EBP - PFAM28P - GREMLIN Contacts

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EBP - Emopamil binding protein

PFAM:	PF05241	Sequences: ILSLAASAALLLAAWLLSGRLLPKSLSRADRLLFCWFAFDGLIHLFLEGYFLYNSLFAQLWKEYAKADSRYLTSDPFVVSLETLTVFLWGPLSLLLVYAIAKRKPYRHPLQLVVSVGQLYGTVLYFATEWLDGGPNLSTSNPLYFWVYFVFMNALWVVIPLLLLYDSWKEIARAFRQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	177 (172)
Sequences:	838 (571)
Seq/√Len:	43.5
META:	0.291

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
108_H	167_S	5.855	1.00
151_F	155_L	3.427	1.00
150_V	154_A	2.659	1.00
122_T	157_V	2.562	1.00
77_F	124_L	2.517	1.00
59_Q	62_K	2.499	1.00
171_I	175_F	2.432	1.00
112_L	164_L	2.418	1.00
52_L	86_V	2.415	1.00
107_R	111_Q	2.392	1.00
51_F	79_V	2.345	1.00
99_A	106_Y	2.258	1.00
4_L	10_L	2.244	1.00
145_F	150_V	2.233	1.00
6_A	9_A	2.208	1.00
89_W	117_G	2.176	1.00
95_L	99_A	2.154	1.00
82_E	85_T	2.136	1.00
63_E	148_Y	2.133	1.00
154_A	158_V	2.049	0.99
48_E	82_E	1.925	0.99
71_Y	125_Y	1.896	0.99
8_A	11_L	1.843	0.99
15_W	19_G	1.831	0.98
86_V	118_Q	1.828	0.98
65_A	72_L	1.770	0.98
125_Y	128_T	1.768	0.98
30_D	107_R	1.762	0.98
134_G	137_L	1.731	0.98
119_L	157_V	1.660	0.97
118_Q	121_G	1.637	0.97
48_E	67_A	1.635	0.97
50_Y	58_A	1.633	0.97
37_F	115_S	1.633	0.97
85_T	121_G	1.558	0.96
44_H	48_E	1.531	0.95
33_L	163_L	1.529	0.95
63_E	66_K	1.506	0.95
40_D	125_Y	1.456	0.94
44_H	49_G	1.449	0.94
48_E	51_F	1.410	0.93
13_A	19_G	1.370	0.92
112_L	171_I	1.368	0.92
71_Y	128_T	1.365	0.92
67_A	82_E	1.356	0.91
108_H	170_E	1.347	0.91
105_P	172_A	1.313	0.90
75_D	79_V	1.303	0.90
109_P	112_L	1.286	0.89
81_L	84_L	1.282	0.89
45_L	94_L	1.280	0.89
37_F	40_D	1.275	0.89
44_H	90_G	1.266	0.88
16_L	27_S	1.249	0.88
41_G	93_S	1.214	0.86
7_S	11_L	1.192	0.85
97_V	100_I	1.173	0.84
141_N	144_Y	1.169	0.84
9_A	16_L	1.167	0.84
70_R	160_P	1.167	0.84
51_F	55_S	1.167	0.84
52_L	81_L	1.163	0.84
40_D	93_S	1.162	0.83
19_G	31_R	1.152	0.83
98_Y	102_K	1.135	0.82
47_L	57_F	1.131	0.82
61_W	82_E	1.130	0.82
107_R	163_L	1.129	0.82
43_I	118_Q	1.127	0.82
120_Y	124_L	1.104	0.80
8_A	17_L	1.100	0.80
13_A	16_L	1.092	0.79
113_V	168_W	1.090	0.79
5_A	13_A	1.089	0.79
155_L	159_I	1.080	0.79
16_L	21_L	1.073	0.78
167_S	170_E	1.066	0.78
69_S	136_N	1.051	0.77
15_W	35_C	1.046	0.76
61_W	65_A	1.040	0.76
147_V	151_F	1.018	0.74
14_A	21_L	1.013	0.74
36_W	160_P	1.013	0.74
156_W	160_P	1.010	0.74
41_G	51_F	1.003	0.73
134_G	139_T	0.992	0.72
12_L	16_L	0.990	0.72
43_I	78_V	0.987	0.72
44_H	85_T	0.983	0.72
115_S	164_L	0.974	0.71
48_E	153_N	0.971	0.71
77_F	125_Y	0.966	0.70
122_T	155_L	0.966	0.70
111_Q	166_D	0.948	0.69
8_A	28_R	0.945	0.69
142_P	147_V	0.931	0.68
80_S	127_A	0.929	0.67
44_H	93_S	0.927	0.67
48_E	120_Y	0.925	0.67
5_A	103_R	0.925	0.67
15_W	20_R	0.924	0.67
10_L	16_L	0.921	0.67
109_P	168_W	0.904	0.65
16_L	171_I	0.895	0.64
38_A	97_V	0.895	0.64
51_F	85_T	0.887	0.64
15_W	21_L	0.882	0.63
118_Q	125_Y	0.877	0.63
70_R	90_G	0.876	0.63
30_D	100_I	0.875	0.63
108_H	111_Q	0.866	0.62
14_A	18_S	0.861	0.61
19_G	173_R	0.852	0.61
82_E	153_N	0.850	0.60
13_A	18_S	0.849	0.60
153_N	156_W	0.842	0.60
28_R	32_L	0.841	0.60
5_A	11_L	0.840	0.60
12_L	17_L	0.837	0.59
37_F	93_S	0.836	0.59
142_P	145_F	0.836	0.59
77_F	120_Y	0.834	0.59
118_Q	122_T	0.833	0.59
98_Y	162_L	0.833	0.59
44_H	160_P	0.833	0.59
84_L	119_L	0.832	0.59
113_V	116_V	0.817	0.57
41_G	94_L	0.814	0.57
9_A	12_L	0.813	0.57
4_L	123_V	0.808	0.57
82_E	86_V	0.799	0.56
108_H	115_S	0.797	0.56
5_A	38_A	0.797	0.56
5_A	9_A	0.795	0.55
24_K	28_R	0.794	0.55
100_I	111_Q	0.793	0.55
118_Q	123_V	0.791	0.55
48_E	85_T	0.785	0.54
61_W	148_Y	0.778	0.54
82_E	90_G	0.778	0.54
28_R	165_Y	0.777	0.54
17_L	28_R	0.765	0.52
64_Y	68_D	0.757	0.52
9_A	22_L	0.756	0.52
63_E	69_S	0.754	0.51
9_A	13_A	0.751	0.51
133_G	138_S	0.745	0.51
88_L	92_L	0.745	0.51
17_L	29_A	0.744	0.50
119_L	164_L	0.733	0.49
128_T	148_Y	0.732	0.49
59_Q	66_K	0.728	0.49
6_A	10_L	0.722	0.48
130_W	134_G	0.720	0.48
163_L	166_D	0.720	0.48
168_W	172_A	0.716	0.48
58_A	61_W	0.708	0.47
163_L	167_S	0.707	0.47
34_F	97_V	0.705	0.47
67_A	137_L	0.705	0.47
119_L	161_L	0.703	0.47
78_V	84_L	0.701	0.46
11_L	20_R	0.694	0.46
162_L	165_Y	0.692	0.46
96_L	114_V	0.687	0.45
29_A	33_L	0.683	0.45
92_L	102_K	0.681	0.44
61_W	85_T	0.679	0.44
81_L	86_V	0.677	0.44
5_A	12_L	0.675	0.44
15_W	83_T	0.675	0.44
44_H	118_Q	0.673	0.44
36_W	41_G	0.671	0.44
18_S	21_L	0.668	0.43
26_L	30_D	0.668	0.43
14_A	17_L	0.667	0.43
21_L	29_A	0.666	0.43
12_L	102_K	0.663	0.43
85_T	120_Y	0.662	0.43
100_I	175_F	0.655	0.42
99_A	104_K	0.652	0.42
11_L	15_W	0.650	0.42
61_W	75_D	0.647	0.41
28_R	94_L	0.646	0.41
12_L	27_S	0.645	0.41
147_V	152_M	0.644	0.41
71_Y	153_N	0.643	0.41
11_L	18_S	0.643	0.41
129_E	149_F	0.637	0.40
62_K	71_Y	0.636	0.40
93_S	96_L	0.636	0.40
13_A	23_P	0.627	0.39
9_A	159_I	0.627	0.39
44_H	70_R	0.625	0.39
62_K	148_Y	0.624	0.39
17_L	27_S	0.621	0.39
51_F	58_A	0.614	0.38
40_D	128_T	0.609	0.38
109_P	164_L	0.605	0.37
122_T	125_Y	0.603	0.37
30_D	97_V	0.603	0.37
39_F	171_I	0.599	0.37
6_A	11_L	0.599	0.37
8_A	24_K	0.599	0.37
32_L	159_I	0.596	0.37
78_V	82_E	0.592	0.36
106_Y	168_W	0.590	0.36
47_L	144_Y	0.590	0.36
68_D	82_E	0.585	0.36
48_E	111_Q	0.584	0.36
151_F	157_V	0.582	0.35
46_F	104_K	0.581	0.35
92_L	107_R	0.573	0.35
32_L	164_L	0.571	0.34
37_F	114_V	0.571	0.34
4_L	14_A	0.567	0.34
24_K	27_S	0.567	0.34
26_L	100_I	0.566	0.34
16_L	20_R	0.564	0.34
9_A	24_K	0.563	0.34
93_S	97_V	0.563	0.34
49_G	85_T	0.558	0.33
33_L	37_F	0.553	0.33
10_L	19_G	0.553	0.33
4_L	32_L	0.551	0.33
67_A	149_F	0.547	0.32
7_S	10_L	0.546	0.32
122_T	126_F	0.545	0.32
11_L	14_A	0.545	0.32
60_L	152_M	0.543	0.32
68_D	153_N	0.541	0.32
18_S	31_R	0.541	0.32
89_W	93_S	0.540	0.32
84_L	88_L	0.540	0.32
33_L	107_R	0.540	0.32
13_A	24_K	0.538	0.32
41_G	44_H	0.534	0.31
9_A	174_A	0.532	0.31
108_H	163_L	0.531	0.31
8_A	12_L	0.530	0.31
79_V	131_L	0.529	0.31
33_L	56_L	0.527	0.31
9_A	14_A	0.527	0.31
135_P	138_S	0.525	0.31
48_E	52_L	0.524	0.31
7_S	15_W	0.521	0.30
85_T	90_G	0.521	0.30
9_A	19_G	0.520	0.30
96_L	107_R	0.513	0.30
64_Y	156_W	0.513	0.30
81_L	122_T	0.510	0.29
5_A	20_R	0.510	0.29
20_R	23_P	0.510	0.29
125_Y	134_G	0.506	0.29
117_G	120_Y	0.505	0.29
12_L	94_L	0.504	0.29
44_H	75_D	0.501	0.29
77_F	150_V	0.500	0.29

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
4zwjA	1	0.9096	17	0.934	Contact Map
4yayA	1	0.5763	10.5	0.94	Contact Map
4ymuD	2	0.6328	6.4	0.946	Contact Map
4xk8I	1	0.1469	6.1	0.946	Contact Map
3v2yA	1	0.9096	6	0.946	Contact Map
2wscI	1	0.1525	5	0.949	Contact Map
1u19A	2	0.9096	4.1	0.951	Contact Map
2z73A	2	0.9153	3.6	0.952	Contact Map
3vw7A	1	0.904	3.4	0.953	Contact Map
4z35A	1	0.9379	3.4	0.953	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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