DUF3080 - PFAM28P - GREMLIN Contacts

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DUF3080 - Protein of unknown function (DUF3080)

PFAM:	PF11279	Sequences: LDDYLQRLARVLDVEAPEPSPPPPLPRLPRRRELLLPIPELRIGLLDFLSLRGCELQQLIAERNSSLGKVADPSQRLLYELRFLRALPACLLPEEEDEELAATLQEALQQKRQQLPAVFWNALLASEEWRQFFSLSSGLLPYPADTSSELLQALAALNQLVQRWLDGDLPADSDELEQHLQTLRKSRLGGQLLRSLALLTAWLNQATALLEQRLARRLCPNGRPTPRARILRNVFQKFYIGEVQPYLAQLDRRYQQLLPLLQALEQQLPAPPPALQPYYQRYLSQQRDSLWQQFRQATRRHVQAWQQLLKQCGLSP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	316 (313)
Sequences:	581 (502)
Seq/√Len:	28.3
META:	0.527

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_S	177_E	6.050	1.00
83_F	87_L	5.441	1.00
75_Q	177_E	4.791	1.00
211_E	300_R	4.161	1.00
239_Y	302_V	3.980	1.00
80_E	118_V	3.119	1.00
230_I	233_N	3.078	1.00
3_D	242_E	2.989	1.00
199_L	250_L	2.940	1.00
63_R	80_E	2.878	1.00
177_E	180_L	2.866	1.00
47_D	103_T	2.858	1.00
87_L	107_A	2.809	1.00
76_R	80_E	2.677	1.00
235_F	305_W	2.579	0.99
181_Q	185_K	2.458	0.99
235_F	246_Y	2.418	0.99
207_T	235_F	2.403	0.99
207_T	304_A	2.338	0.99
83_F	107_A	2.299	0.99
7_R	244_Q	2.219	0.98
193_L	290_L	2.200	0.98
52_R	57_Q	2.173	0.98
74_S	180_L	2.150	0.98
65_S	70_V	2.043	0.97
75_Q	78_L	2.027	0.97
59_L	79_Y	1.973	0.96
299_R	303_Q	1.936	0.96
251_D	295_R	1.933	0.96
196_L	250_L	1.917	0.96
126_S	129_W	1.881	0.95
239_Y	246_Y	1.867	0.95
7_R	233_N	1.863	0.95
172_D	175_E	1.820	0.94
72_D	177_E	1.805	0.94
62_E	82_R	1.796	0.94
28_L	133_F	1.720	0.92
195_S	246_Y	1.707	0.92
10_R	238_F	1.706	0.92
234_V	237_K	1.704	0.92
80_E	111_K	1.675	0.91
39_P	114_Q	1.672	0.91
220_P	225_T	1.672	0.91
309_L	316_P	1.660	0.91
279_Y	282_Y	1.638	0.90
3_D	10_R	1.633	0.90
207_T	300_R	1.611	0.89
196_L	294_F	1.606	0.89
13_D	105_Q	1.602	0.89
44_G	69_K	1.575	0.88
87_L	108_L	1.572	0.88
77_L	122_A	1.567	0.88
221_N	225_T	1.566	0.88
7_R	234_V	1.563	0.88
128_E	184_R	1.542	0.87
305_W	312_C	1.540	0.87
206_A	209_L	1.530	0.87
48_F	132_F	1.524	0.86
301_H	312_C	1.523	0.86
7_R	306_Q	1.499	0.85
34_L	130_R	1.495	0.85
6_Q	10_R	1.443	0.83
275_L	278_Y	1.442	0.83
238_F	242_E	1.442	0.83
74_S	128_E	1.438	0.83
49_L	57_Q	1.422	0.82
234_V	238_F	1.420	0.82
3_D	7_R	1.417	0.82
235_F	239_Y	1.417	0.82
214_L	311_Q	1.416	0.82
114_Q	118_V	1.387	0.81
217_R	311_Q	1.377	0.80
133_F	261_L	1.369	0.80
173_S	218_L	1.364	0.79
115_L	192_L	1.344	0.78
200_T	207_T	1.332	0.78
252_R	307_Q	1.330	0.78
204_N	297_A	1.321	0.77
207_T	297_A	1.311	0.77
7_R	238_F	1.306	0.76
18_E	26_P	1.301	0.76
113_Q	277_P	1.293	0.76
58_Q	61_A	1.281	0.75
74_S	78_L	1.272	0.74
136_S	139_L	1.270	0.74
202_W	254_Y	1.263	0.74
31_R	130_R	1.262	0.74
76_R	118_V	1.258	0.74
71_A	75_Q	1.253	0.73
132_F	190_G	1.250	0.73
251_D	255_Q	1.247	0.73
10_R	230_I	1.247	0.73
156_A	179_H	1.246	0.73
203_L	297_A	1.244	0.73
291_W	295_R	1.241	0.72
8_L	12_L	1.237	0.72
120_W	272_P	1.236	0.72
11_V	133_F	1.229	0.72
3_D	6_Q	1.229	0.72
145_D	250_L	1.222	0.71
57_Q	61_A	1.220	0.71
232_R	236_Q	1.216	0.71
5_L	206_A	1.215	0.71
213_R	311_Q	1.212	0.71
51_L	61_A	1.207	0.70
51_L	71_A	1.201	0.70
48_F	57_Q	1.199	0.70
31_R	127_E	1.196	0.70
4_Y	45_L	1.190	0.69
128_E	206_A	1.190	0.69
24_P	41_L	1.188	0.69
84_L	108_L	1.173	0.68
204_N	293_Q	1.160	0.67
308_L	313_G	1.157	0.67
181_Q	184_R	1.155	0.67
155_A	243_V	1.138	0.66
66_S	256_Q	1.136	0.66
4_Y	301_H	1.134	0.65
42_R	48_F	1.134	0.65
306_Q	312_C	1.133	0.65
7_R	10_R	1.126	0.65
146_T	149_E	1.125	0.65
84_L	87_L	1.123	0.65
298_T	302_V	1.119	0.64
72_D	75_Q	1.118	0.64
41_L	110_Q	1.117	0.64
11_V	231_L	1.100	0.63
89_A	106_E	1.100	0.63
244_Q	248_A	1.099	0.63
250_L	259_P	1.088	0.62
69_K	206_A	1.071	0.61
80_E	122_A	1.070	0.61
59_L	82_R	1.070	0.61
69_K	233_N	1.067	0.61
81_L	85_R	1.061	0.60
18_E	262_Q	1.055	0.60
210_L	214_L	1.048	0.59
43_I	100_L	1.042	0.59
156_A	159_Q	1.039	0.59
48_F	61_A	1.039	0.59
112_R	261_L	1.038	0.58
7_R	11_V	1.037	0.58
42_R	80_E	1.037	0.58
34_L	71_A	1.037	0.58
80_E	116_P	1.031	0.58
123_L	182_T	1.030	0.58
230_I	234_V	1.029	0.58
235_F	309_L	1.027	0.58
188_L	253_R	1.026	0.58
199_L	247_L	1.025	0.57
304_A	309_L	1.023	0.57
183_L	234_V	1.020	0.57
149_E	152_Q	1.008	0.56
61_A	100_L	1.001	0.56
30_R	123_L	1.001	0.56
79_Y	305_W	0.997	0.55
69_K	266_Q	0.994	0.55
199_L	294_F	0.990	0.55
65_S	73_P	0.990	0.55
203_L	291_W	0.984	0.54
8_L	209_L	0.982	0.54
163_R	166_D	0.977	0.54
53_G	57_Q	0.974	0.54
38_I	114_Q	0.971	0.53
36_L	157_L	0.968	0.53
192_L	254_Y	0.962	0.53
10_R	244_Q	0.960	0.52
60_I	290_L	0.959	0.52
228_A	309_L	0.959	0.52
153_A	156_A	0.958	0.52
24_P	36_L	0.955	0.52
230_I	309_L	0.951	0.52
157_L	183_L	0.948	0.52
117_A	154_L	0.946	0.51
254_Y	291_W	0.945	0.51
178_Q	250_L	0.943	0.51
80_E	246_Y	0.941	0.51
105_Q	113_Q	0.939	0.51
163_R	168_D	0.938	0.51
11_V	32_R	0.936	0.51
42_R	257_L	0.931	0.50
57_Q	180_L	0.930	0.50
196_L	254_Y	0.929	0.50
83_F	123_L	0.927	0.50
233_N	244_Q	0.927	0.50
120_W	190_G	0.926	0.50
4_Y	8_L	0.925	0.50
132_F	189_G	0.924	0.50
123_L	129_W	0.921	0.49
10_R	309_L	0.914	0.49
235_F	306_Q	0.914	0.49
81_L	115_L	0.911	0.49
196_L	298_T	0.910	0.49
309_L	314_L	0.909	0.49
8_L	207_T	0.908	0.48
243_V	255_Q	0.906	0.48
78_L	173_S	0.906	0.48
78_L	176_L	0.904	0.48
245_P	305_W	0.903	0.48
8_L	206_A	0.902	0.48
66_S	70_V	0.901	0.48
78_L	177_E	0.898	0.48
91_L	105_Q	0.898	0.48
131_Q	187_R	0.897	0.48
36_L	113_Q	0.896	0.48
239_Y	247_L	0.889	0.47
77_L	119_F	0.888	0.47
84_L	165_L	0.872	0.46
233_N	248_A	0.870	0.46
275_L	279_Y	0.870	0.46
19_P	205_Q	0.864	0.45
70_V	246_Y	0.862	0.45
63_R	69_K	0.859	0.45
3_D	238_F	0.854	0.44
12_L	308_L	0.852	0.44
69_K	111_K	0.851	0.44
272_P	278_Y	0.850	0.44
5_L	190_G	0.846	0.44
276_Q	279_Y	0.844	0.44
43_I	48_F	0.843	0.44
91_L	101_A	0.843	0.44
166_D	262_Q	0.843	0.44
180_L	184_R	0.843	0.44
233_N	237_K	0.843	0.44
38_I	121_N	0.835	0.43
49_L	52_R	0.832	0.43
256_Q	259_P	0.830	0.43
99_E	161_V	0.824	0.42
130_R	133_F	0.821	0.42
239_Y	305_W	0.819	0.42
94_E	310_K	0.818	0.42
188_L	192_L	0.815	0.41
277_P	303_Q	0.813	0.41
21_P	99_E	0.808	0.41
136_S	191_Q	0.807	0.41
107_A	294_F	0.807	0.41
272_P	276_Q	0.802	0.40
48_F	128_E	0.798	0.40
139_L	194_R	0.795	0.40
128_E	189_G	0.794	0.40
288_D	307_Q	0.794	0.40
294_F	305_W	0.792	0.40
190_G	313_G	0.790	0.40
56_L	103_T	0.785	0.39
56_L	77_L	0.785	0.39
234_V	244_Q	0.782	0.39
71_A	130_R	0.781	0.39
11_V	233_N	0.780	0.39
124_L	239_Y	0.778	0.39
243_V	315_S	0.775	0.38
29_P	120_W	0.775	0.38
69_K	114_Q	0.774	0.38
125_A	190_G	0.771	0.38
50_S	80_E	0.766	0.38
21_P	102_A	0.765	0.38
308_L	311_Q	0.765	0.38
152_Q	156_A	0.763	0.38
222_G	302_V	0.760	0.37
43_I	298_T	0.757	0.37
243_V	252_R	0.757	0.37
100_L	283_L	0.756	0.37
92_L	288_D	0.756	0.37
226_P	230_I	0.754	0.37
150_L	261_L	0.753	0.37
218_L	311_Q	0.748	0.36
26_P	206_A	0.745	0.36
272_P	275_L	0.741	0.36
38_I	118_V	0.741	0.36
30_R	241_G	0.740	0.36
37_P	99_E	0.737	0.36
47_D	100_L	0.737	0.36
49_L	126_S	0.736	0.36
109_Q	208_A	0.734	0.35
247_L	298_T	0.734	0.35
228_A	314_L	0.733	0.35
264_L	303_Q	0.732	0.35
82_R	183_L	0.731	0.35
107_A	183_L	0.730	0.35
225_T	229_R	0.728	0.35
93_P	98_E	0.727	0.35
36_L	117_A	0.726	0.35
6_Q	60_I	0.726	0.35
123_L	268_L	0.722	0.35
52_R	61_A	0.722	0.35
45_L	100_L	0.719	0.34
203_L	206_A	0.719	0.34
6_Q	238_F	0.718	0.34
41_L	157_L	0.716	0.34
129_W	180_L	0.716	0.34
160_L	188_L	0.713	0.34
121_N	235_F	0.712	0.34
244_Q	302_V	0.712	0.34
204_N	296_Q	0.709	0.34
34_L	291_W	0.705	0.33
47_D	161_V	0.703	0.33
268_L	272_P	0.702	0.33
242_E	245_P	0.701	0.33
97_D	198_L	0.701	0.33
71_A	133_F	0.700	0.33
100_L	103_T	0.696	0.33
46_L	63_R	0.696	0.33
78_L	180_L	0.694	0.33
41_L	49_L	0.694	0.33
54_C	68_G	0.693	0.33
115_L	119_F	0.690	0.32
54_C	64_N	0.688	0.32
4_Y	7_R	0.688	0.32
119_F	268_L	0.686	0.32
277_P	296_Q	0.686	0.32
239_Y	251_D	0.685	0.32
13_D	156_A	0.682	0.32
71_A	190_G	0.675	0.31
63_R	76_R	0.675	0.31
11_V	244_Q	0.674	0.31
104_L	210_L	0.673	0.31
207_T	211_E	0.672	0.31
94_E	101_A	0.670	0.31
49_L	311_Q	0.669	0.31
121_N	231_L	0.668	0.31
11_V	18_E	0.667	0.31
76_R	161_V	0.666	0.31
219_C	312_C	0.664	0.31
10_R	235_F	0.664	0.31
2_D	243_V	0.662	0.31
188_L	298_T	0.657	0.30
104_L	157_L	0.654	0.30
61_A	64_N	0.653	0.30
3_D	20_S	0.653	0.30
183_L	232_R	0.653	0.30
82_R	165_L	0.652	0.30
77_L	87_L	0.651	0.30
41_L	239_Y	0.650	0.30
227_R	230_I	0.649	0.30
41_L	195_S	0.649	0.30
60_I	111_K	0.648	0.30
69_K	218_L	0.647	0.30
32_R	181_Q	0.645	0.29
12_L	214_L	0.645	0.29
111_K	231_L	0.643	0.29
98_E	102_A	0.640	0.29
235_F	253_R	0.640	0.29
47_D	226_P	0.638	0.29
214_L	304_A	0.637	0.29
127_E	215_A	0.636	0.29
230_I	244_Q	0.634	0.29
201_A	205_Q	0.632	0.29
65_S	190_G	0.631	0.29
222_G	225_T	0.628	0.28
72_D	127_E	0.628	0.28
278_Y	282_Y	0.627	0.28
22_P	25_L	0.627	0.28
199_L	202_W	0.625	0.28
64_N	68_G	0.625	0.28
129_W	133_F	0.624	0.28
80_E	132_F	0.623	0.28
88_P	99_E	0.622	0.28
53_G	61_A	0.622	0.28
70_V	220_P	0.622	0.28
226_P	229_R	0.620	0.28
61_A	121_N	0.620	0.28
50_S	190_G	0.619	0.28
27_R	33_E	0.618	0.28
9_A	108_L	0.616	0.28
149_E	185_K	0.615	0.28
153_A	197_A	0.615	0.28
110_Q	266_Q	0.611	0.27
249_Q	253_R	0.610	0.27
11_V	243_V	0.610	0.27
112_R	158_N	0.609	0.27
15_E	18_E	0.609	0.27
52_R	308_L	0.604	0.27
37_P	109_Q	0.604	0.27
64_N	244_Q	0.603	0.27
53_G	239_Y	0.602	0.27
65_S	125_A	0.602	0.27
176_L	255_Q	0.595	0.26
287_R	291_W	0.595	0.26
46_L	72_D	0.595	0.26
192_L	250_L	0.594	0.26
265_E	268_L	0.594	0.26
147_S	156_A	0.593	0.26
109_Q	300_R	0.592	0.26
70_V	79_Y	0.592	0.26
130_R	239_Y	0.592	0.26
102_A	280_Q	0.592	0.26
25_L	135_L	0.590	0.26
162_Q	289_S	0.589	0.26
9_A	262_Q	0.589	0.26
96_E	102_A	0.586	0.26
84_L	107_A	0.586	0.26
64_N	69_K	0.584	0.26
12_L	209_L	0.584	0.26
228_A	316_P	0.584	0.26
66_S	261_L	0.583	0.26
61_A	254_Y	0.583	0.26
133_F	305_W	0.582	0.26
217_R	226_P	0.580	0.25
50_S	196_L	0.580	0.25
28_L	36_L	0.578	0.25
76_R	142_Y	0.578	0.25
124_L	190_G	0.576	0.25
65_S	189_G	0.575	0.25
142_Y	265_E	0.575	0.25
40_E	204_N	0.573	0.25
90_C	219_C	0.572	0.25
55_E	58_Q	0.570	0.25
83_F	210_L	0.566	0.25
235_F	244_Q	0.564	0.25
241_G	256_Q	0.564	0.25
192_L	253_R	0.564	0.25
62_E	79_Y	0.563	0.24
224_P	314_L	0.561	0.24
136_S	166_D	0.560	0.24
164_W	167_G	0.559	0.24
8_L	179_H	0.556	0.24
54_C	90_C	0.556	0.24
220_P	252_R	0.552	0.24
231_L	305_W	0.551	0.24
9_A	109_Q	0.550	0.24
30_R	113_Q	0.550	0.24
233_N	238_F	0.550	0.24
79_Y	245_P	0.547	0.24
126_S	196_L	0.547	0.24
51_L	246_Y	0.547	0.24
28_L	56_L	0.545	0.23
49_L	193_L	0.543	0.23
28_L	134_S	0.542	0.23
222_G	316_P	0.541	0.23
183_L	250_L	0.540	0.23
50_S	61_A	0.540	0.23
147_S	150_L	0.539	0.23
150_L	296_Q	0.539	0.23
46_L	100_L	0.538	0.23
151_L	243_V	0.537	0.23
239_Y	290_L	0.536	0.23
143_P	191_Q	0.536	0.23
58_Q	248_A	0.536	0.23
80_E	133_F	0.534	0.23
104_L	203_L	0.534	0.23
10_R	233_N	0.531	0.23
102_A	205_Q	0.529	0.23
69_K	246_Y	0.525	0.22
112_R	125_A	0.523	0.22
3_D	149_E	0.523	0.22
24_P	293_Q	0.522	0.22
59_L	305_W	0.522	0.22
60_I	108_L	0.521	0.22
10_R	234_V	0.519	0.22
97_D	284_S	0.517	0.22
13_D	280_Q	0.516	0.22
76_R	177_E	0.515	0.22
65_S	234_V	0.515	0.22
110_Q	195_S	0.514	0.22
102_A	116_P	0.513	0.22
119_F	133_F	0.513	0.22
39_P	118_V	0.511	0.22
29_P	34_L	0.509	0.22
88_P	108_L	0.507	0.21
19_P	152_Q	0.506	0.21
21_P	252_R	0.506	0.21
72_D	183_L	0.505	0.21
120_W	125_A	0.505	0.21
65_S	111_K	0.502	0.21
45_L	184_R	0.502	0.21
48_F	80_E	0.500	0.21
120_W	278_Y	0.500	0.21
229_R	314_L	0.500	0.21
17_P	162_Q	0.500	0.21
60_I	138_G	0.500	0.21
4_Y	46_L	0.500	0.21

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
3hiuA	3	0.212	29.7	0.961	Contact Map
1uptB	2	0.1867	18	0.965	Contact Map
2gyqA	2	0.2342	17.8	0.965	Contact Map
3oghB	2	0.2215	11.4	0.968	Contact Map
2gs4A	5	0.212	9.7	0.969	Contact Map
4yifA	2	0.1013	7.3	0.97	Contact Map
3fmpB	1	0	6.9	0.971	Contact Map
2ozbB	1	0.3418	5.8	0.972	Contact Map
3fhtA	1	0.1487	5.6	0.972	Contact Map
4etrA	1	0.1962	5.4	0.972	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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