DUF3825 - PFAM28P - GREMLIN Contacts

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DUF3825 - Domain of unknown function (DUF3825)

PFAM:	PF12873	Sequences: LAELALPEDWDYSTPSNKPYPILKNYLEYTFRRLQEEGKIVYSDDGKYACFNTGLVTKNYEPIYALFEKNRPPGRQPWFFKGFCKESDRELGKRLLRYFSPLPERANYFDDPSDLIFDPRLELRVNYDHIIEDNIDRFPEELQSMDRNDRNLRNLLEGAIELAKKRVRRNYKTAVPQYYGPKNGKIQLLLPLCLTDPSKPDLALVVEKTDSGFYRGHTCLTLDMAYNNARLIARPDSDW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	239 (236)
Sequences:	830 (704)
Seq/√Len:	45.8
META:	0.865

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
221_T	224_M	7.726	1.00
117_F	123_L	4.908	1.00
30_T	108_Y	3.960	1.00
33_R	37_E	3.768	1.00
157_E	161_E	3.392	1.00
34_L	106_A	3.386	1.00
68_E	81_K	3.171	1.00
36_E	184_G	2.928	1.00
64_Y	102_L	2.909	1.00
167_V	190_L	2.871	1.00
177_Q	228_N	2.836	1.00
105_R	169_R	2.775	1.00
138_F	202_L	2.700	1.00
37_E	107_N	2.662	1.00
129_H	218_T	2.598	1.00
70_N	76_Q	2.472	1.00
174_A	190_L	2.367	1.00
140_E	143_Q	2.363	1.00
194_L	201_D	2.256	1.00
65_A	83_F	2.191	1.00
56_V	169_R	2.184	1.00
70_N	74_G	2.136	1.00
95_L	99_F	2.093	1.00
177_Q	187_Q	1.956	0.99
24_K	28_E	1.926	0.99
70_N	73_P	1.883	0.99
220_L	228_N	1.864	0.99
125_V	160_I	1.834	0.99
70_N	75_R	1.742	0.98
31_F	49_A	1.742	0.98
104_E	168_R	1.669	0.98
123_L	206_V	1.628	0.97
175_V	233_A	1.619	0.97
138_F	156_L	1.619	0.97
11_D	19_P	1.596	0.97
132_E	149_D	1.596	0.97
34_L	37_E	1.578	0.97
177_Q	189_L	1.569	0.97
6_L	60_Y	1.534	0.96
174_A	188_L	1.500	0.96
71_R	79_F	1.487	0.95
185_K	207_E	1.475	0.95
12_Y	21_P	1.474	0.95
121_L	208_K	1.466	0.95
221_T	227_N	1.463	0.95
187_Q	228_N	1.463	0.95
172_K	236_D	1.459	0.95
34_L	38_G	1.456	0.95
111_D	114_D	1.448	0.95
7_P	58_K	1.436	0.94
131_I	138_F	1.434	0.94
134_N	221_T	1.428	0.94
112_P	188_L	1.410	0.94
167_V	174_A	1.406	0.94
119_P	167_V	1.403	0.94
39_K	106_A	1.400	0.94
173_T	193_C	1.398	0.93
31_F	67_F	1.394	0.93
135_I	149_D	1.389	0.93
53_T	83_F	1.378	0.93
118_D	121_L	1.364	0.93
131_I	156_L	1.357	0.92
53_T	159_A	1.351	0.92
170_N	236_D	1.340	0.92
123_L	160_I	1.331	0.92
6_L	169_R	1.330	0.92
192_L	202_L	1.319	0.91
31_F	35_Q	1.317	0.91
95_L	102_L	1.287	0.90
163_A	173_T	1.286	0.90
27_L	65_A	1.277	0.90
69_K	77_P	1.246	0.89
193_C	200_P	1.240	0.89
161_E	164_K	1.240	0.89
61_E	85_K	1.235	0.88
12_Y	22_I	1.227	0.88
172_K	235_P	1.218	0.88
62_P	169_R	1.210	0.87
150_R	197_P	1.210	0.87
23_L	26_Y	1.202	0.87
109_F	170_N	1.198	0.87
11_D	20_Y	1.195	0.87
162_L	165_K	1.186	0.86
54_G	106_A	1.184	0.86
102_L	124_R	1.181	0.86
235_P	239_W	1.176	0.86
5_A	8_E	1.168	0.85
43_S	46_G	1.163	0.85
166_R	173_T	1.153	0.85
39_K	104_E	1.141	0.84
126_N	215_R	1.130	0.83
189_L	228_N	1.127	0.83
40_I	49_A	1.120	0.83
86_E	122_E	1.108	0.82
188_L	232_I	1.096	0.81
37_E	106_A	1.095	0.81
85_K	128_D	1.079	0.80
118_D	174_A	1.078	0.80
60_Y	169_R	1.076	0.80
61_E	87_S	1.056	0.79
129_H	137_R	1.055	0.79
202_L	219_C	1.031	0.77
37_E	205_V	1.029	0.77
47_K	69_K	1.021	0.77
67_F	80_F	1.009	0.76
193_C	206_V	1.000	0.75
221_T	228_N	0.994	0.75
136_D	143_Q	0.990	0.74
11_D	18_K	0.985	0.74
175_V	229_A	0.982	0.74
151_N	155_L	0.979	0.73
5_A	63_I	0.976	0.73
156_L	160_I	0.972	0.73
33_R	36_E	0.962	0.72
1_L	5_A	0.951	0.71
1_L	8_E	0.948	0.71
49_A	67_F	0.943	0.71
230_R	239_W	0.938	0.70
134_N	202_L	0.938	0.70
226_Y	230_R	0.933	0.70
48_Y	66_L	0.931	0.70
141_E	195_T	0.931	0.70
56_V	60_Y	0.928	0.69
29_Y	231_L	0.926	0.69
43_S	47_K	0.921	0.69
80_F	141_E	0.919	0.69
53_T	65_A	0.918	0.69
27_L	43_S	0.902	0.67
21_P	172_K	0.890	0.66
30_T	106_A	0.888	0.66
107_N	120_R	0.887	0.66
173_T	238_D	0.885	0.66
110_D	120_R	0.878	0.65
135_I	138_F	0.878	0.65
184_G	227_N	0.871	0.64
138_F	169_R	0.868	0.64
177_Q	184_G	0.866	0.64
96_L	99_F	0.865	0.64
142_L	195_T	0.864	0.64
54_G	174_A	0.864	0.64
11_D	16_S	0.859	0.63
194_L	216_G	0.857	0.63
172_K	238_D	0.856	0.63
27_L	34_L	0.848	0.62
59_N	127_Y	0.848	0.62
73_P	76_Q	0.847	0.62
58_K	198_S	0.843	0.62
56_V	62_P	0.839	0.62
171_Y	233_A	0.839	0.62
172_K	233_A	0.838	0.61
184_G	187_Q	0.837	0.61
63_I	166_R	0.837	0.61
231_L	237_S	0.829	0.61
188_L	203_A	0.828	0.61
10_W	23_L	0.828	0.61
207_E	217_H	0.827	0.60
117_F	186_I	0.826	0.60
10_W	55_L	0.825	0.60
42_Y	49_A	0.825	0.60
114_D	208_K	0.824	0.60
55_L	176_P	0.823	0.60
113_S	161_E	0.821	0.60
206_V	216_G	0.821	0.60
224_M	228_N	0.816	0.59
46_G	69_K	0.815	0.59
133_D	168_R	0.815	0.59
223_D	233_A	0.814	0.59
195_T	201_D	0.812	0.59
13_S	17_N	0.806	0.58
112_P	115_L	0.805	0.58
209_T	213_F	0.804	0.58
72_P	76_Q	0.804	0.58
1_L	4_L	0.803	0.58
107_N	229_A	0.801	0.58
86_E	165_K	0.796	0.57
117_F	164_K	0.795	0.57
155_L	192_L	0.793	0.57
188_L	234_R	0.787	0.57
31_F	105_R	0.785	0.56
123_L	164_K	0.782	0.56
173_T	188_L	0.779	0.56
40_I	52_N	0.778	0.56
30_T	52_N	0.775	0.55
30_T	118_D	0.770	0.55
114_D	219_C	0.767	0.55
57_T	61_E	0.764	0.54
48_Y	98_Y	0.759	0.54
156_L	192_L	0.759	0.54
187_Q	220_L	0.759	0.54
170_N	179_Y	0.748	0.53
218_T	226_Y	0.746	0.53
33_R	186_I	0.745	0.53
166_R	193_C	0.741	0.52
66_L	84_C	0.739	0.52
28_E	78_W	0.738	0.52
65_A	80_F	0.734	0.51
212_G	216_G	0.734	0.51
13_S	16_S	0.734	0.51
12_Y	15_P	0.733	0.51
160_I	216_G	0.733	0.51
120_R	163_A	0.729	0.51
186_I	205_V	0.727	0.51
224_M	227_N	0.725	0.51
119_P	173_T	0.724	0.50
59_N	128_D	0.723	0.50
177_Q	220_L	0.722	0.50
194_L	203_A	0.720	0.50
54_G	108_Y	0.719	0.50
108_Y	190_L	0.711	0.49
207_E	215_R	0.707	0.49
13_S	20_Y	0.705	0.49
178_Y	194_L	0.703	0.48
111_D	167_V	0.702	0.48
52_N	169_R	0.701	0.48
235_P	238_D	0.699	0.48
15_P	19_P	0.697	0.48
50_C	84_C	0.697	0.48
65_A	186_I	0.695	0.48
51_F	164_K	0.693	0.47
154_N	158_G	0.689	0.47
63_I	117_F	0.688	0.47
115_L	165_K	0.686	0.47
16_S	21_P	0.679	0.46
89_R	126_N	0.678	0.46
31_F	83_F	0.676	0.46
12_Y	31_F	0.672	0.45
163_A	167_V	0.665	0.45
4_L	57_T	0.662	0.44
43_S	48_Y	0.661	0.44
142_L	155_L	0.660	0.44
50_C	86_E	0.657	0.44
51_F	203_A	0.656	0.44
48_Y	59_N	0.654	0.44
11_D	14_T	0.652	0.43
33_R	106_A	0.651	0.43
58_K	74_G	0.647	0.43
51_F	139_P	0.647	0.43
79_F	82_G	0.646	0.43
22_I	194_L	0.644	0.43
160_I	164_K	0.643	0.43
25_N	227_N	0.640	0.42
25_N	29_Y	0.639	0.42
36_E	178_Y	0.636	0.42
16_S	19_P	0.634	0.42
49_A	146_D	0.633	0.42
34_L	39_K	0.633	0.42
57_T	148_N	0.632	0.42
91_L	236_D	0.628	0.41
3_E	7_P	0.628	0.41
160_I	163_A	0.628	0.41
112_P	202_L	0.626	0.41
229_A	233_A	0.623	0.41
130_I	137_R	0.621	0.40
41_V	49_A	0.620	0.40
216_G	237_S	0.619	0.40
124_R	178_Y	0.617	0.40
32_R	195_T	0.617	0.40
83_F	190_L	0.617	0.40
84_C	90_E	0.616	0.40
30_T	33_R	0.616	0.40
80_F	134_N	0.613	0.40
116_I	172_K	0.611	0.40
126_N	179_Y	0.611	0.40
173_T	236_D	0.608	0.39
71_R	74_G	0.608	0.39
137_R	226_Y	0.605	0.39
85_K	88_D	0.604	0.39
22_I	48_Y	0.604	0.39
215_R	236_D	0.602	0.39
131_I	152_L	0.602	0.39
69_K	76_Q	0.601	0.39
31_F	211_S	0.601	0.39
21_P	223_D	0.597	0.38
219_C	224_M	0.597	0.38
220_L	226_Y	0.594	0.38
92_G	96_L	0.591	0.38
10_W	26_Y	0.590	0.38
207_E	216_G	0.590	0.38
15_P	140_E	0.588	0.37
8_E	23_L	0.587	0.37
105_R	168_R	0.585	0.37
117_F	198_S	0.585	0.37
30_T	54_G	0.583	0.37
169_R	232_I	0.582	0.37
119_P	168_R	0.582	0.37
154_N	157_E	0.582	0.37
84_C	87_S	0.581	0.37
12_Y	227_N	0.581	0.37
35_Q	38_G	0.578	0.36
52_N	226_Y	0.575	0.36
78_W	166_R	0.575	0.36
73_P	101_P	0.575	0.36
132_E	186_I	0.574	0.36
89_R	133_D	0.574	0.36
47_K	71_R	0.573	0.36
9_D	22_I	0.572	0.36
29_Y	36_E	0.570	0.36
154_N	162_L	0.569	0.36
191_P	230_R	0.569	0.36
10_W	230_R	0.568	0.36
64_Y	171_Y	0.565	0.35
56_V	173_T	0.564	0.35
141_E	144_S	0.562	0.35
62_P	105_R	0.562	0.35
74_G	77_P	0.562	0.35
67_F	103_P	0.560	0.35
41_V	44_D	0.560	0.35
142_L	149_D	0.557	0.35
63_I	83_F	0.557	0.35
60_Y	162_L	0.556	0.35
59_N	164_K	0.549	0.34
169_R	236_D	0.548	0.34
76_Q	79_F	0.545	0.34
158_G	219_C	0.544	0.33
42_Y	78_W	0.544	0.33
17_N	110_D	0.544	0.33
8_E	26_Y	0.543	0.33
189_L	201_D	0.542	0.33
188_L	214_Y	0.542	0.33
20_Y	160_I	0.541	0.33
37_E	178_Y	0.540	0.33
66_L	223_D	0.539	0.33
6_L	105_R	0.539	0.33
169_R	237_S	0.536	0.33
226_Y	235_P	0.535	0.33
163_A	222_L	0.534	0.33
60_Y	168_R	0.530	0.32
14_T	17_N	0.526	0.32
39_K	108_Y	0.525	0.32
225_A	228_N	0.523	0.32
225_A	239_W	0.522	0.32
109_F	234_R	0.522	0.32
177_Q	205_V	0.521	0.31
32_R	184_G	0.520	0.31
170_N	231_L	0.518	0.31
103_P	171_Y	0.516	0.31
30_T	37_E	0.515	0.31
215_R	234_R	0.515	0.31
76_Q	226_Y	0.514	0.31
165_K	231_L	0.514	0.31
9_D	15_P	0.514	0.31
35_Q	160_I	0.513	0.31
69_K	83_F	0.512	0.31
18_K	168_R	0.511	0.31
1_L	10_W	0.509	0.30
1_L	7_P	0.506	0.30
69_K	147_R	0.506	0.30
31_F	42_Y	0.505	0.30
26_Y	55_L	0.504	0.30
20_Y	60_Y	0.504	0.30
233_A	236_D	0.504	0.30
34_L	170_N	0.504	0.30
223_D	235_P	0.500	0.30
30_T	174_A	0.500	0.30

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
4v06A	1	0.5941	9.2	0.962	Contact Map
1tohA	3	0.5732	8.7	0.963	Contact Map
1g4wR	1	0.2008	4	0.968	Contact Map
1bh9B	1	0.1464	3.1	0.97	Contact Map
1mlwA	1	0.4142	2.9	0.97	Contact Map
1oaoC	1	0.3598	2.3	0.972	Contact Map
4kgmA	5	0.5397	2.2	0.972	Contact Map
1phzA	2	0.5021	2	0.973	Contact Map
2y9yB	1	0.2301	1.9	0.973	Contact Map
2gr8A	3	0.251	1.9	0.973	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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