Vps8 - PFAM28P - GREMLIN Contacts

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Vps8 - Golgi CORVET complex core vacuolar protein 8

PFAM:	PF12816	Sequences: SIFLETLEPYILDGKITSLPPEVVKDLVEHYVSKGRLSRLEEIICHLDISSLDIDQVTTLCKQHNLYDALIYVWNRALNDYVTPLEELLSLLRPLNGDDELEESKEYNAYKLLPYLSYCLTGRAYPTGEPLPEDEAPKAKAEIYDFLFSGRSISWPKPDGDDEPSFPYLRLLLKFDAESFLSVLNEAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (187)
Sequences:	611 (468)
Seq/√Len:	34.2
META:	0.34

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
68_D	125_Y	4.211	1.00
41_E	69_A	3.800	1.00
176_D	179_S	3.559	1.00
79_N	135_E	3.059	1.00
182_S	185_N	2.898	1.00
68_D	111_K	2.663	1.00
14_G	46_H	2.603	1.00
84_P	115_Y	2.577	1.00
163_E	168_Y	2.570	1.00
182_S	186_E	2.478	1.00
155_W	163_E	2.437	1.00
179_S	182_S	2.359	0.99
155_W	164_P	2.303	0.99
120_L	125_Y	2.292	0.99
75_N	115_Y	2.081	0.99
67_Y	146_F	2.058	0.98
4_L	27_L	2.046	0.98
9_P	23_V	2.022	0.98
8_E	12_L	1.955	0.98
166_F	186_E	1.935	0.98
27_L	43_I	1.908	0.97
121_T	186_E	1.904	0.97
66_L	125_Y	1.892	0.97
89_L	92_L	1.875	0.97
9_P	12_L	1.851	0.97
75_N	119_C	1.804	0.96
47_L	54_I	1.754	0.96
81_Y	84_P	1.733	0.95
115_Y	119_C	1.723	0.95
87_E	165_S	1.703	0.95
95_L	99_D	1.668	0.94
2_I	43_I	1.654	0.94
164_P	168_Y	1.650	0.94
155_W	168_Y	1.641	0.94
72_Y	75_N	1.606	0.93
66_L	120_L	1.593	0.93
178_E	185_N	1.581	0.93
180_F	183_V	1.510	0.91
60_L	64_H	1.498	0.90
61_C	75_N	1.484	0.90
159_D	174_K	1.470	0.89
97_G	143_I	1.431	0.88
24_V	47_L	1.405	0.87
165_S	170_R	1.374	0.86
78_L	88_L	1.366	0.86
20_P	61_C	1.364	0.86
109_A	113_L	1.359	0.85
178_E	186_E	1.334	0.84
59_T	119_C	1.334	0.84
46_H	74_W	1.288	0.82
20_P	44_I	1.272	0.81
8_E	31_Y	1.266	0.81
65_N	96_N	1.248	0.80
156_P	171_L	1.245	0.80
156_P	168_Y	1.231	0.79
49_I	172_L	1.226	0.79
41_E	45_C	1.220	0.78
36_R	39_R	1.219	0.78
152_S	158_P	1.218	0.78
18_S	48_D	1.208	0.78
156_P	167_P	1.207	0.78
29_E	78_L	1.192	0.77
21_P	28_V	1.175	0.76
79_N	138_K	1.172	0.76
3_F	26_D	1.152	0.74
45_C	54_I	1.141	0.74
178_E	182_S	1.137	0.73
54_I	77_A	1.125	0.72
60_L	132_P	1.125	0.72
171_L	175_F	1.125	0.72
23_V	104_S	1.113	0.72
165_S	172_L	1.112	0.72
11_I	42_E	1.108	0.71
99_D	116_L	1.105	0.71
154_S	157_K	1.095	0.70
72_Y	148_F	1.094	0.70
125_Y	150_G	1.085	0.70
62_K	87_E	1.061	0.68
50_S	142_E	1.060	0.68
86_E	168_Y	1.054	0.67
23_V	29_E	1.053	0.67
61_C	69_A	1.036	0.66
113_L	119_C	1.035	0.66
136_A	139_A	1.034	0.66
120_L	143_I	1.033	0.66
81_Y	179_S	1.027	0.65
111_K	125_Y	1.025	0.65
45_C	69_A	1.024	0.65
3_F	9_P	1.022	0.65
178_E	181_L	1.020	0.65
144_Y	148_F	1.017	0.65
89_L	136_A	1.007	0.64
86_E	155_W	0.999	0.63
89_L	125_Y	0.996	0.63
113_L	156_P	0.991	0.63
158_P	161_D	0.990	0.62
81_Y	92_L	0.989	0.62
119_C	139_A	0.970	0.61
24_V	43_I	0.970	0.61
6_T	10_Y	0.964	0.60
32_V	40_L	0.957	0.60
48_D	104_S	0.957	0.60
47_L	52_L	0.955	0.60
87_E	177_A	0.954	0.60
55_D	143_I	0.953	0.60
167_P	172_L	0.946	0.59
5_E	30_H	0.935	0.58
44_I	72_Y	0.928	0.57
169_L	187_A	0.920	0.57
80_D	83_T	0.917	0.57
183_V	187_A	0.916	0.56
164_P	167_P	0.913	0.56
14_G	73_V	0.908	0.56
32_V	64_H	0.899	0.55
80_D	122_G	0.896	0.55
59_T	98_D	0.890	0.54
9_P	39_R	0.888	0.54
23_V	149_S	0.884	0.54
31_Y	178_E	0.876	0.53
144_Y	187_A	0.873	0.53
77_A	139_A	0.873	0.53
45_C	58_T	0.872	0.53
53_D	126_P	0.872	0.53
168_Y	171_L	0.871	0.53
22_E	79_N	0.870	0.53
29_E	95_L	0.866	0.52
166_F	178_E	0.864	0.52
88_L	115_Y	0.863	0.52
27_L	56_Q	0.858	0.52
7_L	184_L	0.840	0.50
7_L	81_Y	0.837	0.50
10_Y	30_H	0.837	0.50
164_P	171_L	0.833	0.49
42_E	169_L	0.823	0.49
140_K	144_Y	0.820	0.48
112_L	172_L	0.817	0.48
31_Y	185_N	0.816	0.48
46_H	77_A	0.815	0.48
154_S	175_F	0.812	0.48
23_V	170_R	0.808	0.47
118_Y	121_T	0.806	0.47
71_I	88_L	0.804	0.47
20_P	149_S	0.804	0.47
4_L	170_R	0.798	0.46
85_L	143_I	0.798	0.46
132_P	179_S	0.797	0.46
44_I	180_F	0.797	0.46
179_S	187_A	0.794	0.46
12_L	181_L	0.794	0.46
55_D	59_T	0.787	0.46
99_D	107_Y	0.785	0.45
91_L	149_S	0.782	0.45
131_L	139_A	0.780	0.45
121_T	140_K	0.777	0.45
96_N	100_E	0.776	0.45
68_D	180_F	0.776	0.45
24_V	55_D	0.775	0.45
69_A	187_A	0.769	0.44
38_S	89_L	0.766	0.44
66_L	144_Y	0.764	0.44
46_H	181_L	0.761	0.43
50_S	184_L	0.760	0.43
159_D	162_D	0.759	0.43
144_Y	180_F	0.755	0.43
109_A	139_A	0.753	0.43
75_N	83_T	0.752	0.43
5_E	75_N	0.750	0.42
59_T	100_E	0.750	0.42
138_K	141_A	0.749	0.42
12_L	126_P	0.743	0.42
132_P	135_E	0.741	0.42
55_D	75_N	0.737	0.41
106_E	143_I	0.737	0.41
25_K	56_Q	0.735	0.41
9_P	69_A	0.732	0.41
49_I	52_L	0.728	0.41
19_L	130_P	0.726	0.40
129_E	180_F	0.725	0.40
159_D	171_L	0.722	0.40
21_P	140_K	0.720	0.40
41_E	61_C	0.713	0.39
73_V	165_S	0.710	0.39
75_N	84_P	0.709	0.39
6_T	25_K	0.703	0.39
8_E	46_H	0.700	0.38
70_L	156_P	0.698	0.38
60_L	88_L	0.692	0.38
40_L	58_T	0.683	0.37
14_G	157_K	0.680	0.37
138_K	174_K	0.678	0.37
152_S	160_G	0.669	0.36
150_G	164_P	0.666	0.36
87_E	147_L	0.663	0.35
25_K	54_I	0.662	0.35
23_V	52_L	0.662	0.35
43_I	49_I	0.659	0.35
166_F	182_S	0.653	0.35
74_W	77_A	0.652	0.35
43_I	54_I	0.650	0.34
47_L	74_W	0.650	0.34
114_P	125_Y	0.646	0.34
35_G	99_D	0.646	0.34
128_G	177_A	0.644	0.34
80_D	173_L	0.644	0.34
163_E	166_F	0.644	0.34
21_P	123_R	0.643	0.34
155_W	171_L	0.643	0.34
28_V	60_L	0.642	0.34
109_A	175_F	0.635	0.33
15_K	29_E	0.635	0.33
16_I	65_N	0.634	0.33
25_K	60_L	0.631	0.33
42_E	74_W	0.630	0.33
42_E	45_C	0.627	0.33
166_F	177_A	0.627	0.33
100_E	105_K	0.616	0.32
160_G	165_S	0.614	0.32
173_L	180_F	0.614	0.32
19_L	34_K	0.613	0.32
4_L	56_Q	0.612	0.32
17_T	74_W	0.609	0.31
13_D	59_T	0.607	0.31
169_L	175_F	0.605	0.31
54_I	135_E	0.602	0.31
4_L	24_V	0.602	0.31
54_I	68_D	0.602	0.31
143_I	152_S	0.599	0.31
47_L	85_L	0.596	0.30
151_R	154_S	0.595	0.30
52_L	167_P	0.595	0.30
9_P	47_L	0.594	0.30
2_I	27_L	0.591	0.30
169_L	177_A	0.591	0.30
119_C	148_F	0.591	0.30
110_Y	113_L	0.590	0.30
103_E	147_L	0.590	0.30
81_Y	144_Y	0.589	0.30
7_L	102_E	0.585	0.30
85_L	116_L	0.585	0.30
24_V	40_L	0.577	0.29
49_I	124_A	0.576	0.29
56_Q	69_A	0.573	0.29
48_D	64_H	0.571	0.29
156_P	164_P	0.569	0.29
158_P	164_P	0.569	0.29
28_V	54_I	0.567	0.28
4_L	77_A	0.561	0.28
16_I	55_D	0.558	0.28
56_Q	77_A	0.557	0.28
39_R	88_L	0.557	0.28
113_L	182_S	0.557	0.28
34_K	96_N	0.556	0.28
124_A	172_L	0.551	0.27
42_E	111_K	0.550	0.27
15_K	77_A	0.548	0.27
48_D	147_L	0.544	0.27
24_V	39_R	0.540	0.27
25_K	123_R	0.539	0.27
65_N	71_I	0.539	0.27
164_P	169_L	0.537	0.26
178_E	187_A	0.534	0.26
45_C	73_V	0.533	0.26
45_C	178_E	0.533	0.26
28_V	64_H	0.533	0.26
29_E	98_D	0.524	0.26
153_I	184_L	0.524	0.26
4_L	31_Y	0.524	0.26
14_G	24_V	0.523	0.25
5_E	35_G	0.521	0.25
44_I	103_E	0.521	0.25
83_T	139_A	0.518	0.25
73_V	125_Y	0.514	0.25
31_Y	57_V	0.513	0.25
47_L	64_H	0.507	0.24
98_D	101_L	0.506	0.24
44_I	119_C	0.505	0.24
67_Y	88_L	0.503	0.24
79_N	106_E	0.503	0.24
131_L	182_S	0.502	0.24
127_T	130_P	0.500	0.24

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
3lvgA	3	0.9096	76	0.914	Contact Map
1xi4A	8	0.5266	32.6	0.935	Contact Map
3qilA	3	0.4947	23.3	0.94	Contact Map
1xg7A	2	0.8085	21.5	0.941	Contact Map
4x3iA	1	0.1223	4.6	0.956	Contact Map
4cr2S	1	0.9521	4.3	0.957	Contact Map
3fgaB	2	0.9149	3.4	0.959	Contact Map
4kmoB	1	0.266	3.4	0.959	Contact Map
4yczB	1	0.8298	3.3	0.959	Contact Map
4w60A	1	0.1436	3.3	0.959	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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