GNTR - ECOLI - GREMLIN Contacts

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GNTR - HTH-type transcriptional regulator GntR

UniProt:	P0ACP5	Sequences: MKKKRPVLQDVADRVGVTKMTVSRFLRNPEQVSVALRGKIAAALDELGYIPNRAPDILSNATSRAIGVLLPSLTNQVFAEVLRGIESVTDAHGYQTMLAHYGYKPEMEQERLESMLSWNIDGLILTERTHTPRTLKMIEVAGIPVVELMDSKSPCLDIAVGFDNFEAARQMTTAIIARGHRHIAYLGARLDERTIIKQKGYEQAMLDAGLVPYSVMVEQSSSYSSGIELIRQARREYPQLDGVFCTNDDLAVGAAFECQRLGLKVPDDMAIAGFHGHDIGQVMEPRLASVLTPRERMGSIGAERLLARIRGESVTPKMLDLGFTLSPGGSI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12630
Length:	331 (321)
Sequences:	36279 (26190)
Seq/√Len:	1461.8

ECOLI - GNTR IDNR GALS LACI CYTR GALR MALI PURR CRA RBSR ASCG YCJW EBGR TRER TORT ALSB YTFQ RBSB XYLF YPHF ARAF LSRB DGAL XYLR
BACSU - CCPA KDGR DEGA RBSR NTDR YKVZ MSMR EXUR GANR YVDE 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
165_F	203_Q	3.423	1.00
180_H	241_D	3.287	1.00
14_R	46_E	3.154	1.00
264_K	267_D	3.121	1.00
171_M	272_A	2.649	1.00
198_Q	202_E	2.619	1.00
122_G	305_L	2.600	1.00
180_H	270_A	2.569	1.00
276_G	291_L	2.518	1.00
169_R	207_D	2.377	1.00
34_V	38_G	2.269	1.00
227_I	260_R	2.259	1.00
88_V	91_A	2.236	1.00
42_A	46_E	2.232	1.00
38_G	42_A	2.203	1.00
158_I	308_R	2.203	1.00
88_V	303_E	2.160	1.00
231_R	261_L	2.133	1.00
300_I	303_E	2.094	1.00
169_R	203_Q	2.072	1.00
176_I	208_A	2.042	1.00
169_R	204_A	2.037	1.00
173_T	204_A	2.037	1.00
166_E	170_Q	2.027	1.00
231_R	257_E	2.008	1.00
25_F	40_I	1.966	1.00
89_T	302_A	1.959	1.00
165_F	199_K	1.916	1.00
37_R	41_A	1.914	1.00
173_T	177_A	1.891	1.00
168_A	172_T	1.891	1.00
26_L	44_L	1.888	1.00
167_A	274_F	1.886	1.00
84_G	298_G	1.883	1.00
88_V	299_S	1.870	1.00
9_Q	19_K	1.841	1.00
307_A	312_E	1.837	1.00
175_I	242_G	1.833	1.00
226_G	253_G	1.826	1.00
235_R	261_L	1.822	1.00
258_C	269_M	1.816	1.00
168_A	244_F	1.805	1.00
172_T	201_Y	1.793	1.00
291_L	324_T	1.781	1.00
87_S	295_E	1.770	1.00
173_T	208_A	1.746	1.00
169_R	173_T	1.712	1.00
15_V	43_A	1.697	1.00
227_I	257_E	1.686	1.00
14_R	43_A	1.684	1.00
184_A	240_L	1.652	1.00
263_L	268_D	1.647	1.00
230_I	254_A	1.647	1.00
67_G	120_I	1.643	1.00
170_Q	323_F	1.640	1.00
293_P	296_R	1.639	1.00
185_Y	246_T	1.638	1.00
174_A	178_R	1.635	1.00
84_G	295_E	1.626	1.00
300_I	319_L	1.622	1.00
245_C	254_A	1.618	1.00
264_K	268_D	1.586	1.00
182_H	239_Q	1.577	1.00
257_E	261_L	1.553	1.00
41_A	45_D	1.531	1.00
148_L	301_G	1.528	1.00
166_E	169_R	1.518	1.00
88_V	92_H	1.510	1.00
199_K	203_Q	1.508	1.00
296_R	300_I	1.501	1.00
176_I	204_A	1.491	1.00
174_A	177_A	1.486	1.00
163_D	166_E	1.482	1.00
25_F	44_L	1.466	1.00
259_Q	284_E	1.459	1.00
257_E	260_R	1.448	1.00
41_A	44_L	1.437	1.00
217_V	232_Q	1.433	1.00
11_V	43_A	1.432	1.00
92_H	306_L	1.425	1.00
196_I	199_K	1.419	1.00
272_A	288_A	1.414	1.00
64_R	121_D	1.411	1.00
276_G	328_G	1.407	1.00
202_E	206_L	1.404	1.00
296_R	299_S	1.402	1.00
88_V	302_A	1.376	1.00
220_S	225_S	1.375	1.00
174_A	327_P	1.346	1.00
172_T	176_I	1.343	1.00
258_C	263_L	1.339	1.00
227_I	231_R	1.331	1.00
167_A	323_F	1.321	1.00
230_I	243_V	1.320	1.00
204_A	207_D	1.319	1.00
306_L	310_R	1.316	1.00
231_R	260_R	1.314	1.00
227_I	256_F	1.313	1.00
182_H	241_D	1.310	1.00
184_A	233_A	1.308	1.00
136_K	140_V	1.292	1.00
9_Q	13_D	1.290	1.00
182_H	213_Y	1.288	1.00
172_T	200_G	1.287	1.00
172_T	204_A	1.287	1.00
10_D	13_D	1.283	1.00
168_A	200_G	1.283	1.00
14_R	47_L	1.281	1.00
303_E	307_A	1.277	1.00
66_I	89_T	1.277	1.00
180_H	242_G	1.276	1.00
64_R	94_Y	1.275	1.00
34_V	37_R	1.270	1.00
231_R	235_R	1.251	1.00
33_S	36_L	1.250	1.00
67_G	115_M	1.249	1.00
230_I	258_C	1.246	1.00
24_R	29_P	1.239	1.00
255_A	271_I	1.230	1.00
200_G	204_A	1.229	1.00
165_F	169_R	1.225	1.00
39_K	43_A	1.225	1.00
11_V	15_V	1.213	1.00
89_T	96_T	1.207	1.00
124_I	301_G	1.203	1.00
170_Q	173_T	1.201	1.00
99_A	115_M	1.200	1.00
43_A	46_E	1.199	1.00
43_A	47_L	1.196	1.00
8_L	19_K	1.192	1.00
173_T	207_D	1.190	1.00
181_R	241_D	1.186	1.00
99_A	111_R	1.184	1.00
165_F	196_I	1.181	1.00
85_I	124_I	1.179	1.00
85_I	302_A	1.172	1.00
68_V	85_I	1.165	1.00
232_Q	236_E	1.160	1.00
36_L	39_K	1.157	1.00
113_E	137_M	1.153	1.00
224_S	228_E	1.149	1.00
11_V	47_L	1.136	1.00
295_E	299_S	1.133	1.00
186_L	254_A	1.129	1.00
201_Y	205_M	1.127	1.00
237_Y	240_L	1.110	1.00
253_G	257_E	1.108	1.00
42_A	45_D	1.097	1.00
183_I	205_M	1.090	1.00
203_Q	207_D	1.084	1.00
165_F	200_G	1.082	1.00
92_H	303_E	1.080	1.00
65_A	95_Q	1.077	1.00
171_M	244_F	1.076	1.00
68_V	96_T	1.076	1.00
178_R	327_P	1.070	1.00
205_M	210_L	1.066	1.00
243_V	254_A	1.065	1.00
86_E	90_D	1.062	1.00
38_G	41_A	1.060	1.00
300_I	304_R	1.059	1.00
204_A	208_A	1.058	1.00
248_D	289_S	1.058	1.00
25_F	32_V	1.055	1.00
185_Y	198_Q	1.055	1.00
298_G	302_A	1.054	1.00
8_L	22_V	1.053	1.00
222_S	225_S	1.052	1.00
92_H	310_R	1.051	1.00
65_A	97_M	1.048	1.00
90_D	107_M	1.041	1.00
109_Q	113_E	1.040	1.00
229_L	232_Q	1.038	1.00
182_H	238_P	1.026	1.00
28_N	37_R	1.025	1.00
199_K	202_E	1.024	1.00
176_I	210_L	1.023	1.00
248_D	273_G	1.021	1.00
174_A	288_A	1.021	1.00
226_G	230_I	1.017	1.00
177_A	208_A	1.014	1.00
201_Y	244_F	1.013	1.00
209_G	212_P	1.012	1.00
299_S	303_E	1.007	1.00
282_V	285_P	1.000	1.00
245_C	251_A	0.999	1.00
245_C	250_L	0.994	1.00
44_L	47_L	0.993	1.00
225_S	228_E	0.990	1.00
52_N	58_L	0.989	1.00
228_E	232_Q	0.985	1.00
54_A	57_I	0.985	1.00
107_M	110_E	0.980	1.00
304_R	319_L	0.972	1.00
195_I	199_K	0.969	1.00
305_L	309_I	0.969	1.00
166_E	322_G	0.968	1.00
300_I	321_L	0.961	1.00
94_Y	306_L	0.961	1.00
283_M	286_R	0.960	1.00
91_A	299_S	0.951	1.00
15_V	22_V	0.949	1.00
188_A	221_S	0.946	1.00
223_Y	256_F	0.937	1.00
113_E	117_S	0.932	1.00
178_R	270_A	0.930	1.00
183_I	242_G	0.927	1.00
255_A	283_M	0.925	1.00
230_I	234_R	0.924	1.00
171_M	290_V	0.924	1.00
205_M	212_P	0.922	1.00
255_A	265_V	0.920	1.00
52_N	55_P	0.916	1.00
217_V	229_L	0.916	1.00
202_E	212_P	0.912	1.00
87_S	299_S	0.909	1.00
176_I	181_R	0.906	1.00
259_Q	286_R	0.898	1.00
172_T	205_M	0.898	1.00
124_I	305_L	0.897	1.00
324_T	327_P	0.895	1.00
181_R	210_L	0.894	1.00
293_P	321_L	0.881	1.00
66_I	124_I	0.880	1.00
83_R	87_S	0.879	1.00
68_V	82_L	0.875	1.00
162_F	293_P	0.873	1.00
159_A	318_M	0.873	1.00
28_N	41_A	0.872	1.00
55_P	58_L	0.871	1.00
190_L	218_E	0.868	1.00
85_I	298_G	0.866	1.00
166_E	323_F	0.858	1.00
234_R	257_E	0.852	1.00
184_A	243_V	0.851	1.00
51_P	56_D	0.850	1.00
82_L	86_E	0.847	1.00
163_D	322_G	0.847	1.00
243_V	269_M	0.847	1.00
160_V	304_R	0.844	1.00
258_C	271_I	0.840	1.00
163_D	320_D	0.835	1.00
132_P	136_K	0.831	1.00
219_Q	250_L	0.830	1.00
263_L	269_M	0.829	1.00
248_D	276_G	0.827	1.00
25_F	41_A	0.826	1.00
162_F	323_F	0.821	1.00
304_R	307_A	0.821	1.00
164_N	197_K	0.819	1.00
228_E	231_R	0.819	1.00
7_V	10_D	0.809	1.00
81_V	148_L	0.808	1.00
273_G	289_S	0.805	1.00
35_A	38_G	0.805	1.00
239_Q	263_L	0.802	1.00
291_L	326_S	0.802	1.00
77_V	294_R	0.802	1.00
122_G	309_I	0.799	1.00
210_L	213_Y	0.799	1.00
293_P	324_T	0.797	1.00
63_S	121_D	0.795	1.00
80_E	295_E	0.794	1.00
161_G	320_D	0.794	1.00
203_Q	206_L	0.792	1.00
162_F	292_T	0.788	1.00
85_I	96_T	0.788	1.00
187_G	198_Q	0.785	1.00
302_A	306_L	0.785	1.00
225_S	229_L	0.784	1.00
137_M	140_V	0.778	1.00
17_V	40_I	0.776	1.00
276_G	326_S	0.767	1.00
87_S	91_A	0.765	1.00
104_K	107_M	0.761	1.00
53_R	56_D	0.761	1.00
84_G	299_S	0.760	1.00
161_G	318_M	0.759	1.00
65_A	118_W	0.756	1.00
186_L	245_C	0.756	1.00
196_I	200_G	0.754	1.00
21_T	24_R	0.753	1.00
84_G	88_V	0.753	1.00
182_H	215_V	0.752	1.00
175_I	272_A	0.750	1.00
230_I	233_A	0.749	1.00
35_A	39_K	0.748	1.00
82_L	98_L	0.748	1.00
185_Y	244_F	0.748	1.00
230_I	257_E	0.743	1.00
71_P	78_F	0.743	1.00
191_D	195_I	0.741	1.00
20_M	24_R	0.738	1.00
241_D	270_A	0.730	1.00
252_V	283_M	0.728	1.00
50_I	117_S	0.726	1.00
234_R	261_L	0.725	1.00
110_E	113_E	0.721	1.00
62_T	121_D	0.721	1.00
170_Q	290_V	0.721	1.00
275_H	292_T	0.720	1.00
66_I	302_A	0.719	1.00
215_V	236_E	0.718	1.00
193_R	196_I	0.717	1.00
158_I	317_K	0.717	1.00
256_F	259_Q	0.717	1.00
248_D	251_A	0.717	1.00
67_G	123_L	0.714	1.00
24_R	30_E	0.713	1.00
116_L	141_A	0.713	1.00
174_A	325_L	0.708	1.00
83_R	86_E	0.707	1.00
102_G	107_M	0.706	1.00
86_E	96_T	0.706	1.00
217_V	233_A	0.706	1.00
251_A	273_G	0.705	1.00
281_Q	286_R	0.700	1.00
151_S	318_M	0.699	1.00
244_F	272_A	0.699	1.00
97_M	120_I	0.698	1.00
24_R	31_Q	0.697	1.00
276_G	280_G	0.695	1.00
256_F	286_R	0.693	1.00
107_M	111_R	0.693	1.00
258_C	265_V	0.691	1.00
198_Q	216_M	0.689	1.00
307_A	311_G	0.683	1.00
147_E	152_K	0.682	1.00
219_Q	225_S	0.681	1.00
226_G	229_L	0.680	1.00
232_Q	235_R	0.679	1.00
158_I	304_R	0.678	1.00
139_E	145_V	0.672	1.00
136_K	139_E	0.672	1.00
169_R	200_G	0.672	1.00
236_E	239_Q	0.669	1.00
138_I	145_V	0.668	1.00
106_E	110_E	0.668	1.00
176_I	205_M	0.667	1.00
25_F	37_R	0.663	1.00
69_L	111_R	0.662	1.00
38_G	45_D	0.661	1.00
86_E	100_H	0.660	1.00
183_I	241_D	0.655	1.00
124_I	148_L	0.654	1.00
147_E	157_D	0.654	1.00
247_N	275_H	0.651	1.00
170_Q	174_A	0.650	1.00
62_T	310_R	0.649	1.00
236_E	240_L	0.646	1.00
122_G	146_V	0.646	1.00
217_V	236_E	0.645	1.00
139_E	156_L	0.644	1.00
182_H	212_P	0.642	1.00
50_I	113_E	0.641	1.00
210_L	214_S	0.641	1.00
286_R	328_G	0.637	1.00
9_Q	59_S	0.630	1.00
112_L	123_L	0.629	1.00
256_F	260_R	0.627	1.00
146_V	305_L	0.625	1.00
146_V	308_R	0.621	1.00
83_R	295_E	0.620	1.00
75_N	249_D	0.619	1.00
31_Q	36_L	0.618	1.00
282_V	286_R	0.616	1.00
122_G	301_G	0.615	1.00
221_S	246_T	0.614	1.00
11_V	22_V	0.614	1.00
17_V	36_L	0.614	1.00
39_K	42_A	0.614	1.00
116_L	143_I	0.613	1.00
45_D	48_G	0.612	1.00
212_P	216_M	0.611	1.00
175_I	244_F	0.607	1.00
149_M	164_N	0.607	1.00
97_M	118_W	0.607	1.00
230_I	253_G	0.607	1.00
307_A	317_K	0.605	1.00
185_Y	201_Y	0.604	1.00
84_G	294_R	0.604	1.00
252_V	279_I	0.601	1.00
258_C	261_L	0.599	1.00
22_V	25_F	0.598	1.00
169_R	172_T	0.596	1.00
134_T	137_M	0.596	1.00
146_V	160_V	0.595	1.00
183_I	201_Y	0.594	1.00
80_E	294_R	0.589	1.00
94_Y	309_I	0.588	1.00
201_Y	212_P	0.588	1.00
247_N	250_L	0.588	1.00
255_A	259_Q	0.585	1.00
133_R	136_K	0.584	1.00
164_N	196_I	0.582	1.00
288_A	325_L	0.581	1.00
109_Q	134_T	0.580	1.00
223_Y	279_I	0.580	1.00
24_R	32_V	0.578	1.00
295_E	298_G	0.578	1.00
252_V	277_H	0.574	1.00
280_G	289_S	0.574	1.00
81_V	294_R	0.572	1.00
281_Q	285_P	0.571	1.00
256_F	284_E	0.570	1.00
224_S	227_I	0.570	1.00
259_Q	264_K	0.570	1.00
22_V	44_L	0.569	1.00
145_V	157_D	0.568	1.00
308_R	311_G	0.567	1.00
66_I	122_G	0.567	1.00
66_I	309_I	0.562	1.00
146_V	304_R	0.561	1.00
244_F	274_F	0.561	1.00
94_Y	121_D	0.560	1.00
223_Y	253_G	0.558	1.00
174_A	272_A	0.556	1.00
66_I	94_Y	0.555	1.00
77_V	81_V	0.554	1.00
63_S	95_Q	0.554	1.00
274_F	292_T	0.553	1.00
280_G	287_L	0.550	1.00
171_M	242_G	0.548	1.00
101_Y	108_E	0.547	1.00
229_L	233_A	0.545	1.00
105_P	109_Q	0.544	1.00
99_A	114_S	0.543	1.00
32_V	37_R	0.543	1.00
123_L	143_I	0.542	1.00
160_V	300_I	0.540	1.00
149_M	194_T	0.539	1.00
146_V	301_G	0.538	1.00
245_C	273_G	0.537	1.00
184_A	215_V	0.537	1.00
209_G	213_Y	0.535	1.00
221_S	250_L	0.535	1.00
151_S	159_A	0.535	1.00
304_R	308_R	0.533	1.00
22_V	40_I	0.533	1.00
182_H	240_L	0.532	1.00
28_N	31_Q	0.531	1.00
115_M	120_I	0.531	1.00
50_I	54_A	0.531	1.00
265_V	268_D	0.530	1.00
89_T	94_Y	0.530	1.00
234_R	258_C	0.528	1.00
297_M	321_L	0.527	1.00
263_L	266_P	0.527	1.00
227_I	253_G	0.526	1.00
208_A	211_V	0.525	1.00
83_R	102_G	0.525	1.00
300_I	307_A	0.523	1.00
65_A	121_D	0.520	1.00
56_D	60_N	0.520	1.00
29_P	32_V	0.519	1.00
17_V	22_V	0.519	1.00
76_Q	249_D	0.517	1.00
113_E	116_L	0.517	1.00
120_I	123_L	0.516	1.00
240_L	243_V	0.514	1.00
147_E	159_A	0.514	1.00
162_F	274_F	0.513	1.00
78_F	126_T	0.512	1.00
254_A	258_C	0.512	1.00
88_V	306_L	0.512	1.00
137_M	141_A	0.511	1.00
227_I	230_I	0.511	1.00
15_V	40_I	0.510	1.00
15_V	25_F	0.510	1.00
162_F	167_A	0.509	1.00
89_T	306_L	0.508	1.00
182_H	237_Y	0.506	1.00
215_V	218_E	0.505	1.00
219_Q	226_G	0.505	1.00
320_D	323_F	0.503	1.00
202_E	216_M	0.503	1.00
248_D	277_H	0.502	1.00
85_I	89_T	0.502	1.00
20_M	29_P	0.502	1.00
168_A	201_Y	0.502	1.00
256_F	281_Q	0.500	1.00
63_S	94_Y	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
2o20A	2	0.8218	100	0.051	Contact Map
2hsgA	1	0.9789	100	0.063	Contact Map
3kjxA	2	0.994	100	0.069	Contact Map
3bilA	2	0.7613	100	0.071	Contact Map
3h5oA	2	0.8066	100	0.071	Contact Map
3dbiA	2	0.8157	100	0.072	Contact Map
3e3mA	2	0.7946	100	0.074	Contact Map
1qpzA	2	0.9849	100	0.075	Contact Map
4o5aA	2	0.7976	100	0.076	Contact Map
3jvdA	2	0.7795	100	0.085	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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