LACI - ECOLI - GREMLIN Contacts

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LACI - Lactose operon repressor

UniProt:	P03023	Sequences: MKPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELNYIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVEACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHEDGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAMSGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCYIPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRALADSLMQLARQVSRLESGQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10525
Length:	360 (325)
Sequences:	32536 (24216)
Seq/√Len:	1343.3

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
179_H	240_T	3.446	1.00
164_E	203_K	3.424	1.00
12_Y	44_E	3.235	1.00
263_R	266_A	3.176	1.00
170_G	271_V	2.737	1.00
275_D	290_K	2.620	1.00
179_H	269_S	2.579	1.00
198_L	202_H	2.531	1.00
157_N	307_L	2.519	1.00
121_G	304_L	2.462	1.00
168_R	207_R	2.377	1.00
32_A	36_E	2.278	1.00
40_A	44_E	2.255	1.00
36_E	40_A	2.221	1.00
226_F	259_E	2.206	1.00
86_R	89_Q	2.120	1.00
86_R	302_D	2.118	1.00
175_V	208_N	2.073	1.00
230_M	260_S	2.061	1.00
299_T	302_D	2.037	1.00
23_V	38_V	1.996	1.00
257_I	268_I	1.994	1.00
167_T	171_V	1.992	1.00
168_R	203_K	1.987	1.00
225_G	252_G	1.981	1.00
87_A	301_V	1.969	1.00
82_A	297_G	1.965	1.00
35_R	39_E	1.953	1.00
168_R	204_Y	1.951	1.00
172_E	176_A	1.942	1.00
165_D	169_L	1.937	1.00
177_L	329_T	1.922	1.00
172_E	204_Y	1.909	1.00
24_V	42_M	1.909	1.00
234_N	260_S	1.905	1.00
230_M	256_A	1.899	1.00
166_G	273_Y	1.865	1.00
164_E	199_A	1.848	1.00
167_T	243_L	1.834	1.00
7_Y	17_Y	1.831	1.00
290_K	322_S	1.816	1.00
171_V	201_W	1.762	1.00
306_Q	311_Q	1.750	1.00
172_E	208_N	1.739	1.00
85_S	294_R	1.730	1.00
13_A	41_A	1.707	1.00
86_R	298_Q	1.695	1.00
168_R	172_E	1.678	1.00
174_L	241_A	1.661	1.00
263_R	267_D	1.658	1.00
299_T	317_Q	1.655	1.00
12_Y	41_A	1.653	1.00
226_F	256_A	1.651	1.00
229_T	253_A	1.646	1.00
82_A	294_R	1.637	1.00
262_L	267_D	1.634	1.00
169_L	321_V	1.632	1.00
292_D	295_L	1.629	1.00
184_L	245_A	1.625	1.00
65_G	119_V	1.619	1.00
285_P	327_K	1.611	1.00
23_V	42_M	1.561	1.00
244_V	253_A	1.554	1.00
275_D	326_R	1.546	1.00
258_T	283_I	1.545	1.00
39_E	43_A	1.525	1.00
183_A	239_P	1.516	1.00
162_S	165_D	1.502	1.00
9_V	41_A	1.499	1.00
211_Q	214_A	1.484	1.00
199_A	203_K	1.479	1.00
256_A	260_S	1.479	1.00
148_L	300_S	1.478	1.00
181_Q	211_Q	1.456	1.00
39_E	42_M	1.455	1.00
86_R	90_L	1.448	1.00
175_V	204_Y	1.435	1.00
295_L	299_T	1.421	1.00
271_V	287_T	1.418	1.00
256_A	259_E	1.415	1.00
166_G	321_V	1.410	1.00
173_H	177_L	1.399	1.00
229_T	242_M	1.395	1.00
86_R	301_V	1.388	1.00
90_L	305_L	1.386	1.00
212_P	215_E	1.379	1.00
173_H	325_K	1.378	1.00
64_I	87_A	1.376	1.00
165_D	168_R	1.374	1.00
230_M	259_E	1.367	1.00
167_T	200_G	1.365	1.00
196_L	199_A	1.363	1.00
171_V	200_G	1.358	1.00
257_I	262_L	1.348	1.00
181_Q	238_V	1.347	1.00
173_H	329_T	1.340	1.00
295_L	298_Q	1.333	1.00
171_V	175_V	1.328	1.00
179_H	241_A	1.325	1.00
9_V	13_A	1.319	1.00
171_V	204_Y	1.312	1.00
173_H	176_A	1.305	1.00
32_A	35_R	1.298	1.00
183_A	232_M	1.295	1.00
62_L	92_A	1.294	1.00
202_H	206_T	1.291	1.00
7_Y	11_E	1.288	1.00
172_E	207_R	1.288	1.00
62_L	120_S	1.287	1.00
8_D	11_E	1.277	1.00
31_S	34_T	1.264	1.00
200_G	204_Y	1.259	1.00
229_T	257_I	1.259	1.00
22_R	27_A	1.255	1.00
12_Y	45_L	1.254	1.00
216_R	231_Q	1.252	1.00
302_D	306_Q	1.250	1.00
204_Y	207_R	1.246	1.00
181_Q	240_T	1.234	1.00
226_F	255_R	1.231	1.00
219_D	224_S	1.222	1.00
66_V	83_I	1.219	1.00
87_A	94_V	1.217	1.00
37_K	41_A	1.207	1.00
254_M	270_V	1.207	1.00
83_I	123_I	1.202	1.00
41_A	44_E	1.201	1.00
41_A	45_L	1.201	1.00
230_M	234_N	1.198	1.00
226_F	230_M	1.187	1.00
136_V	140_C	1.186	1.00
9_V	45_L	1.175	1.00
185_L	253_A	1.173	1.00
65_G	114_L	1.169	1.00
164_E	196_L	1.160	1.00
180_Q	240_T	1.156	1.00
97_S	110_A	1.153	1.00
247_D	288_T	1.152	1.00
6_L	17_Y	1.152	1.00
182_I	205_L	1.143	1.00
4_V	45_L	1.140	1.00
123_I	300_S	1.140	1.00
97_S	114_L	1.137	1.00
169_L	172_E	1.136	1.00
252_G	256_A	1.133	1.00
305_L	309_Q	1.129	1.00
164_E	168_R	1.129	1.00
201_W	205_L	1.123	1.00
83_I	301_V	1.120	1.00
34_T	37_K	1.117	1.00
231_Q	235_E	1.110	1.00
242_M	253_A	1.103	1.00
303_R	317_Q	1.100	1.00
66_V	94_V	1.099	1.00
6_L	20_V	1.098	1.00
223_M	227_Q	1.098	1.00
88_D	106_A	1.094	1.00
294_R	298_Q	1.085	1.00
176_A	208_N	1.081	1.00
23_V	30_V	1.081	1.00
177_L	325_K	1.080	1.00
269_S	329_T	1.079	1.00
50_N	56_L	1.079	1.00
203_K	207_R	1.078	1.00
112_H	137_E	1.074	1.00
40_A	43_A	1.071	1.00
247_D	272_G	1.063	1.00
236_G	239_P	1.062	1.00
90_L	302_D	1.060	1.00
36_E	39_E	1.057	1.00
225_G	229_T	1.056	1.00
170_G	243_L	1.048	1.00
50_N	53_A	1.045	1.00
181_Q	237_I	1.043	1.00
175_V	210_I	1.042	1.00
205_L	210_I	1.040	1.00
297_G	301_V	1.038	1.00
184_L	198_L	1.035	1.00
26_Q	35_R	1.030	1.00
204_Y	208_N	1.027	1.00
90_L	309_Q	1.023	1.00
164_E	200_G	1.021	1.00
254_M	264_V	1.019	1.00
84_K	88_D	1.016	1.00
299_T	303_R	1.012	1.00
52_V	55_Q	1.005	1.00
42_M	45_L	0.999	1.00
108_K	112_H	0.991	1.00
292_D	319_L	0.991	1.00
228_Q	231_Q	0.983	1.00
299_T	319_L	0.979	1.00
227_Q	231_Q	0.976	1.00
66_V	80_V	0.974	1.00
244_V	250_A	0.969	1.00
182_I	241_A	0.968	1.00
199_A	202_H	0.967	1.00
304_L	308_S	0.967	1.00
170_G	289_I	0.958	1.00
221_S	224_S	0.956	1.00
13_A	20_V	0.956	1.00
201_W	243_L	0.956	1.00
106_A	109_A	0.953	1.00
63_L	95_V	0.952	1.00
53_A	56_L	0.951	1.00
298_Q	302_D	0.949	1.00
161_F	292_D	0.948	1.00
244_V	249_M	0.945	1.00
165_D	320_P	0.942	1.00
254_M	282_Y	0.937	1.00
158_S	316_N	0.935	1.00
229_T	233_L	0.934	1.00
92_A	305_L	0.933	1.00
290_K	324_V	0.930	1.00
85_S	298_Q	0.924	1.00
49_P	54_Q	0.923	1.00
195_R	199_A	0.919	1.00
180_Q	210_I	0.911	1.00
89_Q	298_Q	0.909	1.00
162_S	318_L	0.898	1.00
177_L	269_S	0.894	1.00
26_Q	39_E	0.890	1.00
171_V	205_L	0.888	1.00
175_V	180_Q	0.883	1.00
322_S	325_K	0.881	1.00
272_G	288_T	0.881	1.00
275_D	279_S	0.874	1.00
83_I	297_G	0.871	1.00
187_G	220_W	0.870	1.00
63_L	93_S	0.868	1.00
123_I	304_L	0.867	1.00
192_V	196_L	0.867	1.00
274_D	291_Q	0.866	1.00
218_G	249_M	0.862	1.00
61_S	120_S	0.860	1.00
262_L	268_I	0.859	1.00
173_H	287_T	0.857	1.00
247_D	275_D	0.855	1.00
157_N	315_G	0.854	1.00
159_I	303_R	0.849	1.00
81_A	85_S	0.846	1.00
23_V	39_E	0.845	1.00
224_S	227_Q	0.845	1.00
247_D	250_A	0.841	1.00
161_F	291_Q	0.839	1.00
157_N	303_R	0.837	1.00
183_A	242_M	0.833	1.00
165_D	321_V	0.832	1.00
216_R	228_Q	0.830	1.00
325_K	329_T	0.829	1.00
222_A	255_R	0.829	1.00
161_F	321_V	0.827	1.00
160_I	318_L	0.824	1.00
242_M	268_I	0.823	1.00
275_D	324_V	0.819	1.00
64_I	123_I	0.818	1.00
233_L	256_A	0.817	1.00
162_S	320_P	0.814	1.00
292_D	322_S	0.811	1.00
15_V	38_V	0.810	1.00
121_G	308_S	0.809	1.00
257_I	270_V	0.808	1.00
173_H	323_L	0.805	1.00
33_K	36_E	0.803	1.00
163_H	197_R	0.797	1.00
190_S	195_R	0.797	1.00
301_V	305_L	0.795	1.00
238_V	262_L	0.791	1.00
303_R	306_Q	0.791	1.00
19_T	22_R	0.787	1.00
269_S	330_L	0.786	1.00
184_L	243_L	0.785	1.00
51_R	54_Q	0.783	1.00
189_L	217_E	0.781	1.00
60_Q	120_S	0.779	1.00
112_H	116_A	0.778	1.00
227_Q	230_M	0.775	1.00
33_K	37_K	0.774	1.00
79_I	148_L	0.767	1.00
78_Q	294_R	0.764	1.00
251_L	282_Y	0.763	1.00
181_Q	214_A	0.761	1.00
75_A	293_F	0.761	1.00
82_A	298_Q	0.759	1.00
65_G	122_L	0.758	1.00
203_K	206_T	0.758	1.00
174_L	271_V	0.757	1.00
64_I	301_V	0.755	1.00
69_S	76_P	0.754	1.00
240_T	269_S	0.753	1.00
22_R	29_H	0.753	1.00
243_L	271_V	0.753	1.00
233_L	260_S	0.752	1.00
196_L	200_G	0.752	1.00
160_I	316_N	0.751	1.00
169_L	289_I	0.750	1.00
83_I	94_V	0.750	1.00
22_R	28_S	0.746	1.00
18_Q	22_R	0.746	1.00
224_S	228_Q	0.746	1.00
287_T	329_T	0.745	1.00
235_E	238_V	0.744	1.00
48_I	116_A	0.744	1.00
229_T	256_A	0.741	1.00
186_A	198_L	0.741	1.00
185_L	244_V	0.729	1.00
109_A	112_H	0.722	1.00
287_T	323_L	0.720	1.00
84_K	98_M	0.716	1.00
175_V	205_L	0.715	1.00
229_T	232_M	0.713	1.00
235_E	239_P	0.713	1.00
138_A	145_A	0.708	1.00
63_L	117_Q	0.704	1.00
60_Q	309_Q	0.703	1.00
229_T	252_G	0.703	1.00
306_Q	310_G	0.700	1.00
5_T	8_D	0.699	1.00
82_A	86_R	0.699	1.00
115_L	141_T	0.699	1.00
137_E	140_C	0.698	1.00
218_G	224_S	0.697	1.00
84_K	94_V	0.695	1.00
255_R	285_P	0.692	1.00
36_E	43_A	0.691	1.00
85_S	89_Q	0.691	1.00
151_S	316_N	0.689	1.00
257_I	264_V	0.685	1.00
225_G	228_Q	0.684	1.00
147_F	156_I	0.679	1.00
182_I	201_W	0.679	1.00
121_G	146_L	0.679	1.00
23_V	35_R	0.678	1.00
257_I	260_S	0.674	1.00
255_R	258_T	0.668	1.00
80_V	96_V	0.667	1.00
279_S	282_Y	0.667	1.00
182_I	240_T	0.665	1.00
258_T	285_P	0.665	1.00
168_R	200_G	0.660	1.00
100_E	106_A	0.660	1.00
214_A	235_E	0.659	1.00
177_L	330_L	0.659	1.00
132_D	136_V	0.657	1.00
4_V	46_N	0.656	1.00
231_Q	234_N	0.656	1.00
105_E	109_A	0.649	1.00
106_A	110_A	0.649	1.00
48_I	112_H	0.646	1.00
139_A	145_A	0.645	1.00
250_A	272_G	0.644	1.00
20_V	23_V	0.643	1.00
7_Y	57_A	0.641	1.00
255_R	283_I	0.639	1.00
95_V	119_V	0.637	1.00
149_D	163_H	0.637	1.00
306_Q	315_G	0.633	1.00
285_P	326_R	0.633	1.00
294_R	297_G	0.633	1.00
81_A	84_K	0.632	1.00
29_H	34_T	0.632	1.00
78_Q	293_F	0.630	1.00
194_A	220_W	0.630	1.00
81_A	294_R	0.629	1.00
37_K	40_A	0.628	1.00
163_H	196_L	0.626	1.00
246_N	274_D	0.626	1.00
20_V	42_M	0.626	1.00
123_I	148_L	0.625	1.00
310_G	313_V	0.624	1.00
251_L	276_T	0.624	1.00
102_S	106_A	0.622	1.00
9_V	20_V	0.621	1.00
198_L	215_E	0.620	1.00
184_L	201_W	0.617	1.00
251_L	278_D	0.616	1.00
4_V	41_A	0.613	1.00
43_A	46_N	0.613	1.00
73_L	248_Q	0.612	1.00
115_L	143_V	0.611	1.00
87_A	305_L	0.610	1.00
296_L	319_L	0.609	1.00
111_V	122_L	0.609	1.00
121_G	300_S	0.608	1.00
168_R	171_V	0.608	1.00
146_L	159_I	0.608	1.00
187_G	194_A	0.607	1.00
145_A	156_I	0.607	1.00
220_W	245_A	0.606	1.00
139_A	156_I	0.605	1.00
79_I	293_F	0.604	1.00
82_A	293_F	0.603	1.00
22_R	30_V	0.602	1.00
15_V	34_T	0.601	1.00
239_P	262_L	0.601	1.00
174_L	243_L	0.600	1.00
255_R	259_E	0.597	1.00
169_L	173_H	0.595	1.00
273_Y	291_Q	0.594	1.00
202_H	212_P	0.592	1.00
92_A	308_S	0.592	1.00
216_R	235_E	0.592	1.00
139_A	155_P	0.589	1.00
75_A	79_I	0.588	1.00
222_A	252_G	0.585	1.00
64_I	308_S	0.585	1.00
92_A	120_S	0.584	1.00
170_G	241_A	0.583	1.00
243_L	273_Y	0.582	1.00
73_L	76_P	0.580	1.00
48_I	52_V	0.579	1.00
181_Q	239_P	0.579	1.00
271_V	329_T	0.579	1.00
81_A	100_E	0.574	1.00
136_V	139_A	0.572	1.00
149_D	193_S	0.568	1.00
244_V	272_G	0.568	1.00
54_Q	58_G	0.566	1.00
67_A	110_A	0.565	1.00
64_I	92_A	0.564	1.00
287_T	325_K	0.563	1.00
80_V	84_K	0.563	1.00
146_L	304_L	0.559	1.00
13_A	23_V	0.556	1.00
177_L	240_T	0.555	1.00
64_I	121_G	0.555	1.00
289_I	321_V	0.555	1.00
216_R	232_M	0.555	1.00
20_V	38_V	0.554	1.00
246_N	249_M	0.554	1.00
259_E	283_I	0.551	1.00
254_M	258_T	0.549	1.00
99_V	107_C	0.547	1.00
108_K	134_I	0.547	1.00
222_A	278_D	0.547	1.00
279_S	288_T	0.546	1.00
303_R	307_L	0.546	1.00
253_A	257_I	0.545	1.00
133_A	136_V	0.544	1.00
284_P	328_T	0.543	1.00
226_F	252_G	0.540	1.00
15_V	20_V	0.539	1.00
255_R	280_S	0.538	1.00
258_T	263_R	0.538	1.00
146_L	300_S	0.537	1.00
146_L	307_L	0.537	1.00
30_V	35_R	0.535	1.00
159_I	299_T	0.534	1.00
151_S	158_S	0.532	1.00
280_S	285_P	0.531	1.00
55_Q	58_G	0.531	1.00
102_S	105_E	0.531	1.00
279_S	286_L	0.530	1.00
112_H	115_L	0.529	1.00
220_W	249_M	0.529	1.00
233_L	257_I	0.528	1.00
253_A	270_V	0.528	1.00
146_L	303_R	0.527	1.00
114_L	119_V	0.527	1.00
173_H	271_V	0.523	1.00
18_Q	27_A	0.522	1.00
74_H	248_Q	0.522	1.00
119_V	122_L	0.521	1.00
70_S	81_A	0.521	1.00
276_T	288_T	0.520	1.00
247_D	276_T	0.519	1.00
161_F	273_Y	0.519	1.00
95_V	117_Q	0.518	1.00
164_E	167_T	0.517	1.00
194_A	245_A	0.516	1.00
104_V	108_K	0.515	1.00
239_P	242_M	0.515	1.00
13_A	38_V	0.514	1.00
26_Q	29_H	0.514	1.00
4_V	12_Y	0.514	1.00
124_I	147_F	0.513	1.00
226_F	229_T	0.513	1.00
161_F	166_G	0.513	1.00
171_V	243_L	0.511	1.00
224_S	249_M	0.511	1.00
28_S	35_R	0.510	1.00
159_I	319_L	0.509	1.00
134_I	137_E	0.506	1.00
19_T	38_V	0.503	1.00
86_R	305_L	0.503	1.00
168_R	208_N	0.503	1.00
262_L	265_G	0.502	1.00
163_H	193_S	0.501	1.00
110_A	113_N	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
1jyeA	2	0.75	100	0.13	Contact Map
3dbiA	2	0.7611	100	0.136	Contact Map
4o5aA	2	0.7444	100	0.147	Contact Map
2hsgA	1	0.8972	100	0.152	Contact Map
3e3mA	2	0.7361	100	0.155	Contact Map
3h5oA	2	0.7417	100	0.155	Contact Map
3kjxA	2	0.9139	100	0.158	Contact Map
1qpzA	2	0.925	100	0.161	Contact Map
3ctpA	2	0.7333	100	0.162	Contact Map
3bilA	2	0.7083	100	0.162	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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