YGIM - ECOLI - GREMLIN Contacts

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YGIM - Uncharacterized protein YgiM

UniProt:	P0ADT8	Sequences: MPKLRLIGLTLLALSATAVSHAEETRYVSDELNTWVRSGPGDHYRLVGTVNAGEEVTLLQTDANTNYAQVKDSSGRTAWIPLKQLSTEPSLRSRVPDLENQVKTLTDKLTNIDNTWNQRTAEMQQKVAQSDSVINGLKEENQKLKNELIVAQKKVDAASVQLDDKQRTIIMQWFMYGGGVLGLGLLLGLVLPHLIPSRKRKDRWMN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12434
Length:	206 (194)
Sequences:	560 (430)
Seq/√Len:	30.9

ECOLI - YGIM

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
174_F	180_V	5.129	1.00
68_A	82_L	4.860	1.00
60_Q	69_Q	4.628	1.00
39_G	44_Y	4.258	1.00
56_V	70_V	3.869	1.00
41_G	44_Y	3.795	1.00
147_E	152_Q	3.383	1.00
28_V	70_V	3.329	1.00
189_L	192_P	3.052	1.00
148_L	151_A	2.686	1.00
59_L	71_K	2.675	1.00
23_E	57_T	2.641	1.00
58_L	68_A	2.532	1.00
173_W	180_V	2.530	1.00
101_Q	106_T	2.378	0.99
109_L	112_I	2.365	0.99
141_N	144_L	2.250	0.99
72_D	76_R	2.178	0.98
102_V	105_L	2.045	0.98
173_W	188_G	2.038	0.98
184_G	192_P	2.023	0.97
91_L	95_V	1.922	0.97
127_V	130_S	1.912	0.96
162_L	165_K	1.906	0.96
155_V	158_A	1.896	0.96
94_R	99_E	1.880	0.96
95_V	98_L	1.853	0.96
116_W	119_R	1.763	0.94
69_Q	77_T	1.719	0.94
143_K	147_E	1.668	0.93
175_M	179_G	1.665	0.92
111_N	115_T	1.643	0.92
181_L	185_L	1.573	0.90
84_Q	178_G	1.529	0.89
61_T	82_L	1.484	0.87
180_V	188_G	1.462	0.86
8_G	15_S	1.462	0.86
130_S	134_I	1.440	0.86
50_V	125_Q	1.438	0.86
108_K	113_D	1.428	0.85
88_E	94_R	1.425	0.85
25_T	55_E	1.396	0.84
100_N	104_T	1.379	0.83
35_W	46_L	1.362	0.82
40_P	79_W	1.361	0.82
192_P	204_W	1.356	0.82
128_A	131_D	1.352	0.82
71_K	77_T	1.346	0.81
36_V	78_A	1.341	0.81
48_G	76_R	1.337	0.81
30_D	45_R	1.336	0.81
27_Y	36_V	1.320	0.80
36_V	80_I	1.319	0.80
124_Q	134_I	1.315	0.80
56_V	85_L	1.311	0.80
94_R	97_D	1.302	0.79
106_T	110_T	1.293	0.79
140_E	145_K	1.292	0.79
28_V	34_T	1.290	0.79
41_G	65_T	1.285	0.78
98_L	102_V	1.283	0.78
124_Q	130_S	1.274	0.78
35_W	48_G	1.266	0.77
28_V	86_S	1.242	0.76
26_R	58_L	1.221	0.75
180_V	193_H	1.185	0.72
33_N	49_T	1.178	0.72
176_Y	192_P	1.160	0.71
185_L	189_L	1.159	0.71
37_R	46_L	1.155	0.70
34_T	80_I	1.149	0.70
164_D	167_R	1.139	0.69
131_D	135_N	1.120	0.68
37_R	83_K	1.108	0.67
57_T	71_K	1.100	0.67
28_V	56_V	1.096	0.66
8_G	14_L	1.073	0.65
178_G	187_L	1.064	0.64
44_Y	81_P	1.059	0.64
126_K	130_S	1.035	0.62
27_Y	30_D	1.027	0.61
27_Y	173_W	1.024	0.61
176_Y	195_I	1.017	0.60
146_N	157_A	1.010	0.60
119_R	123_M	1.009	0.60
191_L	194_L	0.998	0.59
78_A	165_K	0.996	0.59
127_V	134_I	0.996	0.59
96_P	178_G	0.994	0.59
68_A	85_L	0.981	0.58
133_V	136_G	0.980	0.57
61_T	68_A	0.975	0.57
35_W	49_T	0.964	0.56
39_G	45_R	0.956	0.56
131_D	134_I	0.952	0.55
113_D	117_N	0.942	0.54
174_F	192_P	0.934	0.54
177_G	184_G	0.928	0.53
78_A	113_D	0.925	0.53
161_Q	165_K	0.922	0.53
29_S	40_P	0.917	0.52
52_A	79_W	0.916	0.52
171_M	176_Y	0.910	0.52
67_Y	194_L	0.885	0.50
198_R	204_W	0.881	0.50
9_L	15_S	0.879	0.49
39_G	189_L	0.874	0.49
40_P	170_I	0.864	0.48
106_T	156_D	0.856	0.48
79_W	163_D	0.854	0.47
11_L	202_D	0.850	0.47
124_Q	135_N	0.849	0.47
10_T	103_K	0.846	0.47
182_G	189_L	0.840	0.46
117_N	194_L	0.838	0.46
28_V	111_N	0.833	0.46
111_N	114_N	0.827	0.45
32_L	45_R	0.825	0.45
115_T	118_Q	0.824	0.45
176_Y	182_G	0.820	0.45
130_S	133_V	0.820	0.45
79_W	141_N	0.819	0.45
174_F	197_S	0.818	0.44
148_L	191_L	0.815	0.44
139_E	183_L	0.815	0.44
149_I	160_V	0.813	0.44
104_T	186_L	0.811	0.44
188_G	191_L	0.811	0.44
82_L	85_L	0.810	0.44
184_G	189_L	0.806	0.44
38_S	45_R	0.796	0.43
11_L	14_L	0.793	0.43
181_L	188_G	0.791	0.42
73_S	77_T	0.787	0.42
185_L	191_L	0.786	0.42
128_A	132_S	0.783	0.42
16_A	19_V	0.782	0.42
192_P	196_P	0.775	0.41
86_S	110_T	0.775	0.41
174_F	193_H	0.772	0.41
186_L	197_S	0.767	0.40
86_S	150_V	0.760	0.40
8_G	11_L	0.759	0.40
36_V	66_N	0.759	0.40
95_V	108_K	0.758	0.40
34_T	123_M	0.752	0.39
161_Q	166_Q	0.750	0.39
17_T	34_T	0.746	0.39
31_E	83_K	0.746	0.39
28_V	80_I	0.745	0.39
21_H	136_G	0.742	0.39
128_A	135_N	0.740	0.38
9_L	12_L	0.735	0.38
99_E	103_K	0.735	0.38
107_D	113_D	0.733	0.38
133_V	138_K	0.730	0.38
59_L	88_E	0.726	0.37
68_A	123_M	0.723	0.37
116_W	120_T	0.717	0.37
177_G	188_G	0.711	0.36
98_L	172_Q	0.710	0.36
69_Q	198_R	0.705	0.36
134_I	138_K	0.704	0.36
57_T	115_T	0.703	0.36
37_R	91_L	0.702	0.36
17_T	23_E	0.701	0.35
183_L	187_L	0.701	0.35
12_L	20_S	0.696	0.35
37_R	74_S	0.694	0.35
33_N	37_R	0.691	0.35
33_N	83_K	0.686	0.34
185_L	188_G	0.686	0.34
54_E	73_S	0.682	0.34
52_A	90_S	0.679	0.34
183_L	194_L	0.679	0.34
124_Q	131_D	0.677	0.34
129_Q	134_I	0.677	0.34
193_H	197_S	0.668	0.33
124_Q	127_V	0.667	0.33
35_W	90_S	0.662	0.33
151_A	181_L	0.661	0.33
140_E	143_K	0.661	0.33
195_I	203_R	0.659	0.32
175_M	193_H	0.659	0.32
102_V	111_N	0.656	0.32
168_T	172_Q	0.656	0.32
106_T	109_L	0.655	0.32
144_L	182_G	0.653	0.32
30_D	184_G	0.652	0.32
114_N	187_L	0.651	0.32
103_K	114_N	0.648	0.32
154_K	159_S	0.648	0.32
59_L	67_Y	0.646	0.32
182_G	185_L	0.643	0.31
58_L	174_F	0.638	0.31
176_Y	181_L	0.633	0.31
149_I	152_Q	0.633	0.31
180_V	185_L	0.633	0.31
100_N	118_Q	0.632	0.31
54_E	132_S	0.632	0.31
30_D	177_G	0.631	0.30
91_L	141_N	0.630	0.30
135_N	138_K	0.626	0.30
174_F	177_G	0.625	0.30
129_Q	133_V	0.625	0.30
71_K	105_L	0.624	0.30
157_A	188_G	0.624	0.30
110_T	186_L	0.623	0.30
50_V	72_D	0.622	0.30
165_K	170_I	0.621	0.30
37_R	195_I	0.619	0.30
50_V	133_V	0.617	0.30
13_A	18_A	0.617	0.30
105_L	162_L	0.611	0.29
14_L	18_A	0.607	0.29
10_T	64_N	0.607	0.29
30_D	52_A	0.607	0.29
9_L	17_T	0.600	0.28
80_I	161_Q	0.600	0.28
58_L	65_T	0.594	0.28
101_Q	110_T	0.594	0.28
55_E	80_I	0.594	0.28
122_E	159_S	0.593	0.28
140_E	160_V	0.589	0.28
190_V	194_L	0.588	0.28
51_N	85_L	0.588	0.28
67_Y	192_P	0.587	0.28
10_T	14_L	0.586	0.28
57_T	183_L	0.583	0.27
143_K	153_K	0.582	0.27
60_Q	79_W	0.580	0.27
112_I	116_W	0.578	0.27
19_V	24_E	0.575	0.27
174_F	188_G	0.574	0.27
48_G	83_K	0.571	0.27
187_L	196_P	0.568	0.26
32_L	49_T	0.561	0.26
12_L	139_E	0.559	0.26
33_N	48_G	0.559	0.26
91_L	138_K	0.558	0.26
89_P	141_N	0.556	0.26
58_L	105_L	0.553	0.25
125_Q	129_Q	0.553	0.25
24_E	101_Q	0.552	0.25
125_Q	131_D	0.551	0.25
157_A	187_L	0.545	0.25
110_T	150_V	0.545	0.25
37_R	67_Y	0.545	0.25
54_E	151_A	0.545	0.25
8_G	13_A	0.542	0.25
127_V	133_V	0.540	0.25
112_I	199_K	0.540	0.25
49_T	81_P	0.538	0.25
13_A	16_A	0.537	0.24
32_L	36_V	0.536	0.24
29_S	79_W	0.534	0.24
78_A	84_Q	0.532	0.24
51_N	99_E	0.531	0.24
50_V	70_V	0.531	0.24
181_L	184_G	0.530	0.24
44_Y	189_L	0.529	0.24
141_N	171_M	0.528	0.24
47_V	76_R	0.528	0.24
106_T	185_L	0.527	0.24
194_L	199_K	0.526	0.24
95_V	102_V	0.526	0.24
33_N	46_L	0.525	0.24
36_V	175_M	0.524	0.24
140_E	144_L	0.523	0.24
8_G	190_V	0.521	0.24
20_S	23_E	0.520	0.23
86_S	100_N	0.519	0.23
18_A	103_K	0.519	0.23
17_T	107_D	0.518	0.23
86_S	91_L	0.517	0.23
151_A	184_G	0.517	0.23
88_E	186_L	0.516	0.23
77_T	104_T	0.514	0.23
45_R	177_G	0.508	0.23
103_K	186_L	0.508	0.23
9_L	59_L	0.507	0.23
57_T	176_Y	0.506	0.23
36_V	155_V	0.506	0.23
15_S	70_V	0.506	0.23
22_A	143_K	0.505	0.23
44_Y	69_Q	0.505	0.23
67_Y	98_L	0.504	0.23
66_N	159_S	0.503	0.23
37_R	81_P	0.500	0.22
106_T	114_N	0.500	0.22
19_V	22_A	0.500	0.22

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
2kq8A	1	0.3398	99.3	0.749	Contact Map
2kt8A	1	0.3689	99.3	0.75	Contact Map
2krsA	1	0.3592	99.3	0.758	Contact Map
4krtA	1	0.3641	99	0.782	Contact Map
3npfA	2	0.7524	98.7	0.806	Contact Map
3h41A	1	0.9515	98.5	0.818	Contact Map
3m1uA	2	0.932	97.1	0.867	Contact Map
2hbwA	1	0.5437	96.9	0.871	Contact Map
3pe0A	1	0.5146	95.5	0.888	Contact Map
1v1cA	1	0.3058	95.2	0.89	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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