DUF3710 - PFAM28P - GREMLIN Contacts

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DUF3710 - Protein of unknown function (DUF3710)

PFAM:	PF12502	Sequences: GPWDVSEVPDDDGRLDLGSLLVPVPEGMELRLEVDEATGQVVAVTLVLGDSALQLQAFAAPRSGGLWDEVRAEIAASLRKQGGTAEEVEGPFGTELRARVPVATPDGRTTQPARFIGVDGPRWFLRGVISGPAAVDPEAAAPLEEVFRDVVVVRGDEPMPPRDLLPLRLPEEAAEQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	176 (174)
Sequences:	2143 (1341)
Seq/√Len:	101.7
META:	0.709

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
55_L	150_V	4.833	1.00
127_G	147_F	4.327	1.00
116_I	129_I	3.956	1.00
53_L	127_G	3.276	1.00
35_D	38_T	3.107	1.00
51_S	133_A	2.845	1.00
78_L	83_G	2.786	1.00
129_I	143_L	2.629	1.00
118_V	147_F	2.589	1.00
19_S	165_L	2.584	1.00
75_A	96_L	2.520	1.00
53_L	147_F	2.478	1.00
58_F	126_R	2.456	1.00
71_R	87_E	2.262	1.00
65_G	119_D	2.232	1.00
19_S	57_A	2.232	1.00
155_G	159_M	2.159	1.00
89_E	94_T	2.073	1.00
21_L	153_V	2.022	1.00
5_V	153_V	1.975	1.00
46_L	146_V	1.913	1.00
118_V	127_G	1.897	1.00
88_V	97_R	1.856	1.00
17_L	44_V	1.838	1.00
35_D	40_Q	1.830	1.00
115_F	128_V	1.816	1.00
95_E	114_R	1.801	1.00
50_D	132_P	1.718	1.00
76_A	80_K	1.714	1.00
132_P	136_D	1.655	1.00
57_A	165_L	1.652	1.00
67_W	117_G	1.599	1.00
91_P	148_R	1.582	1.00
125_L	150_V	1.559	1.00
8_V	21_L	1.507	1.00
72_A	87_E	1.491	1.00
73_E	162_R	1.487	1.00
56_Q	128_V	1.471	1.00
90_G	95_E	1.464	1.00
92_F	144_E	1.442	1.00
86_E	97_R	1.434	1.00
33_E	43_A	1.419	1.00
125_L	147_F	1.390	1.00
104_T	108_R	1.351	0.99
3_W	9_P	1.334	0.99
3_W	149_D	1.330	0.99
33_E	45_T	1.329	0.99
68_D	94_T	1.312	0.99
25_P	149_D	1.309	0.99
84_T	99_R	1.306	0.99
25_P	28_M	1.287	0.99
53_L	129_I	1.275	0.99
159_M	165_L	1.266	0.99
54_Q	115_F	1.264	0.99
98_A	113_A	1.248	0.99
75_A	79_R	1.244	0.99
78_L	98_A	1.242	0.99
79_R	84_T	1.200	0.99
103_A	108_R	1.181	0.98
81_Q	124_F	1.169	0.98
79_R	85_A	1.169	0.98
33_E	54_Q	1.156	0.98
99_R	110_T	1.140	0.98
137_P	144_E	1.136	0.98
11_D	21_L	1.124	0.98
52_A	130_S	1.120	0.98
65_G	68_D	1.116	0.98
1_G	4_D	1.113	0.98
61_P	65_G	1.104	0.98
118_V	148_R	1.099	0.98
140_A	144_E	1.098	0.98
91_P	144_E	1.092	0.97
62_R	122_R	1.089	0.97
29_E	47_V	1.073	0.97
168_R	171_E	1.068	0.97
64_G	119_D	1.054	0.97
17_L	32_L	1.044	0.97
47_V	52_A	1.039	0.97
9_P	12_D	1.034	0.96
98_A	115_F	1.031	0.96
141_A	145_E	1.027	0.96
20_L	55_L	1.020	0.96
68_D	71_R	1.008	0.96
103_A	109_T	1.003	0.96
6_S	11_D	0.997	0.96
4_D	121_P	0.996	0.96
87_E	94_T	0.995	0.96
161_P	164_L	0.993	0.95
125_L	152_V	0.980	0.95
14_R	21_L	0.975	0.95
41_V	81_Q	0.968	0.95
137_P	141_A	0.965	0.95
28_M	46_L	0.949	0.94
144_E	148_R	0.949	0.94
76_A	79_R	0.944	0.94
70_V	162_R	0.943	0.94
54_Q	98_A	0.936	0.94
48_L	142_P	0.933	0.94
54_Q	113_A	0.924	0.93
11_D	14_R	0.923	0.93
33_E	52_A	0.901	0.93
87_E	96_L	0.891	0.92
8_V	11_D	0.886	0.92
159_M	166_P	0.886	0.92
160_P	165_L	0.878	0.92
121_P	148_R	0.878	0.92
72_A	76_A	0.872	0.91
102_V	111_Q	0.872	0.91
68_D	87_E	0.871	0.91
116_I	147_F	0.868	0.91
5_V	21_L	0.868	0.91
77_S	81_Q	0.857	0.91
132_P	135_V	0.855	0.90
5_V	8_V	0.846	0.90
10_D	14_R	0.845	0.90
75_A	87_E	0.843	0.90
20_L	152_V	0.840	0.90
115_F	126_R	0.840	0.90
124_F	128_V	0.839	0.90
92_F	118_V	0.837	0.89
22_V	150_V	0.834	0.89
129_I	140_A	0.824	0.89
78_L	115_F	0.821	0.89
129_I	147_F	0.813	0.88
45_T	55_L	0.808	0.88
88_V	137_P	0.796	0.87
145_E	149_D	0.793	0.87
130_S	158_P	0.789	0.87
8_V	12_D	0.782	0.86
61_P	66_L	0.780	0.86
14_R	151_V	0.778	0.86
14_R	23_P	0.773	0.85
28_M	33_E	0.772	0.85
76_A	84_T	0.760	0.84
13_G	24_V	0.760	0.84
78_L	99_R	0.756	0.84
61_P	122_R	0.754	0.84
9_P	21_L	0.746	0.83
71_R	94_T	0.744	0.83
56_Q	78_L	0.735	0.82
69_E	72_A	0.734	0.82
22_V	40_Q	0.734	0.82
103_A	106_D	0.728	0.82
55_L	125_L	0.726	0.82
59_A	122_R	0.725	0.82
129_I	144_E	0.719	0.81
138_E	141_A	0.708	0.80
113_A	130_S	0.707	0.80
32_L	36_E	0.705	0.80
106_D	109_T	0.704	0.80
63_S	122_R	0.704	0.80
19_S	159_M	0.699	0.79
102_V	105_P	0.696	0.79
86_E	110_T	0.696	0.79
8_V	23_P	0.695	0.79
30_L	44_V	0.695	0.79
43_A	54_Q	0.686	0.78
6_S	9_P	0.683	0.78
68_D	72_A	0.679	0.77
100_V	135_V	0.678	0.77
148_R	167_L	0.669	0.76
148_R	156_D	0.668	0.76
25_P	142_P	0.666	0.76
31_R	74_I	0.665	0.76
119_D	124_F	0.662	0.75
28_M	48_L	0.661	0.75
36_E	39_G	0.661	0.75
97_R	112_P	0.661	0.75
75_A	85_A	0.658	0.75
77_S	80_K	0.657	0.75
66_L	124_F	0.657	0.75
136_D	139_A	0.655	0.75
116_I	127_G	0.650	0.74
3_W	8_V	0.648	0.74
14_R	61_P	0.646	0.74
66_L	119_D	0.645	0.73
45_T	54_Q	0.645	0.73
154_R	158_P	0.644	0.73
21_L	24_V	0.641	0.73
86_E	99_R	0.639	0.73
61_P	118_V	0.638	0.73
130_S	162_R	0.633	0.72
70_V	73_E	0.632	0.72
68_D	151_V	0.631	0.72
22_V	47_V	0.630	0.72
33_E	42_V	0.630	0.72
45_T	52_A	0.623	0.71
39_G	111_Q	0.622	0.71
104_T	107_G	0.612	0.69
139_A	142_P	0.606	0.69
167_L	171_E	0.605	0.69
80_K	135_V	0.603	0.68
59_A	62_R	0.602	0.68
29_E	34_V	0.602	0.68
45_T	130_S	0.599	0.68
58_F	129_I	0.598	0.68
143_L	169_L	0.597	0.68
29_E	169_L	0.597	0.68
70_V	128_V	0.596	0.67
90_G	118_V	0.595	0.67
157_E	160_P	0.592	0.67
59_A	154_R	0.584	0.66
71_R	75_A	0.581	0.66
30_L	33_E	0.579	0.65
157_E	174_A	0.578	0.65
34_V	41_V	0.578	0.65
5_V	9_P	0.576	0.65
122_R	154_R	0.575	0.65
48_L	51_S	0.574	0.65
117_G	124_F	0.571	0.64
54_Q	134_A	0.570	0.64
40_Q	47_V	0.565	0.63
32_L	64_G	0.565	0.63
35_D	56_Q	0.564	0.63
79_R	137_P	0.560	0.63
59_A	118_V	0.557	0.62
53_L	69_E	0.555	0.62
83_G	96_L	0.554	0.62
70_V	124_F	0.550	0.61
23_P	149_D	0.549	0.61
52_A	111_Q	0.547	0.61
105_P	109_T	0.547	0.61
115_F	124_F	0.546	0.61
132_P	165_L	0.546	0.61
16_D	153_V	0.544	0.60
31_R	47_V	0.544	0.60
78_L	100_V	0.544	0.60
29_E	50_D	0.543	0.60
85_A	94_T	0.543	0.60
44_V	57_A	0.537	0.59
83_G	101_P	0.536	0.59
169_L	172_E	0.536	0.59
41_V	70_V	0.535	0.59
88_V	94_T	0.535	0.59
115_F	119_D	0.530	0.58
27_G	112_P	0.528	0.58
54_Q	128_V	0.528	0.58
8_V	151_V	0.528	0.58
78_L	128_V	0.527	0.58
13_G	91_P	0.527	0.58
25_P	45_T	0.521	0.57
92_F	95_E	0.518	0.57
43_A	158_P	0.517	0.57
160_P	163_D	0.517	0.57
128_V	158_P	0.517	0.57
103_A	158_P	0.516	0.56
158_P	164_L	0.515	0.56
63_S	101_P	0.512	0.56
124_F	130_S	0.512	0.56
12_D	145_E	0.510	0.56
26_E	172_E	0.507	0.55
132_P	139_A	0.507	0.55
43_A	57_A	0.504	0.55
28_M	150_V	0.502	0.54
77_S	128_V	0.502	0.54
114_R	140_A	0.502	0.54
6_S	10_D	0.502	0.54
22_V	46_L	0.501	0.54
150_V	163_D	0.501	0.54
119_D	162_R	0.500	0.54
99_R	112_P	0.500	0.54

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
1jrmA	1	0.5852	6.7	0.959	Contact Map
3fcgA	2	0.2159	5.2	0.961	Contact Map
3lydA	2	0.7784	4.6	0.962	Contact Map
4aneA	4	0.2614	3.5	0.964	Contact Map
2j0pA	1	0.392	3.2	0.965	Contact Map
4mf9A	1	0.392	3.1	0.965	Contact Map
1novD	1	0.1136	2.9	0.966	Contact Map
1f8vD	3	0.1648	2.8	0.966	Contact Map
4ftbD	1	0.1193	2.8	0.966	Contact Map
4cdpA	1	0.3864	2.7	0.966	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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