VPS13_mid_rpt - PFAM28P - GREMLIN Contacts

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VPS13_mid_rpt - Repeating coiled region of VPS13

PFAM:	PF16910	Sequences: FETNPLDEKADQRLSVKLQPLEIVYNPKFVNSLLNFFKPPESAKESIEALTEAAGATLEGLKEQTRAGLEYALEEHKRLDLDIDLKAPVIIIPESSTSKSSNLLVLDLGHLSVTSDLVDKSTLKEIQSKQSQQYSEEDLEELESLMYDKFDVKLTDLQLLIGRSIEDWKSALSSDSSELHLLEPINLDLQLERSIVPKDPNLPKFKVSGHLPSLHVNLSDEKYKALMKLLDVAIP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	235 (229)
Sequences:	1065 (750)
Seq/√Len:	49.6
META:	0.174

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
106_L	159_L	4.575	1.00
84_D	110_H	3.894	1.00
113_V	152_V	3.850	1.00
76_H	115_S	3.630	1.00
27_P	31_N	3.598	1.00
191_L	207_V	3.103	1.00
87_A	109_G	2.977	1.00
156_D	186_N	2.931	1.00
49_A	52_E	2.417	1.00
15_S	82_D	2.403	1.00
33_L	210_H	2.385	1.00
87_A	107_D	2.357	1.00
125_E	128_S	2.255	1.00
17_K	84_D	2.215	1.00
158_Q	184_P	2.213	1.00
192_E	206_K	2.181	1.00
94_E	102_N	2.169	1.00
190_Q	208_S	2.159	1.00
57_T	60_G	2.141	1.00
207_V	216_V	2.117	1.00
223_Y	227_M	1.922	0.99
88_P	107_D	1.813	0.99
48_E	54_A	1.804	0.99
83_I	113_V	1.766	0.99
12_Q	79_L	1.762	0.99
94_E	228_K	1.749	0.99
90_I	126_I	1.745	0.99
10_A	80_D	1.732	0.99
48_E	51_T	1.687	0.98
22_E	94_E	1.684	0.98
147_Y	202_L	1.649	0.98
16_V	135_S	1.624	0.98
206_K	219_S	1.617	0.98
90_I	113_V	1.608	0.98
58_L	62_K	1.600	0.98
121_S	124_K	1.595	0.98
147_Y	150_F	1.574	0.97
16_V	83_I	1.573	0.97
209_G	230_L	1.565	0.97
65_T	69_L	1.557	0.97
19_Q	86_K	1.554	0.97
122_T	125_E	1.541	0.97
166_E	180_H	1.528	0.97
14_L	64_Q	1.522	0.97
39_P	43_A	1.519	0.97
43_A	46_S	1.518	0.97
19_Q	186_N	1.517	0.97
189_L	209_G	1.492	0.96
200_P	218_L	1.480	0.96
153_K	188_D	1.470	0.96
25_Y	32_S	1.469	0.96
160_L	216_V	1.402	0.95
165_I	168_W	1.396	0.95
202_L	205_F	1.395	0.95
186_N	226_L	1.387	0.95
22_E	89_V	1.376	0.94
60_G	90_I	1.369	0.94
29_F	168_W	1.334	0.93
106_L	178_E	1.330	0.93
94_E	104_L	1.328	0.93
33_L	155_T	1.319	0.93
76_H	195_I	1.318	0.93
194_S	202_L	1.313	0.93
73_L	84_D	1.310	0.93
59_E	111_L	1.309	0.93
124_K	128_S	1.298	0.92
54_A	64_Q	1.290	0.92
53_A	81_L	1.290	0.92
47_I	50_L	1.278	0.92
183_E	212_P	1.277	0.92
194_S	199_D	1.272	0.92
148_D	154_L	1.267	0.91
183_E	217_N	1.265	0.91
164_S	167_D	1.237	0.90
104_L	219_S	1.234	0.90
16_V	208_S	1.225	0.90
73_L	214_L	1.224	0.90
26_N	96_S	1.217	0.90
162_G	223_Y	1.214	0.89
14_L	79_L	1.211	0.89
5_P	11_D	1.199	0.89
30_V	112_S	1.195	0.89
9_K	15_S	1.190	0.89
157_L	163_R	1.188	0.88
115_S	195_I	1.161	0.87
2_E	23_I	1.160	0.87
23_I	68_G	1.150	0.87
11_D	92_I	1.131	0.86
89_V	223_Y	1.119	0.85
160_L	222_K	1.113	0.85
211_L	222_K	1.111	0.85
42_S	105_V	1.109	0.85
26_N	29_F	1.105	0.84
76_H	204_K	1.085	0.83
150_F	161_I	1.080	0.83
157_L	185_I	1.079	0.83
137_E	226_L	1.077	0.83
113_V	230_L	1.074	0.83
104_L	181_L	1.073	0.83
192_E	216_V	1.067	0.82
111_L	174_S	1.067	0.82
14_L	177_S	1.062	0.82
3_T	218_L	1.059	0.82
88_P	108_L	1.057	0.82
92_I	106_L	1.044	0.81
193_R	203_P	1.041	0.81
57_T	179_L	1.038	0.81
150_F	160_L	1.037	0.80
183_E	192_E	1.035	0.80
160_L	177_S	1.028	0.80
129_K	132_Q	1.023	0.80
22_E	104_L	1.021	0.79
18_L	168_W	1.019	0.79
47_I	52_E	1.018	0.79
26_N	182_L	1.015	0.79
33_L	197_P	1.011	0.79
180_H	222_K	1.006	0.78
208_S	211_L	0.997	0.78
3_T	12_Q	0.996	0.78
134_Y	137_E	0.993	0.78
12_Q	20_P	0.982	0.77
171_A	174_S	0.976	0.76
146_M	152_V	0.974	0.76
142_L	149_K	0.974	0.76
38_K	151_D	0.967	0.76
106_L	217_N	0.963	0.75
92_I	221_E	0.958	0.75
90_I	223_Y	0.947	0.74
219_S	222_K	0.947	0.74
25_Y	158_Q	0.944	0.74
88_P	109_G	0.943	0.74
15_S	33_L	0.938	0.73
7_D	40_P	0.933	0.73
113_V	171_A	0.927	0.72
115_S	147_Y	0.925	0.72
10_A	36_F	0.919	0.72
105_V	112_S	0.915	0.71
91_I	226_L	0.914	0.71
146_M	202_L	0.913	0.71
183_E	215_H	0.912	0.71
54_A	66_R	0.911	0.71
77_K	115_S	0.910	0.71
91_I	103_L	0.901	0.70
166_E	225_A	0.890	0.69
205_F	227_M	0.887	0.69
206_K	218_L	0.886	0.69
71_Y	91_I	0.885	0.69
89_V	197_P	0.885	0.69
50_L	53_A	0.883	0.69
18_L	89_V	0.882	0.69
152_V	174_S	0.881	0.69
34_L	164_S	0.877	0.68
206_K	220_D	0.875	0.68
137_E	179_L	0.872	0.68
130_Q	133_Q	0.870	0.68
95_S	98_S	0.869	0.68
82_D	114_T	0.868	0.67
160_L	180_H	0.868	0.67
168_W	203_P	0.865	0.67
9_K	80_D	0.865	0.67
68_G	172_L	0.861	0.67
149_K	190_Q	0.860	0.67
12_Q	25_Y	0.858	0.67
21_L	32_S	0.858	0.67
92_I	104_L	0.857	0.66
127_Q	131_S	0.854	0.66
66_R	70_E	0.847	0.66
182_L	185_I	0.846	0.65
102_N	218_L	0.845	0.65
36_F	107_D	0.845	0.65
154_L	158_Q	0.833	0.64
83_I	184_P	0.831	0.64
64_Q	68_G	0.829	0.64
135_S	138_D	0.821	0.63
78_R	195_I	0.820	0.63
125_E	210_H	0.820	0.63
17_K	153_K	0.815	0.63
48_E	52_E	0.814	0.62
161_I	226_L	0.807	0.62
56_A	113_V	0.806	0.62
21_L	156_D	0.805	0.62
34_L	156_D	0.804	0.61
185_I	219_S	0.803	0.61
111_L	154_L	0.799	0.61
104_L	161_I	0.796	0.61
149_K	192_E	0.795	0.61
36_F	43_A	0.794	0.60
30_V	38_K	0.788	0.60
2_E	5_P	0.785	0.60
75_E	144_S	0.785	0.60
152_V	167_D	0.784	0.59
73_L	195_I	0.781	0.59
65_T	162_G	0.781	0.59
80_D	194_S	0.779	0.59
60_G	64_Q	0.778	0.59
29_F	105_V	0.773	0.58
77_K	103_L	0.771	0.58
105_V	108_L	0.768	0.58
78_R	108_L	0.767	0.58
104_L	229_L	0.767	0.58
68_G	146_M	0.766	0.58
11_D	88_P	0.765	0.58
147_Y	206_K	0.763	0.57
72_A	76_H	0.761	0.57
30_V	79_L	0.757	0.57
15_S	111_L	0.754	0.57
22_E	204_K	0.753	0.56
68_G	204_K	0.750	0.56
34_L	113_V	0.748	0.56
101_S	179_L	0.743	0.55
28_K	32_S	0.743	0.55
54_A	65_T	0.740	0.55
65_T	87_A	0.738	0.55
33_L	92_I	0.737	0.55
56_A	106_L	0.736	0.55
59_E	62_K	0.735	0.55
63_E	163_R	0.731	0.54
99_K	178_E	0.731	0.54
211_L	214_L	0.725	0.54
92_I	124_K	0.723	0.53
61_L	187_L	0.722	0.53
121_S	131_S	0.720	0.53
147_Y	222_K	0.706	0.52
131_S	136_E	0.704	0.51
124_K	127_Q	0.701	0.51
192_E	212_P	0.699	0.51
106_L	190_Q	0.698	0.51
106_L	211_L	0.697	0.51
128_S	132_Q	0.696	0.51
83_I	172_L	0.694	0.50
37_F	187_L	0.693	0.50
120_K	123_L	0.690	0.50
68_G	71_Y	0.686	0.50
55_G	62_K	0.686	0.50
150_F	191_L	0.685	0.50
25_Y	30_V	0.685	0.50
218_L	223_Y	0.684	0.49
208_S	218_L	0.678	0.49
14_L	35_N	0.678	0.49
104_L	200_P	0.677	0.49
59_E	92_I	0.675	0.48
67_A	214_L	0.673	0.48
96_S	187_L	0.672	0.48
137_E	140_E	0.670	0.48
170_S	176_S	0.665	0.47
9_K	14_L	0.664	0.47
91_I	215_H	0.662	0.47
31_N	229_L	0.659	0.47
108_L	182_L	0.658	0.47
50_L	59_E	0.657	0.47
126_I	136_E	0.648	0.46
41_E	55_G	0.647	0.46
92_I	114_T	0.643	0.45
90_I	103_L	0.642	0.45
91_I	105_V	0.641	0.45
132_Q	141_E	0.639	0.45
33_L	93_P	0.638	0.45
183_E	211_L	0.638	0.45
144_S	191_L	0.635	0.44
6_L	26_N	0.633	0.44
120_K	124_K	0.633	0.44
145_L	195_I	0.628	0.44
218_L	226_L	0.627	0.44
158_Q	180_H	0.622	0.43
84_D	149_K	0.621	0.43
150_F	167_D	0.620	0.43
20_P	32_S	0.618	0.43
22_E	214_L	0.616	0.43
173_S	226_L	0.616	0.43
25_Y	187_L	0.614	0.42
42_S	113_V	0.612	0.42
23_I	173_S	0.608	0.42
177_S	181_L	0.607	0.42
135_S	140_E	0.606	0.42
131_S	176_S	0.605	0.41
159_L	189_L	0.598	0.41
135_S	177_S	0.596	0.41
59_E	110_H	0.593	0.40
10_A	26_N	0.588	0.40
112_S	229_L	0.584	0.39
167_D	181_L	0.584	0.39
36_F	189_L	0.584	0.39
171_A	180_H	0.581	0.39
91_I	156_D	0.579	0.39
47_I	103_L	0.575	0.38
18_L	66_R	0.575	0.38
89_V	168_W	0.573	0.38
75_E	216_V	0.572	0.38
12_Q	196_V	0.572	0.38
153_K	163_R	0.571	0.38
127_Q	130_Q	0.569	0.38
137_E	176_S	0.569	0.38
21_L	87_A	0.568	0.38
90_I	104_L	0.567	0.38
28_K	186_N	0.567	0.38
114_T	176_S	0.566	0.38
46_S	50_L	0.562	0.37
33_L	196_V	0.559	0.37
104_L	149_K	0.559	0.37
20_P	37_F	0.558	0.37
84_D	212_P	0.556	0.37
26_N	194_S	0.555	0.37
30_V	180_H	0.552	0.36
35_N	100_S	0.549	0.36
103_L	162_G	0.547	0.36
24_V	99_K	0.543	0.35
145_L	223_Y	0.542	0.35
87_A	108_L	0.542	0.35
61_L	99_K	0.542	0.35
3_T	79_L	0.541	0.35
102_N	124_K	0.540	0.35
126_I	131_S	0.540	0.35
22_E	26_N	0.540	0.35
73_L	194_S	0.540	0.35
154_L	182_L	0.537	0.35
220_D	223_Y	0.535	0.35
11_D	81_L	0.534	0.35
30_V	53_A	0.534	0.35
7_D	39_P	0.530	0.34
34_L	178_E	0.527	0.34
152_V	218_L	0.525	0.34
116_D	218_L	0.524	0.34
170_S	173_S	0.522	0.34
94_E	180_H	0.521	0.33
6_L	9_K	0.518	0.33
77_K	195_I	0.515	0.33
102_N	225_A	0.515	0.33
187_L	214_L	0.515	0.33
24_V	193_R	0.515	0.33
212_P	216_V	0.514	0.33
60_G	229_L	0.512	0.33
27_P	87_A	0.511	0.33
115_S	194_S	0.510	0.32
153_K	214_L	0.510	0.32
53_A	223_Y	0.508	0.32
123_L	126_I	0.507	0.32
90_I	112_S	0.507	0.32
13_R	80_D	0.507	0.32
155_T	194_S	0.506	0.32
65_T	107_D	0.504	0.32
116_D	119_D	0.504	0.32
26_N	40_P	0.501	0.32
89_V	105_V	0.500	0.32
63_E	184_P	0.500	0.32

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
2ymyA	2	0.1745	4.6	0.951	Contact Map
2fy7A	1	0.3404	4.4	0.952	Contact Map
1s16A	2	0.2298	3.1	0.955	Contact Map
3ayhA	1	0.5319	2.3	0.958	Contact Map
3lnuA	1	0.2128	2.3	0.958	Contact Map
4bjsA	3	0.1021	2.1	0.959	Contact Map
1knzA	2	0.4894	2	0.96	Contact Map
4g1gA	2	0.2553	1.9	0.96	Contact Map
4d2gD	1	0.0894	1.7	0.961	Contact Map
4e0tA	4	0.3617	1.6	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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