OSMF - ECOLI - GREMLIN Contacts

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OSMF - Putative osmoprotectant uptake system substrate-binding protein OsmF

UniProt:	P33362	Sequences: MPLLKLWAGSLVMLAAVSLPLQAASPVKVGSKIDTEGALLGNIILQVLESHGVPTVNKVQLGTTPVVRGAITSGELDIYPEYTGNGAFFFKDENDAAWKNAQQGYEKVKKLDSEHNKLIWLTPAPANNTWTIAVRQDVAEKNKLTSLADLSRYLQEGGTFKLAASAEFIERADALPAFEKAYGFKLGQDQLLSLAGGDTAVTIKAAAQQTSGVNAAMAYGTDGPVAALGLQTLSDPQGVQPIYAPAPVVRESVLREYPQMAQWLQPVFASLDAKTLQQLNASIAVEGLDAKKVAADYLKQKGWTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12012
Length:	305 (284)
Sequences:	2935 (2151)
Seq/√Len:	127.6

ECOLI - OSMF PROX
BACSU - OPUBC OPUCC
HALSA - Q9HP83

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
282_S	288_L	5.230	1.00
136_Q	229_G	4.241	1.00
148_A	236_P	4.073	1.00
272_D	275_T	3.953	1.00
134_V	144_L	3.425	1.00
145_T	231_Q	3.280	1.00
119_I	251_E	3.168	1.00
295_A	299_K	3.163	1.00
138_V	142_N	3.107	1.00
136_Q	231_Q	2.826	1.00
136_Q	140_E	2.817	1.00
163_A	213_V	2.598	1.00
282_S	296_D	2.575	1.00
30_G	76_L	2.489	1.00
102_Q	106_E	2.477	1.00
45_L	57_N	2.469	1.00
275_T	279_L	2.468	1.00
133_A	218_A	2.432	1.00
270_S	301_K	2.417	1.00
275_T	301_K	2.311	1.00
28_K	56_V	2.310	1.00
251_E	255_R	2.274	1.00
226_A	278_Q	2.251	1.00
213_V	216_A	2.215	1.00
117_K	251_E	2.115	1.00
118_L	248_V	2.111	1.00
69_G	72_T	2.090	1.00
26_P	54_P	2.066	1.00
122_T	265_Q	2.061	1.00
26_P	56_V	2.017	1.00
177_A	239_V	2.011	1.00
42_N	46_Q	2.003	1.00
46_Q	295_A	1.958	1.00
146_S	234_S	1.877	1.00
179_E	185_K	1.873	1.00
283_I	293_V	1.871	1.00
296_D	300_Q	1.859	1.00
51_H	266_P	1.839	1.00
132_I	215_A	1.835	1.00
270_S	297_Y	1.803	1.00
282_S	286_E	1.798	1.00
288_L	296_D	1.790	1.00
47_V	263_W	1.788	1.00
113_S	251_E	1.785	1.00
31_S	41_G	1.769	1.00
39_L	283_I	1.739	1.00
288_L	292_K	1.735	1.00
146_S	236_P	1.718	1.00
145_T	234_S	1.715	1.00
47_V	267_V	1.669	1.00
93_E	111_L	1.645	1.00
100_N	103_Q	1.641	1.00
155_Q	159_T	1.600	1.00
145_T	149_D	1.580	1.00
131_T	232_T	1.577	1.00
134_V	138_V	1.570	1.00
42_N	57_N	1.567	1.00
110_K	114_E	1.565	1.00
271_L	279_L	1.526	1.00
148_A	237_Q	1.496	1.00
113_S	119_I	1.478	1.00
120_W	246_A	1.460	1.00
44_I	80_P	1.442	1.00
119_I	261_A	1.441	1.00
181_A	239_V	1.427	1.00
274_K	277_Q	1.427	1.00
51_H	263_W	1.413	1.00
29_V	78_I	1.399	1.00
91_K	111_L	1.398	1.00
253_V	257_Y	1.394	1.00
86_G	108_V	1.390	1.00
27_V	53_V	1.371	1.00
135_R	138_V	1.370	1.00
47_V	303_W	1.370	1.00
135_R	211_S	1.363	1.00
144_L	153_Y	1.359	1.00
278_Q	282_S	1.355	1.00
254_L	260_M	1.355	1.00
126_A	276_L	1.355	1.00
160_F	215_A	1.350	1.00
131_T	220_G	1.349	1.00
68_R	112_D	1.347	1.00
165_S	219_Y	1.336	1.00
275_T	297_Y	1.334	1.00
28_K	58_K	1.305	1.00
129_T	220_G	1.301	1.00
281_A	286_E	1.297	1.00
44_I	264_L	1.274	1.00
165_S	199_T	1.269	1.00
13_M	16_A	1.269	1.00
35_T	284_A	1.267	1.00
105_Y	109_K	1.259	1.00
46_Q	291_K	1.241	1.00
198_D	202_T	1.236	1.00
142_N	153_Y	1.232	1.00
121_L	249_V	1.224	0.99
292_K	296_D	1.211	0.99
9_G	12_V	1.199	0.99
106_E	109_K	1.194	0.99
289_D	292_K	1.185	0.99
226_A	277_Q	1.170	0.99
127_N	273_A	1.164	0.99
45_L	49_E	1.161	0.99
68_R	72_T	1.158	0.99
291_K	295_A	1.156	0.99
70_A	75_E	1.147	0.99
106_E	110_K	1.137	0.99
41_G	57_N	1.121	0.99
42_N	45_L	1.120	0.99
46_Q	50_S	1.109	0.99
31_S	57_N	1.109	0.99
49_E	55_T	1.107	0.99
154_L	184_F	1.102	0.99
254_L	261_A	1.094	0.99
181_A	237_Q	1.093	0.99
53_V	259_Q	1.092	0.99
144_L	149_D	1.087	0.99
41_G	59_V	1.081	0.99
49_E	57_N	1.072	0.99
149_D	152_R	1.071	0.99
10_S	13_M	1.066	0.99
46_Q	49_E	1.064	0.99
86_G	112_D	1.062	0.99
161_K	214_N	1.057	0.99
33_I	60_Q	1.049	0.98
261_A	265_Q	1.047	0.98
139_A	144_L	1.046	0.98
43_I	297_Y	1.045	0.98
114_E	246_A	1.041	0.98
83_T	105_Y	1.038	0.98
126_A	245_P	1.037	0.98
161_K	187_G	1.036	0.98
42_N	291_K	1.030	0.98
10_S	14_L	1.028	0.98
147_L	184_F	1.024	0.98
121_L	247_P	1.022	0.98
45_L	55_T	1.021	0.98
265_Q	268_F	1.019	0.98
204_K	210_T	1.010	0.98
32_K	79_Y	1.006	0.98
9_G	13_M	1.003	0.98
112_D	120_W	1.002	0.98
172_A	176_P	0.987	0.98
154_L	187_G	0.986	0.98
44_I	247_P	0.985	0.98
103_Q	106_E	0.983	0.98
43_I	267_V	0.976	0.97
150_L	215_A	0.974	0.97
202_T	217_M	0.967	0.97
274_K	278_Q	0.966	0.97
296_D	299_K	0.966	0.97
125_P	269_A	0.964	0.97
37_G	80_P	0.964	0.97
38_A	60_Q	0.960	0.97
211_S	214_N	0.955	0.97
250_R	253_V	0.955	0.97
43_I	46_Q	0.948	0.97
40_L	245_P	0.945	0.97
107_K	111_L	0.943	0.97
140_E	234_S	0.943	0.97
14_L	17_V	0.939	0.97
273_A	277_Q	0.937	0.97
199_T	202_T	0.937	0.97
86_G	120_W	0.937	0.97
260_M	263_W	0.936	0.97
218_A	225_V	0.935	0.97
6_L	10_S	0.932	0.97
164_A	168_F	0.920	0.96
38_A	290_A	0.916	0.96
120_W	248_V	0.915	0.96
109_K	113_S	0.915	0.96
105_Y	123_P	0.908	0.96
77_D	250_R	0.899	0.96
134_V	142_N	0.898	0.96
223_G	284_A	0.898	0.96
8_A	12_V	0.894	0.96
33_I	219_Y	0.893	0.96
131_T	147_L	0.893	0.96
85_N	173_D	0.889	0.96
87_A	104_G	0.879	0.95
135_R	214_N	0.865	0.95
107_K	110_K	0.865	0.95
43_I	47_V	0.862	0.95
71_I	118_L	0.858	0.95
202_T	216_A	0.854	0.95
167_E	171_R	0.853	0.95
271_L	276_L	0.852	0.95
138_V	141_K	0.848	0.94
17_V	20_P	0.846	0.94
31_S	59_V	0.844	0.94
36_E	221_T	0.843	0.94
28_K	55_T	0.841	0.94
290_A	294_A	0.838	0.94
83_T	246_A	0.837	0.94
25_S	257_Y	0.832	0.94
250_R	256_E	0.826	0.94
127_N	220_G	0.820	0.93
253_V	260_M	0.820	0.93
174_A	177_A	0.817	0.93
151_S	184_F	0.812	0.93
70_A	76_L	0.812	0.93
198_D	201_V	0.809	0.93
275_T	278_Q	0.808	0.93
133_A	232_T	0.805	0.93
278_Q	281_A	0.804	0.93
68_R	248_V	0.798	0.92
203_I	224_P	0.795	0.92
209_Q	230_L	0.795	0.92
112_D	248_V	0.795	0.92
31_S	37_G	0.784	0.92
69_G	73_S	0.780	0.91
43_I	279_L	0.779	0.91
137_D	141_K	0.777	0.91
48_L	52_G	0.776	0.91
188_Q	191_L	0.772	0.91
151_S	154_L	0.772	0.91
25_S	53_V	0.767	0.91
224_P	284_A	0.767	0.91
161_K	188_Q	0.766	0.91
151_S	183_G	0.757	0.90
81_E	86_G	0.756	0.90
140_E	229_G	0.754	0.90
249_V	253_V	0.752	0.90
138_V	153_Y	0.746	0.90
138_V	160_F	0.746	0.90
282_S	292_K	0.745	0.90
147_L	233_L	0.740	0.89
113_S	117_K	0.740	0.89
218_A	232_T	0.740	0.89
43_I	298_L	0.734	0.89
165_S	217_M	0.730	0.89
64_T	90_F	0.725	0.88
105_Y	246_A	0.719	0.88
47_V	50_S	0.717	0.88
47_V	298_L	0.716	0.88
35_T	283_I	0.715	0.88
249_V	254_L	0.714	0.87
17_V	23_A	0.713	0.87
78_I	264_L	0.712	0.87
8_A	11_L	0.712	0.87
175_L	179_E	0.708	0.87
252_S	256_E	0.707	0.87
103_Q	107_K	0.707	0.87
265_Q	269_A	0.703	0.87
266_P	303_W	0.699	0.86
7_W	14_L	0.698	0.86
78_I	249_V	0.697	0.86
9_G	15_A	0.697	0.86
121_L	261_A	0.696	0.86
247_P	264_L	0.696	0.86
12_V	17_V	0.691	0.86
163_A	207_A	0.690	0.86
130_W	133_A	0.690	0.86
128_N	132_I	0.689	0.86
6_L	11_L	0.689	0.86
173_D	243_Y	0.683	0.85
143_K	152_R	0.682	0.85
245_P	276_L	0.681	0.85
150_L	160_F	0.680	0.85
165_S	202_T	0.679	0.85
6_L	13_M	0.677	0.85
137_D	300_Q	0.677	0.85
21_L	24_A	0.676	0.84
189_D	192_L	0.674	0.84
281_A	285_V	0.672	0.84
35_T	223_G	0.666	0.84
53_V	257_Y	0.665	0.83
141_K	145_T	0.658	0.83
262_Q	266_P	0.657	0.83
173_D	240_Q	0.656	0.83
139_A	149_D	0.653	0.82
183_G	237_Q	0.652	0.82
29_V	44_I	0.652	0.82
27_V	253_V	0.651	0.82
90_F	112_D	0.651	0.82
34_D	82_Y	0.649	0.82
117_K	143_K	0.649	0.82
96_A	107_K	0.648	0.82
32_K	81_E	0.644	0.81
7_W	11_L	0.644	0.81
153_Y	159_T	0.643	0.81
123_P	244_A	0.643	0.81
175_L	186_L	0.643	0.81
225_V	232_T	0.643	0.81
162_L	175_L	0.639	0.81
93_E	107_K	0.638	0.81
96_A	104_G	0.638	0.81
136_Q	145_T	0.636	0.81
130_W	243_Y	0.634	0.80
182_Y	237_Q	0.633	0.80
262_Q	265_Q	0.632	0.80
153_Y	160_F	0.630	0.80
282_S	300_Q	0.630	0.80
32_K	37_G	0.630	0.80
199_T	203_I	0.628	0.80
223_G	227_A	0.627	0.80
124_A	245_P	0.626	0.80
49_E	54_P	0.624	0.79
178_F	239_V	0.623	0.79
85_N	243_Y	0.621	0.79
12_V	16_A	0.621	0.79
259_Q	262_Q	0.620	0.79
34_D	167_E	0.619	0.79
29_V	57_N	0.619	0.79
133_A	225_V	0.618	0.79
140_E	262_Q	0.618	0.79
61_L	66_V	0.618	0.79
104_G	242_I	0.618	0.79
17_V	21_L	0.617	0.79
209_Q	228_L	0.609	0.78
27_V	257_Y	0.608	0.78
225_V	230_L	0.605	0.77
200_A	203_I	0.603	0.77
226_A	274_K	0.602	0.77
160_F	214_N	0.601	0.77
176_P	180_K	0.601	0.77
34_D	85_N	0.598	0.77
45_L	59_V	0.598	0.77
229_G	238_G	0.597	0.76
208_Q	216_A	0.595	0.76
43_I	271_L	0.595	0.76
48_L	260_M	0.593	0.76
36_E	40_L	0.592	0.76
109_K	119_I	0.592	0.76
226_A	229_G	0.592	0.76
140_E	143_K	0.589	0.75
220_G	232_T	0.589	0.75
27_V	77_D	0.588	0.75
144_L	147_L	0.587	0.75
48_L	53_V	0.586	0.75
168_F	217_M	0.586	0.75
44_I	78_I	0.585	0.75
11_L	14_L	0.585	0.75
134_V	215_A	0.583	0.75
216_A	224_P	0.583	0.75
263_W	267_V	0.582	0.75
138_V	214_N	0.579	0.74
67_V	200_A	0.579	0.74
132_I	147_L	0.577	0.74
151_S	155_Q	0.574	0.74
10_S	17_V	0.574	0.74
188_Q	192_L	0.573	0.73
145_T	152_R	0.571	0.73
86_G	90_F	0.570	0.73
96_A	103_Q	0.567	0.73
141_K	237_Q	0.565	0.72
164_A	169_I	0.565	0.72
106_E	152_R	0.564	0.72
180_K	296_D	0.564	0.72
110_K	255_R	0.564	0.72
12_V	15_A	0.563	0.72
173_D	241_P	0.562	0.72
139_A	147_L	0.561	0.72
288_L	293_V	0.560	0.72
74_G	249_V	0.559	0.72
169_I	214_N	0.558	0.71
179_E	211_S	0.557	0.71
125_P	245_P	0.556	0.71
134_V	233_L	0.555	0.71
138_V	231_Q	0.552	0.71
252_S	255_R	0.550	0.70
84_G	243_Y	0.548	0.70
227_A	285_V	0.548	0.70
132_I	217_M	0.546	0.70
162_L	215_A	0.546	0.70
271_L	275_T	0.545	0.70
32_K	85_N	0.544	0.70
87_A	96_A	0.544	0.70
144_L	148_A	0.543	0.69
224_P	228_L	0.541	0.69
259_Q	263_W	0.541	0.69
64_T	89_F	0.541	0.69
46_Q	298_L	0.541	0.69
117_K	255_R	0.540	0.69
68_R	90_F	0.540	0.69
255_R	258_P	0.540	0.69
90_F	120_W	0.540	0.69
44_I	268_F	0.540	0.69
33_I	63_T	0.539	0.69
32_K	167_E	0.539	0.69
67_V	79_Y	0.539	0.69
133_A	230_L	0.538	0.69
218_A	224_P	0.538	0.69
154_L	186_L	0.538	0.69
43_I	294_A	0.538	0.69
124_A	271_L	0.536	0.68
121_L	265_Q	0.534	0.68
30_G	67_V	0.532	0.68
201_V	207_A	0.532	0.68
137_D	140_E	0.531	0.68
32_K	64_T	0.530	0.68
51_H	260_M	0.529	0.67
8_A	15_A	0.529	0.67
76_L	79_Y	0.529	0.67
32_K	67_V	0.528	0.67
106_E	140_E	0.527	0.67
163_A	192_L	0.525	0.67
50_S	299_K	0.524	0.67
144_L	233_L	0.523	0.67
94_N	107_K	0.523	0.67
128_N	131_T	0.521	0.66
227_A	281_A	0.521	0.66
178_F	184_F	0.521	0.66
132_I	178_F	0.520	0.66
164_A	175_L	0.519	0.66
234_S	255_R	0.518	0.66
152_R	180_K	0.517	0.66
54_P	262_Q	0.516	0.66
129_T	132_I	0.514	0.65
11_L	17_V	0.513	0.65
131_T	218_A	0.513	0.65
139_A	231_Q	0.512	0.65
33_I	167_E	0.511	0.65
114_E	300_Q	0.510	0.65
169_I	175_L	0.510	0.65
90_F	94_N	0.508	0.64
92_D	95_D	0.507	0.64
30_G	61_L	0.506	0.64
64_T	67_V	0.505	0.64
126_A	130_W	0.505	0.64
68_R	86_G	0.504	0.64
35_T	293_V	0.502	0.63
145_T	187_G	0.501	0.63
101_A	238_G	0.500	0.63
62_G	66_V	0.500	0.63
135_R	208_Q	0.500	0.63

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
3o66A	1	0.8852	100	0.298	Contact Map
4ne4A	1	0.9049	100	0.316	Contact Map
3r6uA	1	0.882	100	0.351	Contact Map
1sw5A	1	0.8852	100	0.403	Contact Map
1r9lA	1	0.859	100	0.518	Contact Map
2rinA	1	0.8426	100	0.581	Contact Map
3tmgA	1	0.8131	100	0.625	Contact Map
3l6gA	1	0.7934	100	0.633	Contact Map
2b4lA	1	0.4918	100	0.656	Contact Map
3un6A	1	0.7934	99.6	0.792	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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