DUF2227 - PFAM28P - GREMLIN Contacts

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DUF2227 - Uncharacterized metal-binding protein (DUF2227)

PFAM:	PF09988	Sequences: PSGRTHDRITLLLLPPVAAAAYALTLSPALTLIFAGGFLFGGLMFSPDLDLYSRQYRRWGPLRFLWLPYQKLFRHRSRLSHGPIIGTLLRLLYLALLLTLLLFLLAYLLAAIGGGWGDLLASLQRLLGLLLLLLQLYPEELLALLLGLELGAASHTLADGIGSAYKRLQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	169 (167)
Sequences:	1049 (873)
Seq/√Len:	67.6
META:	0.779

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_I	158_A	5.191	1.00
10_T	42_G	4.916	1.00
83_P	153_A	3.293	1.00
37_G	144_L	3.069	1.00
46_S	55_Q	3.016	1.00
40_F	44_M	2.714	1.00
87_T	148_L	2.617	1.00
56_Y	63_R	2.413	1.00
51_L	70_Q	2.305	1.00
56_Y	70_Q	2.176	1.00
7_D	10_T	2.140	1.00
73_F	89_L	2.127	1.00
77_S	89_L	2.119	1.00
149_E	152_A	2.096	1.00
7_D	58_R	2.041	1.00
87_T	152_A	1.901	1.00
155_H	159_D	1.899	1.00
1_P	5_T	1.848	1.00
53_S	58_R	1.846	1.00
33_I	37_G	1.826	1.00
87_T	149_E	1.785	1.00
53_S	59_W	1.769	1.00
1_P	9_I	1.740	1.00
163_S	166_K	1.740	1.00
156_T	160_G	1.734	1.00
46_S	58_R	1.652	0.99
45_F	94_L	1.608	0.99
83_P	87_T	1.597	0.99
53_S	63_R	1.580	0.99
11_L	15_P	1.556	0.99
30_L	143_A	1.518	0.99
42_G	151_G	1.515	0.99
137_Y	140_E	1.500	0.99
82_G	152_A	1.495	0.99
10_T	151_G	1.494	0.99
45_F	55_Q	1.488	0.99
59_W	66_W	1.484	0.99
5_T	9_I	1.458	0.98
52_Y	70_Q	1.457	0.98
162_G	166_K	1.452	0.98
45_F	151_G	1.441	0.98
44_M	55_Q	1.435	0.98
77_S	82_G	1.420	0.98
115_G	118_D	1.412	0.98
1_P	158_A	1.405	0.98
53_S	56_Y	1.379	0.98
131_L	135_Q	1.350	0.97
21_A	34_F	1.346	0.97
117_G	121_A	1.342	0.97
102_L	106_A	1.332	0.97
82_G	85_I	1.316	0.97
41_G	151_G	1.313	0.97
153_A	156_T	1.293	0.97
109_L	112_I	1.279	0.96
7_D	45_F	1.267	0.96
127_L	131_L	1.249	0.96
116_W	123_L	1.238	0.96
12_L	16_P	1.235	0.96
10_T	154_S	1.224	0.95
13_L	16_P	1.222	0.95
69_Y	90_R	1.220	0.95
92_L	95_A	1.203	0.95
4_R	8_R	1.202	0.95
117_G	120_L	1.200	0.95
38_F	150_L	1.197	0.95
117_G	123_L	1.189	0.95
10_T	14_L	1.166	0.94
111_A	114_G	1.155	0.94
72_L	78_R	1.152	0.94
90_R	93_Y	1.144	0.93
119_L	122_S	1.138	0.93
78_R	85_I	1.126	0.93
10_T	152_A	1.116	0.93
53_S	66_W	1.106	0.92
110_A	114_G	1.099	0.92
41_G	45_F	1.071	0.91
109_L	113_G	1.047	0.90
10_T	43_L	1.031	0.89
53_S	68_P	1.030	0.89
47_P	80_S	1.023	0.89
37_G	72_L	1.023	0.89
34_F	144_L	1.015	0.89
151_G	156_T	1.012	0.88
59_W	62_L	0.997	0.88
120_L	123_L	0.992	0.87
162_G	165_Y	0.992	0.87
47_P	156_T	0.978	0.87
55_Q	86_G	0.973	0.86
21_A	31_T	0.966	0.86
136_L	139_E	0.963	0.86
41_G	148_L	0.957	0.85
18_A	21_A	0.952	0.85
53_S	70_Q	0.951	0.85
7_D	42_G	0.947	0.85
33_I	144_L	0.936	0.84
49_L	66_W	0.928	0.84
68_P	93_Y	0.926	0.84
45_F	53_S	0.919	0.83
65_L	68_P	0.919	0.83
77_S	152_A	0.918	0.83
73_F	78_R	0.911	0.83
4_R	18_A	0.907	0.82
7_D	82_G	0.905	0.82
140_E	144_L	0.897	0.82
42_G	149_E	0.896	0.81
37_G	93_Y	0.889	0.81
56_Y	67_L	0.888	0.81
10_T	77_S	0.884	0.81
38_F	149_E	0.878	0.80
118_D	121_A	0.863	0.79
69_Y	80_S	0.861	0.79
80_S	90_R	0.860	0.79
34_F	38_F	0.856	0.78
7_D	54_R	0.845	0.78
46_S	154_S	0.843	0.77
55_Q	63_R	0.833	0.77
82_G	156_T	0.831	0.76
83_P	148_L	0.831	0.76
56_Y	77_S	0.830	0.76
73_F	80_S	0.830	0.76
3_G	8_R	0.827	0.76
42_G	152_A	0.820	0.75
52_Y	71_K	0.811	0.75
58_R	65_L	0.805	0.74
148_L	152_A	0.805	0.74
41_G	51_L	0.804	0.74
128_G	131_L	0.803	0.74
115_G	122_S	0.801	0.74
14_L	18_A	0.788	0.72
19_A	23_A	0.785	0.72
73_F	77_S	0.770	0.71
7_D	53_S	0.769	0.71
54_R	57_R	0.768	0.70
41_G	46_S	0.755	0.69
67_L	71_K	0.755	0.69
54_R	87_T	0.753	0.69
115_G	120_L	0.752	0.69
47_P	152_A	0.752	0.69
8_R	12_L	0.748	0.68
138_P	142_L	0.748	0.68
65_L	97_L	0.741	0.68
15_P	18_A	0.740	0.68
7_D	70_Q	0.740	0.68
83_P	152_A	0.739	0.68
123_L	126_L	0.728	0.66
38_F	47_P	0.727	0.66
70_Q	152_A	0.720	0.66
91_L	134_L	0.712	0.65
115_G	121_A	0.710	0.64
85_I	149_E	0.710	0.64
118_D	122_S	0.709	0.64
18_A	31_T	0.691	0.62
49_L	59_W	0.676	0.61
125_R	130_L	0.673	0.60
91_L	140_E	0.670	0.60
59_W	65_L	0.669	0.60
17_V	22_Y	0.666	0.60
134_L	137_Y	0.665	0.59
52_Y	67_L	0.655	0.58
38_F	156_T	0.654	0.58
14_L	19_A	0.652	0.58
42_G	154_S	0.651	0.58
48_D	81_H	0.651	0.58
50_D	81_H	0.651	0.58
4_R	74_R	0.649	0.58
90_R	152_A	0.647	0.57
121_A	125_R	0.646	0.57
16_P	19_A	0.644	0.57
17_V	34_F	0.644	0.57
110_A	115_G	0.642	0.57
162_G	167_R	0.642	0.57
132_L	135_Q	0.641	0.57
7_D	46_S	0.641	0.57
34_F	150_L	0.637	0.56
125_R	128_G	0.632	0.56
8_R	30_L	0.632	0.56
104_L	123_L	0.624	0.55
62_L	142_L	0.623	0.54
102_L	107_Y	0.621	0.54
70_Q	83_P	0.617	0.54
59_W	68_P	0.616	0.54
109_L	114_G	0.612	0.53
3_G	148_L	0.605	0.52
83_P	156_T	0.603	0.52
133_L	146_L	0.602	0.52
29_A	33_I	0.601	0.52
71_K	92_L	0.601	0.52
19_A	22_Y	0.599	0.52
44_M	79_L	0.598	0.52
84_I	93_Y	0.597	0.51
3_G	6_H	0.594	0.51
87_T	94_L	0.594	0.51
10_T	148_L	0.592	0.51
112_I	118_D	0.592	0.51
116_W	122_S	0.591	0.51
58_R	68_P	0.591	0.51
138_P	141_L	0.590	0.51
133_L	141_L	0.589	0.50
73_F	79_L	0.584	0.50
141_L	144_L	0.578	0.49
49_L	68_P	0.575	0.49
41_G	152_A	0.573	0.49
116_W	121_A	0.572	0.48
1_P	167_R	0.571	0.48
48_D	75_H	0.569	0.48
50_D	75_H	0.569	0.48
75_H	81_H	0.569	0.48
37_G	151_G	0.566	0.48
59_W	63_R	0.566	0.48
1_P	162_G	0.560	0.47
98_L	128_G	0.549	0.46
101_L	105_L	0.547	0.45
118_D	124_Q	0.546	0.45
123_L	132_L	0.545	0.45
116_W	124_Q	0.544	0.45
152_A	156_T	0.543	0.45
125_R	131_L	0.543	0.45
56_Y	152_A	0.543	0.45
65_L	93_Y	0.543	0.45
68_P	76_R	0.542	0.45
7_D	43_L	0.541	0.45
121_A	132_L	0.541	0.45
49_L	58_R	0.540	0.45
107_Y	111_A	0.538	0.44
87_T	145_L	0.537	0.44
32_L	105_L	0.534	0.44
98_L	114_G	0.532	0.44
42_G	77_S	0.531	0.44
88_L	92_L	0.531	0.44
119_L	123_L	0.527	0.43
8_R	71_K	0.526	0.43
29_A	141_L	0.525	0.43
14_L	38_F	0.524	0.43
112_I	141_L	0.523	0.43
52_Y	57_R	0.522	0.43
149_E	154_S	0.520	0.42
7_D	152_A	0.518	0.42
127_L	133_L	0.517	0.42
81_H	155_H	0.517	0.42
48_D	155_H	0.517	0.42
50_D	155_H	0.517	0.42
61_P	97_L	0.516	0.42
37_G	61_P	0.516	0.42
22_Y	105_L	0.513	0.41
122_S	125_R	0.511	0.41
116_W	120_L	0.508	0.41
35_A	97_L	0.505	0.41
7_D	55_Q	0.502	0.40
35_A	130_L	0.501	0.40
44_M	82_G	0.500	0.40

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
3klyA	3	0.3254	3.9	0.952	Contact Map
2o1qA	4	0.2899	1.8	0.96	Contact Map
4lukA	2	0.3491	1.6	0.961	Contact Map
4fc4A	3	0.3254	1.6	0.961	Contact Map
2b8mA	2	0.1834	1.4	0.963	Contact Map
3tdsE	3	0.3905	1.3	0.963	Contact Map
2ajjA	1	0.142	1.3	0.963	Contact Map
3mp7B	1	0.2189	1.1	0.965	Contact Map
3kcuA	3	0.3314	1	0.966	Contact Map
4ui9G	1	0	1	0.966	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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