DUF4419 - PFAM28P - GREMLIN Contacts

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DUF4419 - Domain of unknown function (DUF4419)

PFAM:	PF14388	Sequences: HGFVAAVHLAYAQHRPLVLSPDDIWLLILQGFAFHVNANAEELRSRFVDHEGKKELVVEFDGGLLDNDWEEVFPEFSDQIAENIGDPELRDLLVPDFSTTTPVERIASEITLMDAMKSYFEYEVYTGCGIPSITLEGTPEDWEKILDRAEKLAEYGEDLEWWTDELRPILDEFVAAAENPGKPDKEFWQSIYKYHSGKGSGPPYISGWITKFFPYDKDGKWNGLKLRRNPLLESWREVLDGVSYPGIDTDDLPSGLSSVPFKWDDYDNGTEYPMELVAGFVGVEQDPETDLALRPEIGWAV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	301 (290)
Sequences:	1150 (1019)
Seq/√Len:	59.8
META:	0.683

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
146_L	171_D	4.796	1.00
172_E	184_D	4.705	1.00
139_P	177_A	4.258	1.00
55_E	123_E	3.505	1.00
101_T	104_E	3.342	1.00
143_E	178_E	3.228	1.00
7_V	17_L	3.191	1.00
54_K	83_N	3.064	1.00
80_I	113_M	2.987	1.00
39_N	42_E	2.900	1.00
136_E	294_R	2.840	1.00
68_D	71_E	2.768	1.00
173_F	176_A	2.684	1.00
153_A	164_D	2.634	1.00
60_F	63_G	2.601	1.00
53_K	121_E	2.584	1.00
79_Q	82_E	2.576	1.00
146_L	174_V	2.560	1.00
32_F	36_V	2.492	1.00
32_F	155_Y	2.456	1.00
149_A	170_L	2.386	1.00
150_E	167_R	2.296	1.00
96_D	144_K	2.285	1.00
144_K	148_R	2.266	1.00
139_P	178_E	2.255	1.00
18_V	292_A	2.229	1.00
76_F	113_M	2.217	1.00
117_K	260_P	2.149	1.00
143_E	147_D	2.109	1.00
8_H	192_Y	2.105	1.00
3_F	27_L	2.100	1.00
28_I	152_L	2.059	1.00
153_A	163_T	2.035	1.00
261_F	274_M	2.033	1.00
44_R	48_V	2.031	1.00
95_P	108_S	2.018	1.00
261_F	276_L	2.001	1.00
145_I	148_R	1.956	1.00
284_E	296_E	1.954	1.00
47_F	119_Y	1.948	1.00
55_E	121_E	1.939	1.00
56_L	79_Q	1.886	1.00
165_E	211_K	1.864	1.00
96_D	108_S	1.841	1.00
286_D	289_T	1.731	0.99
262_K	273_P	1.718	0.99
81_A	90_R	1.698	0.99
27_L	212_F	1.684	0.99
229_N	232_L	1.669	0.99
107_A	297_I	1.662	0.99
72_V	124_V	1.662	0.99
146_L	167_R	1.648	0.99
31_G	214_P	1.647	0.99
60_F	64_L	1.625	0.99
127_G	200_S	1.619	0.99
41_E	44_R	1.595	0.99
126_T	263_W	1.593	0.99
63_G	67_N	1.585	0.99
94_V	109_E	1.579	0.99
63_G	66_D	1.568	0.99
126_T	200_S	1.551	0.98
172_E	175_A	1.530	0.98
20_S	23_D	1.525	0.98
197_G	202_P	1.523	0.98
264_D	269_G	1.523	0.98
153_A	160_E	1.512	0.98
3_F	19_L	1.497	0.98
64_L	67_N	1.479	0.98
6_A	283_V	1.471	0.98
24_I	173_F	1.459	0.98
60_F	67_N	1.455	0.98
44_R	50_H	1.452	0.98
59_E	63_G	1.444	0.98
262_K	271_E	1.434	0.97
280_F	297_I	1.428	0.97
162_W	214_P	1.424	0.97
191_I	208_W	1.422	0.97
22_D	99_T	1.414	0.97
73_F	106_I	1.405	0.97
37_N	118_S	1.398	0.97
39_N	43_L	1.396	0.97
44_R	52_G	1.384	0.97
57_V	123_E	1.374	0.97
6_A	17_L	1.366	0.97
149_A	163_T	1.360	0.96
40_A	43_L	1.351	0.96
160_E	163_T	1.343	0.96
181_G	184_D	1.333	0.96
263_W	274_M	1.331	0.96
37_N	117_K	1.317	0.96
61_D	67_N	1.308	0.96
96_D	105_R	1.307	0.96
42_E	158_D	1.296	0.95
8_H	12_A	1.287	0.95
29_L	111_T	1.275	0.95
36_V	155_Y	1.255	0.94
264_D	271_E	1.234	0.94
48_V	52_G	1.229	0.94
110_I	278_A	1.210	0.93
139_P	143_E	1.195	0.93
22_D	26_L	1.191	0.93
116_M	122_Y	1.190	0.93
258_S	275_E	1.182	0.92
140_E	143_E	1.182	0.92
169_I	211_K	1.182	0.92
23_D	136_E	1.179	0.92
142_W	162_W	1.169	0.92
48_V	119_Y	1.153	0.91
32_F	93_L	1.147	0.91
35_H	215_Y	1.144	0.91
76_F	80_I	1.123	0.90
60_F	75_E	1.122	0.90
23_D	280_F	1.122	0.90
196_S	203_P	1.113	0.90
26_L	297_I	1.109	0.90
126_T	202_P	1.101	0.89
216_D	220_K	1.096	0.89
93_L	112_L	1.096	0.89
60_F	65_L	1.089	0.89
171_D	175_A	1.086	0.89
145_I	149_A	1.082	0.89
123_E	264_D	1.078	0.88
36_V	43_L	1.074	0.88
56_L	83_N	1.066	0.88
3_F	212_F	1.048	0.87
16_P	132_S	1.043	0.87
255_G	280_F	1.037	0.86
43_L	46_R	1.030	0.86
50_H	54_K	1.030	0.86
40_A	44_R	1.026	0.86
27_L	280_F	1.023	0.86
282_G	298_G	1.023	0.86
31_G	35_H	1.022	0.86
35_H	43_L	1.016	0.85
61_D	64_L	1.016	0.85
77_S	112_L	1.007	0.85
20_S	104_E	1.005	0.85
45_S	51_E	0.999	0.84
285_Q	291_L	0.998	0.84
9_L	13_Q	0.995	0.84
151_K	154_E	0.984	0.83
34_F	38_A	0.983	0.83
40_A	119_Y	0.978	0.83
100_T	104_E	0.977	0.83
228_R	232_L	0.958	0.82
22_D	25_W	0.956	0.82
111_T	257_S	0.946	0.81
176_A	184_D	0.944	0.81
22_D	100_T	0.943	0.81
80_I	83_N	0.942	0.81
140_E	144_K	0.935	0.80
169_I	191_I	0.935	0.80
3_F	280_F	0.934	0.80
31_G	215_Y	0.933	0.80
59_E	62_G	0.925	0.79
62_G	67_N	0.921	0.79
175_A	182_K	0.921	0.79
23_D	27_L	0.911	0.78
7_V	209_I	0.908	0.78
23_D	294_R	0.908	0.78
48_V	120_F	0.903	0.78
77_S	80_I	0.895	0.77
2_G	5_A	0.894	0.77
150_E	163_T	0.891	0.77
77_S	109_E	0.891	0.77
15_R	293_L	0.886	0.76
58_V	72_V	0.886	0.76
159_L	162_W	0.883	0.76
178_E	182_K	0.882	0.76
71_E	75_E	0.876	0.76
60_F	66_D	0.867	0.75
80_I	84_I	0.867	0.75
35_H	39_N	0.861	0.74
46_R	154_E	0.860	0.74
72_V	76_F	0.859	0.74
110_I	276_L	0.856	0.74
2_G	6_A	0.856	0.74
50_H	119_Y	0.855	0.74
289_T	292_A	0.849	0.73
12_A	200_S	0.847	0.73
57_V	125_Y	0.845	0.73
205_I	252_L	0.845	0.73
265_D	268_N	0.838	0.72
167_R	171_D	0.836	0.72
28_I	170_L	0.832	0.72
26_L	280_F	0.829	0.71
41_E	48_V	0.828	0.71
174_V	178_E	0.823	0.71
135_L	177_A	0.823	0.71
44_R	120_F	0.811	0.70
142_W	145_I	0.810	0.70
43_L	48_V	0.809	0.70
56_L	261_F	0.808	0.70
158_D	161_W	0.806	0.69
110_I	259_V	0.804	0.69
8_H	193_K	0.798	0.69
213_F	253_P	0.792	0.68
40_A	118_S	0.788	0.68
197_G	200_S	0.785	0.67
108_S	111_T	0.785	0.67
41_E	50_H	0.783	0.67
56_L	80_I	0.782	0.67
1_H	6_A	0.779	0.67
139_P	174_V	0.779	0.67
26_L	30_Q	0.771	0.66
149_A	167_R	0.771	0.66
123_E	251_D	0.763	0.65
171_D	174_V	0.763	0.65
142_W	170_L	0.761	0.65
69_W	73_F	0.756	0.64
115_A	118_S	0.754	0.64
35_H	181_G	0.754	0.64
77_S	90_R	0.748	0.64
200_S	204_Y	0.741	0.63
114_D	117_K	0.741	0.63
73_F	80_I	0.737	0.62
89_L	155_Y	0.737	0.62
113_M	122_Y	0.737	0.62
76_F	124_V	0.736	0.62
84_I	93_L	0.736	0.62
57_V	264_D	0.736	0.62
55_E	262_K	0.735	0.62
95_P	100_T	0.734	0.62
20_S	31_G	0.734	0.62
196_S	200_S	0.734	0.62
265_D	269_G	0.734	0.62
259_V	276_L	0.731	0.62
26_L	107_A	0.731	0.62
49_D	85_G	0.730	0.62
18_V	136_E	0.730	0.62
85_G	89_L	0.728	0.61
103_V	106_I	0.722	0.61
90_R	154_E	0.720	0.61
75_E	79_Q	0.716	0.60
102_P	105_R	0.716	0.60
25_W	97_F	0.713	0.60
74_P	109_E	0.712	0.60
105_R	170_L	0.712	0.60
4_V	213_F	0.710	0.59
58_V	76_F	0.706	0.59
261_F	269_G	0.706	0.59
169_I	208_W	0.705	0.59
35_H	213_F	0.703	0.59
69_W	263_W	0.701	0.59
193_K	200_S	0.701	0.59
124_V	261_F	0.701	0.59
264_D	268_N	0.701	0.59
32_F	163_T	0.700	0.58
175_A	183_P	0.699	0.58
203_P	248_D	0.697	0.58
193_K	202_P	0.696	0.58
11_Y	14_H	0.695	0.58
126_T	267_D	0.693	0.58
30_Q	280_F	0.690	0.57
266_Y	269_G	0.688	0.57
8_H	11_Y	0.687	0.57
113_M	259_V	0.687	0.57
214_P	280_F	0.686	0.57
169_I	187_F	0.684	0.57
36_V	115_A	0.684	0.57
81_A	91_D	0.683	0.57
159_L	215_Y	0.682	0.56
47_F	116_M	0.680	0.56
166_L	169_I	0.679	0.56
155_Y	163_T	0.677	0.56
226_L	229_N	0.677	0.56
62_G	65_L	0.675	0.56
161_W	214_P	0.675	0.56
55_E	264_D	0.672	0.55
40_A	50_H	0.666	0.55
263_W	268_N	0.666	0.55
61_D	65_L	0.665	0.55
83_N	120_F	0.665	0.55
143_E	174_V	0.664	0.54
196_S	202_P	0.663	0.54
126_T	268_N	0.659	0.54
185_K	189_Q	0.658	0.54
274_M	301_V	0.657	0.54
190_S	206_S	0.657	0.54
52_G	119_Y	0.654	0.53
11_Y	190_S	0.653	0.53
192_Y	209_I	0.653	0.53
205_I	249_T	0.652	0.53
48_V	54_K	0.651	0.53
74_P	106_I	0.650	0.53
146_L	150_E	0.650	0.53
62_G	66_D	0.649	0.53
112_L	116_M	0.648	0.53
248_D	251_D	0.648	0.53
73_F	109_E	0.645	0.52
277_V	300_A	0.644	0.52
14_H	128_C	0.643	0.52
131_P	135_L	0.641	0.52
175_A	184_D	0.637	0.51
46_R	158_D	0.636	0.51
58_V	79_Q	0.635	0.51
225_K	228_R	0.635	0.51
40_A	48_V	0.628	0.50
22_D	162_W	0.627	0.50
49_D	171_D	0.627	0.50
277_V	291_L	0.627	0.50
58_V	75_E	0.627	0.50
265_D	272_Y	0.626	0.50
126_T	199_G	0.622	0.50
88_E	91_D	0.621	0.50
146_L	149_A	0.620	0.50
26_L	108_S	0.619	0.49
104_E	297_I	0.619	0.49
16_P	292_A	0.615	0.49
28_I	42_E	0.614	0.49
7_V	293_L	0.613	0.49
107_A	259_V	0.613	0.49
92_L	151_K	0.612	0.49
82_E	154_E	0.612	0.49
174_V	177_A	0.611	0.49
121_E	262_K	0.611	0.49
263_W	267_D	0.610	0.48
238_V	241_G	0.610	0.48
158_D	215_Y	0.609	0.48
12_A	193_K	0.608	0.48
81_A	86_D	0.605	0.48
105_R	108_S	0.605	0.48
173_F	177_A	0.605	0.48
31_G	162_W	0.602	0.47
168_P	188_W	0.601	0.47
3_F	7_V	0.600	0.47
131_P	134_T	0.600	0.47
228_R	231_L	0.598	0.47
187_F	282_G	0.598	0.47
208_W	212_F	0.598	0.47
26_L	111_T	0.595	0.47
165_E	169_I	0.594	0.47
153_A	167_R	0.593	0.46
139_P	176_A	0.593	0.46
50_H	53_K	0.588	0.46
133_I	187_F	0.587	0.46
16_P	130_I	0.587	0.46
173_F	188_W	0.586	0.46
29_L	108_S	0.586	0.46
193_K	201_G	0.585	0.46
143_E	146_L	0.584	0.45
145_I	170_L	0.584	0.45
33_A	190_S	0.583	0.45
28_I	166_L	0.580	0.45
140_E	185_K	0.579	0.45
132_S	135_L	0.578	0.45
111_T	117_K	0.577	0.45
90_R	112_L	0.576	0.45
2_G	11_Y	0.575	0.44
43_L	155_Y	0.574	0.44
29_L	33_A	0.572	0.44
116_M	126_T	0.570	0.44
30_Q	111_T	0.570	0.44
56_L	189_Q	0.568	0.44
54_K	58_V	0.567	0.44
44_R	51_E	0.567	0.44
90_R	255_G	0.565	0.43
165_E	212_F	0.565	0.43
155_Y	280_F	0.564	0.43
283_V	293_L	0.564	0.43
131_P	299_W	0.563	0.43
33_A	37_N	0.562	0.43
2_G	17_L	0.561	0.43
7_V	191_I	0.560	0.43
21_P	25_W	0.560	0.43
73_F	102_P	0.559	0.43
16_P	285_Q	0.559	0.43
138_T	176_A	0.558	0.43
190_S	193_K	0.558	0.43
4_V	205_I	0.558	0.43
105_R	109_E	0.558	0.43
107_A	278_A	0.554	0.42
187_F	213_F	0.554	0.42
67_N	110_I	0.554	0.42
30_Q	285_Q	0.551	0.42
142_W	188_W	0.549	0.42
177_A	183_P	0.546	0.41
162_W	181_G	0.546	0.41
159_L	187_F	0.542	0.41
134_T	166_L	0.541	0.41
199_G	269_G	0.540	0.41
28_I	145_I	0.538	0.40
99_T	141_D	0.538	0.40
284_E	294_R	0.537	0.40
126_T	193_K	0.537	0.40
176_A	188_W	0.537	0.40
133_I	191_I	0.536	0.40
3_F	32_F	0.536	0.40
16_P	30_Q	0.535	0.40
286_D	294_R	0.535	0.40
98_S	144_K	0.534	0.40
114_D	257_S	0.532	0.40
126_T	203_P	0.531	0.40
1_H	34_F	0.530	0.40
142_W	173_F	0.526	0.39
93_L	115_A	0.525	0.39
199_G	249_T	0.524	0.39
51_E	186_E	0.524	0.39
35_H	285_Q	0.524	0.39
79_Q	124_V	0.524	0.39
204_Y	248_D	0.522	0.39
130_I	187_F	0.522	0.39
191_I	195_H	0.522	0.39
75_E	78_D	0.521	0.39
73_F	276_L	0.521	0.39
73_F	76_F	0.521	0.39
152_L	163_T	0.521	0.39
56_L	76_F	0.520	0.39
113_M	273_P	0.518	0.38
58_V	217_K	0.516	0.38
88_E	150_E	0.516	0.38
177_A	181_G	0.516	0.38
55_E	273_P	0.515	0.38
7_V	29_L	0.513	0.38
22_D	176_A	0.513	0.38
16_P	23_D	0.512	0.38
12_A	127_G	0.511	0.38
78_D	112_L	0.511	0.38
41_E	51_E	0.510	0.37
130_I	191_I	0.510	0.37
83_N	259_V	0.509	0.37
186_E	190_S	0.508	0.37
15_R	113_M	0.508	0.37
50_H	83_N	0.508	0.37
40_A	154_E	0.508	0.37
7_V	19_L	0.508	0.37
94_V	100_T	0.508	0.37
135_L	176_A	0.506	0.37
176_A	187_F	0.506	0.37
264_D	267_D	0.505	0.37
17_L	209_I	0.505	0.37
184_D	282_G	0.505	0.37
163_T	167_R	0.504	0.37
193_K	263_W	0.503	0.37
210_T	247_I	0.500	0.36

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
3jrtA	2	0.3355	39.3	0.963	Contact Map
4amgA	2	0.2625	17.7	0.969	Contact Map
4hlnA	1	0.2957	12.6	0.971	Contact Map
4p7aA	2	0.1993	9.5	0.972	Contact Map
3froA	3	0.3056	8.8	0.973	Contact Map
2iyfA	1	0.2724	8.2	0.973	Contact Map
2q83A	1	0.2027	8.1	0.973	Contact Map
4fkzA	2	0.3223	6.6	0.974	Contact Map
4pqgA	2	0.2857	6.3	0.974	Contact Map
3tixB	1	0.2625	5.9	0.975	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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