DUF2057 - PFAM28P - GREMLIN Contacts

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DUF2057 - Uncharacterized protein conserved in bacteria (DUF2057)

PFAM:	PF09829	Sequences: TLTLPEEIELLAVNGQKVSGSLFSGAKSLELDPGEHQIVVRYEKLFREGSDSDEHDLVKSDPIVVTFDASDGQTLTLSLPKIRNEREAKKFAKSPTWALVDENGQPIAVKQDVLPKEGFQLGRDYEKELAEYNRSGGIAAAAVAAAAAAAAAAAAAAVAAAAATAQSQNTAEQMLKYWYLQADPETRKRFLQW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	193 (192)
Sequences:	1096 (853)
Seq/√Len:	61.5
META:	0.339

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_N	36_H	8.836	1.00
183_D	186_T	6.583	1.00
174_M	177_Y	3.315	1.00
174_M	178_W	3.187	1.00
176_K	193_W	2.868	1.00
42_Y	179_Y	2.861	1.00
101_D	105_Q	2.835	1.00
91_F	95_P	2.824	1.00
123_R	128_E	2.643	1.00
178_W	182_A	2.551	1.00
120_Q	123_R	2.232	1.00
4_L	10_L	2.228	1.00
175_L	190_F	2.052	1.00
125_Y	128_E	2.049	1.00
37_Q	133_N	2.043	1.00
143_V	147_A	2.042	1.00
112_D	132_Y	2.041	1.00
58_V	92_A	2.011	1.00
39_V	62_P	1.954	1.00
179_Y	191_L	1.892	1.00
144_A	148_A	1.872	1.00
35_E	66_T	1.843	1.00
120_Q	128_E	1.790	1.00
32_D	36_H	1.695	0.99
145_A	149_A	1.673	0.99
153_A	156_A	1.667	0.99
142_A	145_A	1.603	0.99
178_W	181_Q	1.599	0.99
185_E	189_R	1.578	0.99
33_P	36_H	1.577	0.99
187_R	193_W	1.516	0.98
172_E	189_R	1.509	0.98
39_V	129_L	1.480	0.98
174_M	182_A	1.474	0.98
188_K	192_Q	1.471	0.98
175_L	182_A	1.432	0.98
46_F	88_A	1.425	0.98
13_V	29_L	1.422	0.98
61_D	113_V	1.409	0.97
132_Y	136_G	1.401	0.97
39_V	114_L	1.378	0.97
124_D	128_E	1.369	0.97
169_N	172_E	1.340	0.96
33_P	71_D	1.319	0.96
151_A	154_A	1.313	0.96
31_L	36_H	1.300	0.96
40_V	65_V	1.299	0.96
79_L	82_I	1.277	0.95
116_K	120_Q	1.276	0.95
35_E	68_D	1.262	0.95
172_E	183_D	1.261	0.95
64_V	132_Y	1.255	0.95
141_A	146_A	1.233	0.94
140_A	145_A	1.212	0.94
177_Y	182_A	1.210	0.94
143_V	146_A	1.205	0.94
130_A	134_R	1.203	0.94
75_L	97_W	1.185	0.93
118_G	123_R	1.176	0.93
33_P	72_G	1.169	0.93
12_A	79_L	1.156	0.92
176_K	180_L	1.145	0.92
144_A	149_A	1.140	0.92
15_G	126_E	1.131	0.91
60_S	95_P	1.131	0.91
7_E	44_K	1.127	0.91
152_A	155_A	1.126	0.91
122_G	125_Y	1.120	0.91
141_A	148_A	1.116	0.91
37_Q	124_D	1.105	0.90
45_L	179_Y	1.101	0.90
154_A	161_A	1.091	0.90
185_E	188_K	1.090	0.90
63_I	95_P	1.090	0.90
37_Q	118_G	1.089	0.90
127_K	130_A	1.086	0.89
149_A	153_A	1.081	0.89
41_R	60_S	1.077	0.89
42_Y	58_V	1.068	0.89
143_V	148_A	1.065	0.89
156_A	164_T	1.054	0.88
142_A	146_A	1.054	0.88
97_W	179_Y	1.054	0.88
151_A	160_A	1.052	0.88
112_D	139_A	1.051	0.88
162_A	165_A	1.051	0.88
171_A	174_M	1.051	0.88
147_A	152_A	1.050	0.88
41_R	95_P	1.035	0.87
176_K	189_R	1.034	0.87
141_A	144_A	1.032	0.87
37_Q	64_V	1.026	0.87
167_S	172_E	1.026	0.87
181_Q	187_R	1.015	0.86
163_A	169_N	0.999	0.85
150_A	155_A	0.992	0.85
171_A	178_W	0.984	0.84
184_P	187_R	0.983	0.84
140_A	144_A	0.982	0.84
64_V	129_L	0.976	0.84
140_A	143_V	0.974	0.84
148_A	154_A	0.971	0.83
174_M	181_Q	0.962	0.83
148_A	152_A	0.960	0.83
70_S	73_Q	0.955	0.82
100_V	106_P	0.953	0.82
64_V	112_D	0.946	0.82
14_N	32_D	0.944	0.82
67_F	107_I	0.942	0.82
169_N	173_Q	0.939	0.81
11_L	62_P	0.928	0.81
177_Y	180_L	0.928	0.81
172_E	176_K	0.927	0.81
37_Q	179_Y	0.925	0.80
147_A	150_A	0.925	0.80
145_A	150_A	0.924	0.80
40_V	77_L	0.921	0.80
121_L	125_Y	0.912	0.79
114_L	133_N	0.910	0.79
46_F	179_Y	0.902	0.79
135_S	139_A	0.902	0.79
121_L	128_E	0.873	0.76
66_T	110_K	0.871	0.76
92_A	95_P	0.871	0.76
37_Q	114_L	0.858	0.75
45_L	57_L	0.857	0.75
124_D	127_K	0.855	0.75
41_R	59_K	0.854	0.75
151_A	156_A	0.852	0.75
10_L	29_L	0.852	0.75
168_Q	171_A	0.849	0.74
82_I	88_A	0.845	0.74
11_L	41_R	0.843	0.74
16_Q	26_A	0.843	0.74
1_T	10_L	0.840	0.74
182_A	191_L	0.839	0.73
150_A	154_A	0.836	0.73
69_A	139_A	0.825	0.72
153_A	163_A	0.822	0.72
82_I	91_F	0.814	0.71
155_A	159_A	0.813	0.71
3_T	74_T	0.809	0.71
42_Y	46_F	0.807	0.71
78_S	100_V	0.806	0.70
12_A	129_L	0.801	0.70
142_A	150_A	0.797	0.70
66_T	77_L	0.794	0.69
47_R	50_S	0.793	0.69
75_L	92_A	0.788	0.69
2_L	109_V	0.788	0.69
79_L	132_Y	0.782	0.68
142_A	147_A	0.779	0.68
136_G	139_A	0.778	0.68
157_A	162_A	0.776	0.68
132_Y	137_G	0.775	0.67
107_I	110_K	0.774	0.67
120_Q	125_Y	0.774	0.67
46_F	84_N	0.772	0.67
158_V	165_A	0.770	0.67
177_Y	189_R	0.768	0.67
14_N	183_D	0.766	0.67
42_Y	47_R	0.757	0.66
161_A	165_A	0.752	0.65
186_T	189_R	0.750	0.65
9_E	41_R	0.742	0.64
76_T	86_R	0.741	0.64
105_Q	110_K	0.740	0.64
46_F	79_L	0.738	0.64
33_P	67_F	0.736	0.63
149_A	155_A	0.727	0.62
8_I	79_L	0.723	0.62
161_A	164_T	0.721	0.62
180_L	193_W	0.720	0.62
78_S	103_N	0.718	0.61
154_A	157_A	0.712	0.61
154_A	166_Q	0.708	0.60
176_K	192_Q	0.705	0.60
20_G	27_K	0.701	0.60
18_V	77_L	0.699	0.59
84_N	87_E	0.697	0.59
75_L	179_Y	0.695	0.59
143_V	161_A	0.693	0.59
39_V	64_V	0.691	0.59
124_D	179_Y	0.685	0.58
13_V	54_E	0.681	0.57
115_P	181_Q	0.679	0.57
188_K	191_L	0.676	0.57
177_Y	181_Q	0.674	0.57
12_A	57_L	0.670	0.56
188_K	193_W	0.667	0.56
5_P	122_G	0.667	0.56
176_K	190_F	0.666	0.56
2_L	31_L	0.660	0.55
65_V	99_L	0.659	0.55
143_V	149_A	0.657	0.55
12_A	58_V	0.657	0.55
118_G	121_L	0.656	0.55
40_V	79_L	0.656	0.55
65_V	73_Q	0.653	0.54
82_I	95_P	0.652	0.54
151_A	158_V	0.651	0.54
40_V	129_L	0.650	0.54
89_K	104_G	0.648	0.54
4_L	23_F	0.646	0.54
38_I	156_A	0.645	0.53
70_S	105_Q	0.645	0.53
67_F	139_A	0.643	0.53
171_A	177_Y	0.643	0.53
154_A	158_V	0.639	0.53
79_L	91_F	0.639	0.53
171_A	189_R	0.637	0.52
85_E	89_K	0.636	0.52
122_G	128_E	0.634	0.52
45_L	55_H	0.632	0.52
104_G	136_G	0.627	0.51
146_A	149_A	0.621	0.51
156_A	160_A	0.621	0.51
145_A	148_A	0.620	0.51
5_P	42_Y	0.618	0.50
154_A	167_S	0.617	0.50
152_A	159_A	0.617	0.50
144_A	147_A	0.613	0.50
152_A	160_A	0.612	0.50
182_A	188_K	0.605	0.49
108_A	153_A	0.603	0.49
140_A	148_A	0.602	0.49
145_A	152_A	0.601	0.48
133_N	139_A	0.594	0.48
6_E	42_Y	0.592	0.47
147_A	151_A	0.590	0.47
156_A	166_Q	0.586	0.47
126_E	129_L	0.586	0.47
132_Y	179_Y	0.585	0.47
62_P	66_T	0.582	0.46
157_A	161_A	0.580	0.46
165_A	171_A	0.578	0.46
55_H	64_V	0.577	0.46
67_F	112_D	0.573	0.45
8_I	186_T	0.572	0.45
58_V	61_D	0.572	0.45
9_E	38_I	0.572	0.45
93_K	151_A	0.571	0.45
99_L	107_I	0.570	0.45
161_A	170_T	0.568	0.45
131_E	134_R	0.564	0.44
47_R	51_D	0.564	0.44
11_L	60_S	0.558	0.44
164_T	168_Q	0.558	0.44
90_K	93_K	0.557	0.43
60_S	66_T	0.551	0.43
174_M	193_W	0.551	0.43
87_E	180_L	0.548	0.42
26_A	103_N	0.548	0.42
16_Q	90_K	0.547	0.42
178_W	186_T	0.547	0.42
54_E	85_E	0.546	0.42
2_L	10_L	0.546	0.42
8_I	21_S	0.543	0.42
27_K	64_V	0.542	0.42
88_A	129_L	0.542	0.42
67_F	80_P	0.541	0.42
67_F	99_L	0.540	0.42
114_L	118_G	0.540	0.42
9_E	16_Q	0.536	0.41
163_A	168_Q	0.534	0.41
167_S	171_A	0.534	0.41
36_H	44_K	0.531	0.41
147_A	153_A	0.530	0.40
31_L	34_G	0.528	0.40
140_A	146_A	0.527	0.40
71_D	106_P	0.526	0.40
171_A	181_Q	0.525	0.40
43_E	57_L	0.523	0.40
170_T	173_Q	0.519	0.39
156_A	161_A	0.518	0.39
66_T	88_A	0.517	0.39
11_L	39_V	0.516	0.39
183_D	189_R	0.516	0.39
17_K	25_G	0.516	0.39
12_A	192_Q	0.513	0.39
156_A	159_A	0.512	0.38
49_G	62_P	0.509	0.38
8_I	67_F	0.506	0.38
7_E	121_L	0.506	0.38
190_F	193_W	0.504	0.38
69_A	73_Q	0.504	0.38
95_P	111_Q	0.502	0.37
111_Q	121_L	0.500	0.37

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
2jttC	1	0.1347	13.9	0.94	Contact Map
3kd4A	3	0.3938	13.7	0.94	Contact Map
2k6wA	1	0.3782	13.4	0.941	Contact Map
1x9lA	1	0.399	11.4	0.943	Contact Map
2c34A	1	0.3264	10.8	0.943	Contact Map
2q1fA	1	0.5078	9.8	0.944	Contact Map
1tg7A	1	0.4352	7.5	0.947	Contact Map
2bgoA	1	0.2953	7.4	0.947	Contact Map
2xwxA	2	0.3161	7.3	0.947	Contact Map
2yn5A	3	0.3161	6.2	0.949	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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