DUF4421 - PFAM28P - GREMLIN Contacts

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DUF4421 - Domain of unknown function (DUF4421)

PFAM:	PF14391	Sequences: KYDTTYIESYPDKLTVRLYLSNKYNSFSLSSKGNGQSLRYRPNTSLNLGLGFSYRWLSLGYSFNPPFLNGNKGKTKYLDFQLNLYGRKWGIDLYYQKYKGFYLEDFGDDDDDGDPYYQRPDLKTRSFGLNAYYIFNHKKFSYRAAFSQSEIQKKSAGSFLLGGSYYYGRIKADSSLLPDELSDYFPEEANINKIKYFDIGLGGGYAYNWVFKKNWFLNASLSLGPGLGYKKSKGTYEDLEDSKKKTNFNPNLDGRLALGYNSKRWFAGLSFVYNNYNYGNKSDFSINNSFGNFRLYVGYRF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	301 (299)
Sequences:	2444 (2146)
Seq/√Len:	124.1
META:	0.881

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
159_F	203_G	5.499	1.00
135_F	161_L	5.381	1.00
157_G	205_Y	5.270	1.00
94_Y	128_G	4.440	1.00
157_G	207_Y	4.246	1.00
268_G	296_Y	4.127	1.00
216_F	259_G	3.478	1.00
146_F	218_N	3.404	1.00
75_T	78_L	3.327	1.00
206_A	218_N	3.218	1.00
155_S	207_Y	2.966	1.00
8_E	153_K	2.753	1.00
53_S	58_S	2.577	1.00
266_F	298_G	2.449	1.00
140_F	206_A	2.376	1.00
208_N	216_F	2.376	1.00
119_R	122_L	2.332	1.00
51_G	60_G	2.321	1.00
75_T	83_N	2.237	1.00
78_L	83_N	2.233	1.00
75_T	79_D	2.216	1.00
92_D	255_R	2.155	1.00
136_N	156_A	2.045	1.00
95_Y	125_R	2.041	1.00
16_V	52_F	2.030	1.00
89_W	131_A	2.000	1.00
79_D	83_N	1.981	1.00
167_Y	197_F	1.927	1.00
73_G	77_Y	1.922	1.00
73_G	78_L	1.921	1.00
135_F	159_F	1.915	1.00
90_G	132_Y	1.910	1.00
75_T	81_Q	1.901	1.00
119_R	172_A	1.878	1.00
91_I	131_A	1.877	1.00
164_S	200_G	1.875	1.00
209_W	219_A	1.875	1.00
143_R	150_E	1.859	1.00
88_K	137_H	1.843	1.00
10_Y	151_I	1.813	1.00
119_R	174_S	1.785	1.00
264_R	299_Y	1.774	1.00
107_G	110_D	1.746	1.00
152_Q	208_N	1.740	1.00
219_A	256_L	1.737	1.00
78_L	82_L	1.720	1.00
87_R	150_E	1.700	1.00
211_F	215_W	1.683	1.00
155_S	210_V	1.682	1.00
105_D	109_D	1.673	1.00
42_P	98_Y	1.650	1.00
75_T	80_F	1.649	1.00
53_S	149_S	1.643	1.00
158_S	205_Y	1.635	1.00
211_F	214_N	1.622	1.00
105_D	108_D	1.615	1.00
177_L	181_L	1.604	1.00
93_L	129_L	1.602	1.00
151_I	214_N	1.594	1.00
157_G	209_W	1.586	1.00
145_A	257_A	1.550	1.00
19_Y	62_S	1.522	1.00
17_R	51_G	1.521	1.00
73_G	79_D	1.517	1.00
77_Y	81_Q	1.516	1.00
106_F	109_D	1.493	1.00
134_I	160_L	1.480	1.00
223_L	228_G	1.462	1.00
208_N	218_N	1.460	1.00
17_R	266_F	1.447	1.00
77_Y	83_N	1.441	1.00
79_D	98_Y	1.435	1.00
133_Y	137_H	1.434	1.00
162_G	202_G	1.428	1.00
217_L	258_L	1.428	1.00
259_G	262_S	1.414	1.00
89_W	133_Y	1.412	1.00
19_Y	49_G	1.407	1.00
65_P	68_L	1.366	1.00
24_Y	291_G	1.353	1.00
146_F	206_A	1.349	1.00
172_A	176_L	1.348	1.00
265_W	297_V	1.330	1.00
162_G	203_G	1.305	1.00
145_A	218_N	1.280	1.00
158_S	206_A	1.268	1.00
121_D	172_A	1.267	1.00
53_S	60_G	1.262	1.00
225_P	228_G	1.259	1.00
152_Q	155_S	1.258	1.00
78_L	95_Y	1.251	1.00
211_F	217_L	1.239	0.99
143_R	149_S	1.236	0.99
152_Q	156_A	1.232	0.99
90_G	142_Y	1.218	0.99
139_K	156_A	1.212	0.99
140_F	218_N	1.205	0.99
5_T	154_K	1.187	0.99
134_I	137_H	1.185	0.99
257_A	268_G	1.171	0.99
152_Q	210_V	1.165	0.99
73_G	102_Y	1.163	0.99
165_Y	197_F	1.154	0.99
17_R	60_G	1.150	0.99
121_D	174_S	1.148	0.99
81_Q	96_Q	1.147	0.99
110_D	113_G	1.144	0.99
206_A	220_S	1.143	0.99
102_Y	120_P	1.138	0.99
214_N	262_S	1.135	0.99
186_P	189_A	1.131	0.99
40_Y	119_R	1.128	0.99
85_Y	92_D	1.125	0.99
10_Y	14_L	1.106	0.99
141_S	152_Q	1.104	0.99
202_G	224_G	1.103	0.99
217_L	221_L	1.088	0.99
216_F	296_Y	1.087	0.99
97_K	125_R	1.081	0.99
91_I	129_L	1.073	0.99
97_K	123_K	1.065	0.98
4_T	41_R	1.058	0.98
265_W	299_Y	1.052	0.98
19_Y	23_K	1.045	0.98
224_G	228_G	1.045	0.98
110_D	114_D	1.045	0.98
151_I	263_K	1.039	0.98
6_Y	154_K	1.035	0.98
115_P	118_Q	1.033	0.98
2_Y	7_I	1.018	0.98
136_N	157_G	1.014	0.98
145_A	206_A	1.014	0.98
214_N	260_Y	1.010	0.98
179_D	182_S	1.003	0.98
254_G	273_Y	1.001	0.98
177_L	180_E	0.996	0.98
130_N	164_S	0.995	0.98
73_G	83_N	0.990	0.97
105_D	110_D	0.989	0.97
148_Q	261_N	0.988	0.97
16_V	299_Y	0.982	0.97
185_F	189_A	0.981	0.97
148_Q	206_A	0.980	0.97
92_D	162_G	0.977	0.97
73_G	116_Y	0.968	0.97
4_T	153_K	0.965	0.97
106_F	110_D	0.963	0.97
28_S	37_S	0.961	0.97
17_R	21_S	0.959	0.97
144_A	156_A	0.958	0.97
260_Y	267_A	0.957	0.97
236_Y	239_L	0.956	0.97
10_Y	300_R	0.954	0.97
15_T	19_Y	0.951	0.97
237_E	241_D	0.951	0.97
78_L	81_Q	0.949	0.97
146_F	257_A	0.948	0.97
141_S	150_E	0.947	0.97
142_Y	145_A	0.946	0.97
2_Y	5_T	0.940	0.97
102_Y	118_Q	0.939	0.97
136_N	208_N	0.938	0.97
21_S	62_S	0.935	0.96
229_Y	246_T	0.932	0.96
83_N	92_D	0.931	0.96
4_T	8_E	0.928	0.96
202_G	222_S	0.923	0.96
237_E	240_E	0.917	0.96
178_P	181_L	0.915	0.96
18_L	48_L	0.914	0.96
43_N	102_Y	0.912	0.96
20_L	48_L	0.911	0.96
87_R	272_V	0.907	0.96
175_S	295_L	0.907	0.96
144_A	152_Q	0.906	0.96
133_Y	161_L	0.904	0.96
88_K	134_I	0.902	0.96
119_R	173_D	0.895	0.95
17_R	148_Q	0.883	0.95
174_S	177_L	0.881	0.95
100_G	120_P	0.877	0.95
19_Y	60_G	0.873	0.95
267_A	297_V	0.872	0.95
185_F	191_I	0.870	0.95
255_R	272_V	0.867	0.95
85_Y	272_V	0.861	0.94
144_A	208_N	0.861	0.94
92_D	272_V	0.860	0.94
92_D	130_N	0.859	0.94
215_W	267_A	0.859	0.94
172_A	175_S	0.856	0.94
254_G	271_F	0.854	0.94
108_D	112_D	0.844	0.94
136_N	205_Y	0.844	0.94
278_Y	284_F	0.837	0.94
90_G	93_L	0.834	0.93
198_D	251_N	0.832	0.93
109_D	112_D	0.830	0.93
161_L	203_G	0.830	0.93
134_I	158_S	0.829	0.93
225_P	248_F	0.829	0.93
81_Q	98_Y	0.826	0.93
272_V	294_R	0.824	0.93
80_F	95_Y	0.823	0.93
212_K	215_W	0.821	0.93
20_L	46_L	0.819	0.93
170_I	216_F	0.813	0.92
169_R	193_K	0.812	0.92
49_G	204_G	0.809	0.92
262_S	267_A	0.806	0.92
131_A	161_L	0.803	0.92
102_Y	116_Y	0.798	0.92
81_Q	92_D	0.795	0.92
155_S	205_Y	0.795	0.92
43_N	100_G	0.794	0.92
159_F	163_G	0.791	0.91
196_Y	228_G	0.789	0.91
50_L	61_Y	0.789	0.91
131_A	163_G	0.789	0.91
7_I	87_R	0.789	0.91
26_S	41_R	0.789	0.91
255_R	270_S	0.788	0.91
215_W	260_Y	0.786	0.91
210_V	213_K	0.786	0.91
119_R	209_W	0.781	0.91
73_G	81_Q	0.779	0.91
144_A	148_Q	0.776	0.91
16_V	50_L	0.773	0.90
122_L	172_A	0.766	0.90
124_T	274_N	0.763	0.90
273_Y	289_S	0.761	0.90
42_P	96_Q	0.758	0.90
41_R	104_E	0.757	0.90
207_Y	219_A	0.756	0.90
40_Y	178_P	0.754	0.89
222_S	225_P	0.752	0.89
48_L	65_P	0.752	0.89
291_G	294_R	0.751	0.89
288_N	298_G	0.750	0.89
187_E	190_N	0.748	0.89
17_R	23_K	0.748	0.89
14_L	52_F	0.748	0.89
139_K	154_K	0.747	0.89
141_S	148_Q	0.746	0.89
64_N	68_L	0.746	0.89
125_R	169_R	0.746	0.89
83_N	255_R	0.745	0.89
221_L	229_Y	0.744	0.89
99_K	123_K	0.735	0.88
42_P	148_Q	0.734	0.88
288_N	291_G	0.733	0.88
54_Y	57_L	0.725	0.87
160_L	206_A	0.725	0.87
136_N	152_Q	0.722	0.87
8_E	151_I	0.722	0.87
226_G	230_K	0.721	0.87
157_G	204_G	0.721	0.87
155_S	208_N	0.718	0.87
281_K	284_F	0.717	0.87
14_L	54_Y	0.713	0.87
252_L	275_N	0.713	0.87
22_N	25_N	0.711	0.86
112_D	115_P	0.708	0.86
254_G	258_L	0.706	0.86
215_W	259_G	0.706	0.86
121_D	176_L	0.704	0.86
119_R	175_S	0.703	0.86
52_F	269_L	0.701	0.86
96_Q	200_G	0.700	0.86
202_G	226_G	0.697	0.85
90_G	130_N	0.696	0.85
31_S	36_Q	0.695	0.85
162_G	222_S	0.695	0.85
9_S	12_D	0.692	0.85
225_P	229_Y	0.691	0.85
155_S	209_W	0.688	0.85
132_Y	142_Y	0.686	0.84
88_K	138_K	0.686	0.84
208_N	259_G	0.685	0.84
9_S	143_R	0.685	0.84
108_D	114_D	0.683	0.84
52_F	58_S	0.683	0.84
219_A	254_G	0.682	0.84
153_K	213_K	0.679	0.84
89_W	256_L	0.678	0.84
136_N	207_Y	0.678	0.84
227_L	246_T	0.676	0.84
144_A	150_E	0.673	0.83
274_N	278_Y	0.669	0.83
10_Y	13_K	0.667	0.83
96_Q	255_R	0.666	0.83
80_F	92_D	0.664	0.82
109_D	113_G	0.664	0.82
92_D	206_A	0.660	0.82
175_S	179_D	0.659	0.82
64_N	200_G	0.659	0.82
92_D	146_F	0.658	0.82
2_Y	8_E	0.657	0.82
167_Y	195_K	0.657	0.82
85_Y	90_G	0.657	0.82
86_G	149_S	0.656	0.82
45_S	64_N	0.656	0.82
141_S	145_A	0.652	0.81
278_Y	288_N	0.651	0.81
49_G	162_G	0.650	0.81
79_D	85_Y	0.649	0.81
2_Y	15_T	0.647	0.81
141_S	157_G	0.645	0.81
110_D	115_P	0.645	0.81
169_R	195_K	0.644	0.81
80_F	83_N	0.642	0.80
292_N	295_L	0.639	0.80
38_L	177_L	0.639	0.80
23_K	51_G	0.636	0.80
85_Y	147_S	0.631	0.79
67_F	71_N	0.630	0.79
95_Y	127_F	0.629	0.79
269_L	295_L	0.629	0.79
145_A	152_Q	0.628	0.79
270_S	294_R	0.624	0.78
81_Q	128_G	0.622	0.78
129_L	165_Y	0.621	0.78
179_D	183_D	0.621	0.78
104_E	217_L	0.619	0.78
43_N	73_G	0.617	0.78
181_L	185_F	0.616	0.78
158_S	261_N	0.616	0.78
123_K	171_K	0.614	0.77
52_F	264_R	0.614	0.77
74_K	195_K	0.614	0.77
49_G	65_P	0.611	0.77
148_Q	294_R	0.608	0.77
293_F	297_V	0.608	0.77
76_K	82_L	0.607	0.77
75_T	102_Y	0.603	0.76
56_W	62_S	0.603	0.76
163_G	199_I	0.601	0.76
101_F	124_T	0.599	0.76
19_Y	29_L	0.597	0.75
43_N	260_Y	0.596	0.75
284_F	288_N	0.594	0.75
130_N	253_D	0.592	0.75
8_E	263_K	0.592	0.75
16_V	104_E	0.591	0.75
139_K	152_Q	0.590	0.74
209_W	263_K	0.589	0.74
50_L	59_L	0.585	0.74
99_K	120_P	0.584	0.74
8_E	11_P	0.584	0.74
75_T	118_Q	0.584	0.74
182_S	185_F	0.581	0.73
98_Y	126_S	0.578	0.73
193_K	273_Y	0.576	0.73
10_Y	15_T	0.576	0.73
53_S	151_I	0.576	0.73
64_N	77_Y	0.576	0.73
227_L	285_S	0.572	0.72
14_L	55_R	0.571	0.72
15_T	52_F	0.571	0.72
87_R	143_R	0.570	0.72
281_K	293_F	0.568	0.72
151_I	262_S	0.567	0.72
132_Y	253_D	0.567	0.72
83_N	90_G	0.567	0.72
89_W	201_L	0.563	0.71
84_L	91_I	0.562	0.71
85_Y	148_Q	0.561	0.71
132_Y	145_A	0.561	0.71
275_N	283_D	0.560	0.71
108_D	111_D	0.559	0.70
148_Q	216_F	0.559	0.70
239_L	242_S	0.558	0.70
144_A	257_A	0.558	0.70
220_S	224_G	0.557	0.70
126_S	132_Y	0.557	0.70
184_Y	188_E	0.557	0.70
224_G	227_L	0.556	0.70
31_S	34_N	0.556	0.70
19_Y	27_F	0.554	0.70
15_T	21_S	0.554	0.70
57_L	164_S	0.553	0.70
21_S	24_Y	0.553	0.70
32_K	40_Y	0.553	0.70
92_D	253_D	0.552	0.70
7_I	150_E	0.552	0.70
237_E	242_S	0.551	0.69
35_G	112_D	0.550	0.69
73_G	76_K	0.550	0.69
100_G	103_L	0.549	0.69
209_W	236_Y	0.548	0.69
106_F	111_D	0.546	0.69
146_F	222_S	0.543	0.68
281_K	287_N	0.542	0.68
152_Q	158_S	0.539	0.68
209_W	256_L	0.539	0.68
140_F	222_S	0.538	0.68
13_K	20_L	0.538	0.68
14_L	20_L	0.538	0.68
170_I	183_D	0.537	0.67
227_L	239_L	0.536	0.67
132_Y	160_L	0.534	0.67
134_I	234_G	0.531	0.67
198_D	268_G	0.531	0.67
253_D	288_N	0.530	0.66
18_L	34_N	0.528	0.66
271_F	293_F	0.528	0.66
225_P	286_I	0.527	0.66
209_W	212_K	0.526	0.66
56_W	143_R	0.526	0.66
35_G	241_D	0.526	0.66
7_I	10_Y	0.525	0.66
161_L	201_L	0.524	0.66
270_S	296_Y	0.523	0.65
150_E	247_N	0.522	0.65
183_D	235_T	0.521	0.65
114_D	127_F	0.521	0.65
136_N	235_T	0.521	0.65
126_S	224_G	0.521	0.65
128_G	164_S	0.520	0.65
74_K	245_K	0.520	0.65
276_Y	280_N	0.520	0.65
90_G	134_I	0.517	0.65
256_L	269_L	0.517	0.65
53_S	270_S	0.516	0.64
142_Y	257_A	0.516	0.64
148_Q	268_G	0.515	0.64
58_S	149_S	0.515	0.64
282_S	289_S	0.514	0.64
28_S	180_E	0.513	0.64
273_Y	276_Y	0.512	0.64
16_V	34_N	0.511	0.64
42_P	226_G	0.511	0.64
36_Q	210_V	0.511	0.64
85_Y	146_F	0.510	0.64
141_S	144_A	0.509	0.63
54_Y	251_N	0.508	0.63
79_D	128_G	0.507	0.63
47_N	62_S	0.505	0.63
147_S	196_Y	0.505	0.63
119_R	176_L	0.505	0.63
147_S	208_N	0.504	0.63
37_S	265_W	0.504	0.63
28_S	39_R	0.504	0.63
15_T	266_F	0.504	0.63
75_T	120_P	0.501	0.62
103_L	178_P	0.501	0.62
220_S	223_L	0.500	0.62
140_F	208_N	0.500	0.62

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
1p4tA	2	0.515	51.6	0.936	Contact Map
1xkwA	1	0.8173	39.5	0.941	Contact Map
3efmA	1	0.6844	35.4	0.942	Contact Map
2f1vA	4	0.5249	30.7	0.944	Contact Map
2x27X	1	0.5914	28.8	0.945	Contact Map
3nb3A	2	0.4385	24.9	0.947	Contact Map
2lhfA	1	0.5648	22.8	0.948	Contact Map
3qlbA	1	0.7076	20.5	0.949	Contact Map
1ormA	1	0.4751	20.3	0.949	Contact Map
2ervA	1	0.4718	16.4	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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