DUF3068 - PFAM28P - GREMLIN Contacts

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DUF3068 - Protein of unknown function (DUF3068)

PFAM:	PF11271	Sequences: LGLVLLGLGAFLLVLALLLRFYVVPRLAKLPLDLDSTTVLEGTTATYLDPATLAAGAAPTGVPLTATRTVKGDAASDSDVAVWDVGTTVRDDDGGEDGGLLSATTDRYAFDRRTGEAVGPANCCGGAPVGADAVPREGLVYKFPFGTEKKTYPYFDPTLRKAVPARYVGEETVDGLTVYRFTQTVPPTKVGADLTLTVPGSLVVTLTRYYSNTRTLWVEPVTGAIVKGEEHQRQTLRDPGGEGGAAVVTLLDATLTFTDATVAAQVDLAKDNRDKLRLLGTTLPIVLLVLGLVLLVAGLV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	300 (285)
Sequences:	1626 (1201)
Seq/√Len:	71.2
META:	0.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
147_T	181_F	8.846	1.00
169_G	180_R	3.447	1.00
285_I	289_V	3.387	1.00
151_T	164_P	3.193	1.00
267_D	271_D	3.146	1.00
171_E	178_V	2.944	1.00
176_L	266_V	2.921	1.00
214_R	230_E	2.893	1.00
170_E	177_T	2.889	1.00
17_L	21_F	2.782	1.00
16_A	288_L	2.730	1.00
219_E	273_R	2.717	1.00
180_R	215_T	2.699	1.00
282_T	286_V	2.652	1.00
9_G	291_G	2.617	1.00
149_K	179_Y	2.590	1.00
49_D	52_T	2.571	1.00
263_A	267_D	2.447	1.00
168_V	182_T	2.351	1.00
178_V	226_V	2.329	1.00
189_K	207_T	2.311	1.00
259_D	263_A	2.263	1.00
171_E	217_W	2.215	1.00
42_G	45_A	2.197	1.00
42_G	253_A	2.182	1.00
231_H	254_T	2.168	1.00
173_V	178_V	2.142	1.00
30_L	110_F	2.110	1.00
222_T	272_N	2.104	1.00
167_Y	170_E	2.074	1.00
227_K	256_T	2.055	1.00
151_T	166_R	2.034	1.00
278_L	283_L	2.022	1.00
66_A	255_L	1.944	1.00
231_H	252_D	1.902	1.00
184_T	213_T	1.810	1.00
23_V	27_L	1.802	1.00
182_T	215_T	1.799	1.00
153_P	164_P	1.763	1.00
106_D	136_R	1.726	1.00
171_E	180_R	1.725	1.00
257_F	261_T	1.714	1.00
80_V	118_V	1.706	1.00
176_L	220_P	1.683	1.00
168_V	180_R	1.682	1.00
35_D	69_T	1.653	1.00
45_A	253_A	1.648	0.99
259_D	262_V	1.644	0.99
72_G	81_A	1.633	0.99
147_T	220_P	1.632	0.99
154_Y	165_A	1.629	0.99
165_A	183_Q	1.627	0.99
143_F	181_F	1.618	0.99
176_L	219_E	1.605	0.99
294_L	297_A	1.594	0.99
174_D	263_A	1.594	0.99
172_T	177_T	1.577	0.99
139_L	143_F	1.575	0.99
28_A	146_G	1.569	0.99
24_V	28_A	1.557	0.99
278_L	282_T	1.552	0.99
159_L	163_V	1.544	0.99
116_E	153_P	1.538	0.99
147_T	219_E	1.533	0.99
173_V	227_K	1.526	0.99
167_Y	179_Y	1.511	0.99
182_T	213_T	1.503	0.99
281_T	285_I	1.496	0.99
148_E	152_Y	1.477	0.99
19_L	287_L	1.470	0.99
20_R	288_L	1.443	0.99
189_K	209_Y	1.430	0.99
123_C	126_G	1.424	0.98
68_R	228_G	1.423	0.98
149_K	167_Y	1.415	0.98
282_T	285_I	1.415	0.98
143_F	147_T	1.408	0.98
221_V	273_R	1.407	0.98
227_K	262_V	1.398	0.98
24_V	280_G	1.396	0.98
271_D	275_K	1.387	0.98
217_W	227_K	1.375	0.98
149_K	170_E	1.367	0.98
180_R	217_W	1.355	0.98
178_V	217_W	1.350	0.98
143_F	216_L	1.348	0.98
28_A	276_L	1.348	0.98
154_Y	216_L	1.336	0.98
264_A	268_L	1.322	0.98
200_G	203_V	1.313	0.97
142_K	145_F	1.308	0.97
64_L	253_A	1.274	0.97
117_A	136_R	1.268	0.97
143_F	165_A	1.250	0.97
226_V	265_Q	1.247	0.96
32_L	112_R	1.223	0.96
65_T	92_D	1.219	0.96
52_T	55_A	1.217	0.96
38_T	70_V	1.206	0.96
156_D	210_Y	1.206	0.96
124_C	127_A	1.205	0.96
122_N	125_G	1.188	0.95
152_Y	179_Y	1.172	0.95
73_D	107_R	1.171	0.95
251_L	255_L	1.164	0.95
265_Q	269_A	1.161	0.95
116_E	139_L	1.157	0.95
289_V	296_V	1.153	0.95
183_Q	214_R	1.152	0.95
30_L	142_K	1.148	0.94
83_W	110_F	1.136	0.94
229_E	254_T	1.136	0.94
71_K	84_D	1.128	0.94
277_R	282_T	1.125	0.94
81_A	112_R	1.111	0.93
272_N	279_L	1.110	0.93
12_L	287_L	1.106	0.93
17_L	288_L	1.104	0.93
163_V	183_Q	1.098	0.93
273_R	277_R	1.091	0.93
123_C	129_V	1.084	0.93
2_G	298_G	1.075	0.92
272_N	275_K	1.070	0.92
52_T	56_G	1.069	0.92
123_C	128_P	1.067	0.92
233_R	252_D	1.067	0.92
115_G	139_L	1.048	0.91
48_L	52_T	1.043	0.91
209_Y	235_T	1.038	0.91
291_G	298_G	1.031	0.91
84_D	107_R	1.029	0.90
18_L	22_Y	1.029	0.90
30_L	83_W	1.024	0.90
174_D	266_V	1.014	0.90
261_T	265_Q	1.006	0.89
21_F	25_P	1.005	0.89
41_E	258_T	1.005	0.89
141_Y	261_T	1.004	0.89
170_E	179_Y	1.001	0.89
185_V	188_T	0.991	0.89
279_L	283_L	0.988	0.89
277_R	281_T	0.984	0.88
123_C	127_A	0.982	0.88
176_L	226_V	0.979	0.88
11_F	18_L	0.973	0.88
176_L	270_K	0.972	0.88
7_G	11_F	0.972	0.88
174_D	262_V	0.969	0.88
12_L	290_L	0.960	0.87
32_L	76_S	0.952	0.87
80_V	109_A	0.950	0.87
108_Y	141_Y	0.947	0.86
213_T	231_H	0.947	0.86
159_L	188_T	0.946	0.86
143_F	218_V	0.942	0.86
91_D	94_G	0.937	0.86
267_D	292_L	0.929	0.85
64_L	101_L	0.926	0.85
13_L	290_L	0.924	0.85
117_A	140_V	0.923	0.85
125_G	128_P	0.922	0.85
159_L	190_V	0.905	0.84
8_L	32_L	0.905	0.84
155_F	276_L	0.905	0.84
190_V	234_Q	0.904	0.84
131_A	135_P	0.896	0.83
293_V	297_A	0.894	0.83
130_G	133_A	0.888	0.83
27_L	30_L	0.887	0.83
226_V	269_A	0.886	0.82
229_E	256_T	0.885	0.82
149_K	152_Y	0.882	0.82
212_N	230_E	0.882	0.82
111_D	114_T	0.880	0.82
262_V	266_V	0.875	0.82
211_S	214_R	0.874	0.82
39_V	258_T	0.873	0.82
108_Y	140_V	0.872	0.81
156_D	219_E	0.870	0.81
227_K	257_F	0.870	0.81
217_W	229_E	0.859	0.80
168_V	213_T	0.853	0.80
137_E	162_A	0.848	0.80
17_L	20_R	0.840	0.79
124_C	130_G	0.839	0.79
278_L	284_P	0.839	0.79
75_A	82_V	0.836	0.79
134_V	155_F	0.833	0.78
224_A	272_N	0.830	0.78
124_C	128_P	0.830	0.78
105_T	211_S	0.827	0.78
22_Y	26_R	0.823	0.78
278_L	286_V	0.823	0.78
289_V	293_V	0.822	0.77
48_L	53_L	0.822	0.77
126_G	297_A	0.822	0.77
209_Y	237_R	0.821	0.77
187_P	211_S	0.820	0.77
269_A	273_R	0.818	0.77
127_A	130_G	0.817	0.77
270_K	274_D	0.815	0.77
195_T	203_V	0.809	0.76
241_G	244_G	0.809	0.76
212_N	255_L	0.808	0.76
260_A	264_A	0.806	0.76
186_P	211_S	0.804	0.76
6_L	298_G	0.804	0.76
42_G	64_L	0.798	0.75
81_A	110_F	0.798	0.75
274_D	278_L	0.797	0.75
224_A	269_A	0.797	0.75
198_V	203_V	0.794	0.75
159_L	250_L	0.792	0.75
249_T	252_D	0.791	0.75
274_D	282_T	0.784	0.74
122_N	126_G	0.782	0.74
6_L	295_L	0.781	0.74
218_V	225_I	0.778	0.74
238_D	241_G	0.778	0.74
86_G	103_A	0.774	0.73
40_L	228_G	0.770	0.73
233_R	249_T	0.768	0.73
258_T	261_T	0.762	0.72
4_V	296_V	0.760	0.72
257_F	265_Q	0.756	0.71
19_L	283_L	0.750	0.71
83_W	87_T	0.748	0.71
283_L	287_L	0.748	0.71
26_R	29_K	0.747	0.70
290_L	297_A	0.744	0.70
111_D	118_V	0.744	0.70
153_P	165_A	0.736	0.69
124_C	131_A	0.736	0.69
40_L	68_R	0.730	0.69
150_K	179_Y	0.727	0.68
13_L	291_G	0.724	0.68
222_T	226_V	0.723	0.68
97_D	100_L	0.723	0.68
162_A	183_Q	0.719	0.68
292_L	296_V	0.718	0.67
264_A	267_D	0.717	0.67
167_Y	266_V	0.717	0.67
142_K	222_T	0.715	0.67
89_V	155_F	0.708	0.66
266_V	270_K	0.707	0.66
203_V	206_L	0.706	0.66
126_G	129_V	0.705	0.66
68_R	87_T	0.702	0.66
165_A	216_L	0.702	0.66
30_L	145_F	0.701	0.66
75_A	84_D	0.699	0.65
262_V	267_D	0.698	0.65
16_A	21_F	0.689	0.64
53_L	56_G	0.686	0.64
37_T	222_T	0.686	0.64
166_R	174_D	0.685	0.64
47_Y	91_D	0.681	0.63
29_K	42_G	0.677	0.63
67_T	236_L	0.674	0.63
287_L	294_L	0.672	0.62
108_Y	115_G	0.667	0.62
198_V	202_L	0.665	0.61
6_L	299_L	0.663	0.61
216_L	225_I	0.663	0.61
82_V	109_A	0.662	0.61
63_P	92_D	0.660	0.61
107_R	226_V	0.659	0.61
47_Y	62_V	0.658	0.61
216_L	228_G	0.652	0.60
130_G	134_V	0.650	0.60
164_P	183_Q	0.648	0.59
109_A	118_V	0.648	0.59
73_D	84_D	0.647	0.59
217_W	220_P	0.646	0.59
29_K	113_R	0.646	0.59
154_Y	158_T	0.645	0.59
85_V	141_Y	0.644	0.59
81_A	225_I	0.641	0.59
37_T	67_T	0.640	0.59
197_T	200_G	0.638	0.58
173_V	266_V	0.637	0.58
172_T	267_D	0.633	0.58
49_D	65_T	0.630	0.57
195_T	200_G	0.630	0.57
146_G	221_V	0.627	0.57
230_E	290_L	0.625	0.57
127_A	132_D	0.624	0.57
44_T	61_G	0.623	0.57
19_L	23_V	0.623	0.57
207_T	240_G	0.622	0.56
155_F	257_F	0.621	0.56
117_A	139_L	0.620	0.56
156_D	214_R	0.620	0.56
82_V	118_V	0.617	0.56
7_G	14_V	0.615	0.56
181_F	298_G	0.615	0.56
125_G	129_V	0.613	0.55
179_Y	220_P	0.613	0.55
44_T	63_P	0.612	0.55
125_G	130_G	0.608	0.55
9_G	298_G	0.608	0.55
93_D	100_L	0.607	0.55
124_C	132_D	0.607	0.55
36_S	104_T	0.606	0.54
128_P	133_A	0.606	0.54
161_K	188_T	0.605	0.54
104_T	157_P	0.603	0.54
267_D	270_K	0.603	0.54
10_A	14_V	0.602	0.54
296_V	299_L	0.601	0.54
156_D	185_V	0.600	0.54
9_G	13_L	0.599	0.54
20_R	107_R	0.598	0.53
27_L	145_F	0.597	0.53
11_F	40_L	0.595	0.53
35_D	71_K	0.594	0.53
23_V	30_L	0.592	0.53
2_G	6_L	0.592	0.53
128_P	131_A	0.592	0.53
36_S	102_S	0.589	0.52
123_C	131_A	0.589	0.52
150_K	166_R	0.589	0.52
6_L	34_L	0.588	0.52
275_K	279_L	0.587	0.52
31_P	152_Y	0.585	0.52
265_Q	268_L	0.584	0.52
136_R	140_V	0.581	0.51
237_R	243_G	0.580	0.51
21_F	276_L	0.580	0.51
39_V	46_T	0.577	0.51
83_W	141_Y	0.577	0.51
84_D	167_Y	0.576	0.51
10_A	54_A	0.576	0.51
140_V	155_F	0.575	0.51
240_G	244_G	0.575	0.51
16_A	82_V	0.575	0.51
197_T	205_T	0.573	0.50
139_L	153_P	0.571	0.50
225_I	257_F	0.571	0.50
41_E	63_P	0.571	0.50
155_F	268_L	0.570	0.50
250_L	262_V	0.567	0.50
116_E	138_G	0.567	0.50
131_A	134_V	0.565	0.49
15_L	74_A	0.564	0.49
265_Q	273_R	0.563	0.49
9_G	295_L	0.563	0.49
208_R	234_Q	0.560	0.49
67_T	75_A	0.560	0.49
8_L	61_G	0.558	0.49
25_P	284_P	0.558	0.49
16_A	284_P	0.556	0.48
198_V	235_T	0.555	0.48
218_V	227_K	0.555	0.48
52_T	239_P	0.554	0.48
244_G	276_L	0.552	0.48
29_K	78_S	0.550	0.48
81_A	85_V	0.549	0.47
145_F	256_T	0.548	0.47
5_L	10_A	0.548	0.47
62_V	115_G	0.548	0.47
204_V	208_R	0.547	0.47
80_V	213_T	0.547	0.47
285_I	297_A	0.546	0.47
222_T	269_A	0.546	0.47
4_V	260_A	0.546	0.47
286_V	290_L	0.546	0.47
112_R	156_D	0.543	0.47
8_L	15_L	0.542	0.47
67_T	88_T	0.539	0.46
201_S	296_V	0.539	0.46
30_L	33_D	0.536	0.46
61_G	295_L	0.536	0.46
181_F	261_T	0.535	0.46
41_E	76_S	0.534	0.46
197_T	202_L	0.534	0.46
5_L	290_L	0.534	0.46
5_L	169_G	0.534	0.46
293_V	296_V	0.532	0.45
195_T	201_S	0.531	0.45
35_D	86_G	0.531	0.45
155_F	209_Y	0.530	0.45
80_V	91_D	0.530	0.45
47_Y	255_L	0.528	0.45
156_D	230_E	0.528	0.45
187_P	190_V	0.528	0.45
86_G	91_D	0.528	0.45
143_F	154_Y	0.527	0.45
34_L	72_G	0.527	0.45
47_Y	81_A	0.525	0.45
221_V	277_R	0.524	0.44
60_T	219_E	0.524	0.44
189_K	195_T	0.524	0.44
222_T	283_L	0.523	0.44
274_D	281_T	0.523	0.44
237_R	244_G	0.520	0.44
168_V	215_T	0.518	0.44
4_V	126_G	0.518	0.44
169_G	219_E	0.517	0.44
20_R	24_V	0.515	0.43
52_T	84_D	0.514	0.43
199_P	202_L	0.514	0.43
68_R	212_N	0.513	0.43
276_L	284_P	0.513	0.43
47_Y	55_A	0.513	0.43
189_K	259_D	0.512	0.43
40_L	140_V	0.511	0.43
64_L	89_V	0.510	0.43
47_Y	101_L	0.510	0.43
84_D	149_K	0.509	0.43
61_G	161_K	0.509	0.43
85_V	106_D	0.508	0.43
50_P	56_G	0.508	0.43
238_D	243_G	0.508	0.43
198_V	236_L	0.507	0.42
66_A	206_L	0.506	0.42
198_V	201_S	0.505	0.42
196_L	203_V	0.504	0.42
22_Y	27_L	0.503	0.42
49_D	91_D	0.503	0.42
41_E	77_D	0.503	0.42
67_T	90_R	0.502	0.42
229_E	262_V	0.502	0.42
8_L	95_G	0.501	0.42
90_R	130_G	0.501	0.42
49_D	218_V	0.501	0.42
24_V	276_L	0.500	0.42
123_C	130_G	0.500	0.42

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
4q4fA	1	0.8233	63.7	0.94	Contact Map
2byoA	1	0.5833	17.4	0.956	Contact Map
3mh9C	1	0.6233	13	0.959	Contact Map
2mc7A	1	0.0867	8.3	0.962	Contact Map
1s7qA	1	0	7.9	0.963	Contact Map
2kluA	1	0.09	6.2	0.964	Contact Map
4qa8A	1	0.5767	5.3	0.966	Contact Map
4um9B	2	0	4.3	0.967	Contact Map
2qjyB	1	0.5767	4.2	0.967	Contact Map
2j5lA	1	0	3.9	0.968	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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