DUF3087 - PFAM28P - GREMLIN Contacts

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DUF3087 - Protein of unknown function (DUF3087)

PFAM:	PF11286	Sequences: MQLQPIDKERYRKHLRRVTLIIAAILAVLSLLLSTLLIALFGEPGGSNFRLNLLGVILGLLLTAALLRKLKTHPWMAEVVYVWQLKQSLNRITRKMHKVKAAVEAGDPDAMKILRFYYLGLRQLYQLDDNTLTLSELVREIDELDERMEALGLDLDQDRFDPAWL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	165 (165)
Sequences:	560 (360)
Seq/√Len:	28.0
META:	0.532

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
49_F	53_L	3.879	1.00
10_R	14_H	3.478	1.00
106_G	151_L	3.195	1.00
89_L	120_G	3.112	1.00
111_M	148_M	3.082	1.00
88_S	160_F	3.003	1.00
18_V	79_V	2.884	1.00
12_R	16_R	2.644	0.99
100_K	140_E	2.374	0.99
117_Y	121_L	2.350	0.99
29_L	59_G	2.344	0.99
93_T	96_M	2.225	0.98
26_L	30_S	2.162	0.98
16_R	19_T	2.146	0.98
80_V	84_Q	2.136	0.98
42_G	48_N	1.918	0.95
17_R	75_W	1.889	0.95
91_R	165_L	1.822	0.94
103_V	111_M	1.809	0.94
141_I	145_D	1.787	0.93
117_Y	160_F	1.739	0.92
12_R	15_L	1.734	0.92
147_R	153_L	1.728	0.92
147_R	151_L	1.683	0.91
121_L	137_L	1.659	0.90
122_R	141_I	1.637	0.90
137_L	144_L	1.608	0.89
106_G	150_A	1.593	0.88
89_L	124_L	1.582	0.88
73_H	76_M	1.578	0.88
31_L	35_T	1.577	0.88
12_R	19_T	1.533	0.86
106_G	147_R	1.530	0.86
1_M	8_K	1.476	0.84
93_T	125_Y	1.466	0.84
111_M	144_L	1.463	0.84
124_L	132_L	1.435	0.82
35_T	42_G	1.422	0.82
24_A	61_L	1.412	0.81
53_L	57_I	1.394	0.80
143_E	161_D	1.375	0.80
90_N	94_R	1.366	0.79
4_Q	36_L	1.355	0.79
93_T	133_T	1.339	0.78
92_I	116_F	1.334	0.77
6_I	78_E	1.329	0.77
142_D	146_E	1.313	0.76
49_F	57_I	1.312	0.76
25_I	59_G	1.292	0.75
146_E	150_A	1.235	0.72
29_L	33_L	1.229	0.71
157_Q	164_W	1.224	0.71
24_A	28_V	1.200	0.69
148_M	153_L	1.199	0.69
42_G	51_L	1.195	0.69
101_A	149_E	1.166	0.67
96_M	99_V	1.159	0.67
99_V	114_L	1.153	0.66
103_V	114_L	1.140	0.65
37_L	51_L	1.138	0.65
66_L	70_L	1.134	0.65
138_V	142_D	1.133	0.65
89_L	121_L	1.115	0.64
50_R	54_L	1.113	0.63
96_M	114_L	1.105	0.63
70_L	76_M	1.099	0.62
53_L	100_K	1.098	0.62
34_S	89_L	1.076	0.61
107_D	159_R	1.073	0.61
54_L	59_G	1.055	0.59
97_H	101_A	1.025	0.57
140_E	143_E	1.017	0.56
159_R	164_W	1.017	0.56
135_S	142_D	1.015	0.56
61_L	65_A	1.015	0.56
26_L	31_L	1.015	0.56
61_L	75_W	1.014	0.56
121_L	124_L	1.005	0.56
35_T	48_N	1.004	0.55
85_L	120_G	1.002	0.55
63_T	121_L	1.002	0.55
154_D	157_Q	0.992	0.55
96_M	113_I	0.991	0.54
4_Q	77_A	0.980	0.54
131_T	134_L	0.974	0.53
99_V	113_I	0.974	0.53
15_L	90_N	0.959	0.52
84_Q	87_Q	0.955	0.52
133_T	153_L	0.953	0.52
38_I	49_F	0.945	0.51
34_S	37_L	0.941	0.51
43_E	47_S	0.939	0.50
19_T	23_A	0.936	0.50
25_I	116_F	0.932	0.50
97_H	102_A	0.926	0.49
91_R	162_P	0.925	0.49
120_G	124_L	0.922	0.49
108_P	146_E	0.922	0.49
16_R	116_F	0.917	0.49
76_M	115_R	0.907	0.48
152_G	161_D	0.899	0.47
136_E	140_E	0.898	0.47
148_M	155_L	0.895	0.47
115_R	157_Q	0.894	0.47
2_Q	28_V	0.893	0.47
109_D	165_L	0.892	0.47
106_G	153_L	0.889	0.47
145_D	155_L	0.882	0.46
8_K	129_D	0.882	0.46
9_E	13_K	0.873	0.45
13_K	28_V	0.869	0.45
125_Y	133_T	0.869	0.45
87_Q	91_R	0.867	0.45
28_V	57_I	0.866	0.45
63_T	120_G	0.865	0.45
131_T	144_L	0.859	0.44
108_P	143_E	0.859	0.44
26_L	40_L	0.858	0.44
20_L	133_T	0.856	0.44
36_L	96_M	0.854	0.44
99_V	145_D	0.854	0.44
121_L	160_F	0.845	0.43
104_E	147_R	0.843	0.43
60_L	73_H	0.843	0.43
51_L	59_G	0.842	0.43
52_N	56_V	0.839	0.43
76_M	141_I	0.838	0.43
146_E	149_E	0.838	0.43
36_L	100_K	0.837	0.43
71_K	87_Q	0.835	0.43
18_V	21_I	0.834	0.42
122_R	138_V	0.834	0.42
49_F	56_V	0.833	0.42
75_W	84_Q	0.828	0.42
100_K	147_R	0.819	0.41
29_L	114_L	0.819	0.41
137_L	141_I	0.814	0.41
4_Q	54_L	0.808	0.41
12_R	96_M	0.804	0.40
19_T	60_L	0.801	0.40
37_L	100_K	0.793	0.39
51_L	122_R	0.790	0.39
53_L	75_W	0.783	0.39
28_V	149_E	0.778	0.38
87_Q	94_R	0.758	0.37
41_F	65_A	0.757	0.37
11_Y	92_I	0.756	0.37
76_M	124_L	0.754	0.37
135_S	139_R	0.742	0.36
88_S	132_L	0.739	0.36
132_L	137_L	0.737	0.35
89_L	137_L	0.726	0.35
109_D	154_D	0.725	0.35
1_M	90_N	0.724	0.34
78_E	113_I	0.724	0.34
62_L	155_L	0.721	0.34
40_L	64_A	0.720	0.34
48_N	56_V	0.716	0.34
83_W	87_Q	0.716	0.34
22_I	48_N	0.714	0.34
33_L	58_L	0.710	0.34
11_Y	82_V	0.710	0.34
37_L	58_L	0.706	0.33
41_F	109_D	0.705	0.33
113_I	160_F	0.702	0.33
121_L	125_Y	0.700	0.33
142_D	145_D	0.700	0.33
132_L	136_E	0.699	0.33
126_Q	134_L	0.697	0.33
67_L	80_V	0.697	0.33
36_L	39_A	0.694	0.32
13_K	30_S	0.682	0.32
103_V	144_L	0.676	0.31
31_L	91_R	0.667	0.31
46_G	58_L	0.666	0.31
135_S	138_V	0.659	0.30
114_L	117_Y	0.650	0.30
57_I	160_F	0.647	0.29
100_K	109_D	0.645	0.29
75_W	112_K	0.643	0.29
29_L	42_G	0.642	0.29
2_Q	153_L	0.641	0.29
72_T	134_L	0.640	0.29
2_Q	159_R	0.639	0.29
3_L	78_E	0.637	0.29
23_A	128_D	0.634	0.29
71_K	80_V	0.633	0.28
36_L	163_A	0.632	0.28
21_I	87_Q	0.624	0.28
6_I	129_D	0.624	0.28
23_A	30_S	0.623	0.28
16_R	34_S	0.622	0.28
103_V	147_R	0.621	0.28
129_D	132_L	0.620	0.28
35_T	39_A	0.614	0.27
94_R	133_T	0.613	0.27
87_Q	124_L	0.611	0.27
10_R	158_D	0.603	0.27
103_V	115_R	0.600	0.26
112_K	164_W	0.600	0.26
32_L	35_T	0.597	0.26
19_T	67_L	0.596	0.26
142_D	149_E	0.594	0.26
112_K	125_Y	0.594	0.26
74_P	78_E	0.591	0.26
3_L	148_M	0.591	0.26
114_L	143_E	0.589	0.26
19_T	22_I	0.588	0.26
139_R	155_L	0.581	0.25
6_I	71_K	0.579	0.25
68_R	162_P	0.578	0.25
27_A	32_L	0.575	0.25
74_P	80_V	0.569	0.25
65_A	69_K	0.567	0.25
26_L	71_K	0.561	0.24
13_K	17_R	0.560	0.24
95_K	111_M	0.559	0.24
96_M	115_R	0.555	0.24
108_P	153_L	0.553	0.24
14_H	78_E	0.552	0.24
34_S	120_G	0.550	0.24
28_V	36_L	0.546	0.23
120_G	152_G	0.544	0.23
16_R	22_I	0.542	0.23
84_Q	111_M	0.542	0.23
37_L	49_F	0.537	0.23
97_H	116_F	0.537	0.23
82_V	94_R	0.535	0.23
125_Y	129_D	0.534	0.23
26_L	38_I	0.532	0.23
95_K	99_V	0.530	0.22
6_I	121_L	0.529	0.22
1_M	6_I	0.528	0.22
22_I	42_G	0.525	0.22
1_M	82_V	0.523	0.22
76_M	85_L	0.522	0.22
154_D	158_D	0.520	0.22
64_A	72_T	0.520	0.22
27_A	85_L	0.518	0.22
84_Q	124_L	0.517	0.22
114_L	140_E	0.517	0.22
15_L	19_T	0.515	0.22
119_L	164_W	0.511	0.21
63_T	100_K	0.505	0.21
99_V	157_Q	0.502	0.21
69_K	108_P	0.501	0.21
57_I	61_L	0.500	0.21
139_R	142_D	0.500	0.21

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
4qq0A	1	0.5152	60.9	0.94	Contact Map
2m8rA	1	0.2545	32.8	0.95	Contact Map
4n9nA	2	0.6364	25.5	0.952	Contact Map
4djkA	2	0.497	25	0.952	Contact Map
3ixzA	1	0.4788	18	0.956	Contact Map
2c9kA	1	0.7818	17.8	0.956	Contact Map
4xmmE	1	0.5394	16	0.957	Contact Map
1ji6A	1	0.7636	15.1	0.957	Contact Map
3pjsK	4	0.6545	14.5	0.957	Contact Map
2zxeA	1	0.4788	13.3	0.958	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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