DUF4868 - PFAM28P - GREMLIN Contacts

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DUF4868 - Domain of unknown function (DUF4868)

PFAM:	PF16162	Sequences: LKNIKGYVIRFGDGDKKIYAFRKISPSKVLKKSKGLFLLFFSDNTLKKLDDDVFKIDPDFDFLIIDGDLFILNKSNFERIFGLEEAYKEAADEKIEEIEELNLISDFEDLKELVGLSNKRIARKLAKIAKSGYLLYLNEDIIEKLKEVPKLGLEIKFDDNGKIIIDDKKDLKLFLKLLNDDYLTSELT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	188 (183)
Sequences:	1807 (1525)
Seq/√Len:	112.7
META:	0.806

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_R	57_D	3.458	1.00
99_E	111_K	3.381	1.00
176_K	181_D	2.848	1.00
180_D	185_S	2.661	1.00
156_K	166_D	2.608	1.00
64_I	69_L	2.554	1.00
137_L	140_D	2.378	1.00
106_D	109_D	2.356	1.00
180_D	183_L	2.186	1.00
96_E	99_E	2.159	1.00
16_K	66_D	2.115	1.00
78_E	123_R	2.105	1.00
77_F	83_L	2.065	1.00
146_K	149_P	2.045	1.00
141_I	144_K	2.024	1.00
143_E	146_K	2.014	1.00
71_I	77_F	1.984	1.00
141_I	149_P	1.949	1.00
105_S	158_D	1.945	1.00
138_N	141_I	1.911	1.00
137_L	141_I	1.906	1.00
176_K	182_Y	1.858	1.00
124_K	181_D	1.851	1.00
108_E	112_E	1.850	1.00
85_E	88_K	1.842	1.00
90_A	93_E	1.800	1.00
95_I	107_F	1.770	1.00
75_S	79_R	1.769	1.00
141_I	145_L	1.739	1.00
99_E	108_E	1.724	1.00
91_A	94_K	1.694	1.00
124_K	179_N	1.691	1.00
87_Y	123_R	1.677	1.00
174_F	178_L	1.596	1.00
136_Y	141_I	1.591	1.00
91_A	125_L	1.558	1.00
96_E	111_K	1.510	1.00
8_V	19_Y	1.504	1.00
156_K	164_I	1.503	1.00
49_L	53_V	1.489	1.00
165_I	174_F	1.458	1.00
29_V	33_S	1.446	1.00
154_E	157_F	1.441	1.00
62_F	77_F	1.438	1.00
62_F	71_I	1.438	1.00
109_D	112_E	1.436	1.00
4_I	7_Y	1.428	1.00
6_G	80_I	1.416	1.00
144_K	148_V	1.413	1.00
139_E	142_I	1.406	1.00
140_D	145_L	1.402	1.00
180_D	188_T	1.393	1.00
24_I	29_V	1.386	1.00
63_L	72_L	1.373	1.00
141_I	146_K	1.347	1.00
137_L	142_I	1.342	1.00
145_L	149_P	1.331	1.00
172_K	176_K	1.317	1.00
96_E	100_E	1.309	1.00
20_A	24_I	1.302	0.99
87_Y	122_A	1.247	0.99
118_N	123_R	1.247	0.99
120_R	172_K	1.245	0.99
10_R	17_K	1.228	0.99
99_E	107_F	1.192	0.99
22_R	61_D	1.186	0.99
28_K	31_K	1.177	0.99
46_L	78_E	1.158	0.99
76_N	79_R	1.155	0.99
21_F	64_I	1.147	0.99
24_I	28_K	1.138	0.99
163_I	167_D	1.136	0.99
144_K	147_E	1.123	0.98
5_K	23_K	1.120	0.98
142_I	146_K	1.104	0.98
137_L	149_P	1.104	0.98
153_L	157_F	1.098	0.98
140_D	143_E	1.092	0.98
180_D	187_L	1.080	0.98
13_D	16_K	1.063	0.98
96_E	108_E	1.062	0.98
118_N	122_A	1.059	0.98
29_V	32_K	1.045	0.98
114_V	165_I	1.044	0.98
20_A	30_L	1.035	0.97
121_I	125_L	1.034	0.97
22_R	29_V	1.033	0.97
105_S	162_K	1.029	0.97
119_K	122_A	1.028	0.97
26_P	33_S	1.027	0.97
91_A	165_I	1.018	0.97
158_D	164_I	1.018	0.97
74_K	77_F	1.018	0.97
77_F	94_K	1.016	0.97
22_R	60_F	1.012	0.97
183_L	188_T	1.009	0.97
124_K	172_K	0.992	0.97
107_F	111_K	0.990	0.97
167_D	170_D	0.990	0.97
43_D	96_E	0.987	0.97
98_I	125_L	0.974	0.96
27_S	32_K	0.971	0.96
138_N	142_I	0.969	0.96
142_I	145_L	0.969	0.96
139_E	145_L	0.966	0.96
118_N	172_K	0.961	0.96
77_F	93_E	0.953	0.96
19_Y	22_R	0.952	0.96
62_F	80_I	0.950	0.96
32_K	35_G	0.948	0.96
22_R	25_S	0.948	0.96
46_L	110_L	0.938	0.95
132_G	135_L	0.933	0.95
65_I	70_F	0.933	0.95
24_I	31_K	0.931	0.95
93_E	97_E	0.921	0.95
30_L	35_G	0.917	0.95
90_A	129_A	0.915	0.95
165_I	171_L	0.912	0.95
136_Y	139_E	0.908	0.94
119_K	123_R	0.903	0.94
110_L	114_V	0.902	0.94
14_G	17_K	0.901	0.94
31_K	34_K	0.896	0.94
10_R	19_Y	0.892	0.94
85_E	89_E	0.884	0.94
92_D	111_K	0.854	0.92
84_E	119_K	0.841	0.92
183_L	187_L	0.838	0.92
66_D	112_E	0.838	0.92
149_P	153_L	0.837	0.92
21_F	62_F	0.830	0.91
27_S	34_K	0.828	0.91
115_G	153_L	0.827	0.91
175_L	179_N	0.826	0.91
74_K	86_A	0.816	0.91
83_L	183_L	0.810	0.90
125_L	128_I	0.806	0.90
93_E	96_E	0.802	0.90
154_E	159_D	0.802	0.90
137_L	145_L	0.802	0.90
110_L	113_L	0.794	0.89
11_F	15_D	0.791	0.89
104_I	165_I	0.785	0.89
25_S	30_L	0.785	0.89
74_K	78_E	0.784	0.89
59_D	73_N	0.783	0.89
87_Y	119_K	0.781	0.89
94_K	98_I	0.779	0.89
9_I	13_D	0.776	0.88
121_I	126_A	0.775	0.88
134_L	137_L	0.774	0.88
4_I	9_I	0.769	0.88
6_G	10_R	0.767	0.88
71_I	88_K	0.765	0.88
24_I	30_L	0.764	0.88
10_R	13_D	0.759	0.87
21_F	25_S	0.759	0.87
147_E	150_K	0.755	0.87
60_F	78_E	0.754	0.87
118_N	168_K	0.754	0.87
113_L	121_I	0.753	0.87
16_K	19_Y	0.753	0.87
139_E	143_E	0.752	0.87
23_K	26_P	0.751	0.87
91_A	129_A	0.746	0.86
26_P	32_K	0.742	0.86
152_G	159_D	0.737	0.86
61_D	77_F	0.736	0.86
167_D	171_L	0.735	0.86
12_G	15_D	0.733	0.85
60_F	176_K	0.733	0.85
84_E	128_I	0.722	0.85
145_L	148_V	0.719	0.84
21_F	30_L	0.719	0.84
27_S	55_K	0.719	0.84
184_T	187_L	0.718	0.84
105_S	164_I	0.716	0.84
134_L	138_N	0.712	0.84
141_I	148_V	0.712	0.84
63_L	105_S	0.709	0.83
152_G	155_I	0.706	0.83
22_R	27_S	0.697	0.82
146_K	157_F	0.691	0.82
9_I	12_G	0.691	0.82
28_K	33_S	0.690	0.82
151_L	155_I	0.684	0.81
24_I	33_S	0.679	0.81
118_N	121_I	0.678	0.81
121_I	172_K	0.677	0.81
139_E	161_G	0.676	0.80
61_D	145_L	0.676	0.80
31_K	35_G	0.675	0.80
26_P	31_K	0.673	0.80
18_I	32_K	0.673	0.80
38_L	41_F	0.672	0.80
106_D	111_K	0.672	0.80
99_E	102_N	0.671	0.80
131_S	134_L	0.665	0.79
91_A	122_A	0.664	0.79
46_L	57_D	0.663	0.79
88_K	117_S	0.658	0.79
54_F	58_P	0.657	0.79
53_V	178_L	0.657	0.79
41_F	67_G	0.653	0.78
90_A	94_K	0.649	0.78
170_D	174_F	0.649	0.78
55_K	87_Y	0.648	0.78
15_D	71_I	0.646	0.77
22_R	59_D	0.646	0.77
148_V	151_L	0.641	0.77
95_I	125_L	0.640	0.77
157_F	160_N	0.637	0.76
87_Y	98_I	0.634	0.76
185_S	188_T	0.630	0.76
99_E	117_S	0.628	0.75
179_N	185_S	0.627	0.75
21_F	33_S	0.621	0.75
139_E	146_K	0.619	0.74
9_I	60_F	0.617	0.74
22_R	26_P	0.617	0.74
136_Y	142_I	0.611	0.73
168_K	171_L	0.611	0.73
104_I	107_F	0.609	0.73
91_A	127_K	0.608	0.73
138_N	148_V	0.607	0.73
45_T	117_S	0.605	0.73
138_N	145_L	0.603	0.72
44_N	100_E	0.601	0.72
21_F	26_P	0.596	0.72
145_L	150_K	0.587	0.70
87_Y	173_L	0.587	0.70
4_I	80_I	0.585	0.70
5_K	8_V	0.579	0.69
111_K	115_G	0.579	0.69
66_D	76_N	0.579	0.69
65_I	103_L	0.573	0.69
5_K	15_D	0.569	0.68
18_I	73_N	0.568	0.68
165_I	178_L	0.565	0.68
142_I	148_V	0.564	0.67
56_I	128_I	0.560	0.67
84_E	176_K	0.559	0.67
8_V	21_F	0.558	0.67
165_I	168_K	0.554	0.66
126_A	129_A	0.552	0.66
30_L	33_S	0.541	0.64
6_G	65_I	0.538	0.64
18_I	23_K	0.536	0.63
117_S	150_K	0.532	0.63
21_F	80_I	0.530	0.63
83_L	91_A	0.529	0.62
158_D	161_G	0.527	0.62
122_A	127_K	0.525	0.62
153_L	156_K	0.520	0.61
43_D	130_K	0.520	0.61
172_K	179_N	0.519	0.61
21_F	29_V	0.515	0.60
8_V	25_S	0.515	0.60
157_F	161_G	0.513	0.60
144_K	158_D	0.510	0.60
54_F	80_I	0.510	0.60
164_I	167_D	0.508	0.59
54_F	61_D	0.508	0.59
161_G	165_I	0.507	0.59
35_G	38_L	0.507	0.59
63_L	120_R	0.507	0.59
50_D	147_E	0.506	0.59
26_P	29_V	0.505	0.59
156_K	169_K	0.503	0.59
93_E	157_F	0.503	0.59
83_L	133_Y	0.502	0.58
100_E	146_K	0.501	0.58
91_A	95_I	0.500	0.58

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
1jyoA	2	0.5266	3.8	0.94	Contact Map
2mysB	1	0.2447	3.4	0.941	Contact Map
1mvfD	1	0.234	3.2	0.943	Contact Map
4uwjA	1	0.2819	3.1	0.943	Contact Map
4c68A	1	0.383	2	0.948	Contact Map
4c7iA	1	0.383	2	0.948	Contact Map
1iicA	1	0.3989	1.7	0.95	Contact Map
1sauA	1	0.3245	1.6	0.951	Contact Map
3fwbA	1	0.2872	1.6	0.951	Contact Map
1xtzA	3	0.2606	1.6	0.951	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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