DUF4855 - PFAM28P - GREMLIN Contacts

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DUF4855 - Domain of unknown function (DUF4855)

PFAM:	PF16147	Sequences: DLVLIYNGGYHRTGDWTKEDFLPYVAYVDEDGKKDWLFDGFLFLEFSDGSGRGFAPGYGGKPATKEDWEWYLDRLFAPGGNLDALDEAVGEAKAKLGKPDYKRKVVLMIPYPIPGQTDFGDLDGDGLDFSFSLEDRIKAVKWYIDEVLERFNAANYKNLELAGFYWLAESISTDPDDEELVKAVADYVHSKGLKFYWIPYYGAPGYDDWKELGFDAAYLQPNYFFNEDVPDSRLDDAAALAKKYGMGVEMEFDERVLTDPAFRDRLYDYLDAGVEYGYMKNAALAYYQGGGALYDLARSTDPEDRELYDDLYQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	313 (309)
Sequences:	624 (561)
Seq/√Len:	31.9
META:	0.821

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
18_K	91_E	4.298	1.00
102_K	160_E	4.273	1.00
146_E	149_E	4.227	1.00
189_H	215_D	3.993	1.00
185_A	189_H	3.394	1.00
185_A	195_F	3.383	1.00
107_L	147_V	3.233	1.00
104_K	160_E	3.122	1.00
125_D	129_F	3.106	1.00
146_E	150_R	3.087	1.00
86_D	157_K	3.071	1.00
145_D	187_Y	2.944	1.00
73_D	150_R	2.833	1.00
83_D	156_Y	2.726	1.00
195_F	214_F	2.693	1.00
35_D	312_Y	2.487	1.00
121_D	125_D	2.467	0.99
148_L	151_F	2.390	0.99
266_L	311_L	2.388	0.99
218_Y	285_A	2.377	0.99
234_L	272_A	2.339	0.99
217_A	246_M	2.292	0.99
121_D	126_G	2.240	0.99
121_D	129_F	2.218	0.99
43_F	85_L	2.168	0.99
125_D	138_K	2.155	0.99
129_F	139_A	2.146	0.98
86_D	159_L	2.136	0.98
29_D	33_K	2.101	0.98
93_K	158_N	2.084	0.98
187_Y	191_K	2.080	0.98
141_K	187_Y	2.061	0.98
123_D	138_K	2.008	0.98
72_L	146_E	2.007	0.98
21_F	85_L	1.974	0.97
109_I	140_V	1.964	0.97
41_F	103_R	1.960	0.97
267_Y	310_D	1.917	0.97
109_I	184_V	1.916	0.97
90_G	158_N	1.915	0.97
89_V	103_R	1.887	0.97
209_W	217_A	1.829	0.96
273_G	278_Y	1.823	0.96
237_A	248_V	1.822	0.96
305_R	309_D	1.818	0.96
273_G	279_M	1.817	0.96
26_A	92_A	1.794	0.95
34_K	95_K	1.771	0.95
82_L	107_L	1.760	0.95
83_D	87_E	1.758	0.95
2_L	106_V	1.754	0.95
224_F	253_D	1.719	0.94
148_L	164_F	1.716	0.94
72_L	147_V	1.710	0.94
149_E	153_A	1.684	0.93
5_I	21_F	1.674	0.93
111_Y	168_A	1.659	0.93
25_V	41_F	1.652	0.93
208_D	211_E	1.638	0.93
164_F	193_L	1.635	0.92
44_L	108_M	1.634	0.92
24_Y	288_Q	1.627	0.92
141_K	145_D	1.608	0.92
198_I	249_E	1.592	0.91
255_R	262_F	1.580	0.91
6_Y	44_L	1.579	0.91
106_V	196_Y	1.569	0.91
219_L	240_L	1.558	0.90
82_L	159_L	1.481	0.88
3_V	24_Y	1.477	0.88
85_L	105_V	1.477	0.88
169_E	220_Q	1.474	0.88
88_A	92_A	1.473	0.88
126_G	129_F	1.458	0.87
274_V	310_D	1.457	0.87
181_V	212_L	1.444	0.87
219_L	237_A	1.438	0.87
293_L	311_L	1.428	0.86
220_Q	251_E	1.425	0.86
122_L	138_K	1.410	0.85
274_V	279_M	1.410	0.85
82_L	154_A	1.389	0.85
238_A	273_G	1.383	0.84
51_G	54_F	1.376	0.84
225_F	269_Y	1.375	0.84
128_D	131_F	1.359	0.83
165_Y	251_E	1.351	0.83
148_L	193_L	1.349	0.83
64_T	67_D	1.344	0.83
209_W	246_M	1.339	0.82
223_Y	234_L	1.338	0.82
224_F	255_R	1.337	0.82
145_D	191_K	1.335	0.82
69_E	73_D	1.334	0.82
137_I	183_A	1.333	0.82
119_F	273_G	1.325	0.82
25_V	89_V	1.309	0.81
80_G	84_A	1.301	0.80
16_W	139_A	1.288	0.80
188_V	195_F	1.277	0.79
2_L	40_G	1.276	0.79
7_N	74_R	1.243	0.77
108_M	167_L	1.241	0.77
272_A	276_Y	1.240	0.77
112_P	140_V	1.232	0.77
238_A	278_Y	1.225	0.76
120_G	142_W	1.207	0.75
119_F	142_W	1.187	0.74
71_Y	75_L	1.186	0.74
110_P	247_G	1.185	0.74
86_D	158_N	1.176	0.73
165_Y	220_Q	1.171	0.73
218_Y	247_G	1.160	0.72
37_L	312_Y	1.149	0.71
288_Q	294_Y	1.143	0.71
219_L	241_A	1.142	0.71
94_A	157_K	1.140	0.71
221_P	269_Y	1.134	0.70
202_G	219_L	1.131	0.70
123_D	129_F	1.129	0.70
79_G	83_D	1.115	0.69
16_W	106_V	1.112	0.69
17_T	20_D	1.102	0.68
127_L	131_F	1.096	0.68
200_Y	203_A	1.096	0.68
18_K	87_E	1.082	0.67
297_A	305_R	1.079	0.66
86_D	154_A	1.076	0.66
86_D	156_Y	1.073	0.66
288_Q	291_G	1.071	0.66
296_L	307_L	1.064	0.65
206_Y	219_L	1.064	0.65
218_Y	283_A	1.060	0.65
263_R	267_Y	1.054	0.65
110_P	143_Y	1.051	0.64
305_R	308_Y	1.050	0.64
220_Q	287_Y	1.050	0.64
274_V	312_Y	1.046	0.64
171_I	212_L	1.044	0.64
42_L	198_I	1.044	0.64
117_T	130_S	1.044	0.64
3_V	288_Q	1.043	0.64
231_D	268_D	1.040	0.64
229_V	233_R	1.038	0.63
138_K	141_K	1.036	0.63
12_R	45_E	1.028	0.63
250_M	270_L	1.028	0.63
144_I	191_K	1.013	0.61
36_W	89_V	1.012	0.61
125_D	131_F	1.011	0.61
137_I	180_L	1.009	0.61
46_F	58_Y	1.007	0.61
187_Y	190_S	0.996	0.60
169_E	251_E	0.994	0.60
144_I	187_Y	0.992	0.60
147_V	164_F	0.987	0.59
64_T	116_Q	0.981	0.59
296_L	311_L	0.979	0.59
237_A	241_A	0.969	0.58
76_F	195_F	0.955	0.57
68_W	112_P	0.950	0.56
278_Y	282_A	0.949	0.56
250_M	286_Y	0.943	0.56
70_W	74_R	0.937	0.55
46_F	167_L	0.932	0.55
254_E	292_A	0.930	0.55
208_D	212_L	0.930	0.55
165_Y	249_E	0.929	0.55
306_E	310_D	0.923	0.54
195_F	219_L	0.923	0.54
93_K	101_Y	0.912	0.53
30_E	33_K	0.908	0.53
27_Y	34_K	0.908	0.53
184_V	209_W	0.901	0.52
86_D	90_G	0.901	0.52
112_P	136_R	0.898	0.52
265_R	269_Y	0.896	0.52
21_F	43_F	0.895	0.52
82_L	156_Y	0.895	0.52
122_L	129_F	0.890	0.52
112_P	166_W	0.881	0.51
144_I	188_V	0.880	0.51
165_Y	169_E	0.879	0.51
64_T	118_D	0.876	0.50
199_P	220_Q	0.872	0.50
266_L	296_L	0.872	0.50
251_E	287_Y	0.868	0.50
90_G	157_K	0.861	0.49
75_L	107_L	0.860	0.49
75_L	81_N	0.857	0.49
1_D	284_L	0.857	0.49
72_L	149_E	0.856	0.49
65_K	69_E	0.854	0.49
235_D	276_Y	0.852	0.48
65_K	121_D	0.852	0.48
119_F	122_L	0.850	0.48
264_D	268_D	0.846	0.48
131_F	134_E	0.841	0.48
25_V	92_A	0.835	0.47
126_G	131_F	0.833	0.47
90_G	93_K	0.830	0.47
223_Y	272_A	0.825	0.46
36_W	101_Y	0.824	0.46
45_E	108_M	0.819	0.46
265_R	272_A	0.819	0.46
127_L	139_A	0.816	0.46
86_D	100_D	0.815	0.45
225_F	265_R	0.814	0.45
169_E	199_P	0.810	0.45
247_G	282_A	0.808	0.45
27_Y	35_D	0.806	0.45
16_W	42_L	0.805	0.45
54_F	58_Y	0.805	0.45
233_R	237_A	0.804	0.45
307_L	311_L	0.800	0.44
225_F	241_A	0.798	0.44
87_E	90_G	0.792	0.44
27_Y	308_Y	0.790	0.43
156_Y	234_L	0.790	0.43
111_Y	166_W	0.786	0.43
253_D	289_G	0.786	0.43
267_Y	271_D	0.784	0.43
156_Y	228_D	0.784	0.43
227_E	277_G	0.783	0.43
252_F	256_V	0.782	0.43
271_D	275_E	0.782	0.43
4_L	198_I	0.781	0.43
271_D	310_D	0.779	0.43
5_I	41_F	0.779	0.43
84_A	286_Y	0.777	0.42
65_K	119_F	0.777	0.42
78_P	83_D	0.774	0.42
19_E	152_N	0.772	0.42
170_S	212_L	0.770	0.42
150_R	153_A	0.769	0.42
203_A	208_D	0.769	0.42
90_G	105_V	0.768	0.42
76_F	84_A	0.768	0.42
302_P	305_R	0.766	0.41
184_V	195_F	0.765	0.41
200_Y	289_G	0.765	0.41
223_Y	293_L	0.763	0.41
43_F	205_G	0.762	0.41
149_E	154_A	0.759	0.41
1_D	286_Y	0.759	0.41
26_A	36_W	0.754	0.41
23_P	297_A	0.750	0.40
27_Y	312_Y	0.748	0.40
279_M	312_Y	0.747	0.40
178_E	208_D	0.745	0.40
198_I	265_R	0.743	0.40
78_P	154_A	0.742	0.40
111_Y	177_D	0.736	0.39
198_I	225_F	0.736	0.39
40_G	218_Y	0.731	0.39
144_I	164_F	0.730	0.39
206_Y	240_L	0.729	0.39
170_S	204_P	0.728	0.39
118_D	128_D	0.726	0.38
62_P	111_Y	0.724	0.38
71_Y	108_M	0.723	0.38
288_Q	292_A	0.721	0.38
220_Q	249_E	0.719	0.38
159_L	231_D	0.718	0.38
8_G	217_A	0.713	0.37
304_D	310_D	0.712	0.37
104_K	162_A	0.710	0.37
247_G	309_D	0.709	0.37
251_E	269_Y	0.707	0.37
41_F	71_Y	0.704	0.37
75_L	180_L	0.704	0.37
247_G	285_A	0.703	0.37
294_Y	298_R	0.703	0.37
23_P	294_Y	0.700	0.36
286_Y	311_L	0.698	0.36
21_F	25_V	0.692	0.36
119_F	279_M	0.690	0.36
1_D	159_L	0.689	0.36
31_D	271_D	0.684	0.35
76_F	257_L	0.682	0.35
119_F	238_A	0.682	0.35
49_G	70_W	0.682	0.35
170_S	254_E	0.680	0.35
291_G	295_D	0.679	0.35
11_H	141_K	0.675	0.34
232_S	236_D	0.674	0.34
123_D	126_G	0.673	0.34
3_V	9_G	0.672	0.34
201_Y	233_R	0.670	0.34
220_Q	225_F	0.669	0.34
42_L	285_A	0.669	0.34
248_V	278_Y	0.669	0.34
225_F	251_E	0.668	0.34
79_G	149_E	0.666	0.34
148_L	191_K	0.666	0.34
108_M	237_A	0.665	0.34
110_P	147_V	0.665	0.34
44_L	198_I	0.665	0.34
263_R	307_L	0.661	0.33
299_S	304_D	0.659	0.33
198_I	251_E	0.659	0.33
72_L	150_R	0.659	0.33
26_A	34_K	0.658	0.33
65_K	120_G	0.655	0.33
252_F	292_A	0.654	0.33
235_D	272_A	0.653	0.33
28_V	305_R	0.653	0.33
136_R	181_V	0.652	0.33
168_A	177_D	0.652	0.33
36_W	99_P	0.651	0.33
44_L	167_L	0.650	0.33
71_Y	245_G	0.649	0.33
165_Y	199_P	0.645	0.32
7_N	75_L	0.644	0.32
39_D	165_Y	0.642	0.32
91_E	151_F	0.640	0.32
124_G	127_L	0.639	0.32
124_G	245_G	0.636	0.32
239_A	243_K	0.635	0.32
155_N	161_L	0.634	0.32
273_G	284_L	0.634	0.32
152_N	182_K	0.632	0.31
77_A	80_G	0.629	0.31
207_D	244_Y	0.626	0.31
23_P	85_L	0.624	0.31
147_V	156_Y	0.622	0.31
68_W	139_A	0.620	0.31
199_P	251_E	0.620	0.31
92_A	308_Y	0.619	0.30
37_L	51_G	0.619	0.30
247_G	266_L	0.617	0.30
272_A	278_Y	0.614	0.30
52_R	56_P	0.614	0.30
235_D	239_A	0.614	0.30
169_E	287_Y	0.613	0.30
91_E	94_A	0.612	0.30
88_A	96_L	0.612	0.30
199_P	225_F	0.610	0.30
136_R	201_Y	0.610	0.30
120_G	135_D	0.610	0.30
45_E	167_L	0.609	0.30
79_G	87_E	0.609	0.30
44_L	109_I	0.606	0.30
201_Y	219_L	0.606	0.30
123_D	131_F	0.605	0.30
201_Y	236_D	0.604	0.29
20_D	291_G	0.603	0.29
97_G	155_N	0.602	0.29
109_I	203_A	0.599	0.29
252_F	311_L	0.599	0.29
144_I	183_A	0.599	0.29
138_K	250_M	0.598	0.29
15_D	158_N	0.595	0.29
103_R	312_Y	0.594	0.29
194_K	215_D	0.593	0.29
309_D	312_Y	0.590	0.28
106_V	285_A	0.590	0.28
152_N	300_T	0.589	0.28
140_V	184_V	0.588	0.28
26_A	95_K	0.586	0.28
23_P	43_F	0.581	0.28
16_W	24_Y	0.580	0.28
198_I	220_Q	0.580	0.28
107_L	188_V	0.578	0.28
274_V	278_Y	0.578	0.28
107_L	110_P	0.577	0.28
141_K	190_S	0.577	0.28
27_Y	136_R	0.576	0.28
1_D	65_K	0.574	0.27
164_F	187_Y	0.574	0.27
63_A	139_A	0.572	0.27
25_V	36_W	0.572	0.27
250_M	266_L	0.572	0.27
51_G	70_W	0.569	0.27
136_R	307_L	0.568	0.27
166_W	177_D	0.566	0.27
38_F	286_Y	0.565	0.27
224_F	265_R	0.563	0.27
100_D	190_S	0.561	0.27
1_D	19_E	0.560	0.27
92_A	96_L	0.558	0.26
5_I	24_Y	0.558	0.26
126_G	138_K	0.555	0.26
235_D	268_D	0.555	0.26
89_V	92_A	0.553	0.26
200_Y	205_G	0.553	0.26
152_N	157_K	0.553	0.26
96_L	123_D	0.553	0.26
66_E	141_K	0.551	0.26
144_I	210_K	0.550	0.26
28_V	297_A	0.550	0.26
18_K	96_L	0.550	0.26
116_Q	234_L	0.549	0.26
83_D	154_A	0.548	0.26
8_G	247_G	0.548	0.26
92_A	128_D	0.547	0.26
208_D	246_M	0.546	0.26
69_E	72_L	0.545	0.26
213_G	233_R	0.544	0.26
7_N	81_N	0.543	0.25
162_A	180_L	0.543	0.25
151_F	159_L	0.542	0.25
164_F	188_V	0.542	0.25
44_L	220_Q	0.542	0.25
39_D	104_K	0.540	0.25
106_V	163_G	0.538	0.25
221_P	251_E	0.538	0.25
257_L	303_E	0.537	0.25
119_F	218_Y	0.537	0.25
74_R	81_N	0.536	0.25
1_D	7_N	0.536	0.25
270_L	279_M	0.534	0.25
107_L	270_L	0.534	0.25
105_V	210_K	0.532	0.25
186_D	223_Y	0.532	0.25
14_G	20_D	0.531	0.25
234_L	237_A	0.528	0.25
35_D	140_V	0.527	0.24
137_I	203_A	0.527	0.24
215_D	247_G	0.526	0.24
1_D	280_K	0.526	0.24
22_L	91_E	0.525	0.24
7_N	201_Y	0.525	0.24
218_Y	311_L	0.523	0.24
119_F	131_F	0.523	0.24
165_Y	198_I	0.523	0.24
45_E	51_G	0.522	0.24
93_K	103_R	0.522	0.24
107_L	116_Q	0.520	0.24
210_K	245_G	0.519	0.24
100_D	300_T	0.519	0.24
55_A	58_Y	0.519	0.24
269_Y	287_Y	0.518	0.24
38_F	41_F	0.517	0.24
42_L	156_Y	0.517	0.24
94_A	155_N	0.517	0.24
27_Y	69_E	0.515	0.24
124_G	129_F	0.514	0.24
186_D	190_S	0.514	0.24
270_L	297_A	0.514	0.24
71_Y	180_L	0.514	0.24
32_G	138_K	0.513	0.24
143_Y	209_W	0.513	0.24
79_G	156_Y	0.513	0.24
289_G	292_A	0.513	0.24
72_L	107_L	0.512	0.24
308_Y	312_Y	0.512	0.24
203_A	207_D	0.511	0.24
201_Y	240_L	0.510	0.23
205_G	219_L	0.508	0.23
50_S	67_D	0.507	0.23
248_V	273_G	0.505	0.23
78_P	123_D	0.505	0.23
161_L	164_F	0.505	0.23
293_L	296_L	0.504	0.23
63_A	67_D	0.504	0.23
224_F	252_F	0.504	0.23
10_Y	14_G	0.504	0.23
144_I	223_Y	0.503	0.23
185_A	235_D	0.503	0.23
41_F	85_L	0.502	0.23
239_A	293_L	0.501	0.23
77_A	160_E	0.501	0.23
169_E	225_F	0.500	0.23

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
1bqcA	1	0.4537	75.1	0.957	Contact Map
1ceoA	1	0.4537	56.6	0.962	Contact Map
2whlA	1	0.4441	56.5	0.962	Contact Map
3w0kA	1	0.4441	51.5	0.963	Contact Map
4yheA	1	0.5112	51.2	0.964	Contact Map
3p6lA	2	0.5559	50.2	0.964	Contact Map
1h4pA	1	0.5655	50.2	0.964	Contact Map
3aofA	1	0.4633	48.1	0.964	Contact Map
3hjeA	1	0.4409	47.6	0.964	Contact Map
4aweA	1	0.5272	46.6	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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