
52_N	219_R	0.981	0.83
116_G	139_L	0.969	0.82
125_S	128_T	0.968	0.82
15_V	127_E	0.967	0.82
29_S	157_L	0.961	0.81
26_D	78_W	0.957	0.81
29_S	43_E	0.947	0.81
35_F	153_D	0.947	0.81
86_S	89_E	0.943	0.80
167_R	171_R	0.942	0.80
120_L	133_I	0.942	0.80
180_K	183_P	0.941	0.80
122_L	133_I	0.934	0.80
2_T	5_L	0.934	0.80
183_P	186_W	0.932	0.79
49_T	161_F	0.924	0.79
100_S	104_S	0.923	0.79
1_F	14_Q	0.922	0.79
181_E	186_W	0.920	0.79
90_L	109_Y	0.918	0.78
174_R	186_W	0.910	0.78
13_L	101_G	0.906	0.78
70_E	117_S	0.905	0.77
69_L	170_Y	0.891	0.76
118_A	137_L	0.881	0.76
174_R	189_Y	0.879	0.75
67_K	150_Q	0.872	0.75
213_R	221_I	0.872	0.75
40_T	109_Y	0.869	0.75
25_E	34_P	0.859	0.74
3_E	8_K	0.842	0.72
22_I	75_A	0.841	0.72
14_Q	17_I	0.837	0.72
198_I	209_Y	0.829	0.71
174_R	187_W	0.818	0.70
64_I	124_K	0.814	0.70
80_K	146_L	0.810	0.69
36_A	79_N	0.807	0.69
128_T	224_Y	0.804	0.69
6_V	179_V	0.801	0.68
13_L	153_D	0.799	0.68
55_P	136_D	0.797	0.68
16_T	19_N	0.796	0.68
210_I	213_R	0.792	0.67
77_Y	94_F	0.790	0.67
172_K	195_L	0.785	0.67
177_V	182_N	0.785	0.67
178_P	181_E	0.780	0.66
22_I	76_V	0.777	0.66
8_K	13_L	0.777	0.66
192_N	195_L	0.777	0.66
11_D	24_Y	0.772	0.65
114_V	168_Q	0.771	0.65
189_Y	202_N	0.768	0.65
79_N	122_L	0.767	0.65
21_H	40_T	0.766	0.65
221_I	225_K	0.763	0.65
177_V	181_E	0.760	0.64
82_L	85_L	0.753	0.64
175_P	187_W	0.753	0.64
79_N	98_I	0.750	0.63
81_S	90_L	0.748	0.63
121_T	134_D	0.744	0.63
41_L	114_V	0.743	0.62
111_L	149_D	0.743	0.62
16_T	155_L	0.742	0.62
189_Y	210_I	0.740	0.62
65_I	78_W	0.738	0.62
12_N	17_I	0.737	0.62
216_D	219_R	0.734	0.62
85_L	89_E	0.731	0.61
195_L	198_I	0.730	0.61
17_I	71_L	0.729	0.61
89_E	92_E	0.728	0.61
82_L	120_L	0.727	0.61
187_W	220_Y	0.726	0.61
48_T	193_A	0.718	0.60
163_R	189_Y	0.717	0.60
154_I	170_Y	0.717	0.60
116_G	217_R	0.716	0.60
35_F	38_G	0.715	0.60
178_P	182_N	0.714	0.59
207_W	211_K	0.710	0.59
17_I	21_H	0.703	0.58
12_N	57_F	0.702	0.58
1_F	153_D	0.699	0.58
123_N	131_P	0.695	0.57
8_K	217_R	0.693	0.57
170_Y	189_Y	0.689	0.57
44_L	158_L	0.689	0.57
66_H	121_T	0.688	0.57
191_I	195_L	0.687	0.56
132_K	150_Q	0.686	0.56
46_A	116_G	0.685	0.56
5_L	160_S	0.684	0.56
192_N	199_R	0.681	0.56
11_D	217_R	0.680	0.56
184_R	187_W	0.680	0.56
14_Q	43_E	0.678	0.55
49_T	68_L	0.676	0.55
179_V	182_N	0.676	0.55
63_K	154_I	0.675	0.55
4_S	214_R	0.675	0.55
163_R	218_K	0.673	0.55
41_L	194_V	0.671	0.55
76_V	104_S	0.668	0.54
24_Y	42_E	0.668	0.54
6_V	88_E	0.665	0.54
170_Y	197_E	0.664	0.54
173_Y	192_N	0.662	0.54
149_D	153_D	0.662	0.54
89_E	93_K	0.661	0.54
65_I	146_L	0.660	0.54
12_N	131_P	0.659	0.53
76_V	130_T	0.659	0.53
38_G	150_Q	0.658	0.53
40_T	77_Y	0.653	0.53
147_D	201_R	0.652	0.53
64_I	120_L	0.651	0.53
164_F	189_Y	0.650	0.52
173_Y	189_Y	0.650	0.52
53_W	66_H	0.648	0.52
37_F	78_W	0.647	0.52
85_L	93_K	0.646	0.52
130_T	203_R	0.645	0.52
8_K	213_R	0.645	0.52
208_E	211_K	0.644	0.52
33_H	74_L	0.642	0.52
207_W	210_I	0.642	0.52
112_K	141_E	0.641	0.51
79_N	115_S	0.641	0.51
93_K	102_D	0.640	0.51
146_L	188_K	0.639	0.51
14_Q	44_L	0.638	0.51
8_K	118_A	0.638	0.51
173_Y	196_E	0.635	0.51
25_E	94_F	0.632	0.50
2_T	9_I	0.630	0.50
5_L	12_N	0.625	0.50
116_G	151_Y	0.620	0.49
51_E	67_K	0.619	0.49
91_L	95_K	0.618	0.49
212_E	222_E	0.616	0.49
170_Y	173_Y	0.613	0.48
185_A	192_N	0.613	0.48
24_Y	71_L	0.611	0.48
42_E	176_K	0.611	0.48
218_K	225_K	0.607	0.48
174_R	179_V	0.606	0.47
99_A	105_P	0.605	0.47
19_N	138_E	0.604	0.47
2_T	45_S	0.603	0.47
122_L	214_R	0.601	0.47
68_L	71_L	0.600	0.47
88_E	104_S	0.599	0.47
179_V	183_P	0.599	0.47
112_K	145_V	0.596	0.46
115_S	146_L	0.596	0.46
189_Y	197_E	0.592	0.46
11_D	124_K	0.591	0.46
213_R	217_R	0.589	0.46
30_N	43_E	0.586	0.45
200_E	203_R	0.584	0.45
96_S	101_G	0.581	0.45
102_D	106_K	0.580	0.45
24_Y	35_F	0.580	0.45
135_A	149_D	0.577	0.44
101_G	105_P	0.575	0.44
12_N	53_W	0.573	0.44
28_I	178_P	0.569	0.43
18_K	135_A	0.569	0.43
107_H	183_P	0.568	0.43
8_K	57_F	0.564	0.43
36_A	206_S	0.561	0.43
49_T	57_F	0.559	0.42
183_P	217_R	0.559	0.42
6_V	10_I	0.555	0.42
17_I	136_D	0.555	0.42
185_A	212_E	0.555	0.42
214_R	224_Y	0.555	0.42
69_L	135_A	0.555	0.42
13_L	95_K	0.555	0.42
142_I	189_Y	0.554	0.42
6_V	9_I	0.554	0.42
1_F	194_V	0.553	0.42
84_D	87_P	0.551	0.41
82_L	97_G	0.551	0.41
65_I	126_G	0.549	0.41
187_W	198_I	0.549	0.41
89_E	96_S	0.549	0.41
172_K	196_E	0.548	0.41
59_D	117_S	0.544	0.41
57_F	221_I	0.543	0.41
206_S	209_Y	0.543	0.41
51_E	101_G	0.543	0.41
177_V	185_A	0.542	0.40
35_F	77_Y	0.542	0.40
59_D	62_S	0.538	0.40
207_W	217_R	0.537	0.40
30_N	110_I	0.536	0.40
8_K	12_N	0.536	0.40
32_G	76_V	0.535	0.40
25_E	79_N	0.535	0.40
94_F	116_G	0.535	0.40
39_I	84_D	0.534	0.40
18_K	39_I	0.533	0.40
61_T	157_L	0.532	0.39
121_T	166_R	0.531	0.39
121_T	136_D	0.531	0.39
111_L	193_A	0.527	0.39
110_I	165_I	0.526	0.39
40_T	151_Y	0.526	0.39
100_S	198_I	0.524	0.39
10_I	184_R	0.524	0.39
124_K	127_E	0.523	0.38
4_S	118_A	0.521	0.38
70_E	142_I	0.520	0.38
125_S	129_D	0.517	0.38
118_A	156_K	0.514	0.38
13_L	151_Y	0.513	0.37
29_S	75_A	0.511	0.37
20_I	32_G	0.509	0.37
82_L	184_R	0.509	0.37
26_D	35_F	0.508	0.37
206_S	214_R	0.507	0.37
49_T	78_W	0.507	0.37
17_I	20_I	0.507	0.37
209_Y	212_E	0.506	0.37
39_I	103_N	0.506	0.37
199_R	202_N	0.505	0.37
122_L	160_S	0.505	0.37
36_A	117_S	0.503	0.36
123_N	172_K	0.501	0.36
12_N	49_T	0.500	0.36

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4x3iA	1	0.3186	13	0.945	Contact Map
2la3A	1	0.4248	6.5	0.952	Contact Map
1nh2D	1	0.1681	4.5	0.955	Contact Map
3c6vA	3	0.2611	4.5	0.955	Contact Map
1sz7A	2	0.1858	4.5	0.955	Contact Map
3kanA	3	0.1858	4.2	0.956	Contact Map
3jtzA	2	0.3363	3.2	0.959	Contact Map
3ju0A	1	0.3363	3	0.959	Contact Map
1hfoA	3	0.1726	2.5	0.961	Contact Map
1d4tA	1	0.4248	2.4	0.961	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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