MELR - ECOLI - GREMLIN Contacts

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MELR - Melibiose operon regulatory protein

UniProt:	P0ACH8	Sequences: MNTDTFMCSSDEKQTRSPLSLYSEYQRMEIEFRAPHIMPTSHWHGQVEVNVPFDGDVEYLINNEKVNINQGHITLFWACTPHQLTDTGTCQSMAIFNLPMHLFLSWPLDKDLINHVTHGMVIKSLATQQLSPFEVRRWQQELNSPNEQIRQLAIDEIGLMLKRFSLSGWEPILVNKTSRTHKNSVSRHAQFYVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRVMQLTMKQYITAMRINHVRALLSDTDKSILDIALTAGFRSSSRFYSTFGKYVGMSPQQYRKLSQQRRQTFPG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11230
Length:	302 (249)
Sequences:	31565 (27284)
Seq/√Len:	1729.1

ECOLI - MELR RHAR YQHC RHAS YIDL YPDC CHBR YDIP YIJO ARAC RCLR YEAM YBCM FEAR APPY GADX GADW ADIY ENVY EUTR YDEO YKGA MARA SOXS ROB XYLR
BACSU - YDEC YFIF YISR YBFI BTR YOBQ YTDP YESS ADAA YDEE YESN

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
249_R	282_V	3.356	1.00
234_L	242_A	3.329	1.00
257_K	265_T	3.125	1.00
201_A	243_M	3.051	1.00
245_I	282_V	3.041	1.00
247_H	250_A	2.939	1.00
211_N	221_A	2.891	1.00
199_F	203_N	2.799	1.00
203_N	206_Q	2.780	1.00
242_A	281_Y	2.684	1.00
278_F	289_Y	2.424	1.00
248_V	274_F	2.398	1.00
251_L	265_T	2.346	1.00
196_M	224_A	2.309	1.00
228_F	239_Y	2.223	1.00
209_T	212_D	2.119	1.00
284_M	292_L	2.094	1.00
251_L	266_A	2.055	1.00
257_K	261_D	2.034	1.00
200_I	240_I	1.938	1.00
204_Y	243_M	1.919	1.00
58_E	65_K	1.919	1.00
199_F	216_H	1.899	1.00
237_K	241_T	1.897	1.00
58_E	67_N	1.868	1.00
251_L	257_K	1.852	1.00
245_I	281_Y	1.852	1.00
196_M	217_V	1.844	1.00
193_V	232_M	1.815	1.00
197_L	232_M	1.800	1.00
198_G	202_E	1.753	1.00
213_V	236_M	1.739	1.00
271_S	275_Y	1.719	1.00
258_S	261_D	1.714	1.00
210_I	225_M	1.703	1.00
277_T	280_K	1.695	1.00
60_L	65_K	1.691	1.00
56_D	67_N	1.674	1.00
250_A	254_D	1.665	1.00
243_M	247_H	1.655	1.00
223_Y	227_I	1.653	1.00
252_L	259_I	1.648	1.00
249_R	289_Y	1.637	1.00
234_L	238_Q	1.631	1.00
224_A	236_M	1.615	1.00
247_H	251_L	1.607	1.00
199_F	208_L	1.601	1.00
236_M	240_I	1.579	1.00
223_Y	226_G	1.569	1.00
53_F	94_A	1.555	1.00
260_L	271_S	1.552	1.00
201_A	239_Y	1.515	1.00
56_D	69_N	1.509	1.00
273_R	277_T	1.507	1.00
268_F	277_T	1.505	1.00
284_M	288_Q	1.493	1.00
219_L	223_Y	1.482	1.00
204_Y	247_H	1.476	1.00
261_D	265_T	1.468	1.00
69_N	72_H	1.458	1.00
54_D	92_S	1.452	1.00
261_D	264_L	1.451	1.00
260_L	264_L	1.436	1.00
287_Q	291_K	1.432	1.00
132_P	136_R	1.430	1.00
190_Q	231_V	1.422	1.00
212_D	216_H	1.419	1.00
222_N	226_G	1.415	1.00
163_R	167_S	1.406	1.00
262_I	266_A	1.405	1.00
205_D	265_T	1.401	1.00
221_A	225_M	1.401	1.00
58_E	85_T	1.400	1.00
60_L	83_Q	1.400	1.00
272_S	275_Y	1.400	1.00
47_V	78_A	1.400	1.00
225_M	236_M	1.397	1.00
248_V	266_A	1.396	1.00
159_L	163_R	1.394	1.00
255_T	290_R	1.379	1.00
197_L	201_A	1.363	1.00
200_I	243_M	1.352	1.00
247_H	266_A	1.337	1.00
211_N	215_E	1.335	1.00
62_N	80_T	1.332	1.00
241_T	277_T	1.309	1.00
235_T	238_Q	1.308	1.00
206_Q	212_D	1.306	1.00
242_A	246_N	1.296	1.00
192_Y	219_L	1.283	1.00
219_L	224_A	1.258	1.00
275_Y	285_S	1.248	1.00
220_N	223_Y	1.224	1.00
196_M	213_V	1.217	1.00
156_E	159_L	1.205	1.00
243_M	246_N	1.198	1.00
275_Y	287_Q	1.179	1.00
249_R	253_S	1.178	1.00
155_D	158_G	1.165	1.00
208_L	213_V	1.163	1.00
54_D	70_Q	1.157	1.00
160_M	163_R	1.145	1.00
77_W	80_T	1.140	1.00
207_A	269_R	1.136	1.00
246_N	249_R	1.127	1.00
257_K	262_I	1.109	1.00
276_S	280_K	1.106	1.00
44_H	82_H	1.086	1.00
210_I	236_M	1.085	1.00
288_Q	291_K	1.084	1.00
48_E	82_H	1.078	1.00
155_D	159_L	1.068	1.00
136_R	140_Q	1.065	1.00
191_F	195_Q	1.063	1.00
227_I	230_R	1.056	1.00
285_S	288_Q	1.047	1.00
205_D	247_H	1.045	1.00
125_L	128_Q	1.040	1.00
156_E	160_M	1.040	1.00
42_H	82_H	1.039	1.00
192_Y	217_V	1.037	1.00
199_F	217_V	1.037	1.00
41_S	81_P	1.025	1.00
53_F	92_S	1.025	1.00
154_I	158_G	1.020	1.00
133_F	137_R	1.019	1.00
241_T	280_K	1.007	1.00
197_L	239_Y	1.006	1.00
192_Y	227_I	1.002	1.00
212_D	215_E	0.999	1.00
194_S	198_G	0.996	1.00
259_I	262_I	0.995	1.00
287_Q	290_R	0.992	1.00
227_I	231_V	0.987	1.00
214_A	221_A	0.978	1.00
251_L	262_I	0.974	1.00
44_H	48_E	0.973	1.00
195_Q	216_H	0.972	1.00
244_R	266_A	0.953	1.00
145_P	149_I	0.952	1.00
270_S	276_S	0.949	1.00
237_K	273_R	0.946	1.00
52_P	57_V	0.941	1.00
133_F	136_R	0.940	1.00
200_I	236_M	0.934	1.00
213_V	216_H	0.931	1.00
238_Q	242_A	0.922	1.00
275_Y	279_G	0.917	1.00
249_R	278_F	0.910	1.00
60_L	63_N	0.909	1.00
277_T	281_Y	0.907	1.00
162_K	166_L	0.906	1.00
245_I	277_T	0.905	1.00
282_V	289_Y	0.896	1.00
255_T	262_I	0.895	1.00
207_A	212_D	0.894	1.00
217_V	224_A	0.892	1.00
210_I	221_A	0.891	1.00
219_L	227_I	0.890	1.00
199_F	213_V	0.889	1.00
127_T	131_S	0.886	1.00
150_R	154_I	0.883	1.00
222_N	225_M	0.878	1.00
195_Q	198_G	0.878	1.00
288_Q	292_L	0.878	1.00
252_L	290_R	0.872	1.00
241_T	281_Y	0.869	1.00
155_D	162_K	0.867	1.00
238_Q	241_T	0.863	1.00
273_R	276_S	0.858	1.00
252_L	262_I	0.851	1.00
60_L	85_T	0.848	1.00
204_Y	240_I	0.845	1.00
47_V	75_L	0.844	1.00
228_F	236_M	0.843	1.00
195_Q	217_V	0.842	1.00
193_V	227_I	0.839	1.00
57_V	68_I	0.837	1.00
123_K	127_T	0.835	1.00
193_V	196_M	0.835	1.00
129_Q	133_F	0.834	1.00
279_G	285_S	0.833	1.00
228_F	232_M	0.832	1.00
159_L	166_L	0.830	1.00
203_N	216_H	0.824	1.00
160_M	166_L	0.819	1.00
158_G	162_K	0.817	1.00
58_E	87_T	0.815	1.00
263_A	271_S	0.814	1.00
193_V	231_V	0.806	1.00
56_D	87_T	0.804	1.00
130_L	133_F	0.803	1.00
124_S	128_Q	0.797	1.00
204_Y	266_A	0.796	1.00
196_M	228_F	0.791	1.00
200_I	239_Y	0.784	1.00
238_Q	281_Y	0.777	1.00
100_M	104_L	0.776	1.00
203_N	212_D	0.773	1.00
163_R	166_L	0.773	1.00
57_V	67_N	0.770	1.00
41_S	83_Q	0.770	1.00
237_K	240_I	0.770	1.00
59_Y	74_T	0.769	1.00
112_L	116_V	0.768	1.00
248_V	251_L	0.768	1.00
48_E	97_N	0.767	1.00
50_N	95_I	0.767	1.00
160_M	164_F	0.762	1.00
226_G	230_R	0.760	1.00
253_S	289_Y	0.759	1.00
152_L	159_L	0.755	1.00
51_V	73_I	0.754	1.00
204_Y	208_L	0.753	1.00
245_I	274_F	0.752	1.00
279_G	288_Q	0.747	1.00
61_I	64_E	0.747	1.00
152_L	156_E	0.743	1.00
160_M	165_S	0.742	1.00
194_S	197_L	0.736	1.00
272_S	285_S	0.731	1.00
270_S	273_R	0.730	1.00
196_M	199_F	0.729	1.00
264_L	269_R	0.729	1.00
112_L	115_H	0.728	1.00
197_L	228_F	0.725	1.00
189_A	230_R	0.725	1.00
137_R	141_E	0.725	1.00
121_V	124_S	0.723	1.00
68_I	74_T	0.723	1.00
225_M	229_Q	0.722	1.00
128_Q	132_P	0.718	1.00
196_M	236_M	0.717	1.00
149_I	153_A	0.716	1.00
239_Y	243_M	0.715	1.00
190_Q	227_I	0.712	1.00
156_E	163_R	0.710	1.00
213_V	224_A	0.710	1.00
129_Q	132_P	0.710	1.00
284_M	289_Y	0.704	1.00
159_L	162_K	0.702	1.00
225_M	235_T	0.700	1.00
201_A	247_H	0.697	1.00
124_S	127_T	0.697	1.00
153_A	156_E	0.697	1.00
256_D	262_I	0.692	1.00
151_Q	154_I	0.685	1.00
57_V	84_L	0.683	1.00
225_M	237_K	0.683	1.00
208_L	212_D	0.681	1.00
109_D	113_I	0.677	1.00
204_Y	244_R	0.676	1.00
141_E	145_P	0.676	1.00
262_I	290_R	0.675	1.00
192_Y	195_Q	0.675	1.00
76_F	82_H	0.673	1.00
46_Q	97_N	0.670	1.00
130_L	134_E	0.670	1.00
208_L	244_R	0.664	1.00
52_P	93_M	0.662	1.00
269_R	273_R	0.661	1.00
117_T	120_M	0.660	1.00
50_N	76_F	0.659	1.00
272_S	276_S	0.658	1.00
50_N	93_M	0.656	1.00
240_I	244_R	0.653	1.00
151_Q	155_D	0.653	1.00
134_E	137_R	0.651	1.00
246_N	281_Y	0.650	1.00
199_F	212_D	0.648	1.00
158_G	168_G	0.647	1.00
258_S	262_I	0.645	1.00
193_V	197_L	0.644	1.00
104_L	108_L	0.639	1.00
50_N	59_Y	0.635	1.00
229_Q	235_T	0.634	1.00
111_D	114_N	0.631	1.00
213_V	217_V	0.630	1.00
52_P	55_G	0.629	1.00
245_I	268_F	0.629	1.00
196_M	200_I	0.629	1.00
190_Q	194_S	0.622	1.00
278_F	284_M	0.620	1.00
153_A	160_M	0.619	1.00
196_M	216_H	0.618	1.00
270_S	280_K	0.616	1.00
193_V	224_A	0.616	1.00
140_Q	144_S	0.615	1.00
52_P	68_I	0.615	1.00
139_Q	143_N	0.614	1.00
189_A	231_V	0.612	1.00
111_D	115_H	0.611	1.00
119_G	123_K	0.610	1.00
210_I	237_K	0.607	1.00
109_D	115_H	0.607	1.00
112_L	117_T	0.606	1.00
187_R	190_Q	0.603	1.00
50_N	74_T	0.603	1.00
189_A	192_Y	0.602	1.00
153_A	166_L	0.601	1.00
134_E	138_W	0.599	1.00
248_V	262_I	0.598	1.00
232_M	239_Y	0.597	1.00
166_L	170_E	0.597	1.00
137_R	140_Q	0.596	1.00
43_W	81_P	0.593	1.00
130_L	137_R	0.591	1.00
170_E	177_T	0.589	1.00
127_T	130_L	0.588	1.00
215_E	218_K	0.582	1.00
49_V	75_L	0.578	1.00
62_N	81_P	0.578	1.00
214_A	217_V	0.576	1.00
198_G	201_A	0.575	1.00
157_I	160_M	0.574	1.00
110_K	114_N	0.574	1.00
234_L	239_Y	0.573	1.00
274_F	286_P	0.573	1.00
101_H	104_L	0.570	1.00
125_L	129_Q	0.569	1.00
240_I	243_M	0.568	1.00
141_E	144_S	0.568	1.00
210_I	222_N	0.567	1.00
152_L	155_D	0.566	1.00
49_V	73_I	0.565	1.00
207_A	244_R	0.557	1.00
259_I	287_Q	0.555	1.00
133_F	140_Q	0.554	1.00
271_S	274_F	0.550	1.00
59_Y	84_L	0.549	1.00
241_T	245_I	0.546	1.00
191_F	231_V	0.546	1.00
251_L	254_D	0.546	1.00
146_N	149_I	0.545	1.00
200_I	208_L	0.544	1.00
160_M	167_S	0.543	1.00
100_M	103_F	0.543	1.00
250_A	253_S	0.542	1.00
246_N	282_V	0.542	1.00
224_A	232_M	0.539	1.00
121_V	125_L	0.538	1.00
162_K	168_G	0.537	1.00
277_T	282_V	0.534	1.00
59_Y	76_F	0.533	1.00
157_I	164_F	0.527	1.00
148_Q	152_L	0.527	1.00
274_F	278_F	0.526	1.00
151_Q	162_K	0.525	1.00
148_Q	151_Q	0.525	1.00
56_D	90_C	0.524	1.00
268_F	273_R	0.524	1.00
263_A	268_F	0.523	1.00
213_V	244_R	0.522	1.00
254_D	257_K	0.521	1.00
259_I	271_S	0.520	1.00
208_L	240_I	0.519	1.00
161_L	165_S	0.518	1.00
101_H	105_S	0.518	1.00
217_V	221_A	0.517	1.00
229_Q	232_M	0.517	1.00
45_G	99_P	0.515	1.00
150_R	153_A	0.513	1.00
113_I	117_T	0.512	1.00
135_V	139_Q	0.512	1.00
264_L	271_S	0.512	1.00
114_N	118_H	0.510	1.00
191_F	194_S	0.510	1.00
61_I	76_F	0.509	1.00
252_L	289_Y	0.507	1.00
114_N	117_T	0.507	1.00
131_S	139_Q	0.506	1.00
45_G	79_C	0.502	1.00
203_N	208_L	0.502	1.00
241_T	273_R	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
3gbgA	1	0.8278	100	0.265	Contact Map
1bl0A	1	0.3775	100	0.481	Contact Map
3oouA	1	0.3477	100	0.485	Contact Map
3oioA	1	0.3709	100	0.488	Contact Map
3mn2A	1	0.351	100	0.493	Contact Map
3w6vA	1	0.3675	100	0.494	Contact Map
3mklA	1	0.3675	100	0.496	Contact Map
2k9sA	1	0.351	100	0.501	Contact Map
3lsgA	2	0.3377	100	0.507	Contact Map
1d5yA	1	0.3775	99.9	0.515	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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