DGAL - ECOLI - GREMLIN Contacts

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DGAL - D-galactose-binding periplasmic protein

UniProt:	P0AEE5	Sequences: MNKKVLTLSAVMASMLFGAAAHAADTRIGVTIYKYDDNFMSVVRKAIEQDAKAAPDVQLLMNDSQNDQSKQNDQIDVLLAKGVKALAINLVDPAAAGTVIEKARGQNVPVVFFNKEPSRKALDSYDKAYYVGTDSKESGIIQGDLIAKHWAANQGWDLNKDGQIQFVLLKGEPGHPDAEARTTYVIKELNDKGIKTEQLQLDTAMWDTAQAKDKMDAWLSGPNANKIEVVIANNDAMAMGAVEALKAHNKSSIPVFGVDALPEALALVKSGALAGTVLNDANNQAKATFDLAKNLADGKGAADGTNWKIDNKVVRVPYVGVDKDNLAEFSKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10593
Length:	332 (284)
Sequences:	38555 (28996)
Seq/√Len:	1720.6

ECOLI - DGAL LSRB XYLF ARAF YTFQ RBSB ALSB GALR YPHF GALS PURR CYTR ASCG LACI MALI CRA IDNR TORT RBSR YCJW GNTR TRER EBGR XYLR
BACSU - RBSB CCPA DEGA KDGR ARAR RBSR NTDR YKVZ EXUR MSMR GANR YVDE CCPB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
136_K	187_K	3.499	1.00
163_Q	228_E	3.370	1.00
85_A	292_A	2.792	1.00
142_Q	256_F	2.671	1.00
182_T	186_I	2.619	1.00
260_A	278_L	2.590	1.00
129_Y	295_L	2.548	1.00
163_Q	254_P	2.477	1.00
50_D	53_A	2.313	1.00
140_I	191_D	2.293	1.00
212_K	247_A	2.291	1.00
216_D	248_H	2.247	1.00
140_I	187_K	2.179	1.00
50_D	290_D	2.162	1.00
144_D	188_E	2.137	1.00
140_I	188_E	2.131	1.00
137_E	141_I	2.101	1.00
287_A	290_D	2.088	1.00
216_D	244_A	2.070	1.00
51_A	289_F	2.043	1.00
136_K	183_T	2.018	1.00
146_I	229_V	1.996	1.00
138_S	258_V	1.988	1.00
294_N	299_K	1.956	1.00
139_G	143_G	1.954	1.00
165_Q	197_E	1.941	1.00
50_D	286_K	1.934	1.00
46_A	285_A	1.923	1.00
144_D	148_K	1.910	1.00
147_A	192_K	1.909	1.00
211_A	240_G	1.880	1.00
149_H	326_L	1.833	1.00
29_G	83_V	1.808	1.00
144_D	192_K	1.799	1.00
49_Q	282_N	1.793	1.00
220_S	248_H	1.793	1.00
139_G	231_I	1.774	1.00
245_L	253_I	1.767	1.00
143_G	185_V	1.749	1.00
278_L	319_V	1.746	1.00
167_V	227_I	1.740	1.00
140_I	144_D	1.738	1.00
232_A	241_A	1.712	1.00
168_L	233_N	1.687	1.00
212_K	244_A	1.671	1.00
215_M	241_A	1.666	1.00
280_D	283_N	1.661	1.00
113_F	288_T	1.648	1.00
183_T	187_K	1.640	1.00
165_Q	226_K	1.631	1.00
145_L	149_H	1.620	1.00
46_A	282_N	1.618	1.00
137_E	140_I	1.608	1.00
246_K	270_S	1.605	1.00
244_A	248_H	1.569	1.00
145_L	148_K	1.569	1.00
141_I	318_Y	1.561	1.00
287_A	314_V	1.558	1.00
147_A	188_E	1.546	1.00
16_L	19_A	1.539	1.00
202_D	217_A	1.502	1.00
293_K	297_D	1.501	1.00
180_A	183_T	1.499	1.00
186_I	190_N	1.492	1.00
272_A	324_D	1.487	1.00
50_D	55_P	1.477	1.00
283_N	287_A	1.459	1.00
134_D	137_E	1.456	1.00
205_M	210_Q	1.454	1.00
212_K	243_E	1.452	1.00
244_A	247_A	1.421	1.00
26_T	84_K	1.417	1.00
55_P	293_K	1.416	1.00
283_N	286_K	1.409	1.00
50_D	289_F	1.403	1.00
29_G	78_L	1.391	1.00
165_Q	228_E	1.388	1.00
143_G	147_A	1.376	1.00
101_E	105_G	1.371	1.00
167_V	218_W	1.366	1.00
139_G	184_Y	1.355	1.00
145_L	322_D	1.350	1.00
138_S	318_Y	1.340	1.00
216_D	247_A	1.338	1.00
76_D	102_K	1.334	1.00
212_K	216_D	1.325	1.00
143_G	184_Y	1.319	1.00
136_K	140_I	1.302	1.00
215_M	245_L	1.301	1.00
26_T	57_V	1.296	1.00
290_D	294_N	1.293	1.00
51_A	59_L	1.289	1.00
163_Q	229_V	1.284	1.00
143_G	188_E	1.280	1.00
87_A	288_T	1.280	1.00
62_N	74_Q	1.276	1.00
184_Y	188_E	1.272	1.00
260_A	323_K	1.271	1.00
215_M	230_V	1.263	1.00
246_K	272_A	1.263	1.00
216_D	220_S	1.256	1.00
188_E	191_D	1.246	1.00
141_I	144_D	1.244	1.00
27_R	58_Q	1.244	1.00
164_I	228_E	1.225	1.00
48_E	52_K	1.224	1.00
47_I	289_F	1.220	1.00
62_N	78_L	1.218	1.00
197_E	200_Q	1.211	1.00
28_I	51_A	1.203	1.00
30_V	47_I	1.196	1.00
282_N	286_K	1.184	1.00
209_A	213_D	1.171	1.00
27_R	60_L	1.171	1.00
185_V	189_L	1.170	1.00
242_V	255_V	1.153	1.00
240_G	244_A	1.146	1.00
136_K	184_Y	1.145	1.00
217_A	221_G	1.141	1.00
207_D	210_Q	1.139	1.00
148_K	192_K	1.137	1.00
168_L	182_T	1.126	1.00
136_K	180_A	1.118	1.00
224_A	227_I	1.116	1.00
185_V	231_I	1.098	1.00
144_D	191_D	1.095	1.00
256_F	274_A	1.093	1.00
179_E	183_T	1.083	1.00
169_L	241_A	1.081	1.00
254_P	326_L	1.078	1.00
230_V	241_A	1.076	1.00
291_L	314_V	1.072	1.00
187_K	191_D	1.071	1.00
30_V	59_L	1.063	1.00
149_H	254_P	1.062	1.00
142_Q	231_I	1.057	1.00
213_D	217_A	1.056	1.00
235_D	276_T	1.055	1.00
72_N	76_D	1.053	1.00
221_G	224_A	1.051	1.00
214_K	217_A	1.051	1.00
15_M	18_G	1.048	1.00
47_I	87_A	1.048	1.00
232_A	237_M	1.047	1.00
210_Q	213_D	1.044	1.00
166_F	189_L	1.043	1.00
52_K	70_K	1.042	1.00
287_A	291_L	1.042	1.00
44_R	48_E	1.038	1.00
55_P	290_D	1.036	1.00
70_K	73_D	1.035	1.00
208_T	243_E	1.032	1.00
183_T	186_I	1.031	1.00
11_V	14_S	1.029	1.00
235_D	257_G	1.021	1.00
165_Q	225_N	1.018	1.00
149_H	322_D	1.017	1.00
285_A	289_F	1.014	1.00
211_A	215_M	1.014	1.00
286_K	290_D	1.013	1.00
67_D	70_K	1.010	1.00
76_D	80_A	0.996	1.00
55_P	297_D	0.993	1.00
53_A	286_K	0.981	1.00
137_E	317_P	0.981	1.00
171_G	206_W	0.980	1.00
292_A	296_A	0.979	1.00
145_L	326_L	0.979	1.00
57_V	293_K	0.978	1.00
45_K	49_Q	0.977	1.00
202_D	214_K	0.976	1.00
215_M	219_L	0.966	1.00
173_P	203_T	0.962	1.00
188_E	192_K	0.960	1.00
232_A	238_A	0.959	1.00
142_Q	277_V	0.952	1.00
143_G	189_L	0.951	1.00
176_P	180_A	0.945	1.00
39_F	281_A	0.931	1.00
242_V	269_K	0.930	1.00
97_G	101_E	0.929	1.00
166_F	229_V	0.928	1.00
319_V	322_D	0.924	1.00
287_A	316_V	0.916	1.00
129_Y	291_L	0.914	1.00
28_I	87_A	0.912	1.00
235_D	260_A	0.908	1.00
147_A	194_I	0.908	1.00
189_L	194_I	0.901	1.00
134_D	315_R	0.889	1.00
174_G	179_E	0.886	1.00
47_I	285_A	0.883	1.00
87_A	292_A	0.882	1.00
49_Q	286_K	0.881	1.00
49_Q	53_A	0.880	1.00
213_D	216_D	0.877	1.00
219_L	244_A	0.877	1.00
133_T	280_D	0.876	1.00
200_Q	221_G	0.875	1.00
27_R	81_K	0.872	1.00
149_H	163_Q	0.870	1.00
85_A	296_A	0.857	1.00
14_S	17_F	0.855	1.00
230_V	253_I	0.854	1.00
133_T	279_N	0.853	1.00
280_D	319_V	0.851	1.00
43_V	113_F	0.851	1.00
245_L	255_V	0.845	1.00
210_Q	214_K	0.845	1.00
13_A	18_G	0.844	1.00
204_A	237_M	0.841	1.00
187_K	190_N	0.839	1.00
238_A	257_G	0.839	1.00
47_I	59_L	0.834	1.00
243_E	246_K	0.833	1.00
31_T	74_Q	0.829	1.00
130_Y	313_V	0.828	1.00
186_I	196_T	0.825	1.00
70_K	74_Q	0.822	1.00
167_V	230_V	0.822	1.00
30_V	44_R	0.819	1.00
12_M	80_A	0.817	1.00
102_K	105_G	0.815	1.00
257_G	276_T	0.812	1.00
131_V	291_L	0.812	1.00
291_L	294_N	0.812	1.00
147_A	164_I	0.807	1.00
196_T	199_L	0.804	1.00
135_S	181_R	0.804	1.00
170_K	182_T	0.803	1.00
60_L	81_K	0.797	1.00
289_F	293_K	0.794	1.00
25_D	84_K	0.791	1.00
164_I	194_I	0.790	1.00
44_R	61_M	0.789	1.00
280_D	316_V	0.787	1.00
146_I	256_F	0.786	1.00
73_D	76_D	0.784	1.00
116_E	313_V	0.782	1.00
259_D	279_N	0.777	1.00
60_L	83_V	0.777	1.00
219_L	248_H	0.776	1.00
168_L	231_I	0.775	1.00
46_A	286_K	0.773	1.00
33_Y	40_M	0.768	1.00
132_G	313_V	0.767	1.00
45_K	48_E	0.767	1.00
215_M	218_W	0.765	1.00
14_S	20_A	0.763	1.00
215_M	244_A	0.757	1.00
278_L	321_V	0.756	1.00
65_Q	70_K	0.753	1.00
133_T	318_Y	0.753	1.00
85_A	111_V	0.749	1.00
103_A	110_V	0.747	1.00
137_E	318_Y	0.746	1.00
186_I	201_L	0.745	1.00
42_V	282_N	0.744	1.00
180_A	184_Y	0.742	1.00
145_L	274_A	0.742	1.00
235_D	238_A	0.740	1.00
132_G	315_R	0.739	1.00
10_A	13_A	0.738	1.00
169_L	232_A	0.737	1.00
266_A	270_S	0.737	1.00
104_R	128_A	0.736	1.00
165_Q	200_Q	0.735	1.00
140_I	184_Y	0.735	1.00
145_L	320_G	0.734	1.00
217_A	220_S	0.727	1.00
25_D	58_Q	0.725	1.00
260_A	321_V	0.722	1.00
234_N	259_D	0.720	1.00
267_L	272_A	0.719	1.00
178_A	206_W	0.715	1.00
87_A	113_F	0.715	1.00
134_D	317_P	0.714	1.00
99_V	102_K	0.712	1.00
29_G	86_L	0.712	1.00
182_T	201_L	0.710	1.00
69_S	73_D	0.709	1.00
24_A	84_K	0.705	1.00
189_L	196_T	0.699	1.00
198_Q	201_L	0.697	1.00
101_E	104_R	0.696	1.00
111_V	295_L	0.695	1.00
221_G	227_I	0.693	1.00
46_A	50_D	0.691	1.00
204_A	210_Q	0.691	1.00
24_A	297_D	0.690	1.00
112_F	117_P	0.689	1.00
72_N	99_V	0.686	1.00
79_L	106_Q	0.686	1.00
260_A	266_A	0.684	1.00
147_A	193_G	0.683	1.00
8_L	11_V	0.682	1.00
28_I	289_F	0.678	1.00
75_I	86_L	0.677	1.00
202_D	221_G	0.677	1.00
202_D	218_W	0.675	1.00
206_W	233_N	0.673	1.00
221_G	225_N	0.671	1.00
243_E	272_A	0.670	1.00
37_D	236_A	0.670	1.00
19_A	22_H	0.670	1.00
114_N	177_D	0.667	1.00
48_E	59_L	0.666	1.00
79_L	108_V	0.663	1.00
211_A	214_K	0.663	1.00
141_I	277_V	0.662	1.00
231_I	256_F	0.660	1.00
85_A	288_T	0.658	1.00
322_D	326_L	0.657	1.00
168_L	185_V	0.654	1.00
114_N	135_S	0.647	1.00
298_G	301_A	0.646	1.00
294_N	298_G	0.644	1.00
221_G	226_K	0.641	1.00
147_A	189_L	0.641	1.00
167_V	200_Q	0.640	1.00
266_A	269_K	0.635	1.00
28_I	85_A	0.634	1.00
243_E	247_A	0.634	1.00
12_M	76_D	0.628	1.00
234_N	237_M	0.628	1.00
239_M	269_K	0.624	1.00
242_V	246_K	0.622	1.00
199_L	202_D	0.622	1.00
171_G	178_A	0.620	1.00
68_Q	72_N	0.619	1.00
111_V	131_V	0.617	1.00
146_I	231_I	0.617	1.00
12_M	16_L	0.616	1.00
186_I	198_Q	0.615	1.00
112_F	130_Y	0.613	1.00
28_I	296_A	0.612	1.00
98_T	101_E	0.610	1.00
245_L	248_H	0.610	1.00
40_M	89_N	0.606	1.00
12_M	15_M	0.605	1.00
228_E	254_P	0.605	1.00
104_R	110_V	0.602	1.00
46_A	281_A	0.601	1.00
235_D	261_L	0.600	1.00
163_Q	195_K	0.598	1.00
215_M	240_G	0.597	1.00
181_R	279_N	0.594	1.00
231_I	258_V	0.591	1.00
142_Q	229_V	0.591	1.00
57_V	84_K	0.588	1.00
42_V	281_A	0.586	1.00
39_F	43_V	0.584	1.00
206_W	237_M	0.581	1.00
258_V	279_N	0.580	1.00
43_V	281_A	0.579	1.00
51_A	57_V	0.577	1.00
238_A	273_L	0.575	1.00
166_F	228_E	0.574	1.00
45_K	65_Q	0.574	1.00
86_L	108_V	0.573	1.00
282_N	285_A	0.572	1.00
209_A	212_K	0.572	1.00
111_V	292_A	0.567	1.00
45_K	282_N	0.566	1.00
214_K	218_W	0.566	1.00
243_E	270_S	0.564	1.00
135_S	180_A	0.562	1.00
208_T	240_G	0.562	1.00
73_D	77_V	0.560	1.00
102_K	106_Q	0.559	1.00
232_A	257_G	0.558	1.00
18_G	22_H	0.558	1.00
165_Q	227_I	0.557	1.00
74_Q	77_V	0.557	1.00
135_S	177_D	0.557	1.00
165_Q	224_A	0.556	1.00
114_N	284_Q	0.556	1.00
116_E	130_Y	0.555	1.00
11_V	17_F	0.555	1.00
243_E	267_L	0.554	1.00
62_N	77_V	0.551	1.00
27_R	84_K	0.551	1.00
27_R	83_V	0.551	1.00
57_V	296_A	0.551	1.00
239_M	261_L	0.548	1.00
28_I	57_V	0.548	1.00
141_I	145_L	0.545	1.00
145_L	256_F	0.545	1.00
132_G	135_S	0.544	1.00
78_L	83_V	0.544	1.00
178_A	233_N	0.543	1.00
26_T	296_A	0.543	1.00
229_V	254_P	0.542	1.00
111_V	291_L	0.541	1.00
238_A	255_V	0.539	1.00
166_F	185_V	0.538	1.00
120_K	128_A	0.537	1.00
291_L	295_L	0.535	1.00
196_T	201_L	0.534	1.00
212_K	215_M	0.529	1.00
140_I	143_G	0.529	1.00
104_R	121_A	0.528	1.00
315_R	318_Y	0.525	1.00
272_A	323_K	0.523	1.00
295_L	298_G	0.522	1.00
72_N	102_K	0.522	1.00
111_V	288_T	0.522	1.00
241_A	245_L	0.520	1.00
212_K	240_G	0.520	1.00
77_V	80_A	0.519	1.00
48_E	63_D	0.518	1.00
17_F	20_A	0.516	1.00
112_F	128_A	0.516	1.00
284_Q	316_V	0.516	1.00
38_N	236_A	0.516	1.00
51_A	293_K	0.515	1.00
26_T	297_D	0.511	1.00
181_R	259_D	0.510	1.00
110_V	128_A	0.508	1.00
64_S	71_Q	0.506	1.00
85_A	109_P	0.506	1.00
208_T	236_A	0.504	1.00
77_V	81_K	0.501	1.00
198_Q	202_D	0.501	1.00
169_L	214_K	0.500	1.00
164_I	229_V	0.500	1.00

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
2hsgA	1	0.8735	100	0.221	Contact Map
2iksA	2	0.8223	100	0.224	Contact Map
3huuA	2	0.7922	100	0.225	Contact Map
3brqA	2	0.8193	100	0.228	Contact Map
3dbiA	2	0.8253	100	0.239	Contact Map
4wt7A	1	0.8524	100	0.241	Contact Map
1qpzA	2	0.9006	100	0.241	Contact Map
2o20A	2	0.8193	100	0.243	Contact Map
3e3mA	2	0.7982	100	0.244	Contact Map
3h5oA	2	0.8042	100	0.245	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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