DUF4220 - PFAM28P - GREMLIN Contacts

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DUF4220 - Domain of unknown function (DUF4220)

PFAM:	PF13968	Sequences: WLAYLLADSVATYALGLLSSSPNQLVAFWAPFLLLHLGGPDTITAYSLEDNELWLRHLLTLVVQVAVALYVFYKSWPNLLAAAILRIPLWLLFVVGIIKYGERTWALRSASRNSKLVADYMMEGYRSSAKLVTVDKIWECSLLSPDSDSGPRLKDLCLAFALFKLLKRLFVDLIVLSEADLDKSRDFFLKGDLDAERAFKVIEVELSFMYDFLYTKAPVLHTWRLISLLLTLVAALVLFALSYPSGHDSDKHGYSRVDVAITYVLLVGAILLEVYSLLMLLFSDWTKVWLICKYVRRRKRRWSGSIGQYNLLSSY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	315 (295)
Sequences:	1434 (1184)
Seq/√Len:	68.9
META:	0.041

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_S	12_T	3.458	1.00
1_W	4_Y	3.252	1.00
122_M	125_Y	3.189	1.00
257_V	261_I	3.112	1.00
117_V	120_Y	2.720	1.00
160_F	163_F	2.650	1.00
105_W	109_S	2.599	1.00
163_F	166_L	2.383	1.00
224_R	227_S	2.330	1.00
16_G	19_S	2.285	1.00
238_L	242_S	2.278	1.00
124_G	127_S	2.204	1.00
28_F	266_L	2.198	1.00
184_S	188_F	2.133	1.00
236_L	240_A	2.112	1.00
205_E	208_F	2.106	1.00
144_S	147_S	2.080	1.00
283_S	286_T	2.069	1.00
129_A	132_V	1.999	1.00
163_F	167_K	1.993	1.00
116_L	120_Y	1.988	1.00
181_L	185_R	1.973	1.00
150_G	155_D	1.968	1.00
286_T	290_L	1.917	1.00
13_Y	33_L	1.889	1.00
227_S	231_T	1.880	1.00
224_R	228_L	1.864	1.00
28_F	92_L	1.849	1.00
115_K	118_A	1.829	1.00
47_S	55_L	1.809	1.00
118_A	121_M	1.805	1.00
228_L	231_T	1.805	1.00
8_D	57_H	1.770	1.00
159_A	167_K	1.759	1.00
155_D	197_R	1.752	1.00
114_S	117_V	1.728	1.00
181_L	184_S	1.725	1.00
28_F	32_F	1.706	1.00
260_A	264_V	1.697	1.00
185_R	189_L	1.692	1.00
158_L	161_A	1.691	1.00
54_W	57_H	1.689	1.00
57_H	64_Q	1.673	0.99
18_L	31_P	1.668	0.99
8_D	12_T	1.661	0.99
79_L	84_I	1.638	0.99
32_F	35_L	1.637	0.99
32_F	48_L	1.621	0.99
61_L	64_Q	1.620	0.99
31_P	36_H	1.607	0.99
13_Y	19_S	1.590	0.99
43_I	46_Y	1.588	0.99
122_M	126_R	1.587	0.99
300_R	304_G	1.581	0.99
182_D	185_R	1.572	0.99
178_E	181_L	1.561	0.99
205_E	211_D	1.539	0.99
156_L	163_F	1.538	0.99
234_A	238_L	1.523	0.99
165_L	209_M	1.522	0.99
12_T	60_T	1.522	0.99
238_L	241_L	1.505	0.99
122_M	128_S	1.503	0.99
208_F	211_D	1.502	0.99
79_L	82_A	1.495	0.99
235_A	239_F	1.491	0.99
224_R	239_F	1.477	0.99
15_L	68_A	1.471	0.99
45_A	56_R	1.463	0.99
147_S	153_L	1.458	0.99
45_A	50_D	1.457	0.99
47_S	50_D	1.444	0.98
237_V	241_L	1.442	0.98
102_E	216_K	1.438	0.98
165_L	168_R	1.437	0.98
142_L	145_P	1.425	0.98
93_F	96_G	1.415	0.98
11_A	15_L	1.408	0.98
163_F	208_F	1.404	0.98
31_P	37_L	1.404	0.98
50_D	54_W	1.394	0.98
159_A	204_V	1.394	0.98
38_G	103_R	1.388	0.98
53_L	56_R	1.379	0.98
115_K	119_D	1.377	0.98
96_G	100_Y	1.374	0.98
6_L	13_Y	1.368	0.98
181_L	188_F	1.350	0.98
7_A	11_A	1.346	0.98
44_T	51_N	1.332	0.97
225_L	228_L	1.332	0.97
208_F	284_D	1.331	0.97
141_S	145_P	1.329	0.97
64_Q	70_Y	1.316	0.97
34_L	37_L	1.315	0.97
264_V	279_M	1.311	0.97
51_N	56_R	1.289	0.97
207_S	211_D	1.279	0.97
217_A	222_T	1.276	0.97
160_F	167_K	1.274	0.97
172_D	179_A	1.274	0.97
161_A	165_L	1.269	0.97
106_A	110_A	1.268	0.96
146_D	151_P	1.245	0.96
292_C	295_V	1.243	0.96
142_L	147_S	1.242	0.96
35_L	40_P	1.231	0.96
13_Y	17_L	1.226	0.96
161_A	164_K	1.217	0.96
7_A	19_S	1.216	0.96
121_M	125_Y	1.216	0.96
170_F	173_L	1.213	0.95
2_L	6_L	1.212	0.95
8_D	31_P	1.211	0.95
201_V	205_E	1.210	0.95
50_D	56_R	1.210	0.95
293_K	296_R	1.209	0.95
18_L	26_V	1.205	0.95
199_F	208_F	1.205	0.95
199_F	205_E	1.197	0.95
101_G	105_W	1.197	0.95
180_D	184_S	1.196	0.95
69_L	72_F	1.194	0.95
25_L	258_D	1.192	0.95
57_H	104_T	1.192	0.95
41_D	44_T	1.191	0.95
136_K	140_C	1.186	0.95
1_W	56_R	1.176	0.95
186_D	190_K	1.172	0.95
36_H	39_G	1.172	0.95
147_S	152_R	1.170	0.95
7_A	16_G	1.170	0.95
133_T	138_W	1.166	0.94
183_K	187_F	1.163	0.94
38_G	54_W	1.163	0.94
98_I	156_L	1.133	0.94
236_L	266_L	1.132	0.93
26_V	72_F	1.129	0.93
183_K	186_D	1.123	0.93
114_S	120_Y	1.120	0.93
49_E	107_L	1.119	0.93
179_A	184_S	1.105	0.93
15_L	308_Q	1.099	0.92
44_T	50_D	1.094	0.92
227_S	230_L	1.090	0.92
56_R	64_Q	1.086	0.92
17_L	26_V	1.078	0.92
203_E	211_D	1.078	0.92
135_D	139_E	1.061	0.91
200_K	203_E	1.057	0.91
116_L	121_M	1.041	0.90
46_Y	50_D	1.037	0.90
193_L	197_R	1.036	0.90
168_R	178_E	1.035	0.90
65_V	69_L	1.034	0.90
4_Y	50_D	1.021	0.89
57_H	61_L	1.015	0.89
8_D	36_H	1.012	0.89
107_L	111_S	1.011	0.89
159_A	172_D	1.010	0.89
224_R	231_T	1.008	0.89
37_L	44_T	1.007	0.89
18_L	74_K	1.006	0.89
80_L	84_I	1.004	0.89
82_A	85_L	0.998	0.88
166_L	169_L	0.996	0.88
228_L	277_L	0.994	0.88
76_W	221_H	0.992	0.88
163_F	205_E	0.991	0.88
45_A	53_L	0.989	0.88
134_V	138_W	0.988	0.88
224_R	230_L	0.985	0.88
46_Y	56_R	0.983	0.87
169_L	172_D	0.981	0.87
306_I	309_Y	0.980	0.87
37_L	214_Y	0.976	0.87
123_E	126_R	0.970	0.87
228_L	234_A	0.969	0.87
103_R	109_S	0.965	0.87
117_V	121_M	0.963	0.86
165_L	169_L	0.958	0.86
234_A	242_S	0.943	0.85
30_A	39_G	0.934	0.85
4_Y	216_K	0.925	0.84
49_E	56_R	0.924	0.84
200_K	234_A	0.919	0.84
121_M	124_G	0.919	0.84
73_Y	284_D	0.917	0.84
10_V	63_V	0.916	0.84
177_S	181_L	0.916	0.84
167_K	205_E	0.907	0.83
14_A	171_V	0.902	0.83
54_W	64_Q	0.900	0.82
174_I	199_F	0.898	0.82
107_L	266_L	0.896	0.82
6_L	264_V	0.894	0.82
13_Y	80_L	0.892	0.82
158_L	168_R	0.886	0.81
115_K	121_M	0.881	0.81
156_L	165_L	0.877	0.81
96_G	102_E	0.876	0.81
44_T	49_E	0.867	0.80
298_R	308_Q	0.867	0.80
45_A	214_Y	0.865	0.80
12_T	15_L	0.865	0.80
50_D	215_T	0.865	0.80
44_T	57_H	0.864	0.80
58_L	61_L	0.863	0.80
199_F	287_K	0.862	0.80
11_A	57_H	0.858	0.79
36_H	49_E	0.858	0.79
54_W	58_L	0.857	0.79
143_L	151_P	0.850	0.79
133_T	140_C	0.847	0.78
142_L	146_D	0.847	0.78
305_S	310_N	0.847	0.78
3_A	13_Y	0.843	0.78
251_K	254_Y	0.843	0.78
163_F	171_V	0.843	0.78
136_K	147_S	0.836	0.77
155_D	158_L	0.836	0.77
143_L	147_S	0.833	0.77
115_K	120_Y	0.828	0.77
148_D	152_R	0.828	0.77
2_L	5_L	0.826	0.77
265_L	269_A	0.826	0.77
170_F	186_D	0.824	0.76
79_L	83_A	0.821	0.76
52_E	261_I	0.820	0.76
35_L	92_L	0.819	0.76
285_W	288_V	0.815	0.76
66_A	69_L	0.814	0.76
182_D	186_D	0.812	0.75
146_D	149_S	0.811	0.75
8_D	54_W	0.810	0.75
136_K	139_E	0.809	0.75
14_A	17_L	0.804	0.75
99_K	103_R	0.800	0.74
18_L	68_A	0.797	0.74
248_D	251_K	0.797	0.74
34_L	39_G	0.796	0.74
61_L	100_Y	0.794	0.74
1_W	5_L	0.790	0.73
220_L	269_A	0.785	0.73
203_E	302_W	0.784	0.73
51_N	54_W	0.783	0.73
179_A	186_D	0.781	0.73
159_A	162_L	0.775	0.72
13_Y	71_V	0.773	0.72
165_L	178_E	0.773	0.72
211_D	214_Y	0.772	0.72
280_L	284_D	0.769	0.71
155_D	188_F	0.768	0.71
156_L	204_V	0.762	0.71
209_M	213_L	0.761	0.71
212_F	218_P	0.761	0.71
180_D	188_F	0.758	0.70
59_L	104_T	0.758	0.70
151_P	154_K	0.758	0.70
129_A	147_S	0.758	0.70
110_A	212_F	0.757	0.70
277_L	282_F	0.757	0.70
145_P	150_G	0.757	0.70
147_S	151_P	0.756	0.70
166_L	174_I	0.754	0.70
42_T	210_Y	0.752	0.70
4_Y	37_L	0.751	0.70
32_F	266_L	0.750	0.69
38_G	44_T	0.749	0.69
55_L	65_V	0.745	0.69
116_L	119_D	0.744	0.69
226_I	230_L	0.744	0.69
36_H	40_P	0.743	0.69
101_G	196_E	0.741	0.69
8_D	32_F	0.738	0.68
284_D	301_R	0.735	0.68
42_T	216_K	0.729	0.67
285_W	290_L	0.727	0.67
134_V	137_I	0.724	0.67
214_Y	303_S	0.723	0.67
160_F	166_L	0.723	0.67
39_G	44_T	0.721	0.66
7_A	13_Y	0.721	0.66
162_L	168_R	0.720	0.66
11_A	37_L	0.716	0.66
29_W	36_H	0.716	0.66
147_S	150_G	0.712	0.65
185_R	188_F	0.710	0.65
48_L	75_S	0.708	0.65
205_E	285_W	0.706	0.65
31_P	40_P	0.704	0.65
105_W	277_L	0.701	0.64
141_S	148_D	0.699	0.64
3_A	66_A	0.697	0.64
153_L	196_E	0.695	0.64
187_F	202_I	0.695	0.64
7_A	100_Y	0.690	0.63
157_C	160_F	0.690	0.63
51_N	110_A	0.687	0.63
282_F	287_K	0.687	0.63
177_S	188_F	0.687	0.63
4_Y	8_D	0.684	0.62
100_Y	104_T	0.683	0.62
61_L	65_V	0.680	0.62
169_L	174_I	0.678	0.62
141_S	151_P	0.677	0.62
276_S	283_S	0.676	0.61
30_A	227_S	0.675	0.61
7_A	269_A	0.674	0.61
172_D	204_V	0.672	0.61
207_S	304_G	0.670	0.61
156_L	162_L	0.669	0.61
13_Y	47_S	0.668	0.61
95_V	237_V	0.665	0.60
94_V	298_R	0.664	0.60
43_I	50_D	0.663	0.60
106_A	200_K	0.663	0.60
202_I	263_Y	0.662	0.60
157_C	164_K	0.661	0.60
207_S	275_Y	0.660	0.60
139_E	143_L	0.657	0.59
213_L	216_K	0.655	0.59
19_S	39_G	0.651	0.59
38_G	45_A	0.650	0.58
121_M	137_I	0.650	0.58
37_L	45_A	0.649	0.58
265_L	276_S	0.649	0.58
157_C	161_A	0.647	0.58
149_S	154_K	0.646	0.58
51_N	75_S	0.642	0.58
60_T	73_Y	0.636	0.57
282_F	307_G	0.636	0.57
45_A	64_Q	0.636	0.57
142_L	151_P	0.635	0.57
178_E	185_R	0.635	0.57
41_D	56_R	0.631	0.56
12_T	17_L	0.629	0.56
170_F	211_D	0.627	0.56
119_D	216_K	0.627	0.56
184_S	191_G	0.627	0.56
144_S	148_D	0.626	0.56
31_P	34_L	0.626	0.56
270_I	278_L	0.625	0.55
26_V	225_L	0.621	0.55
8_D	11_A	0.617	0.55
210_Y	215_T	0.616	0.54
41_D	99_K	0.614	0.54
96_G	99_K	0.613	0.54
94_V	158_L	0.612	0.54
199_F	211_D	0.610	0.54
3_A	162_L	0.608	0.53
125_Y	128_S	0.607	0.53
19_S	26_V	0.606	0.53
259_V	263_Y	0.603	0.53
211_D	273_E	0.602	0.53
44_T	215_T	0.602	0.53
164_K	179_A	0.601	0.53
3_A	309_Y	0.601	0.53
100_Y	213_L	0.597	0.52
185_R	306_I	0.597	0.52
37_L	49_E	0.596	0.52
57_H	60_T	0.595	0.52
199_F	288_V	0.595	0.52
69_L	97_I	0.594	0.52
174_I	177_S	0.593	0.52
38_G	96_G	0.591	0.51
83_A	94_V	0.591	0.51
187_F	197_R	0.588	0.51
171_V	177_S	0.584	0.51
114_S	118_A	0.583	0.50
92_L	231_T	0.582	0.50
213_L	219_V	0.582	0.50
96_G	263_Y	0.582	0.50
16_G	58_L	0.582	0.50
160_F	208_F	0.580	0.50
258_D	272_L	0.580	0.50
34_L	43_I	0.579	0.50
143_L	148_D	0.579	0.50
214_Y	241_L	0.578	0.50
234_A	240_A	0.576	0.50
10_V	276_S	0.572	0.49
140_C	148_D	0.572	0.49
149_S	152_R	0.570	0.49
166_L	208_F	0.569	0.49
169_L	173_L	0.569	0.49
128_S	134_V	0.568	0.49
169_L	197_R	0.568	0.49
32_F	61_L	0.568	0.49
164_K	167_K	0.567	0.49
5_L	8_D	0.566	0.48
33_L	55_L	0.566	0.48
292_C	296_R	0.564	0.48
164_K	168_R	0.563	0.48
150_G	153_L	0.563	0.48
71_V	99_K	0.562	0.48
148_D	151_P	0.561	0.48
8_D	37_L	0.559	0.48
63_V	312_L	0.559	0.48
102_E	106_A	0.558	0.47
138_W	159_A	0.558	0.47
37_L	50_D	0.552	0.47
124_G	154_K	0.551	0.47
68_A	72_F	0.549	0.46
12_T	108_R	0.548	0.46
260_A	271_L	0.547	0.46
53_L	96_G	0.546	0.46
158_L	166_L	0.546	0.46
219_V	222_T	0.545	0.46
198_A	203_E	0.543	0.46
159_A	211_D	0.543	0.46
49_E	54_W	0.541	0.45
178_E	206_L	0.540	0.45
32_F	37_L	0.540	0.45
216_K	268_G	0.537	0.45
152_R	155_D	0.536	0.45
92_L	241_L	0.533	0.44
122_M	127_S	0.533	0.44
148_D	153_L	0.533	0.44
1_W	64_Q	0.532	0.44
141_S	278_L	0.532	0.44
105_W	266_L	0.532	0.44
11_A	64_Q	0.527	0.44
229_L	234_A	0.524	0.43
182_D	196_E	0.523	0.43
40_P	47_S	0.523	0.43
68_A	308_Q	0.520	0.43
307_G	313_S	0.519	0.43
94_V	98_I	0.518	0.43
46_Y	82_A	0.516	0.42
188_F	191_G	0.516	0.42
200_K	301_R	0.514	0.42
65_V	72_F	0.513	0.42
81_A	85_L	0.513	0.42
212_F	285_W	0.513	0.42
44_T	48_L	0.511	0.42
33_L	37_L	0.511	0.42
169_L	177_S	0.510	0.42
44_T	107_L	0.509	0.42
40_P	163_F	0.508	0.42
96_G	216_K	0.504	0.41
153_L	306_I	0.500	0.41
40_P	48_L	0.500	0.41

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
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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
3zd0A	1	0.1524	5.4	0.974	Contact Map
4lx3B	1	0.1143	3.2	0.977	Contact Map
2j9uA	1	0.2571	2.4	0.978	Contact Map
2kebA	1	0.1079	1.9	0.98	Contact Map
2j9wA	1	0.2794	1.6	0.98	Contact Map
2mtsA	1	0.1397	1.5	0.981	Contact Map
4ysxD	1	0.2984	1.5	0.981	Contact Map
2ab9A	1	0.0984	1.4	0.981	Contact Map
4ytpD	1	0.2889	1.2	0.982	Contact Map
4xtrG	1	0.0698	1.1	0.982	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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