DUF4007 - PFAM28P - GREMLIN Contacts

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DUF4007 - Protein of unknown function (DUF4007)

PFAM:	PF13182	Sequences: FSGHETFPLRYGWLKKGYDAVKEDPDNKNVFSDEDAIVRLGVGKNMVKSIRYWLLAFGLIEEDKKKRGLELTELGKLLFGDDGWDPYLEDPATLWLLHWLLASNPERATTWYWFFNEFNKPEFTREELLEALKRYAREERGGKKVSENTLKRDVDCFLRTYVPRRKSKKDPEDSLDSPLAELGLIREVGKGKGYRFNRGPKPSLPPEIFLYALLDFWERRSPGTISFEELAYGPGSPGRVFKLDENSLIERLEELEELTGAIRYSETAGLRQLQFKKDPEDPLEILEKYY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	290 (285)
Sequences:	2522 (2091)
Seq/√Len:	123.9
META:	0.847

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_V	50_I	5.094	1.00
15_K	19_D	4.523	1.00
74_L	100_L	4.121	1.00
92_A	205_P	3.676	1.00
17_G	54_L	3.674	1.00
206_P	254_E	3.533	1.00
77_L	84_W	3.381	1.00
59_L	75_G	3.353	1.00
133_K	147_E	3.264	1.00
61_E	70_E	3.132	1.00
229_E	233_G	3.034	1.00
21_V	60_I	2.990	1.00
78_L	93_T	2.873	1.00
5_E	48_K	2.831	1.00
128_L	154_V	2.776	1.00
212_A	241_F	2.767	1.00
97_L	179_L	2.740	1.00
88_L	93_T	2.692	1.00
129_L	154_V	2.682	1.00
124_T	127_E	2.572	1.00
57_F	97_L	2.519	1.00
114_F	157_F	2.498	1.00
213_L	230_L	2.477	1.00
206_P	251_R	2.467	1.00
244_D	247_S	2.427	1.00
196_F	242_K	2.422	1.00
114_F	128_L	2.415	1.00
215_D	282_P	2.400	1.00
77_L	287_E	2.297	1.00
22_K	76_K	2.253	1.00
114_F	196_F	2.246	1.00
92_A	208_I	2.161	1.00
231_A	248_L	2.158	1.00
117_E	234_P	2.097	1.00
5_E	49_S	2.018	1.00
110_T	157_F	2.008	1.00
209_F	248_L	2.004	1.00
58_G	100_L	2.002	1.00
99_W	215_D	2.001	1.00
74_L	78_L	1.998	1.00
18_Y	76_K	1.979	1.00
37_I	47_V	1.819	1.00
148_N	152_R	1.778	1.00
217_W	275_F	1.771	1.00
54_L	60_I	1.750	1.00
17_G	50_I	1.740	1.00
125_R	151_K	1.727	1.00
90_D	289_Y	1.702	1.00
103_S	215_D	1.696	1.00
18_Y	71_L	1.695	1.00
92_A	289_Y	1.673	1.00
76_K	80_G	1.663	1.00
113_W	131_A	1.657	1.00
209_F	251_R	1.642	1.00
18_Y	80_G	1.623	1.00
58_G	104_N	1.595	1.00
186_R	197_N	1.589	1.00
52_Y	108_A	1.581	1.00
96_L	208_I	1.575	1.00
56_A	101_L	1.563	1.00
20_A	30_V	1.555	1.00
117_E	135_Y	1.549	1.00
100_L	103_S	1.542	1.00
213_L	273_L	1.529	1.00
102_A	240_V	1.490	1.00
60_I	69_L	1.485	1.00
73_E	76_K	1.473	1.00
132_L	150_L	1.461	1.00
263_R	276_K	1.459	1.00
57_F	101_L	1.439	1.00
44_K	48_K	1.433	1.00
100_L	211_Y	1.426	1.00
152_R	155_D	1.395	1.00
103_S	240_V	1.383	1.00
113_W	132_L	1.358	1.00
63_D	70_E	1.345	1.00
116_N	240_V	1.345	1.00
204_L	243_L	1.332	1.00
12_G	178_P	1.327	1.00
133_K	150_L	1.324	1.00
281_D	284_E	1.303	1.00
35_D	39_R	1.288	1.00
148_N	151_K	1.287	1.00
256_E	260_G	1.276	1.00
125_R	155_D	1.262	1.00
147_E	151_K	1.245	1.00
265_S	274_Q	1.232	0.99
230_L	248_L	1.213	0.99
129_L	150_L	1.201	0.99
14_L	57_F	1.191	0.99
88_L	94_L	1.187	0.99
220_R	229_E	1.187	0.99
284_E	287_E	1.184	0.99
24_D	33_D	1.176	0.99
115_F	157_F	1.170	0.99
210_L	285_I	1.141	0.99
9_L	177_S	1.141	0.99
59_L	74_L	1.136	0.99
9_L	57_F	1.129	0.99
230_L	237_P	1.127	0.99
110_T	132_L	1.123	0.99
24_D	29_N	1.114	0.99
73_E	283_L	1.113	0.99
209_F	213_L	1.111	0.99
112_Y	235_G	1.094	0.99
211_Y	215_D	1.087	0.99
136_A	145_V	1.084	0.99
210_L	255_L	1.083	0.99
95_W	248_L	1.069	0.98
2_S	149_T	1.065	0.98
5_E	45_N	1.049	0.98
33_D	39_R	1.048	0.98
118_F	131_A	1.048	0.98
123_F	194_Y	1.044	0.98
94_L	160_T	1.037	0.98
11_Y	178_P	1.031	0.98
157_F	160_T	1.028	0.98
8_P	159_R	1.024	0.98
112_Y	116_N	1.018	0.98
71_L	76_K	1.015	0.98
207_E	289_Y	1.014	0.98
256_E	263_R	1.008	0.98
55_L	69_L	1.008	0.98
283_L	287_E	1.007	0.98
55_L	107_R	1.005	0.98
102_A	112_Y	0.998	0.98
109_T	132_L	0.990	0.97
23_E	39_R	0.978	0.97
36_A	47_V	0.975	0.97
149_T	153_D	0.974	0.97
129_L	147_E	0.972	0.97
252_L	256_E	0.970	0.97
6_T	155_D	0.967	0.97
58_G	74_L	0.963	0.97
118_F	123_F	0.962	0.97
100_L	215_D	0.961	0.97
80_G	83_G	0.961	0.97
209_F	243_L	0.961	0.97
230_L	273_L	0.960	0.97
72_T	75_G	0.959	0.97
217_W	225_I	0.955	0.97
110_T	153_D	0.955	0.97
216_F	236_S	0.951	0.97
103_S	235_G	0.949	0.97
151_K	155_D	0.947	0.97
112_Y	117_E	0.944	0.97
52_Y	55_L	0.924	0.96
122_E	188_V	0.920	0.96
51_R	62_E	0.920	0.96
225_I	230_L	0.919	0.96
10_R	13_W	0.913	0.96
158_L	194_Y	0.910	0.96
8_P	49_S	0.900	0.96
120_K	127_E	0.897	0.95
17_G	40_L	0.896	0.95
128_L	204_L	0.892	0.95
227_F	264_Y	0.891	0.95
146_S	149_T	0.890	0.95
152_R	156_C	0.888	0.95
99_W	216_F	0.885	0.95
225_I	275_F	0.870	0.95
218_E	282_P	0.868	0.95
267_T	270_L	0.866	0.95
212_A	236_S	0.866	0.95
36_A	48_K	0.864	0.94
41_G	46_M	0.864	0.94
19_D	23_E	0.862	0.94
30_V	40_L	0.859	0.94
209_F	230_L	0.857	0.94
71_L	75_G	0.854	0.94
57_F	179_L	0.852	0.94
111_W	156_C	0.850	0.94
74_L	96_L	0.849	0.94
214_L	262_I	0.849	0.94
110_T	113_W	0.844	0.94
6_T	150_L	0.844	0.94
213_L	255_L	0.843	0.94
284_E	288_K	0.841	0.94
196_F	201_K	0.839	0.94
227_F	252_L	0.831	0.93
36_A	44_K	0.828	0.93
160_T	179_L	0.827	0.93
65_K	68_G	0.826	0.93
227_F	249_I	0.826	0.93
215_D	219_R	0.826	0.93
158_L	185_I	0.813	0.92
115_F	184_L	0.812	0.92
266_E	271_R	0.806	0.92
30_V	33_D	0.806	0.92
216_F	237_P	0.805	0.92
85_D	98_H	0.803	0.92
236_S	245_E	0.801	0.92
113_W	135_Y	0.799	0.92
101_L	108_A	0.797	0.92
261_A	277_K	0.797	0.92
252_L	273_L	0.796	0.92
227_F	248_L	0.790	0.91
176_D	180_A	0.788	0.91
251_R	254_E	0.787	0.91
114_F	118_F	0.787	0.91
4_H	7_F	0.787	0.91
145_V	153_D	0.786	0.91
209_F	237_P	0.785	0.91
224_T	274_Q	0.784	0.91
84_W	287_E	0.782	0.91
74_L	283_L	0.782	0.91
275_F	279_P	0.782	0.91
20_A	39_R	0.781	0.91
246_N	250_E	0.776	0.91
2_S	6_T	0.772	0.90
9_L	94_L	0.771	0.90
73_E	77_L	0.764	0.90
207_E	258_L	0.762	0.90
80_G	86_P	0.759	0.90
160_T	177_S	0.756	0.89
211_Y	283_L	0.750	0.89
286_L	290_Y	0.748	0.89
79_F	86_P	0.748	0.89
206_P	258_L	0.746	0.89
132_L	136_A	0.745	0.89
228_E	271_R	0.743	0.89
96_L	211_Y	0.741	0.89
30_V	39_R	0.738	0.88
144_K	147_E	0.734	0.88
243_L	248_L	0.733	0.88
95_W	237_P	0.729	0.88
282_P	285_I	0.726	0.87
37_I	209_F	0.726	0.87
123_F	158_L	0.723	0.87
2_S	152_R	0.723	0.87
237_P	261_A	0.718	0.87
242_K	266_E	0.715	0.87
121_P	173_D	0.714	0.87
224_T	272_Q	0.712	0.86
3_G	8_P	0.711	0.86
201_K	204_L	0.711	0.86
29_N	33_D	0.706	0.86
43_G	53_W	0.704	0.86
96_L	241_F	0.701	0.86
186_R	195_R	0.698	0.85
47_V	89_E	0.694	0.85
55_L	62_E	0.694	0.85
56_A	108_A	0.693	0.85
187_E	271_R	0.690	0.85
52_Y	111_W	0.690	0.85
256_E	259_T	0.684	0.84
129_L	151_K	0.684	0.84
212_A	237_P	0.682	0.84
46_M	52_Y	0.681	0.84
22_K	71_L	0.681	0.84
21_V	65_K	0.677	0.84
109_T	153_D	0.669	0.83
109_T	135_Y	0.669	0.83
11_Y	181_E	0.669	0.83
238_G	248_L	0.663	0.82
40_L	46_M	0.662	0.82
250_E	254_E	0.661	0.82
131_A	135_Y	0.658	0.82
110_T	156_C	0.652	0.81
3_G	9_L	0.652	0.81
17_G	90_D	0.649	0.81
18_Y	22_K	0.644	0.80
125_R	154_V	0.644	0.80
18_Y	79_F	0.642	0.80
61_E	151_K	0.642	0.80
9_L	179_L	0.640	0.80
214_L	218_E	0.640	0.80
227_F	271_R	0.638	0.80
145_V	149_T	0.638	0.80
13_W	46_M	0.638	0.80
143_K	262_I	0.638	0.80
16_K	46_M	0.636	0.80
245_E	272_Q	0.635	0.80
15_K	83_G	0.634	0.79
162_V	185_I	0.633	0.79
7_F	43_G	0.631	0.79
102_A	132_L	0.631	0.79
20_A	99_W	0.630	0.79
87_Y	108_A	0.630	0.79
175_L	178_P	0.629	0.79
2_S	8_P	0.625	0.78
13_W	53_W	0.625	0.78
205_P	289_Y	0.625	0.78
282_P	286_L	0.624	0.78
209_F	236_S	0.622	0.78
201_K	247_S	0.621	0.78
256_E	273_L	0.620	0.78
94_L	97_L	0.620	0.78
99_W	103_S	0.619	0.78
266_E	270_L	0.615	0.77
88_L	97_L	0.613	0.77
124_T	193_G	0.613	0.77
130_E	133_K	0.612	0.77
10_R	46_M	0.612	0.77
226_S	229_E	0.611	0.77
12_G	177_S	0.609	0.77
102_A	115_F	0.609	0.77
11_Y	37_I	0.606	0.76
153_D	269_G	0.605	0.76
63_D	68_G	0.604	0.76
90_D	101_L	0.604	0.76
24_D	30_V	0.603	0.76
13_W	16_K	0.601	0.76
155_D	159_R	0.600	0.76
130_E	134_R	0.599	0.76
62_E	69_L	0.599	0.76
25_P	29_N	0.596	0.75
265_S	276_K	0.595	0.75
46_M	53_W	0.595	0.75
267_T	272_Q	0.595	0.75
116_N	238_G	0.594	0.75
2_S	9_L	0.591	0.75
271_R	274_Q	0.590	0.74
124_T	253_E	0.589	0.74
190_K	247_S	0.588	0.74
163_P	200_P	0.588	0.74
14_L	18_Y	0.587	0.74
201_K	242_K	0.584	0.74
79_F	96_L	0.583	0.74
250_E	253_E	0.583	0.74
35_D	38_V	0.582	0.73
71_L	223_G	0.582	0.73
127_E	131_A	0.582	0.73
88_L	178_P	0.581	0.73
46_M	49_S	0.580	0.73
144_K	253_E	0.579	0.73
188_V	195_R	0.578	0.73
15_K	81_D	0.575	0.73
159_R	176_D	0.575	0.73
155_D	164_R	0.574	0.72
211_Y	282_P	0.574	0.72
116_N	235_G	0.572	0.72
264_Y	271_R	0.572	0.72
11_Y	99_W	0.572	0.72
238_G	245_E	0.571	0.72
222_P	262_I	0.570	0.72
98_H	240_V	0.565	0.71
3_G	125_R	0.564	0.71
46_M	56_A	0.564	0.71
89_E	95_W	0.563	0.71
12_G	18_Y	0.563	0.71
58_G	106_E	0.560	0.71
214_L	282_P	0.560	0.71
129_L	133_K	0.560	0.71
111_W	177_S	0.559	0.70
218_E	250_E	0.558	0.70
49_S	53_W	0.557	0.70
201_K	248_L	0.557	0.70
78_L	84_W	0.557	0.70
116_N	149_T	0.557	0.70
93_T	113_W	0.557	0.70
108_A	153_D	0.556	0.70
261_A	276_K	0.554	0.70
91_P	181_E	0.553	0.70
4_H	161_Y	0.552	0.69
22_K	26_D	0.552	0.69
79_F	83_G	0.551	0.69
65_K	263_R	0.550	0.69
6_T	156_C	0.549	0.69
283_L	286_L	0.547	0.69
61_E	257_E	0.547	0.69
111_W	235_G	0.547	0.69
144_K	159_R	0.546	0.69
239_R	265_S	0.546	0.69
99_W	212_A	0.546	0.69
153_D	156_C	0.545	0.69
123_F	185_I	0.543	0.68
52_Y	153_D	0.543	0.68
255_L	259_T	0.542	0.68
43_G	46_M	0.542	0.68
231_A	245_E	0.541	0.68
247_S	251_R	0.541	0.68
201_K	241_F	0.540	0.68
6_T	153_D	0.540	0.68
183_G	197_N	0.540	0.68
254_E	258_L	0.539	0.68
253_E	273_L	0.538	0.68
90_D	273_L	0.537	0.67
81_D	84_W	0.536	0.67
217_W	221_S	0.536	0.67
38_V	50_I	0.535	0.67
59_L	72_T	0.534	0.67
37_I	44_K	0.533	0.67
6_T	117_E	0.533	0.67
42_V	153_D	0.531	0.67
164_R	180_A	0.531	0.67
277_K	283_L	0.530	0.66
77_L	283_L	0.529	0.66
59_L	79_F	0.529	0.66
146_S	152_R	0.529	0.66
177_S	181_E	0.529	0.66
9_L	160_T	0.529	0.66
61_E	73_E	0.527	0.66
9_L	14_L	0.527	0.66
126_E	192_K	0.526	0.66
92_A	101_L	0.526	0.66
103_S	112_Y	0.526	0.66
146_S	175_L	0.525	0.66
122_E	175_L	0.523	0.65
113_W	117_E	0.522	0.65
99_W	241_F	0.521	0.65
152_R	159_R	0.520	0.65
115_F	153_D	0.519	0.65
197_N	226_S	0.519	0.65
21_V	177_S	0.519	0.65
253_E	264_Y	0.519	0.65
21_V	30_V	0.518	0.65
49_S	148_N	0.517	0.64
127_E	227_F	0.515	0.64
196_F	199_G	0.513	0.64
18_Y	54_L	0.513	0.64
6_T	120_K	0.513	0.64
6_T	185_I	0.512	0.64
121_P	188_V	0.511	0.64
113_W	156_C	0.510	0.63
29_N	32_S	0.509	0.63
4_H	45_N	0.508	0.63
3_G	15_K	0.506	0.63
106_E	211_Y	0.506	0.63
61_E	198_R	0.506	0.63
15_K	86_P	0.503	0.62
166_K	262_I	0.503	0.62
197_N	201_K	0.502	0.62
67_R	88_L	0.502	0.62
262_I	275_F	0.502	0.62
86_P	134_R	0.500	0.62
48_K	111_W	0.500	0.62
54_L	59_L	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
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
1xmkA	1	0.2655	63.2	0.953	Contact Map
3w6kB	2	0.269	39.5	0.959	Contact Map
1oaoC	1	0.2483	33.6	0.96	Contact Map
2wteA	2	0.2724	33.4	0.96	Contact Map
3w6jB	2	0.2586	30.3	0.961	Contact Map
4i98B	2	0.2517	30	0.961	Contact Map
2pg4A	3	0.3069	25.6	0.963	Contact Map
2xvcA	1	0.1931	24.2	0.963	Contact Map
4p9fA	1	0.2655	23.3	0.963	Contact Map
2h09A	2	0.4207	21.6	0.964	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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