DUF3396 - PFAM28P - GREMLIN Contacts

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DUF3396 - Protein of unknown function (DUF3396)

PFAM:	PF11876	Sequences: DYEFEVFGRREWQEELDDGLSYLRFTLPLEFLEEHGPERFRELVLELAERLPPEHGYAGLALNLPPDREDAEPLEYALAQRYPGLDVDDPVSTSLRLGDGIKGVNWLTFLGDPLLEKLGGLEALRAALPPPPDIVVHPYGGGVVIQAGEAPELGDVNRGPVPPAYRAVARLLKPIRAEELGSLHFGSPDGEPRFDEEETERWLRRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	206 (198)
Sequences:	979 (773)
Seq/√Len:	54.9
META:	0.577

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_R	155_D	3.945	1.00
44_V	109_F	3.810	1.00
79_A	87_V	3.443	1.00
134_I	168_V	3.400	1.00
105_N	108_T	3.040	1.00
147_A	168_V	2.725	1.00
202_W	205_R	2.606	1.00
107_L	146_Q	2.579	1.00
59_G	105_N	2.490	1.00
62_L	85_L	2.476	1.00
115_L	124_L	2.444	1.00
115_L	143_V	2.440	1.00
41_R	146_Q	2.411	1.00
27_L	43_L	2.208	1.00
135_V	146_Q	2.158	1.00
139_Y	142_G	2.128	1.00
146_Q	149_E	2.017	1.00
43_L	47_L	2.008	1.00
124_L	171_L	1.989	1.00
49_E	140_G	1.980	1.00
105_N	147_A	1.945	1.00
112_D	141_G	1.925	1.00
166_R	169_A	1.867	0.99
101_I	175_I	1.853	0.99
76_Y	80_Q	1.832	0.99
173_K	176_R	1.802	0.99
169_A	176_R	1.783	0.99
83_P	160_P	1.772	0.99
131_P	167_A	1.772	0.99
100_G	169_A	1.768	0.99
134_I	164_A	1.744	0.99
168_V	172_L	1.683	0.99
162_P	166_R	1.650	0.99
20_L	55_H	1.646	0.99
41_R	45_L	1.632	0.99
83_P	163_P	1.628	0.99
62_L	78_L	1.613	0.98
105_N	165_Y	1.578	0.98
176_R	204_R	1.556	0.98
48_A	139_Y	1.539	0.98
118_L	174_P	1.534	0.98
45_L	144_V	1.532	0.98
110_L	115_L	1.521	0.98
100_G	117_K	1.512	0.98
102_K	108_T	1.502	0.97
11_E	14_E	1.501	0.97
128_L	145_I	1.482	0.97
121_L	138_P	1.479	0.97
137_H	146_Q	1.469	0.97
80_Q	201_R	1.458	0.97
155_D	158_R	1.452	0.97
32_L	40_F	1.450	0.97
121_L	125_R	1.432	0.97
48_A	109_F	1.430	0.97
56_G	109_F	1.429	0.97
169_A	173_K	1.388	0.96
107_L	144_V	1.385	0.96
22_Y	90_P	1.380	0.96
48_A	56_G	1.356	0.95
154_G	168_V	1.323	0.95
148_G	164_A	1.305	0.94
40_F	44_V	1.301	0.94
110_L	175_I	1.275	0.94
56_G	145_I	1.266	0.93
86_D	102_K	1.260	0.93
59_G	101_I	1.246	0.93
31_F	35_H	1.229	0.92
114_L	118_L	1.226	0.92
115_L	120_G	1.223	0.92
180_L	183_L	1.216	0.92
12_W	16_L	1.196	0.91
57_Y	105_N	1.194	0.91
75_E	87_V	1.192	0.91
25_F	47_L	1.191	0.91
202_W	206_F	1.191	0.91
134_I	145_I	1.189	0.91
108_T	147_A	1.174	0.90
8_G	11_E	1.169	0.90
52_P	139_Y	1.148	0.89
152_E	163_P	1.143	0.89
32_L	36_G	1.137	0.89
38_E	41_R	1.134	0.89
55_H	102_K	1.132	0.89
171_L	174_P	1.130	0.89
100_G	114_L	1.127	0.88
7_F	10_R	1.124	0.88
115_L	119_G	1.114	0.88
125_R	128_L	1.105	0.87
77_A	157_N	1.099	0.87
113_P	116_E	1.096	0.87
10_R	13_Q	1.085	0.86
147_A	154_G	1.078	0.86
83_P	120_G	1.076	0.86
127_A	171_L	1.074	0.86
72_E	75_E	1.067	0.86
84_G	154_G	1.059	0.85
133_D	136_V	1.059	0.85
101_I	145_I	0.990	0.81
23_L	49_E	0.981	0.80
87_V	184_H	0.978	0.80
46_E	49_E	0.966	0.79
103_G	205_R	0.958	0.79
115_L	136_V	0.943	0.78
59_G	176_R	0.943	0.78
57_Y	102_K	0.942	0.78
161_V	166_R	0.938	0.77
7_F	13_Q	0.928	0.77
8_G	13_Q	0.926	0.76
182_S	186_G	0.920	0.76
57_Y	88_D	0.917	0.76
201_R	204_R	0.915	0.75
81_R	157_N	0.913	0.75
83_P	86_D	0.909	0.75
149_E	174_P	0.901	0.74
79_A	198_E	0.897	0.74
9_R	19_G	0.893	0.74
124_L	143_V	0.891	0.74
53_P	162_P	0.889	0.73
144_V	147_A	0.885	0.73
39_R	42_E	0.883	0.73
110_L	174_P	0.881	0.73
182_S	185_F	0.881	0.73
99_D	117_K	0.880	0.73
128_L	168_V	0.875	0.72
127_A	167_A	0.874	0.72
41_R	137_H	0.873	0.72
56_G	105_N	0.873	0.72
64_L	73_P	0.873	0.72
194_F	197_E	0.870	0.72
178_E	181_G	0.861	0.71
152_E	162_P	0.854	0.70
64_L	88_D	0.850	0.70
53_P	139_Y	0.845	0.70
64_L	75_E	0.842	0.69
104_V	145_I	0.836	0.69
10_R	14_E	0.834	0.68
40_F	147_A	0.830	0.68
7_F	14_E	0.830	0.68
79_A	102_K	0.828	0.68
23_L	50_R	0.828	0.68
53_P	142_G	0.825	0.68
124_L	172_L	0.818	0.67
51_L	126_A	0.817	0.67
55_H	63_N	0.810	0.66
111_G	175_I	0.808	0.66
48_A	53_P	0.801	0.65
58_A	144_V	0.800	0.65
42_E	46_E	0.798	0.65
152_E	160_P	0.793	0.65
40_F	183_L	0.793	0.65
53_P	109_F	0.793	0.65
130_P	133_D	0.792	0.64
8_G	12_W	0.791	0.64
62_L	75_E	0.784	0.64
147_A	165_Y	0.766	0.62
39_R	51_L	0.763	0.62
109_F	144_V	0.760	0.61
169_A	172_L	0.759	0.61
177_A	181_G	0.759	0.61
83_P	161_V	0.757	0.61
83_P	166_R	0.757	0.61
41_R	107_L	0.755	0.61
45_L	49_E	0.754	0.61
37_P	45_L	0.750	0.60
40_F	162_P	0.742	0.59
120_G	123_A	0.735	0.59
103_G	177_A	0.732	0.58
43_L	174_P	0.730	0.58
132_P	201_R	0.727	0.58
119_G	128_L	0.726	0.58
128_L	171_L	0.722	0.57
121_L	127_A	0.721	0.57
169_A	177_A	0.720	0.57
52_P	176_R	0.713	0.56
39_R	85_L	0.713	0.56
185_F	188_P	0.713	0.56
95_L	143_V	0.712	0.56
11_E	16_L	0.711	0.56
59_G	144_V	0.701	0.55
157_N	181_G	0.700	0.55
7_F	18_D	0.699	0.55
123_A	200_E	0.698	0.55
78_L	176_R	0.696	0.55
190_G	193_R	0.696	0.55
105_N	168_V	0.695	0.54
149_E	153_L	0.695	0.54
57_Y	86_D	0.688	0.54
86_D	105_N	0.688	0.54
47_L	55_H	0.684	0.53
110_L	172_L	0.683	0.53
76_Y	184_H	0.682	0.53
88_D	102_K	0.682	0.53
153_L	161_V	0.673	0.52
31_F	51_L	0.673	0.52
50_R	53_P	0.671	0.52
9_R	13_Q	0.670	0.52
44_V	56_G	0.665	0.51
112_D	122_E	0.659	0.51
148_G	166_R	0.657	0.50
101_I	104_V	0.657	0.50
61_A	158_R	0.656	0.50
128_L	134_I	0.656	0.50
74_L	96_R	0.655	0.50
34_E	116_E	0.649	0.50
23_L	92_S	0.647	0.49
153_L	168_V	0.643	0.49
93_T	97_L	0.640	0.49
199_T	203_L	0.640	0.49
55_H	139_Y	0.637	0.48
136_V	142_G	0.637	0.48
134_I	139_Y	0.634	0.48
148_G	162_P	0.630	0.47
7_F	11_E	0.628	0.47
60_L	77_A	0.625	0.47
104_V	172_L	0.624	0.47
111_G	114_L	0.624	0.47
103_G	169_A	0.622	0.47
28_P	56_G	0.618	0.46
56_G	103_G	0.618	0.46
127_A	143_V	0.618	0.46
200_E	204_R	0.615	0.46
43_L	58_A	0.614	0.46
101_I	105_N	0.612	0.46
185_F	201_R	0.611	0.45
174_P	179_E	0.611	0.45
134_I	148_G	0.611	0.45
112_D	116_E	0.610	0.45
140_G	173_K	0.604	0.45
59_G	103_G	0.604	0.45
145_I	172_L	0.604	0.45
152_E	164_A	0.602	0.45
75_E	169_A	0.601	0.44
78_L	104_V	0.600	0.44
155_D	160_P	0.600	0.44
121_L	143_V	0.600	0.44
133_D	138_P	0.599	0.44
36_G	56_G	0.598	0.44
134_I	138_P	0.598	0.44
149_E	160_P	0.596	0.44
30_E	34_E	0.592	0.43
109_F	113_P	0.590	0.43
159_G	162_P	0.585	0.43
69_E	92_S	0.581	0.42
184_H	187_S	0.581	0.42
7_F	16_L	0.581	0.42
165_Y	199_T	0.580	0.42
13_Q	16_L	0.578	0.42
20_L	109_F	0.575	0.42
82_Y	153_L	0.569	0.41
187_S	190_G	0.569	0.41
145_I	168_V	0.568	0.41
159_G	166_R	0.567	0.41
110_L	149_E	0.567	0.41
132_P	141_G	0.566	0.41
59_G	165_Y	0.566	0.41
198_E	201_R	0.565	0.41
14_E	17_D	0.564	0.41
39_R	122_E	0.560	0.40
94_S	174_P	0.560	0.40
150_A	160_P	0.556	0.40
162_P	186_G	0.555	0.40
67_D	79_A	0.555	0.40
138_P	142_G	0.554	0.39
112_D	138_P	0.549	0.39
23_L	76_Y	0.549	0.39
31_F	182_S	0.548	0.39
71_A	75_E	0.545	0.39
8_G	108_T	0.542	0.38
27_L	40_F	0.541	0.38
53_P	112_D	0.538	0.38
93_T	96_R	0.537	0.38
79_A	104_V	0.536	0.38
58_A	199_T	0.534	0.37
54_E	102_K	0.533	0.37
148_G	163_P	0.532	0.37
180_L	185_F	0.530	0.37
180_L	187_S	0.529	0.37
29_L	62_L	0.529	0.37
200_E	203_L	0.527	0.37
110_L	145_I	0.526	0.37
51_L	102_K	0.525	0.37
65_P	143_V	0.522	0.36
143_V	171_L	0.521	0.36
131_P	134_I	0.521	0.36
101_I	166_R	0.517	0.36
56_G	124_L	0.516	0.36
56_G	168_V	0.515	0.36
59_G	199_T	0.513	0.35
180_L	203_L	0.513	0.35
26_T	148_G	0.511	0.35
61_A	118_L	0.510	0.35
138_P	168_V	0.510	0.35
142_G	146_Q	0.509	0.35
22_Y	105_N	0.508	0.35
162_P	173_K	0.506	0.35
162_P	168_V	0.502	0.34
193_R	197_E	0.500	0.34

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
3i12A	2	0.5777	10.1	0.948	Contact Map
1rv3A	3	0.432	9.3	0.949	Contact Map
3tqtA	2	0.5874	8	0.951	Contact Map
3e5nA	2	0.5194	6.1	0.953	Contact Map
3bczA	1	0.8398	5.7	0.954	Contact Map
4c5cA	2	0.5243	5.6	0.954	Contact Map
3lwbA	2	0.5534	5.3	0.955	Contact Map
1ehiA	2	0.6117	4.5	0.956	Contact Map
3ck1A	4	0.2476	4.4	0.956	Contact Map
4uz0A	1	0.2816	3.7	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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