DUF239 - PFAM28P - GREMLIN Contacts

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DUF239 - Domain of unknown function (DUF239)

PFAM:	PF03080	Sequences: INVWNPKVESPDEFSLSQIWVVSGSGGGLNTIEAGWQVYPSLYGDNNPRLFIYWTDGYQKTGCYNLLCPGFVQTSNSIALGAAISPVSTYGGTQYEITILIWKDPKTGNWWLYYGEVGYWPASLFTGLLASGATLVQWGGEVVSSRGGHTSTQMGSGHFPSEGFGKAAYFRNIQYVDSSNKGVLPPPANLTTYADNPNCYDIIDGGYSGDWGTYFYYGGP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	220 (218)
Sequences:	1679 (1322)
Seq/√Len:	89.6
META:	0.379

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_C	68_C	4.608	1.00
160_P	201_D	4.232	1.00
45_D	49_R	4.071	1.00
90_Y	158_H	4.001	1.00
158_H	162_E	3.941	1.00
32_I	125_F	3.628	1.00
37_Q	43_Y	3.422	1.00
42_L	67_L	3.365	1.00
34_A	101_I	3.227	1.00
56_D	61_T	3.100	1.00
20_W	139_G	3.081	1.00
5_N	48_P	2.958	1.00
96_E	171_R	2.757	1.00
109_N	122_A	2.571	1.00
38_V	48_P	2.254	1.00
140_G	154_M	2.224	1.00
79_A	82_A	2.194	1.00
42_L	65_N	2.168	1.00
75_S	116_E	2.076	1.00
171_R	211_W	2.071	1.00
84_I	97_I	1.993	1.00
55_T	58_Y	1.850	1.00
48_P	87_V	1.836	1.00
5_N	47_N	1.835	1.00
77_S	116_E	1.793	1.00
3_V	84_I	1.785	1.00
90_Y	166_K	1.778	1.00
13_E	152_T	1.748	1.00
54_W	124_L	1.727	1.00
18_Q	33_E	1.662	1.00
50_L	99_I	1.636	1.00
54_W	70_G	1.575	1.00
16_L	141_E	1.574	1.00
73_Q	77_S	1.573	1.00
17_S	217_Y	1.562	1.00
128_L	131_S	1.547	1.00
91_G	166_K	1.546	1.00
18_Q	51_F	1.535	1.00
121_P	124_L	1.527	1.00
73_Q	119_Y	1.523	1.00
149_H	152_T	1.522	1.00
47_N	83_A	1.514	1.00
14_F	39_Y	1.496	1.00
13_E	144_S	1.495	1.00
202_I	215_F	1.477	1.00
22_V	31_T	1.464	0.99
161_S	201_D	1.457	0.99
52_I	80_L	1.449	0.99
78_I	117_V	1.447	0.99
17_S	170_F	1.442	0.99
90_Y	162_E	1.440	0.99
100_L	176_V	1.423	0.99
162_E	166_K	1.393	0.99
2_N	94_Q	1.388	0.99
37_Q	64_Y	1.386	0.99
142_V	154_M	1.380	0.99
13_E	149_H	1.354	0.99
159_F	201_D	1.351	0.99
56_D	60_K	1.311	0.99
17_S	36_W	1.287	0.99
18_Q	141_E	1.280	0.99
168_A	217_Y	1.266	0.98
16_L	33_E	1.265	0.98
50_L	84_I	1.259	0.98
142_V	152_T	1.259	0.98
163_G	216_Y	1.232	0.98
34_A	112_L	1.210	0.98
33_E	141_E	1.205	0.98
89_T	92_G	1.202	0.98
194_A	201_D	1.194	0.98
138_W	173_I	1.190	0.98
53_Y	61_T	1.186	0.98
112_L	120_W	1.177	0.98
36_W	48_P	1.172	0.98
51_F	141_E	1.170	0.97
72_V	121_P	1.164	0.97
211_W	214_Y	1.152	0.97
78_I	114_Y	1.147	0.97
104_D	107_T	1.147	0.97
97_I	114_Y	1.147	0.97
74_T	119_Y	1.139	0.97
8_V	15_S	1.131	0.97
88_S	94_Q	1.124	0.97
170_F	215_F	1.119	0.97
163_G	167_A	1.109	0.97
1_I	17_S	1.105	0.96
156_S	167_A	1.104	0.96
49_R	80_L	1.100	0.96
4_W	156_S	1.097	0.96
94_Q	164_F	1.093	0.96
58_Y	61_T	1.093	0.96
52_I	66_L	1.090	0.96
78_I	82_A	1.080	0.96
144_S	150_T	1.077	0.96
101_I	112_L	1.063	0.96
3_V	38_V	1.053	0.95
105_P	122_A	1.052	0.95
86_P	95_Y	1.051	0.95
144_S	149_H	1.030	0.95
140_G	217_Y	1.029	0.95
156_S	169_Y	1.024	0.95
53_Y	64_Y	1.022	0.94
144_S	147_G	1.015	0.94
54_W	62_G	1.013	0.94
74_T	111_W	1.011	0.94
18_Q	31_T	1.009	0.94
96_E	169_Y	1.005	0.94
13_E	143_V	1.003	0.94
99_I	114_Y	0.987	0.93
43_Y	65_N	0.981	0.93
56_D	63_C	0.979	0.93
156_S	216_Y	0.977	0.93
18_Q	58_Y	0.974	0.93
17_S	139_G	0.968	0.93
21_V	133_A	0.967	0.93
194_A	197_P	0.966	0.93
22_V	137_Q	0.960	0.92
20_W	31_T	0.955	0.92
7_K	153_Q	0.951	0.92
75_S	78_I	0.945	0.92
8_V	40_P	0.939	0.92
16_L	31_T	0.937	0.91
103_K	108_G	0.931	0.91
160_P	194_A	0.926	0.91
13_E	142_V	0.925	0.91
54_W	120_W	0.922	0.91
206_G	213_T	0.921	0.91
55_T	61_T	0.914	0.90
57_G	60_K	0.911	0.90
4_W	88_S	0.906	0.90
144_S	152_T	0.901	0.90
159_F	220_P	0.892	0.89
26_G	57_G	0.884	0.89
66_L	71_F	0.881	0.89
17_S	168_A	0.880	0.89
134_T	178_S	0.877	0.89
14_F	37_Q	0.877	0.89
101_I	120_W	0.874	0.88
92_G	133_A	0.871	0.88
23_S	128_L	0.870	0.88
208_S	214_Y	0.864	0.88
68_C	199_C	0.863	0.88
170_F	217_Y	0.860	0.88
39_Y	42_L	0.858	0.87
109_N	119_Y	0.850	0.87
170_F	173_I	0.849	0.87
1_I	11_P	0.847	0.87
215_F	219_G	0.840	0.86
34_A	50_L	0.834	0.86
9_E	12_D	0.830	0.86
43_Y	49_R	0.830	0.86
111_W	119_Y	0.827	0.85
136_V	175_Y	0.818	0.85
55_T	62_G	0.814	0.85
20_W	33_E	0.814	0.85
40_P	43_Y	0.811	0.84
194_A	202_I	0.808	0.84
158_H	166_K	0.806	0.84
34_A	99_I	0.796	0.83
30_N	126_T	0.794	0.83
177_D	180_N	0.785	0.82
94_Q	169_Y	0.785	0.82
150_T	153_Q	0.777	0.82
54_W	69_P	0.775	0.82
196_N	199_C	0.770	0.81
14_F	18_Q	0.769	0.81
188_A	193_Y	0.768	0.81
71_F	80_L	0.763	0.81
71_F	199_C	0.759	0.80
88_S	156_S	0.753	0.80
2_N	165_G	0.749	0.79
75_S	119_Y	0.749	0.79
63_C	177_D	0.746	0.79
25_S	28_G	0.743	0.79
73_Q	76_N	0.741	0.79
51_F	64_Y	0.741	0.79
11_P	46_N	0.736	0.78
27_G	59_Q	0.735	0.78
53_Y	62_G	0.733	0.78
43_Y	67_L	0.732	0.78
40_P	46_N	0.725	0.77
21_V	34_A	0.723	0.77
57_G	61_T	0.717	0.76
101_I	122_A	0.716	0.76
43_Y	64_Y	0.715	0.76
19_I	34_A	0.714	0.76
133_A	136_V	0.712	0.76
1_I	170_F	0.712	0.76
31_T	37_Q	0.709	0.75
186_P	191_T	0.706	0.75
6_P	15_S	0.705	0.75
14_F	141_E	0.699	0.74
63_C	139_G	0.698	0.74
18_Q	55_T	0.697	0.74
95_Y	99_I	0.697	0.74
32_I	126_T	0.696	0.74
43_Y	47_N	0.695	0.74
33_E	36_W	0.692	0.74
66_L	74_T	0.690	0.73
128_L	132_G	0.689	0.73
53_Y	141_E	0.687	0.73
100_L	113_Y	0.687	0.73
30_N	125_F	0.686	0.73
88_S	92_G	0.685	0.73
71_F	117_V	0.683	0.73
33_E	48_P	0.682	0.73
55_T	139_G	0.678	0.72
207_Y	210_D	0.676	0.72
16_L	37_Q	0.670	0.71
203_I	215_F	0.669	0.71
151_S	199_C	0.667	0.71
22_V	26_G	0.663	0.71
22_V	135_L	0.660	0.70
21_V	32_I	0.655	0.70
18_Q	53_Y	0.653	0.69
167_A	216_Y	0.651	0.69
23_S	126_T	0.648	0.69
53_Y	56_D	0.647	0.69
56_D	59_Q	0.637	0.67
97_I	101_I	0.635	0.67
125_F	139_G	0.635	0.67
50_L	112_L	0.632	0.67
96_E	172_N	0.632	0.67
54_W	61_T	0.632	0.67
9_E	13_E	0.630	0.67
164_F	169_Y	0.629	0.66
70_G	121_P	0.627	0.66
40_P	133_A	0.625	0.66
165_G	216_Y	0.625	0.66
160_P	167_A	0.624	0.66
136_V	177_D	0.622	0.66
89_T	93_T	0.622	0.66
209_G	214_Y	0.622	0.66
9_E	148_G	0.618	0.65
13_E	150_T	0.616	0.65
159_F	197_P	0.612	0.64
84_I	87_V	0.612	0.64
41_S	46_N	0.611	0.64
16_L	64_Y	0.611	0.64
78_I	100_L	0.611	0.64
73_Q	111_W	0.610	0.64
21_V	30_N	0.608	0.64
156_S	164_F	0.606	0.64
183_V	186_P	0.604	0.63
75_S	80_L	0.601	0.63
20_W	58_Y	0.597	0.62
32_I	129_L	0.596	0.62
89_T	116_E	0.594	0.62
31_T	58_Y	0.593	0.62
2_N	90_Y	0.592	0.62
22_V	136_V	0.591	0.62
51_F	138_W	0.591	0.62
83_A	202_I	0.590	0.62
102_W	105_P	0.589	0.61
19_I	138_W	0.584	0.61
71_F	74_T	0.584	0.61
6_P	141_E	0.584	0.61
6_P	153_Q	0.582	0.61
51_F	111_W	0.580	0.60
165_G	202_I	0.579	0.60
42_L	64_Y	0.575	0.60
19_I	101_I	0.572	0.59
3_V	97_I	0.570	0.59
1_I	19_I	0.568	0.59
40_P	50_L	0.568	0.59
62_G	70_G	0.568	0.59
16_L	39_Y	0.566	0.58
24_G	128_L	0.565	0.58
142_V	195_D	0.565	0.58
97_I	100_L	0.565	0.58
80_L	196_N	0.564	0.58
84_I	171_R	0.560	0.58
30_N	170_F	0.557	0.57
68_C	139_G	0.557	0.57
31_T	39_Y	0.556	0.57
55_T	156_S	0.555	0.57
204_D	213_T	0.553	0.57
160_P	170_F	0.553	0.57
32_I	54_W	0.552	0.57
205_G	209_G	0.552	0.57
39_Y	43_Y	0.550	0.56
54_W	63_C	0.549	0.56
60_K	198_N	0.547	0.56
160_P	164_F	0.547	0.56
127_G	131_S	0.547	0.56
81_G	216_Y	0.545	0.56
96_E	216_Y	0.545	0.56
174_Q	212_G	0.545	0.56
3_V	36_W	0.542	0.55
33_E	51_F	0.541	0.55
5_N	46_N	0.540	0.55
53_Y	65_N	0.540	0.55
156_S	160_P	0.537	0.54
8_V	38_V	0.537	0.54
207_Y	213_T	0.537	0.54
160_P	169_Y	0.535	0.54
174_Q	186_P	0.535	0.54
32_I	40_P	0.535	0.54
84_I	114_Y	0.533	0.54
41_S	176_V	0.531	0.54
70_G	126_T	0.530	0.54
196_N	212_G	0.529	0.53
198_N	203_I	0.527	0.53
31_T	137_Q	0.526	0.53
88_S	165_G	0.523	0.53
97_I	174_Q	0.523	0.53
173_I	215_F	0.522	0.52
78_I	129_L	0.522	0.52
82_A	159_F	0.521	0.52
211_W	216_Y	0.521	0.52
118_G	121_P	0.520	0.52
87_V	90_Y	0.518	0.52
104_D	109_N	0.518	0.52
102_W	113_Y	0.518	0.52
28_G	57_G	0.517	0.52
89_T	117_V	0.516	0.52
142_V	151_S	0.513	0.51
209_G	213_T	0.513	0.51
75_S	82_A	0.513	0.51
23_S	167_A	0.513	0.51
6_P	33_E	0.512	0.51
185_P	190_L	0.511	0.51
122_A	131_S	0.510	0.51
11_P	15_S	0.504	0.50
14_F	22_V	0.501	0.50
70_G	124_L	0.500	0.49
4_W	163_G	0.500	0.49

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
2jt4A	1	0.3045	3.1	0.968	Contact Map
1nm7A	1	0.2455	2.6	0.969	Contact Map
2ct4A	1	0.3045	2.3	0.97	Contact Map
2lx7A	1	0.2591	2.3	0.97	Contact Map
1x6gA	1	0.2773	2.2	0.97	Contact Map
2v1qA	1	0.2545	2.2	0.97	Contact Map
2bt9A	3	0.4045	2.1	0.971	Contact Map
2cudA	1	0.3409	1.9	0.971	Contact Map
2iimA	2	0.2636	1.8	0.972	Contact Map
2a28A	1	0.2364	1.7	0.972	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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