DUF4203 - PFAM28P - GREMLIN Contacts

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DUF4203 - Domain of unknown function (DUF4203)

PFAM:	PF13886	Sequences: VLAILLILGGLLLCFFGYRLFRIVLFIYGFILGALLGASLIGALFGDPGFLSTTAMLVAALVGGLVGALLLYLFYFVGVALLGAGLGALLGLLLLAALPGGLITGDPPRWLFGVVIALAVAGAVLALFLQRYVIIVATAFGGAWTIVLGILALAGGGPKEFLLNLLPRAANVWVLYPLTPASWVYLAAWLVLALLGIVVQF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	201 (194)
Sequences:	2704 (2191)
Seq/√Len:	157.3
META:	0.756

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
140_F	193_A	5.649	1.00
80_A	123_A	3.188	1.00
11_L	146_I	3.056	1.00
33_G	67_G	2.877	1.00
30_F	64_G	2.832	1.00
124_V	128_F	2.704	1.00
84_A	119_A	2.653	1.00
150_I	154_A	2.632	1.00
7_I	149_G	2.624	1.00
18_Y	131_R	2.517	1.00
54_T	58_V	2.466	1.00
135_I	197_I	2.423	1.00
14_C	196_G	2.397	1.00
15_F	199_V	2.314	1.00
105_G	108_P	2.262	1.00
173_W	176_Y	2.056	1.00
139_A	197_I	2.041	1.00
182_S	185_Y	2.016	1.00
26_F	68_A	1.989	1.00
136_V	197_I	1.940	1.00
3_A	149_G	1.931	1.00
26_F	72_Y	1.888	1.00
62_V	66_V	1.799	1.00
76_F	130_Q	1.791	1.00
194_L	198_V	1.790	1.00
113_G	117_A	1.773	1.00
37_G	41_I	1.773	1.00
14_C	192_L	1.771	1.00
86_L	137_A	1.747	1.00
122_G	126_A	1.745	1.00
125_L	128_F	1.739	1.00
146_I	192_L	1.735	1.00
34_A	60_A	1.700	1.00
189_W	193_A	1.699	1.00
183_W	187_A	1.678	1.00
91_G	95_L	1.623	1.00
184_V	188_A	1.576	1.00
85_G	88_A	1.496	1.00
173_W	177_P	1.494	1.00
29_G	33_G	1.494	1.00
59_A	63_G	1.493	1.00
30_F	68_A	1.472	1.00
15_F	196_G	1.466	1.00
95_L	98_L	1.444	1.00
33_G	37_G	1.425	1.00
7_I	146_I	1.405	1.00
38_A	56_M	1.387	1.00
168_R	171_N	1.381	1.00
116_I	120_V	1.358	1.00
58_V	62_V	1.333	1.00
38_A	42_G	1.328	1.00
184_V	187_A	1.320	1.00
29_G	71_L	1.317	1.00
29_G	67_G	1.314	1.00
179_T	182_S	1.306	1.00
151_L	157_G	1.306	1.00
139_A	193_A	1.302	1.00
107_P	111_L	1.300	1.00
144_W	189_W	1.298	1.00
94_L	97_A	1.297	1.00
144_W	148_L	1.251	1.00
120_V	123_A	1.244	1.00
190_L	194_L	1.218	1.00
83_G	122_G	1.216	1.00
193_A	197_I	1.214	1.00
113_G	128_F	1.211	1.00
21_F	25_L	1.209	1.00
10_G	149_G	1.197	1.00
165_L	168_R	1.195	1.00
178_L	181_A	1.182	1.00
75_Y	130_Q	1.177	1.00
83_G	124_V	1.173	1.00
172_V	175_L	1.168	1.00
176_Y	180_P	1.167	1.00
174_V	179_T	1.132	1.00
172_V	176_Y	1.128	1.00
55_A	58_V	1.124	1.00
147_V	189_W	1.124	1.00
63_G	67_G	1.121	1.00
147_V	188_A	1.121	1.00
108_P	112_F	1.121	1.00
151_L	185_Y	1.120	1.00
41_I	59_A	1.108	1.00
167_P	170_A	1.092	0.99
177_P	181_A	1.092	0.99
55_A	59_A	1.091	0.99
119_A	123_A	1.087	0.99
87_G	95_L	1.086	0.99
13_L	24_V	1.057	0.99
196_G	200_Q	1.040	0.99
118_L	122_G	1.036	0.99
173_W	180_P	1.029	0.99
172_V	178_L	1.028	0.99
63_G	70_L	1.028	0.99
148_L	151_L	1.024	0.99
65_L	69_L	1.022	0.99
155_G	185_Y	1.021	0.99
18_Y	130_Q	1.021	0.99
80_A	127_L	1.017	0.99
176_Y	179_T	1.015	0.99
103_I	106_D	1.012	0.99
30_F	75_Y	1.000	0.99
52_S	55_A	0.980	0.99
164_N	167_P	0.978	0.99
173_W	179_T	0.975	0.99
3_A	153_L	0.971	0.99
177_P	180_P	0.967	0.99
174_V	178_L	0.966	0.99
15_F	195_L	0.953	0.99
12_L	24_V	0.946	0.98
34_A	38_A	0.941	0.98
16_F	20_L	0.939	0.98
188_A	195_L	0.938	0.98
135_I	139_A	0.934	0.98
8_L	36_L	0.933	0.98
103_I	107_P	0.927	0.98
151_L	155_G	0.907	0.98
31_I	39_S	0.901	0.98
104_T	107_P	0.895	0.98
87_G	91_G	0.893	0.98
16_F	199_V	0.892	0.98
106_D	109_R	0.888	0.98
94_L	98_L	0.888	0.98
182_S	189_W	0.886	0.98
88_A	119_A	0.883	0.98
80_A	84_A	0.878	0.98
153_L	157_G	0.876	0.97
21_F	138_T	0.862	0.97
133_V	137_A	0.862	0.97
14_C	146_I	0.862	0.97
118_L	128_F	0.856	0.97
28_Y	141_G	0.849	0.97
57_L	61_L	0.846	0.97
169_A	172_V	0.842	0.97
83_G	123_A	0.842	0.97
113_G	121_A	0.839	0.97
148_L	156_G	0.830	0.96
22_R	75_Y	0.828	0.96
117_A	120_V	0.828	0.96
124_V	127_L	0.827	0.96
98_L	198_V	0.818	0.96
4_I	8_L	0.814	0.96
18_Y	134_I	0.812	0.96
106_D	111_L	0.809	0.96
120_V	124_V	0.808	0.96
13_L	141_G	0.805	0.96
148_L	157_G	0.804	0.96
175_L	180_P	0.804	0.96
23_I	27_I	0.798	0.96
69_L	73_L	0.798	0.96
143_A	189_W	0.793	0.95
25_L	78_G	0.789	0.95
8_L	11_L	0.784	0.95
143_A	147_V	0.783	0.95
91_G	94_L	0.782	0.95
157_G	185_Y	0.775	0.95
164_N	168_R	0.771	0.95
157_G	160_E	0.768	0.95
26_F	34_A	0.767	0.95
22_R	74_F	0.765	0.95
92_L	95_L	0.762	0.94
174_V	181_A	0.761	0.94
82_L	137_A	0.757	0.94
175_L	181_A	0.755	0.94
15_F	139_A	0.746	0.94
103_I	119_A	0.743	0.94
115_V	119_A	0.738	0.93
84_A	135_I	0.738	0.93
78_G	130_Q	0.737	0.93
148_L	160_E	0.736	0.93
132_Y	136_V	0.728	0.93
175_L	178_L	0.726	0.93
117_A	121_A	0.722	0.93
67_G	71_L	0.719	0.92
166_L	169_A	0.718	0.92
10_G	145_T	0.717	0.92
38_A	63_G	0.716	0.92
5_L	170_A	0.715	0.92
62_V	69_L	0.708	0.92
60_A	70_L	0.707	0.92
9_G	13_L	0.702	0.92
98_L	104_T	0.701	0.92
93_L	111_L	0.700	0.91
74_F	152_A	0.698	0.91
188_A	192_L	0.698	0.91
61_L	65_L	0.697	0.91
130_Q	133_V	0.693	0.91
78_G	88_A	0.688	0.91
150_I	153_L	0.685	0.91
180_P	190_L	0.685	0.91
20_L	138_T	0.684	0.91
83_G	126_A	0.682	0.90
166_L	171_N	0.673	0.90
113_G	120_V	0.670	0.90
184_V	189_W	0.669	0.90
7_I	11_L	0.666	0.89
53_T	57_L	0.661	0.89
85_G	92_L	0.660	0.89
160_E	163_L	0.656	0.89
75_Y	134_I	0.651	0.88
109_R	112_F	0.645	0.88
89_L	189_W	0.639	0.87
42_G	56_M	0.639	0.87
136_V	168_R	0.637	0.87
27_I	37_G	0.635	0.87
73_L	79_V	0.633	0.87
173_W	178_L	0.628	0.86
191_V	194_L	0.627	0.86
186_L	190_L	0.626	0.86
172_V	177_P	0.625	0.86
79_V	130_Q	0.625	0.86
13_L	28_Y	0.621	0.86
58_V	97_A	0.620	0.86
167_P	171_N	0.619	0.86
154_A	157_G	0.615	0.85
107_P	110_W	0.614	0.85
123_A	127_L	0.614	0.85
42_G	46_G	0.611	0.85
6_L	148_L	0.611	0.85
32_L	141_G	0.607	0.84
156_G	181_A	0.606	0.84
195_L	198_V	0.604	0.84
9_G	31_I	0.603	0.84
25_L	29_G	0.602	0.84
116_I	126_A	0.602	0.84
102_L	106_D	0.601	0.84
20_L	30_F	0.601	0.84
21_F	134_I	0.599	0.84
102_L	105_G	0.597	0.84
157_G	161_F	0.597	0.84
106_D	110_W	0.597	0.84
91_G	118_L	0.597	0.84
41_I	60_A	0.597	0.84
90_L	154_A	0.596	0.83
114_V	118_L	0.593	0.83
132_Y	135_I	0.591	0.83
58_V	170_A	0.591	0.83
26_F	38_A	0.589	0.83
55_A	69_L	0.587	0.82
144_W	151_L	0.586	0.82
39_S	43_A	0.586	0.82
22_R	72_Y	0.584	0.82
28_Y	32_L	0.582	0.82
41_I	44_L	0.582	0.82
169_A	178_L	0.573	0.81
93_L	97_A	0.573	0.81
165_L	170_A	0.572	0.81
165_L	169_A	0.570	0.81
162_L	194_L	0.570	0.81
86_L	136_V	0.568	0.80
144_W	147_V	0.568	0.80
137_A	140_F	0.563	0.80
117_A	128_F	0.562	0.80
5_L	90_L	0.561	0.80
116_I	119_A	0.561	0.80
28_Y	41_I	0.560	0.79
64_G	169_A	0.560	0.79
102_L	107_P	0.559	0.79
174_V	180_P	0.558	0.79
156_G	185_Y	0.556	0.79
7_I	150_I	0.550	0.78
84_A	123_A	0.541	0.77
25_L	75_Y	0.540	0.77
152_A	155_G	0.540	0.77
140_F	189_W	0.539	0.77
37_G	64_G	0.538	0.77
26_F	41_I	0.532	0.76
154_A	184_V	0.529	0.76
58_V	65_L	0.529	0.76
185_Y	189_W	0.524	0.75
20_L	141_G	0.524	0.75
164_N	171_N	0.523	0.75
16_F	22_R	0.523	0.75
127_L	131_R	0.522	0.75
69_L	191_V	0.521	0.74
49_G	52_S	0.519	0.74
28_Y	145_T	0.516	0.74
51_L	55_A	0.516	0.74
89_L	95_L	0.515	0.74
61_L	169_A	0.515	0.74
55_A	73_L	0.513	0.73
28_Y	85_G	0.511	0.73
42_G	51_L	0.510	0.73
148_L	158_P	0.509	0.73
42_G	45_F	0.509	0.73
5_L	9_G	0.505	0.72
36_L	40_L	0.504	0.72
134_I	138_T	0.503	0.72
15_F	21_F	0.502	0.72
89_L	126_A	0.500	0.71
84_A	134_I	0.500	0.71

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
2ls4A	1	0.1194	3.2	0.934	Contact Map
3j01B	1	0.4776	2.9	0.936	Contact Map
4ev6A	3	0.3831	2.3	0.939	Contact Map
4i0uA	4	0.3731	2.2	0.939	Contact Map
2looA	1	0.4776	2	0.941	Contact Map
5a63B	1	0.2985	1.7	0.943	Contact Map
2zxeG	1	0.1791	1.7	0.944	Contact Map
2ifoA	8	0.1244	1.6	0.944	Contact Map
3o7qA	1	0.6468	1.6	0.944	Contact Map
4p6vB	1	0.5821	1.4	0.946	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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