DUF4125 - PFAM28P - GREMLIN Contacts

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DUF4125 - Protein of unknown function (DUF4125)

PFAM:	PF13526	Sequences: EELIEEIIELEWEMFQKVNNEGGRASCQDDPETFRIMRKSQFSTWSEETLESYLDDLEEAKAEGRNLLTEKYARMMESTAPEEYEEIKDLLPPLSEEKKPLIEEIVAIQVEWQEELAEKYPKLAGRGRPLHSSEDTPGGTSFETYLRGELETYSDKTLELYYRDILELKKEGRNLAEEILENTVKLYGYASLEEAEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	197 (195)
Sequences:	918 (750)
Seq/√Len:	53.7
META:	0.818

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
173_R	178_E	4.039	1.00
65_R	70_E	3.706	1.00
119_K	177_E	3.131	1.00
24_R	29_D	2.851	1.00
80_A	83_E	2.797	1.00
52_S	157_T	2.582	1.00
13_E	61_K	2.563	1.00
49_T	164_D	2.438	1.00
102_I	151_E	2.413	1.00
14_M	67_L	2.270	1.00
46_S	49_T	2.243	1.00
30_D	33_T	2.226	1.00
85_E	88_K	2.151	1.00
74_R	84_Y	2.150	1.00
190_A	194_E	2.106	1.00
56_D	157_T	2.067	1.00
52_S	56_D	2.048	1.00
60_A	67_L	2.009	1.00
184_V	195_A	1.970	1.00
167_E	171_E	1.968	1.00
46_S	164_D	1.963	1.00
97_E	155_D	1.946	1.00
168_L	175_L	1.935	1.00
113_Q	176_A	1.899	0.99
114_E	131_H	1.893	0.99
181_E	185_K	1.864	0.99
77_E	99_K	1.841	0.99
73_A	87_I	1.817	0.99
20_N	23_G	1.807	0.99
162_Y	166_L	1.795	0.99
74_R	151_E	1.786	0.99
55_D	156_K	1.782	0.99
31_P	35_R	1.759	0.99
52_S	160_L	1.758	0.99
12_W	16_Q	1.742	0.99
129_P	139_G	1.722	0.99
113_Q	142_F	1.673	0.99
123_L	195_A	1.668	0.99
95_S	155_D	1.659	0.99
33_T	187_Y	1.614	0.98
123_L	184_V	1.607	0.98
146_L	161_Y	1.590	0.98
132_S	135_D	1.589	0.98
168_L	178_E	1.559	0.98
10_L	61_K	1.548	0.98
117_A	130_L	1.546	0.98
48_E	163_R	1.539	0.98
103_E	147_R	1.519	0.97
104_E	162_Y	1.506	0.97
112_W	175_L	1.494	0.97
6_E	58_E	1.478	0.97
25_A	28_Q	1.472	0.97
115_E	119_K	1.470	0.97
135_D	144_T	1.455	0.97
21_E	80_A	1.440	0.96
77_E	88_K	1.438	0.96
3_L	50_L	1.432	0.96
110_V	130_L	1.412	0.96
112_W	174_N	1.383	0.96
54_L	58_E	1.375	0.95
177_E	181_E	1.322	0.94
33_T	37_M	1.319	0.94
83_E	86_E	1.290	0.94
116_L	180_L	1.288	0.93
56_D	154_S	1.285	0.93
42_F	53_Y	1.249	0.92
104_E	166_L	1.226	0.92
12_W	31_P	1.225	0.92
42_F	45_W	1.218	0.91
5_E	39_K	1.212	0.91
4_I	7_I	1.203	0.91
102_I	106_V	1.184	0.90
16_Q	24_R	1.184	0.90
144_T	148_G	1.171	0.90
60_A	157_T	1.158	0.89
95_S	98_K	1.149	0.89
141_S	144_T	1.147	0.89
114_E	118_E	1.147	0.89
168_L	173_R	1.142	0.89
98_K	102_I	1.134	0.88
18_V	28_Q	1.126	0.88
94_L	98_K	1.113	0.87
111_E	169_K	1.109	0.87
105_I	158_L	1.105	0.87
143_E	147_R	1.104	0.87
156_K	160_L	1.102	0.87
164_D	168_L	1.093	0.86
15_F	27_C	1.090	0.86
109_Q	176_A	1.077	0.85
43_S	186_L	1.044	0.84
74_R	98_K	1.042	0.83
96_E	100_P	1.039	0.83
116_L	177_E	1.038	0.83
77_E	84_Y	1.024	0.82
18_V	68_L	1.011	0.82
103_E	106_V	1.010	0.81
109_Q	146_L	1.002	0.81
44_T	179_I	0.999	0.81
37_M	41_Q	0.996	0.81
15_F	18_V	0.996	0.81
8_I	35_R	0.994	0.80
67_L	74_R	0.990	0.80
140_T	144_T	0.989	0.80
20_N	25_A	0.979	0.79
177_E	192_L	0.969	0.79
108_I	162_Y	0.962	0.78
106_V	147_R	0.960	0.78
101_L	159_E	0.960	0.78
53_Y	153_Y	0.952	0.77
22_G	25_A	0.944	0.77
108_I	169_K	0.923	0.75
184_V	189_Y	0.922	0.75
37_M	40_S	0.920	0.75
104_E	107_A	0.920	0.75
98_K	155_D	0.908	0.74
41_Q	141_S	0.906	0.74
52_S	57_L	0.893	0.73
94_L	151_E	0.893	0.73
84_Y	88_K	0.891	0.73
18_V	27_C	0.875	0.71
5_E	9_E	0.872	0.71
178_E	181_E	0.868	0.71
116_L	124_A	0.867	0.71
83_E	87_I	0.867	0.71
112_W	195_A	0.859	0.70
43_S	182_N	0.859	0.70
9_E	31_P	0.859	0.70
117_A	124_A	0.854	0.69
118_E	167_E	0.851	0.69
74_R	94_L	0.851	0.69
105_I	165_I	0.848	0.69
42_F	176_A	0.845	0.69
14_M	98_K	0.844	0.69
175_L	196_E	0.837	0.68
17_K	68_L	0.831	0.67
71_K	145_Y	0.830	0.67
27_C	145_Y	0.818	0.66
36_I	187_Y	0.816	0.66
34_F	38_R	0.812	0.66
6_E	54_L	0.803	0.65
113_Q	124_A	0.803	0.65
21_E	83_E	0.801	0.64
16_Q	68_L	0.799	0.64
128_R	145_Y	0.792	0.64
29_D	32_E	0.783	0.63
8_I	39_K	0.782	0.63
156_K	159_E	0.782	0.63
120_Y	193_E	0.781	0.62
135_D	141_S	0.770	0.61
98_K	151_E	0.763	0.61
49_T	161_Y	0.762	0.61
57_L	157_T	0.758	0.60
13_E	17_K	0.758	0.60
41_Q	161_Y	0.754	0.60
75_M	145_Y	0.750	0.59
159_E	163_R	0.749	0.59
16_Q	42_F	0.745	0.59
109_Q	113_Q	0.744	0.59
106_V	162_Y	0.741	0.58
18_V	33_T	0.741	0.58
16_Q	29_D	0.740	0.58
41_Q	179_I	0.738	0.58
52_S	60_A	0.735	0.58
108_I	111_E	0.731	0.57
73_A	112_W	0.727	0.57
82_E	85_E	0.727	0.57
21_E	88_K	0.721	0.56
28_Q	75_M	0.717	0.56
21_E	148_G	0.714	0.56
175_L	179_I	0.712	0.55
12_W	157_T	0.710	0.55
44_T	182_N	0.710	0.55
84_Y	151_E	0.705	0.55
42_F	57_L	0.701	0.54
7_I	11_E	0.700	0.54
74_R	176_A	0.698	0.54
10_L	54_L	0.694	0.53
112_W	123_L	0.694	0.53
177_E	180_L	0.693	0.53
122_K	196_E	0.691	0.53
115_E	177_E	0.690	0.53
140_T	148_G	0.690	0.53
189_Y	194_E	0.690	0.53
30_D	41_Q	0.688	0.53
164_D	175_L	0.686	0.53
148_G	160_L	0.685	0.53
161_Y	165_I	0.677	0.52
72_Y	145_Y	0.676	0.52
79_T	84_Y	0.674	0.51
75_M	128_R	0.672	0.51
76_M	79_T	0.669	0.51
5_E	35_R	0.667	0.51
109_Q	142_F	0.661	0.50
120_Y	177_E	0.659	0.50
45_W	161_Y	0.658	0.50
20_N	28_Q	0.657	0.50
166_L	170_K	0.657	0.50
53_Y	67_L	0.657	0.50
101_L	162_Y	0.652	0.49
26_S	32_E	0.649	0.49
129_P	132_S	0.649	0.49
55_D	59_E	0.648	0.49
70_E	152_T	0.645	0.48
113_Q	183_T	0.642	0.48
46_S	98_K	0.642	0.48
177_E	193_E	0.641	0.48
76_M	145_Y	0.639	0.48
154_S	157_T	0.637	0.47
40_S	45_W	0.636	0.47
128_R	140_T	0.635	0.47
42_F	49_T	0.634	0.47
42_F	109_Q	0.632	0.47
110_V	143_E	0.631	0.47
59_E	156_K	0.628	0.46
14_M	102_I	0.628	0.46
51_E	55_D	0.627	0.46
45_W	49_T	0.625	0.46
109_Q	161_Y	0.625	0.46
48_E	51_E	0.625	0.46
52_S	154_S	0.623	0.46
72_Y	75_M	0.620	0.46
47_E	51_E	0.620	0.46
112_W	146_L	0.618	0.45
52_S	156_K	0.616	0.45
27_C	75_M	0.615	0.45
44_T	178_E	0.611	0.45
12_W	25_A	0.609	0.44
33_T	40_S	0.605	0.44
180_L	187_Y	0.604	0.44
33_T	152_T	0.603	0.44
80_A	85_E	0.601	0.44
45_W	113_Q	0.597	0.43
37_M	113_Q	0.593	0.43
185_K	193_E	0.593	0.43
109_Q	112_W	0.592	0.43
41_Q	109_Q	0.590	0.42
142_F	176_A	0.589	0.42
49_T	160_L	0.587	0.42
39_K	186_L	0.581	0.42
64_G	71_K	0.580	0.41
69_T	90_L	0.579	0.41
67_L	153_Y	0.579	0.41
10_L	13_E	0.577	0.41
39_K	43_S	0.576	0.41
53_Y	57_L	0.574	0.41
110_V	141_S	0.566	0.40
12_W	32_E	0.564	0.40
155_D	159_E	0.559	0.39
160_L	164_D	0.556	0.39
103_E	177_E	0.555	0.39
51_E	60_A	0.554	0.39
110_V	185_K	0.553	0.39
14_M	57_L	0.552	0.39
125_G	189_Y	0.552	0.39
6_E	9_E	0.550	0.38
50_L	108_I	0.548	0.38
25_A	34_F	0.545	0.38
185_K	194_E	0.544	0.38
40_S	43_S	0.543	0.38
185_K	190_A	0.543	0.38
101_L	158_L	0.541	0.38
146_L	183_T	0.538	0.37
110_V	142_F	0.536	0.37
96_E	155_D	0.535	0.37
9_E	35_R	0.534	0.37
15_F	25_A	0.531	0.37
80_A	86_E	0.531	0.37
163_R	172_G	0.529	0.36
79_T	187_Y	0.528	0.36
18_V	45_W	0.526	0.36
59_E	62_A	0.523	0.36
12_W	140_T	0.520	0.35
115_E	170_K	0.519	0.35
45_W	153_Y	0.519	0.35
123_L	180_L	0.517	0.35
152_T	158_L	0.517	0.35
76_M	112_W	0.515	0.35
46_S	160_L	0.514	0.35
189_Y	195_A	0.514	0.35
129_P	158_L	0.510	0.34
2_E	6_E	0.510	0.34
81_P	85_E	0.510	0.34
102_I	158_L	0.508	0.34
135_D	143_E	0.507	0.34
190_A	193_E	0.507	0.34
64_G	172_G	0.507	0.34
112_W	130_L	0.507	0.34
112_W	161_Y	0.505	0.34
132_S	147_R	0.504	0.34
167_E	190_A	0.502	0.34
41_Q	128_R	0.501	0.34
158_L	183_T	0.500	0.34

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
2bb6A	1	0.5076	17.1	0.961	Contact Map
4ivnA	2	0.3401	11.6	0.964	Contact Map
2zc2A	1	0.3807	10.8	0.964	Contact Map
1lddA	4	0.2284	8.2	0.966	Contact Map
4ozvA	1	0.6802	8.2	0.966	Contact Map
1wpbA	6	0.4772	7.4	0.967	Contact Map
3iwfA	2	0.3503	7.2	0.967	Contact Map
2j96A	2	0.6599	5.8	0.968	Contact Map
2rnnA	1	0.2741	5.6	0.969	Contact Map
1kvdB	4	0.1472	5.3	0.969	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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