OSMY - ECOLI - GREMLIN Contacts

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OSMY - Osmotically-inducible protein Y

UniProt:	P0AFH8	Sequences: MTMTRLKISKTLLAVMLTSAVATGSAYAENNAQTTNESAGQKVDSSMNKVGNFMDDSAITAKVKAALVDHDNIKSTDISVKTDQKVVTLSGFVESQAQAEEAVKVAKGVEGVTSVSDKLHVRDAKEGSVKGYAGDTATTSEIKAKLLADDIVPSRHVKVETTDGVVQLSGTVDSQAQSDRAESIAKAVDGVKSVKNDLKTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11391
Length:	201 (181)
Sequences:	953 (663)
Seq/√Len:	49.3

ECOLI - OSMY YRAP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
139_T	161_T	5.458	1.00
63_V	106_A	4.484	1.00
81_K	90_S	3.431	1.00
22_A	25_S	3.223	1.00
60_T	82_T	2.931	1.00
182_E	186_K	2.897	1.00
137_A	141_E	2.632	1.00
138_T	161_T	2.527	1.00
147_L	154_S	2.409	1.00
51_G	55_D	2.381	1.00
93_V	119_L	2.281	1.00
89_L	102_A	2.214	1.00
182_E	196_N	2.177	1.00
101_E	104_K	2.125	1.00
172_V	198_L	2.118	1.00
77_D	127_G	2.114	1.00
175_Q	179_D	2.085	1.00
59_I	87_V	2.050	1.00
157_V	172_V	2.048	1.00
120_H	167_Q	2.040	1.00
157_V	181_A	2.030	1.00
103_V	117_D	1.929	0.99
106_A	109_V	1.918	0.99
145_K	188_V	1.880	0.99
178_S	198_L	1.821	0.99
81_K	158_K	1.818	0.99
57_S	60_T	1.798	0.99
89_L	106_A	1.738	0.99
178_S	182_E	1.728	0.99
77_D	132_Y	1.702	0.98
142_I	185_A	1.663	0.98
59_I	82_T	1.661	0.98
127_G	132_Y	1.659	0.98
87_V	112_V	1.648	0.98
149_D	184_I	1.642	0.98
149_D	180_R	1.635	0.98
59_I	112_V	1.602	0.98
131_G	134_G	1.526	0.97
120_H	165_V	1.461	0.96
96_Q	100_E	1.424	0.95
86_V	114_S	1.401	0.95
88_T	169_S	1.397	0.95
183_S	186_K	1.379	0.94
47_M	177_Q	1.374	0.94
152_V	180_R	1.365	0.94
46_S	53_F	1.358	0.94
103_V	107_K	1.352	0.94
43_V	50_V	1.349	0.94
24_G	27_Y	1.318	0.93
57_S	82_T	1.316	0.93
77_D	162_T	1.312	0.93
70_H	101_E	1.296	0.92
152_V	157_V	1.296	0.92
159_V	168_L	1.260	0.91
185_A	194_V	1.257	0.91
92_F	163_D	1.252	0.91
112_V	115_V	1.252	0.91
63_V	109_V	1.252	0.91
107_K	114_S	1.245	0.90
151_I	180_R	1.242	0.90
49_K	55_D	1.226	0.90
67_L	102_A	1.224	0.90
78_I	102_A	1.220	0.90
179_D	196_N	1.214	0.89
141_E	145_K	1.204	0.89
165_V	195_K	1.204	0.89
99_A	103_V	1.203	0.89
88_T	167_Q	1.195	0.89
167_Q	195_K	1.184	0.88
146_L	152_V	1.165	0.87
139_T	143_K	1.161	0.87
106_A	115_V	1.160	0.87
83_D	169_S	1.154	0.87
26_A	29_E	1.149	0.87
137_A	140_S	1.146	0.86
178_S	196_N	1.144	0.86
77_D	92_F	1.136	0.86
63_V	87_V	1.134	0.86
35_T	38_S	1.120	0.85
21_V	24_G	1.119	0.85
183_S	187_A	1.107	0.84
38_S	44_D	1.097	0.84
172_V	178_S	1.087	0.83
92_F	131_G	1.079	0.83
17_L	20_A	1.071	0.82
141_E	189_D	1.065	0.82
96_Q	99_A	1.062	0.82
93_V	99_A	1.047	0.81
92_F	127_G	1.038	0.80
95_S	98_Q	1.027	0.80
140_S	144_A	1.024	0.79
84_Q	171_T	1.011	0.79
95_S	121_V	0.999	0.78
168_L	185_A	0.997	0.78
30_N	37_E	0.988	0.77
104_K	107_K	0.984	0.77
85_K	188_V	0.973	0.76
102_A	119_L	0.960	0.75
89_L	119_L	0.950	0.74
92_F	162_T	0.948	0.74
51_G	109_V	0.942	0.73
38_S	41_Q	0.940	0.73
30_N	38_S	0.936	0.73
18_T	21_V	0.935	0.73
134_G	141_E	0.929	0.72
94_E	98_Q	0.926	0.72
66_A	70_H	0.923	0.72
141_E	190_G	0.918	0.72
85_K	111_G	0.915	0.71
55_D	62_K	0.913	0.71
161_T	166_V	0.912	0.71
30_N	40_G	0.909	0.71
143_K	159_V	0.901	0.70
147_L	153_P	0.899	0.70
78_I	89_L	0.899	0.70
48_N	83_D	0.895	0.70
80_V	106_A	0.884	0.69
103_V	121_V	0.874	0.68
55_D	111_G	0.871	0.67
37_E	41_Q	0.858	0.66
85_K	113_T	0.845	0.65
142_I	166_V	0.842	0.65
182_E	194_V	0.838	0.64
93_V	102_A	0.835	0.64
16_M	19_S	0.827	0.63
84_Q	199_K	0.826	0.63
51_G	62_K	0.824	0.63
36_N	39_A	0.815	0.62
152_V	181_A	0.812	0.62
105_V	138_T	0.805	0.61
81_K	160_E	0.797	0.61
41_Q	44_D	0.793	0.60
134_G	164_G	0.781	0.59
76_T	93_V	0.776	0.58
90_S	127_G	0.775	0.58
70_H	73_I	0.767	0.58
121_V	195_K	0.765	0.57
73_I	98_Q	0.761	0.57
157_V	198_L	0.751	0.56
164_G	192_K	0.737	0.55
136_T	161_T	0.737	0.55
166_V	191_V	0.733	0.54
142_I	188_V	0.732	0.54
16_M	20_A	0.732	0.54
158_K	161_T	0.732	0.54
121_V	124_A	0.728	0.54
25_S	29_E	0.728	0.54
52_N	85_K	0.723	0.53
145_K	184_I	0.719	0.53
55_D	58_A	0.711	0.52
138_T	177_Q	0.701	0.51
117_D	134_G	0.698	0.51
13_L	18_T	0.696	0.50
138_T	164_G	0.693	0.50
99_A	119_L	0.691	0.50
26_A	30_N	0.690	0.50
186_K	193_S	0.688	0.50
168_L	181_A	0.686	0.49
127_G	131_G	0.685	0.49
43_V	53_F	0.685	0.49
152_V	177_Q	0.681	0.49
64_K	80_V	0.676	0.48
145_K	187_A	0.670	0.48
15_V	18_T	0.669	0.48
52_N	84_Q	0.669	0.48
21_V	26_A	0.668	0.48
59_I	111_G	0.668	0.48
15_V	19_S	0.668	0.48
58_A	62_K	0.665	0.47
151_I	176_A	0.665	0.47
40_G	46_S	0.664	0.47
46_S	194_V	0.663	0.47
137_A	144_A	0.661	0.47
168_L	198_L	0.658	0.47
146_L	165_V	0.656	0.46
62_K	109_V	0.654	0.46
19_S	179_D	0.654	0.46
20_A	25_S	0.654	0.46
93_V	121_V	0.654	0.46
67_L	95_S	0.651	0.46
80_V	169_S	0.649	0.46
40_G	44_D	0.643	0.45
110_E	159_V	0.641	0.45
136_T	140_S	0.636	0.44
36_N	44_D	0.634	0.44
79_S	162_T	0.631	0.44
35_T	39_A	0.626	0.43
39_A	42_K	0.622	0.43
14_A	21_V	0.622	0.43
16_M	21_V	0.617	0.42
19_S	130_K	0.616	0.42
139_T	158_K	0.615	0.42
50_V	53_F	0.615	0.42
51_G	58_A	0.614	0.42
29_E	90_S	0.611	0.42
84_Q	143_K	0.609	0.42
133_A	144_A	0.607	0.41
13_L	16_M	0.604	0.41
149_D	156_H	0.603	0.41
183_S	188_V	0.603	0.41
115_V	121_V	0.602	0.41
17_L	115_V	0.602	0.41
95_S	129_V	0.600	0.41
67_L	80_V	0.600	0.41
23_T	28_A	0.598	0.41
15_V	128_S	0.596	0.40
148_A	193_S	0.595	0.40
63_V	89_L	0.593	0.40
123_D	128_S	0.590	0.40
131_G	164_G	0.589	0.40
139_T	159_V	0.586	0.39
86_V	116_S	0.585	0.39
89_L	103_V	0.582	0.39
40_G	43_V	0.580	0.39
88_T	118_K	0.578	0.39
127_G	163_D	0.578	0.39
100_E	104_K	0.577	0.38
138_T	141_E	0.576	0.38
51_G	177_Q	0.574	0.38
154_S	188_V	0.573	0.38
138_T	185_A	0.571	0.38
86_V	115_V	0.571	0.38
12_L	95_S	0.571	0.38
165_V	193_S	0.570	0.38
29_E	36_N	0.569	0.38
19_S	121_V	0.568	0.38
135_D	161_T	0.568	0.38
115_V	119_L	0.567	0.38
40_G	65_A	0.566	0.37
117_D	167_Q	0.565	0.37
191_V	194_V	0.560	0.37
62_K	105_V	0.560	0.37
173_D	195_K	0.560	0.37
60_T	64_K	0.558	0.37
79_S	90_S	0.557	0.37
139_T	166_V	0.555	0.36
61_A	65_A	0.555	0.36
63_V	115_V	0.551	0.36
173_D	176_A	0.550	0.36
167_Q	197_D	0.550	0.36
116_S	197_D	0.548	0.36
138_T	166_V	0.546	0.36
14_A	20_A	0.544	0.35
59_I	160_E	0.543	0.35
78_I	94_E	0.542	0.35
20_A	176_A	0.541	0.35
91_G	170_G	0.541	0.35
36_N	130_K	0.541	0.35
45_S	153_P	0.539	0.35
103_V	115_V	0.536	0.35
122_R	163_D	0.535	0.35
30_N	35_T	0.534	0.34
29_E	171_T	0.531	0.34
136_T	139_T	0.525	0.34
110_E	115_V	0.524	0.34
90_S	177_Q	0.524	0.34
144_A	148_A	0.524	0.34
82_T	85_K	0.522	0.33
41_Q	45_S	0.522	0.33
122_R	152_V	0.522	0.33
39_A	66_A	0.521	0.33
182_E	198_L	0.517	0.33
129_V	151_I	0.517	0.33
43_V	122_R	0.517	0.33
101_E	105_V	0.514	0.33
153_P	156_H	0.514	0.33
120_H	163_D	0.513	0.33
88_T	195_K	0.512	0.32
169_S	197_D	0.507	0.32
63_V	82_T	0.506	0.32
21_V	153_P	0.503	0.32
169_S	195_K	0.500	0.31

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
2kgsA	1	0.607	99.9	0.614	Contact Map
4alzA	1	0.6219	99.9	0.616	Contact Map
2l26A	1	0.597	98.4	0.83	Contact Map
4qq0A	1	0.8358	95.9	0.888	Contact Map
4wzzA	1	0.6915	62.5	0.932	Contact Map
4yv7A	1	0.6766	52	0.936	Contact Map
4uu4A	1	0.6866	49.7	0.937	Contact Map
4kysA	1	0.6119	49.4	0.937	Contact Map
4r9fA	1	0.6816	34.4	0.942	Contact Map
3tlkA	1	0.7363	27.7	0.945	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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