DUF3500 - PFAM28P - GREMLIN Contacts

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DUF3500 - Protein of unknown function (DUF3500)

PFAM:	PF12006	Sequences: GASTAAMAAAANAFLASLDPEQRAKATFPFDDPERRRWHNIPFYVERKGLPLKEMTPAQREAALALLRAGLSARGYEKARDIMRLEEVLGEELYYFSIFGTPSATGPWGWRFEGHHLSLNFTVVDGDQVVMTPSFFGANPAEVREGPGKGLRVLGAEEDLARALLNSLDAEQRKKAILSDTAPDDILTANRDNAPLPPEGIPASELTAAQRALLLDLIEEYVGRLPDELAAARMAEIKAALDKTHFAWAGGTEPGSPHYYRIQGPTFLIEYDNTQNQNANHIHTVWRDPNNDFGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	295 (290)
Sequences:	7360 (5164)
Seq/√Len:	303.2
META:	0.908

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
201_I	206_L	4.455	1.00
175_K	205_E	3.607	1.00
251_G	256_S	3.496	1.00
203_A	214_L	3.030	1.00
165_L	252_T	2.749	1.00
17_S	62_A	2.715	1.00
25_K	54_E	2.710	1.00
215_L	238_K	2.646	1.00
253_E	256_S	2.444	1.00
165_L	177_I	2.358	1.00
211_R	242_D	2.346	1.00
169_D	172_Q	2.329	1.00
77_E	81_D	2.327	1.00
172_Q	210_Q	2.308	1.00
28_F	97_S	2.289	1.00
19_D	22_Q	2.214	1.00
160_L	220_E	2.167	1.00
64_L	80_R	2.166	1.00
152_R	159_D	2.149	1.00
79_A	117_L	2.116	1.00
15_L	27_T	2.096	1.00
169_D	207_T	2.070	1.00
14_F	26_A	2.029	1.00
14_F	63_A	2.018	1.00
64_L	76_Y	1.967	1.00
227_D	231_A	1.958	1.00
11_A	66_L	1.939	1.00
240_A	266_T	1.924	1.00
219_E	223_G	1.919	1.00
235_A	239_A	1.907	1.00
96_F	112_F	1.894	1.00
215_L	241_L	1.866	1.00
61_E	65_A	1.864	1.00
171_E	174_K	1.845	1.00
167_S	213_L	1.823	1.00
202_P	245_H	1.799	1.00
235_A	238_K	1.795	1.00
29_P	32_D	1.781	1.00
170_A	173_R	1.767	1.00
50_L	55_M	1.722	1.00
23_R	27_T	1.717	1.00
143_V	146_G	1.692	1.00
207_T	210_Q	1.685	1.00
222_V	234_M	1.657	1.00
178_L	247_A	1.651	1.00
202_P	243_K	1.635	1.00
162_R	166_N	1.632	1.00
219_E	234_M	1.616	1.00
173_R	177_I	1.609	1.00
68_R	76_Y	1.608	1.00
163_A	213_L	1.595	1.00
7_M	70_G	1.588	1.00
203_A	211_R	1.563	1.00
12_N	101_T	1.562	1.00
14_F	18_L	1.554	1.00
76_Y	80_R	1.546	1.00
78_K	220_E	1.537	1.00
34_E	37_R	1.518	1.00
172_Q	201_I	1.515	1.00
185_D	188_T	1.515	1.00
170_A	174_K	1.510	1.00
208_A	211_R	1.495	1.00
191_R	194_A	1.484	1.00
113_E	118_S	1.481	1.00
142_E	152_R	1.477	1.00
8_A	12_N	1.457	1.00
12_N	16_A	1.451	1.00
70_G	110_W	1.445	1.00
287_R	292_D	1.429	1.00
56_T	59_Q	1.423	1.00
87_E	90_G	1.412	1.00
30_F	122_T	1.404	1.00
212_A	216_D	1.392	1.00
202_P	205_E	1.377	1.00
5_A	9_A	1.371	1.00
177_I	252_T	1.371	1.00
18_L	26_A	1.346	1.00
156_A	220_E	1.345	1.00
87_E	91_E	1.330	1.00
7_M	123_V	1.328	1.00
38_W	42_P	1.324	1.00
80_R	83_M	1.323	1.00
262_I	269_I	1.322	1.00
152_R	158_E	1.320	1.00
85_L	153_V	1.317	1.00
148_G	151_L	1.317	1.00
73_A	77_E	1.316	1.00
231_A	235_A	1.312	1.00
213_L	216_D	1.311	1.00
72_S	75_G	1.311	1.00
160_L	163_A	1.307	1.00
52_L	63_A	1.298	1.00
21_E	24_A	1.296	1.00
107_P	124_V	1.291	1.00
70_G	121_F	1.287	1.00
65_A	68_R	1.283	1.00
22_Q	50_L	1.279	1.00
57_P	61_E	1.274	1.00
51_P	54_E	1.263	1.00
51_P	95_Y	1.261	1.00
221_Y	284_T	1.260	1.00
233_R	236_E	1.259	1.00
221_Y	260_Y	1.245	1.00
146_G	150_G	1.232	1.00
160_L	213_L	1.228	1.00
169_D	210_Q	1.217	1.00
167_S	210_Q	1.212	1.00
22_Q	59_Q	1.210	1.00
9_A	13_A	1.204	1.00
11_A	98_I	1.198	1.00
152_R	155_G	1.189	1.00
164_L	214_L	1.178	1.00
145_E	149_K	1.175	1.00
198_P	245_H	1.173	1.00
43_F	46_E	1.173	1.00
147_P	150_G	1.171	1.00
28_F	34_E	1.166	1.00
215_L	234_M	1.163	1.00
13_A	65_A	1.152	1.00
40_N	189_A	1.147	1.00
60_R	92_E	1.144	1.00
15_L	26_A	1.144	1.00
38_W	41_I	1.141	1.00
257_P	279_A	1.139	1.00
218_I	269_I	1.137	1.00
155_G	159_D	1.127	1.00
168_L	206_L	1.124	1.00
84_R	148_G	1.122	1.00
159_D	163_A	1.119	1.00
203_A	206_L	1.113	1.00
214_L	262_I	1.113	1.00
166_N	253_E	1.112	1.00
20_P	23_R	1.111	1.00
164_L	213_L	1.095	1.00
164_L	206_L	1.094	1.00
168_L	176_A	1.091	1.00
78_K	157_E	1.087	1.00
157_E	220_E	1.086	1.00
55_M	63_A	1.080	1.00
162_R	254_P	1.079	1.00
175_K	201_I	1.078	1.00
136_F	224_R	1.070	1.00
198_P	263_Q	1.064	1.00
17_S	59_Q	1.057	1.00
81_D	84_R	1.052	1.00
208_A	212_A	1.045	1.00
203_A	241_L	1.034	1.00
39_H	190_N	1.034	1.00
173_R	252_T	1.024	1.00
117_L	136_F	1.020	1.00
53_K	92_E	1.012	1.00
63_A	96_F	1.009	1.00
160_L	217_L	1.009	1.00
30_F	35_R	1.005	1.00
185_D	189_A	1.004	1.00
74_R	78_K	0.998	1.00
163_A	216_D	0.990	1.00
39_H	45_V	0.987	1.00
165_L	176_A	0.985	1.00
67_L	112_F	0.976	1.00
250_G	253_E	0.974	1.00
82_I	136_F	0.973	1.00
243_K	265_P	0.972	1.00
188_T	191_R	0.971	1.00
13_A	62_A	0.969	1.00
8_A	104_A	0.965	1.00
241_L	244_T	0.964	1.00
158_E	162_R	0.964	1.00
166_N	254_P	0.961	1.00
81_D	153_V	0.960	1.00
178_L	249_A	0.959	1.00
201_I	205_E	0.959	1.00
79_A	136_F	0.958	1.00
160_L	216_D	0.958	1.00
172_Q	207_T	0.957	1.00
78_K	224_R	0.953	1.00
81_D	151_L	0.949	1.00
57_P	60_R	0.947	1.00
240_A	265_P	0.947	1.00
58_A	61_E	0.942	1.00
267_F	289_P	0.938	1.00
250_G	254_P	0.934	1.00
181_T	184_D	0.931	1.00
142_E	254_P	0.928	1.00
258_H	271_Y	0.927	1.00
257_P	274_T	0.923	1.00
138_A	153_V	0.920	1.00
162_R	271_Y	0.914	1.00
188_T	194_A	0.910	1.00
61_E	68_R	0.906	1.00
52_L	96_F	0.900	1.00
83_M	112_F	0.900	1.00
209_A	212_A	0.892	1.00
267_F	286_W	0.883	1.00
121_F	131_M	0.878	1.00
13_A	16_A	0.877	1.00
35_R	122_T	0.873	1.00
218_I	241_L	0.871	1.00
14_F	55_M	0.868	1.00
244_T	262_I	0.868	1.00
165_L	173_R	0.867	1.00
215_L	219_E	0.866	1.00
39_H	42_P	0.865	1.00
51_P	93_L	0.863	1.00
55_M	59_Q	0.862	1.00
37_R	45_V	0.861	1.00
204_S	242_D	0.857	1.00
263_Q	289_P	0.855	1.00
143_V	148_G	0.850	1.00
112_F	117_L	0.850	1.00
20_P	24_A	0.849	1.00
67_L	79_A	0.848	1.00
225_L	233_R	0.848	1.00
224_R	233_R	0.844	1.00
158_E	271_Y	0.841	1.00
187_L	194_A	0.839	1.00
244_T	267_F	0.838	1.00
216_D	219_E	0.838	1.00
156_A	160_L	0.838	1.00
109_G	120_N	0.831	1.00
128_Q	131_M	0.820	1.00
259_Y	270_E	0.820	1.00
189_A	192_D	0.820	1.00
218_I	244_T	0.818	1.00
229_L	232_A	0.810	1.00
53_K	93_L	0.810	1.00
166_N	173_R	0.808	1.00
180_D	183_P	0.808	1.00
64_L	68_R	0.807	1.00
80_R	84_R	0.806	1.00
74_R	223_G	0.805	1.00
39_H	44_Y	0.802	1.00
225_L	229_L	0.800	1.00
105_T	125_D	0.794	1.00
28_F	48_K	0.790	1.00
134_S	224_R	0.789	1.00
211_R	215_L	0.789	1.00
161_A	217_L	0.789	1.00
7_M	110_W	0.788	0.99
220_E	223_G	0.787	0.99
143_V	151_L	0.784	0.99
36_R	192_D	0.782	0.99
259_Y	272_D	0.781	0.99
74_R	77_E	0.779	0.99
275_Q	278_N	0.777	0.99
41_I	44_Y	0.775	0.99
125_D	128_Q	0.772	0.99
111_R	120_N	0.771	0.99
5_A	8_A	0.764	0.99
61_E	64_L	0.757	0.99
15_L	98_I	0.756	0.99
66_L	96_F	0.756	0.99
15_L	23_R	0.756	0.99
234_M	238_K	0.755	0.99
163_A	166_N	0.754	0.99
84_R	151_L	0.753	0.99
101_T	106_G	0.751	0.99
182_A	249_A	0.749	0.99
71_L	119_L	0.747	0.99
134_S	225_L	0.746	0.99
32_D	35_R	0.745	0.99
68_R	80_R	0.743	0.99
4_T	8_A	0.742	0.99
184_D	187_L	0.737	0.99
104_A	107_P	0.737	0.99
176_A	201_I	0.737	0.99
164_L	168_L	0.733	0.99
64_L	67_L	0.733	0.99
199_E	247_A	0.732	0.99
6_A	9_A	0.729	0.99
156_A	216_D	0.728	0.99
37_R	120_N	0.727	0.99
131_M	225_L	0.726	0.99
101_T	104_A	0.724	0.99
195_P	263_Q	0.720	0.99
41_I	190_N	0.718	0.99
35_R	38_W	0.717	0.99
223_G	231_A	0.713	0.99
34_E	111_R	0.711	0.99
58_A	62_A	0.710	0.99
34_E	99_F	0.709	0.99
175_K	202_P	0.707	0.99
64_L	83_M	0.704	0.99
9_A	12_N	0.704	0.99
223_G	230_A	0.702	0.99
213_L	220_E	0.695	0.99
184_D	189_A	0.692	0.99
68_R	73_A	0.689	0.99
14_F	96_F	0.689	0.99
155_G	158_E	0.688	0.99
141_A	282_I	0.686	0.99
156_A	159_D	0.686	0.99
162_R	255_G	0.684	0.99
161_A	246_F	0.681	0.99
226_P	233_R	0.678	0.98
157_E	224_R	0.675	0.98
62_A	65_A	0.675	0.98
238_K	241_L	0.674	0.98
41_I	45_V	0.673	0.98
223_G	227_D	0.672	0.98
13_A	17_S	0.670	0.98
110_W	121_F	0.668	0.98
166_N	252_T	0.666	0.98
65_A	69_A	0.665	0.98
101_T	105_T	0.665	0.98
161_A	260_Y	0.664	0.98
37_R	41_I	0.660	0.98
116_H	281_H	0.660	0.98
42_P	47_R	0.659	0.98
223_G	234_M	0.658	0.98
240_A	244_T	0.657	0.98
217_L	220_E	0.656	0.98
35_R	42_P	0.656	0.98
84_R	87_E	0.654	0.98
240_A	243_K	0.654	0.98
139_N	276_N	0.649	0.98
34_E	48_K	0.649	0.98
37_R	40_N	0.648	0.98
189_A	194_A	0.646	0.98
52_L	64_L	0.646	0.98
219_E	222_V	0.645	0.98
71_L	79_A	0.645	0.98
119_L	134_S	0.644	0.98
186_I	189_A	0.643	0.98
21_E	25_K	0.640	0.98
30_F	34_E	0.637	0.98
6_A	10_A	0.637	0.98
26_A	55_M	0.635	0.98
162_R	251_G	0.635	0.98
85_L	88_V	0.632	0.98
27_T	98_I	0.631	0.98
265_P	289_P	0.631	0.98
8_A	101_T	0.631	0.98
131_M	233_R	0.629	0.98
8_A	11_A	0.625	0.97
103_S	106_G	0.620	0.97
241_L	264_G	0.618	0.97
66_L	69_A	0.616	0.97
233_R	237_I	0.616	0.97
288_D	291_N	0.613	0.97
236_E	240_A	0.611	0.97
142_E	150_G	0.610	0.97
289_P	293_F	0.609	0.97
37_R	48_K	0.607	0.97
19_D	59_Q	0.604	0.97
6_A	226_P	0.603	0.97
86_E	90_G	0.601	0.97
273_N	279_A	0.596	0.97
219_E	238_K	0.594	0.97
226_P	229_L	0.594	0.97
178_L	182_A	0.592	0.96
85_L	138_A	0.591	0.96
73_A	227_D	0.591	0.96
39_H	46_E	0.589	0.96
183_P	187_L	0.587	0.96
127_D	232_A	0.575	0.96
48_K	97_S	0.574	0.96
210_Q	213_L	0.572	0.96
221_Y	269_I	0.570	0.96
266_T	288_D	0.569	0.96
266_T	290_N	0.569	0.96
12_N	104_A	0.568	0.96
115_H	140_P	0.567	0.96
79_A	83_M	0.561	0.95
49_G	52_L	0.560	0.95
183_P	186_I	0.557	0.95
157_E	260_Y	0.556	0.95
39_H	43_F	0.556	0.95
162_R	253_E	0.554	0.95
146_G	149_K	0.553	0.95
166_N	251_G	0.553	0.95
209_A	213_L	0.552	0.95
91_E	146_G	0.551	0.95
31_D	34_E	0.551	0.95
274_T	279_A	0.550	0.95
144_R	149_K	0.550	0.95
275_Q	280_N	0.549	0.95
26_A	50_L	0.548	0.95
171_E	175_K	0.545	0.94
35_R	40_N	0.545	0.94
36_R	40_N	0.544	0.94
222_V	233_R	0.544	0.94
143_V	147_P	0.544	0.94
187_L	190_N	0.543	0.94
22_Q	25_K	0.543	0.94
184_D	257_P	0.542	0.94
199_E	245_H	0.541	0.94
103_S	107_P	0.540	0.94
222_V	230_A	0.540	0.94
77_E	80_R	0.540	0.94
10_A	69_A	0.539	0.94
188_T	268_L	0.538	0.94
190_N	194_A	0.538	0.94
184_D	274_T	0.536	0.94
211_R	241_L	0.534	0.94
131_M	229_L	0.534	0.94
107_P	125_D	0.532	0.94
51_P	55_M	0.529	0.94
18_L	22_Q	0.529	0.94
70_G	226_P	0.528	0.93
55_M	96_F	0.527	0.93
33_P	36_R	0.526	0.93
161_A	167_S	0.526	0.93
67_L	96_F	0.526	0.93
258_H	273_N	0.525	0.93
171_E	205_E	0.524	0.93
215_L	244_T	0.523	0.93
33_P	37_R	0.523	0.93
47_R	113_E	0.523	0.93
7_M	69_A	0.523	0.93
106_G	124_V	0.523	0.93
234_M	237_I	0.521	0.93
86_E	139_N	0.521	0.93
233_R	291_N	0.519	0.93
8_A	103_S	0.518	0.93
212_A	238_K	0.517	0.93
273_N	276_N	0.516	0.93
19_D	56_T	0.516	0.93
216_D	220_E	0.515	0.93
218_I	267_F	0.515	0.93
276_N	280_N	0.512	0.92
67_L	76_Y	0.512	0.92
97_S	113_E	0.511	0.92
204_S	243_K	0.510	0.92
245_H	263_Q	0.510	0.92
78_K	156_A	0.509	0.92
35_R	109_G	0.508	0.92
116_H	283_H	0.508	0.92
275_Q	282_I	0.507	0.92
160_L	167_S	0.505	0.92
38_W	49_G	0.505	0.92
271_Y	282_I	0.503	0.92
236_E	290_N	0.503	0.92
244_T	264_G	0.503	0.92
110_W	123_V	0.500	0.92

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
3u65B	1	0.2881	41.4	0.96	Contact Map
2pfyA	1	0.2847	40.6	0.961	Contact Map
2hpgA	1	0.2881	38	0.961	Contact Map
4nguA	1	0.3017	37.5	0.961	Contact Map
4pe3A	1	0.3085	37.3	0.961	Contact Map
4pbqA	1	0.2915	35.3	0.962	Contact Map
4ovsA	1	0.2915	33.6	0.962	Contact Map
2pfzA	1	0.2983	28.7	0.964	Contact Map
4n8gA	3	0.3288	28.7	0.964	Contact Map
2zzvA	2	0.3356	25.1	0.965	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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