DUF3179 - PFAM28P - GREMLIN Contacts

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DUF3179 - Protein of unknown function (DUF3179)

PFAM:	PF11376	Sequences: KDGIPAIDNPKFVSAAEADEYLDDDDPVIGVEINGEARAYPLRILGWHEIVNDTVGGVPVAVTYCPLCGTGIVFDRRVDGRVLTFGVSGLLYNSNLVMYDRQTESLWQQFTGEAIVGPLTGTRLEELPSVTTTWGEWKARHPDTLVLSRDTGFSRDYGRNPYGGYDDSASDPLLFPVPNPDDRLPPKERVLGVRVGGEAKAYPLSELRKEGVINDTVGGTPVVVVWDPGTASALDYRRVDGRTLTFEADADGTGSTIDGEAVSGPLKGEQLERVPAHVAFWFAWAAFHPDTE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	292 (288)
Sequences:	6315 (5087)
Seq/√Len:	299.7
META:	0.931

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
202_Y	215_D	4.204	1.00
32_E	37_A	3.956	1.00
75_D	125_E	3.374	1.00
137_W	144_T	3.328	1.00
24_D	135_G	3.230	1.00
73_V	129_S	3.018	1.00
36_E	145_L	2.844	1.00
29_I	71_G	2.842	1.00
200_K	215_D	2.687	1.00
188_E	205_S	2.659	1.00
24_D	138_K	2.628	1.00
79_D	122_T	2.589	1.00
83_L	102_Q	2.516	1.00
30_G	137_W	2.493	1.00
58_V	75_D	2.428	1.00
84_T	102_Q	2.334	1.00
194_R	199_A	2.327	1.00
81_R	102_Q	2.319	1.00
8_D	101_R	2.260	1.00
30_G	144_T	2.246	1.00
84_T	101_R	2.227	1.00
28_V	39_A	2.190	1.00
13_V	148_S	2.188	1.00
26_D	43_R	2.137	1.00
61_A	76_R	2.124	1.00
259_G	262_V	2.095	1.00
113_E	123_R	2.084	1.00
76_R	82_V	2.051	1.00
39_A	137_W	1.939	1.00
11_K	150_D	1.919	1.00
54_T	57_G	1.910	1.00
216_T	221_P	1.884	1.00
36_E	56_G	1.810	1.00
192_G	284_W	1.804	1.00
50_I	98_M	1.789	1.00
97_V	115_I	1.773	1.00
70_T	110_F	1.751	1.00
70_T	279_A	1.713	1.00
36_E	55_V	1.690	1.00
92_Y	108_Q	1.663	1.00
32_E	35_G	1.650	1.00
156_D	159_R	1.646	1.00
40_Y	53_D	1.633	1.00
260_E	270_Q	1.600	1.00
108_Q	111_T	1.600	1.00
78_V	122_T	1.590	1.00
216_T	219_G	1.590	1.00
103_T	119_L	1.588	1.00
105_S	114_A	1.578	1.00
47_W	155_R	1.569	1.00
33_I	58_V	1.560	1.00
195_V	220_T	1.557	1.00
203_P	206_E	1.554	1.00
284_W	291_T	1.554	1.00
39_A	144_T	1.536	1.00
95_N	109_Q	1.518	1.00
13_V	21_Y	1.514	1.00
75_D	127_L	1.500	1.00
136_E	227_D	1.500	1.00
42_L	131_T	1.493	1.00
259_G	264_G	1.490	1.00
88_S	106_L	1.481	1.00
191_L	276_A	1.479	1.00
86_G	99_Y	1.473	1.00
214_N	223_V	1.451	1.00
31_V	55_V	1.447	1.00
13_V	18_A	1.447	1.00
206_E	210_E	1.447	1.00
255_S	261_A	1.400	1.00
60_V	127_L	1.400	1.00
6_A	84_T	1.392	1.00
38_R	53_D	1.385	1.00
19_D	134_W	1.375	1.00
1_K	6_A	1.373	1.00
201_A	291_T	1.369	1.00
12_F	38_R	1.365	1.00
77_R	82_V	1.360	1.00
65_C	68_C	1.342	1.00
185_P	188_E	1.336	1.00
50_I	63_T	1.328	1.00
136_E	139_A	1.324	1.00
241_G	244_L	1.319	1.00
256_T	263_S	1.315	1.00
14_S	17_E	1.306	1.00
236_Y	239_V	1.303	1.00
148_S	151_T	1.300	1.00
21_Y	149_R	1.294	1.00
90_L	106_L	1.291	1.00
264_G	268_G	1.285	1.00
59_P	77_R	1.280	1.00
261_A	264_G	1.261	1.00
114_A	119_L	1.251	1.00
133_T	136_E	1.246	1.00
6_A	99_Y	1.246	1.00
198_E	218_G	1.244	1.00
31_V	60_V	1.244	1.00
281_W	285_A	1.238	1.00
259_G	263_S	1.236	1.00
212_V	223_V	1.233	1.00
15_A	138_K	1.232	1.00
55_V	60_V	1.227	1.00
78_V	81_R	1.223	1.00
38_R	145_L	1.216	1.00
188_E	203_P	1.214	1.00
78_V	83_L	1.209	1.00
173_L	177_V	1.203	1.00
1_K	104_E	1.185	1.00
33_I	36_E	1.183	1.00
63_T	109_Q	1.180	1.00
34_N	56_G	1.174	1.00
43_R	149_R	1.174	1.00
237_R	243_T	1.168	1.00
132_T	140_R	1.151	1.00
260_E	263_S	1.150	1.00
285_A	291_T	1.123	1.00
14_S	145_L	1.113	1.00
60_V	73_V	1.100	1.00
114_A	122_T	1.098	1.00
240_D	269_E	1.094	1.00
87_V	96_L	1.084	1.00
232_S	235_D	1.081	1.00
148_S	152_G	1.075	1.00
217_V	222_V	1.075	1.00
177_V	180_P	1.070	1.00
135_G	139_A	1.067	1.00
23_D	26_D	1.066	1.00
51_V	147_L	1.062	1.00
22_L	26_D	1.059	1.00
134_W	146_V	1.056	1.00
34_N	58_V	1.056	1.00
83_L	119_L	1.052	1.00
239_V	269_E	1.052	1.00
81_R	119_L	1.052	1.00
119_L	122_T	1.046	1.00
173_L	176_P	1.034	1.00
241_G	246_F	1.030	1.00
169_A	173_L	1.029	1.00
62_V	73_V	1.026	1.00
160_N	166_D	1.021	1.00
15_A	144_T	1.020	1.00
184_L	190_V	1.020	1.00
58_V	77_R	1.007	1.00
54_T	59_P	1.004	1.00
50_I	61_A	1.000	1.00
194_R	288_H	1.000	1.00
29_I	129_S	0.999	1.00
239_V	243_T	0.996	1.00
160_N	163_G	0.995	1.00
243_T	246_F	0.994	1.00
207_L	211_G	0.989	1.00
134_W	138_K	0.988	1.00
37_A	144_T	0.987	1.00
30_G	39_A	0.987	1.00
238_R	243_T	0.984	1.00
48_H	157_Y	0.976	1.00
12_F	145_L	0.970	1.00
168_S	171_D	0.965	1.00
212_V	225_V	0.965	1.00
59_P	82_V	0.963	1.00
22_L	134_W	0.962	1.00
110_F	279_A	0.962	1.00
259_G	266_L	0.958	1.00
105_S	119_L	0.954	1.00
242_R	245_T	0.952	1.00
200_K	217_V	0.949	1.00
198_E	217_V	0.943	1.00
227_D	230_T	0.941	1.00
22_L	43_R	0.938	1.00
250_A	253_T	0.938	1.00
257_I	261_A	0.937	1.00
175_F	179_N	0.937	1.00
30_G	37_A	0.936	1.00
13_V	17_E	0.936	1.00
165_Y	187_K	0.935	1.00
30_G	132_T	0.935	1.00
258_D	261_A	0.932	1.00
261_A	268_G	0.930	1.00
191_L	235_D	0.927	1.00
264_G	267_K	0.927	1.00
266_L	269_E	0.922	1.00
93_N	178_P	0.917	1.00
6_A	87_V	0.914	1.00
18_A	21_Y	0.911	1.00
138_K	144_T	0.904	1.00
207_L	226_W	0.902	1.00
202_Y	224_V	0.899	1.00
258_D	263_S	0.897	1.00
214_N	221_P	0.894	1.00
240_D	243_T	0.891	1.00
77_R	80_G	0.889	1.00
239_V	242_R	0.886	1.00
257_I	262_V	0.885	1.00
263_S	267_K	0.885	1.00
168_S	173_L	0.882	1.00
12_F	53_D	0.881	1.00
258_D	262_V	0.880	1.00
25_D	231_A	0.873	1.00
12_F	55_V	0.869	1.00
46_G	160_N	0.868	1.00
244_L	248_A	0.868	1.00
255_S	266_L	0.867	1.00
279_A	283_A	0.866	1.00
108_Q	115_I	0.858	1.00
86_G	101_R	0.857	1.00
246_F	249_D	0.855	1.00
239_V	246_F	0.854	1.00
12_F	147_L	0.850	1.00
162_Y	165_Y	0.850	1.00
97_V	106_L	0.848	1.00
181_D	285_A	0.847	1.00
72_I	126_E	0.845	1.00
193_V	217_V	0.844	1.00
257_I	260_E	0.839	1.00
261_A	266_L	0.838	1.00
43_R	158_G	0.836	1.00
44_I	147_L	0.830	1.00
100_D	103_T	0.828	1.00
31_V	127_L	0.828	1.00
54_T	82_V	0.825	1.00
237_R	241_G	0.825	1.00
94_S	177_V	0.823	1.00
46_G	66_P	0.822	1.00
8_D	84_T	0.822	1.00
134_W	144_T	0.822	1.00
243_T	247_E	0.816	1.00
268_G	271_L	0.814	1.00
199_A	288_H	0.813	1.00
190_V	201_A	0.803	1.00
250_A	256_T	0.803	1.00
107_W	114_A	0.802	1.00
37_A	141_H	0.800	1.00
281_W	291_T	0.800	1.00
238_R	241_G	0.795	1.00
95_N	283_A	0.794	1.00
7_I	147_L	0.791	0.99
87_V	99_Y	0.783	0.99
69_G	189_R	0.783	0.99
2_D	86_G	0.783	0.99
95_N	287_F	0.782	0.99
73_V	127_L	0.780	0.99
25_D	135_G	0.774	0.99
189_R	278_V	0.769	0.99
240_D	246_F	0.768	0.99
7_I	12_F	0.761	0.99
210_E	213_I	0.760	0.99
141_H	144_T	0.756	0.99
31_V	129_S	0.755	0.99
76_R	83_L	0.755	0.99
68_C	95_N	0.755	0.99
242_R	246_F	0.752	0.99
1_K	90_L	0.752	0.99
239_V	244_L	0.752	0.99
151_T	155_R	0.747	0.99
258_D	264_G	0.747	0.99
1_K	99_Y	0.742	0.99
67_L	91_L	0.740	0.99
22_L	146_V	0.732	0.99
245_T	249_D	0.725	0.99
61_A	85_F	0.724	0.99
192_G	199_A	0.723	0.99
261_A	265_P	0.722	0.99
93_N	286_A	0.721	0.99
18_A	148_S	0.721	0.99
195_V	198_E	0.720	0.99
84_T	99_Y	0.718	0.99
173_L	186_P	0.718	0.99
236_Y	272_E	0.718	0.99
215_D	222_V	0.714	0.99
260_E	264_G	0.714	0.99
236_Y	243_T	0.714	0.99
2_D	99_Y	0.710	0.99
36_E	60_V	0.708	0.99
85_F	107_W	0.707	0.99
195_V	218_G	0.706	0.99
36_E	57_G	0.705	0.99
170_S	187_K	0.696	0.99
237_R	272_E	0.694	0.99
184_L	206_E	0.693	0.99
222_V	274_V	0.692	0.99
95_N	110_F	0.690	0.99
42_L	46_G	0.690	0.99
244_L	249_D	0.690	0.99
194_R	197_G	0.689	0.99
47_W	156_D	0.688	0.99
137_W	141_H	0.687	0.99
196_G	220_T	0.684	0.99
226_W	230_T	0.681	0.98
50_I	96_L	0.680	0.98
49_E	88_S	0.678	0.98
52_N	61_A	0.676	0.98
105_S	117_G	0.676	0.98
78_V	119_L	0.675	0.98
223_V	271_L	0.673	0.98
21_Y	43_R	0.670	0.98
58_V	76_R	0.669	0.98
170_S	173_L	0.668	0.98
71_G	131_T	0.664	0.98
245_T	248_A	0.664	0.98
19_D	138_K	0.663	0.98
236_Y	246_F	0.663	0.98
202_Y	213_I	0.663	0.98
151_T	157_Y	0.661	0.98
74_F	112_G	0.659	0.98
263_S	266_L	0.657	0.98
192_G	288_H	0.657	0.98
196_G	219_G	0.655	0.98
220_T	237_R	0.652	0.98
201_A	281_W	0.651	0.98
255_S	264_G	0.649	0.98
257_I	264_G	0.649	0.98
92_Y	106_L	0.647	0.98
239_V	245_T	0.645	0.98
31_V	73_V	0.645	0.98
184_L	203_P	0.644	0.98
193_V	222_V	0.641	0.98
267_K	270_Q	0.639	0.98
220_T	236_Y	0.638	0.98
230_T	233_A	0.631	0.98
105_S	116_V	0.630	0.97
55_V	145_L	0.628	0.97
264_G	271_L	0.625	0.97
108_Q	287_F	0.624	0.97
231_A	235_D	0.624	0.97
193_V	202_Y	0.623	0.97
168_S	172_P	0.619	0.97
33_I	56_G	0.619	0.97
50_I	66_P	0.618	0.97
5_P	155_R	0.617	0.97
80_G	83_L	0.617	0.97
92_Y	95_N	0.617	0.97
255_S	259_G	0.616	0.97
132_T	136_E	0.615	0.97
92_Y	97_V	0.615	0.97
97_V	108_Q	0.613	0.97
175_F	178_P	0.612	0.97
126_E	275_P	0.612	0.97
226_W	231_A	0.611	0.97
265_P	268_G	0.610	0.97
32_E	141_H	0.606	0.97
34_N	57_G	0.604	0.97
262_V	265_P	0.603	0.97
151_T	154_S	0.601	0.97
126_E	129_S	0.597	0.97
273_R	276_A	0.597	0.97
184_L	188_E	0.597	0.97
88_S	91_L	0.597	0.97
14_S	18_A	0.596	0.96
259_G	267_K	0.594	0.96
7_I	11_K	0.592	0.96
15_A	134_W	0.591	0.96
116_V	120_T	0.585	0.96
204_L	278_V	0.583	0.96
262_V	266_L	0.583	0.96
35_G	56_G	0.582	0.96
211_G	248_A	0.580	0.96
240_D	244_L	0.578	0.96
174_L	177_V	0.577	0.96
94_S	282_F	0.575	0.96
29_I	42_L	0.574	0.96
263_S	268_G	0.573	0.96
265_P	269_E	0.573	0.96
26_D	134_W	0.572	0.96
204_L	226_W	0.570	0.95
65_C	96_L	0.570	0.95
277_H	288_H	0.569	0.95
67_L	94_S	0.569	0.95
260_E	267_K	0.569	0.95
226_W	233_A	0.568	0.95
95_N	108_Q	0.568	0.95
53_D	60_V	0.567	0.95
46_G	163_G	0.565	0.95
103_T	107_W	0.564	0.95
83_L	122_T	0.563	0.95
206_E	209_K	0.563	0.95
71_G	129_S	0.563	0.95
12_F	40_Y	0.562	0.95
110_F	288_H	0.560	0.95
205_S	208_R	0.560	0.95
195_V	202_Y	0.557	0.95
202_Y	222_V	0.556	0.95
183_R	285_A	0.555	0.95
31_V	38_R	0.555	0.95
66_P	162_Y	0.554	0.95
245_T	253_T	0.554	0.95
1_K	8_D	0.553	0.95
46_G	161_P	0.551	0.95
171_D	187_K	0.551	0.95
193_V	200_K	0.551	0.95
176_P	179_N	0.545	0.94
196_G	218_G	0.544	0.94
58_V	127_L	0.544	0.94
98_M	112_G	0.543	0.94
181_D	184_L	0.540	0.94
33_I	38_R	0.539	0.94
215_D	224_V	0.539	0.94
179_N	285_A	0.539	0.94
132_T	144_T	0.538	0.94
221_P	238_R	0.538	0.94
29_I	73_V	0.537	0.94
114_A	120_T	0.536	0.94
288_H	291_T	0.535	0.94
272_E	275_P	0.534	0.94
63_T	96_L	0.533	0.94
37_A	137_W	0.531	0.93
44_I	151_T	0.530	0.93
106_L	116_V	0.530	0.93
148_S	153_F	0.528	0.93
236_Y	244_L	0.528	0.93
224_V	233_A	0.528	0.93
32_E	36_E	0.525	0.93
172_P	177_V	0.524	0.93
214_N	237_R	0.522	0.93
279_A	288_H	0.522	0.93
176_P	180_P	0.521	0.93
52_N	84_T	0.521	0.93
159_R	163_G	0.519	0.93
91_L	94_S	0.519	0.93
241_G	245_T	0.517	0.93
30_G	141_H	0.516	0.93
264_G	270_Q	0.514	0.92
184_L	285_A	0.514	0.92
110_F	283_A	0.511	0.92
227_D	234_L	0.508	0.92
239_V	248_A	0.508	0.92
157_Y	162_Y	0.507	0.92
238_R	242_R	0.507	0.92
284_W	288_H	0.506	0.92
110_F	192_G	0.505	0.92
100_D	107_W	0.505	0.92
255_S	268_G	0.503	0.92
169_A	177_V	0.501	0.91
174_L	179_N	0.500	0.91

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
2zylA	3	0.3664	21.2	0.963	Contact Map
5amhA	1	0.3048	18	0.965	Contact Map
4qdcA	3	0.3836	16.2	0.965	Contact Map
3gkeA	3	0.3459	15.1	0.966	Contact Map
3c0dA	1	0.3185	14.9	0.966	Contact Map
4qdfB	3	0.3493	14.4	0.966	Contact Map
1o73A	1	0.4075	9.9	0.968	Contact Map
2jzaA	1	0.3288	9.3	0.969	Contact Map
3gcfA	5	0.3836	8.1	0.97	Contact Map
2bmoA	3	0.4418	6.7	0.971	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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