EBGR - ECOLI - GREMLIN Contacts

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EBGR - HTH-type transcriptional regulator EbgR

UniProt:	P06846	Sequences: MATLKDIAIEAGVSLATVSRVLNDDPTLNVKEETKHRILEIAEKLEYKTSSARKLQTGAVNQHHILAIYSYQQELEINDPYYLAIRHGIETQCEKLGIELTNCYEHSGLPDIKNVTGILIVGKPTPALRAAASALTDNICFIDFHEPGSGYDAVDIDLARISKEIIDFYINQGVNRIGFIGGEDEPGKADIREVAFAEYGRLKQVVREEDIWRGGFSSSSGYELAKQMLAREDYPKALFVASDSIAIGVLRAIHERGLNIPQDISLISVNDIPTARFTFPPLSTVRIHSEMMGSQGVNLVYEKARDGRALPLLVFVPSKLKLRGTTR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10254
Length:	327 (313)
Sequences:	33565 (24723)
Seq/√Len:	1397.4

ECOLI - EBGR GALS RBSR GALR PURR CRA GNTR ASCG CYTR IDNR MALI LACI YCJW TRER TORT ALSB YTFQ RBSB XYLF ARAF YPHF XYLR LSRB DGAL
BACSU - GANR YVDE MSMR CCPA KDGR RBSR NTDR EXUR DEGA YKVZ 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
159_A	198_E	3.282	1.00
174_V	236_K	3.140	1.00
10_E	44_K	3.071	1.00
259_N	262_Q	3.057	1.00
165_I	267_I	2.677	1.00
174_V	265_S	2.557	1.00
193_E	197_A	2.536	1.00
117_G	300_V	2.450	1.00
271_D	286_R	2.426	1.00
163_K	202_L	2.314	1.00
152_D	303_K	2.267	1.00
32_E	36_H	2.255	1.00
40_E	44_K	2.189	1.00
222_Y	255_E	2.165	1.00
36_H	40_E	2.131	1.00
226_K	256_R	2.123	1.00
92_Q	298_N	2.080	1.00
170_I	203_K	2.072	1.00
92_Q	95_K	2.061	1.00
167_D	199_Y	2.032	1.00
160_R	164_E	2.007	1.00
295_Q	298_N	1.988	1.00
226_K	252_A	1.984	1.00
163_K	198_E	1.974	1.00
21_V	38_I	1.963	1.00
163_K	199_Y	1.942	1.00
93_C	297_V	1.931	1.00
25_D	29_N	1.927	1.00
22_L	42_A	1.916	1.00
35_K	39_L	1.899	1.00
5_K	15_L	1.875	1.00
159_A	194_V	1.873	1.00
162_S	166_I	1.858	1.00
161_I	269_V	1.843	1.00
167_D	171_N	1.831	1.00
166_I	196_F	1.811	1.00
162_S	239_F	1.806	1.00
286_R	319_K	1.806	1.00
253_I	264_I	1.801	1.00
88_G	293_G	1.800	1.00
169_Y	237_A	1.798	1.00
92_Q	294_S	1.775	1.00
221_G	248_G	1.764	1.00
10_E	41_I	1.764	1.00
167_D	203_K	1.750	1.00
230_A	256_R	1.747	1.00
281_P	324_G	1.743	1.00
11_A	41_I	1.739	1.00
295_Q	314_V	1.725	1.00
302_E	307_G	1.704	1.00
179_F	241_A	1.686	1.00
91_T	290_E	1.674	1.00
163_K	167_D	1.662	1.00
222_Y	252_A	1.658	1.00
240_V	249_V	1.629	1.00
67_A	115_V	1.626	1.00
164_E	318_S	1.623	1.00
88_G	290_E	1.617	1.00
288_H	291_M	1.616	1.00
254_H	279_F	1.611	1.00
258_L	263_D	1.607	1.00
259_N	263_D	1.600	1.00
225_A	249_V	1.595	1.00
178_G	235_P	1.592	1.00
252_A	256_R	1.587	1.00
168_F	172_Q	1.565	1.00
142_I	296_G	1.564	1.00
92_Q	96_L	1.539	1.00
39_L	43_E	1.516	1.00
291_M	295_Q	1.501	1.00
212_W	227_Q	1.488	1.00
176_R	207_R	1.481	1.00
252_A	255_E	1.478	1.00
157_D	160_R	1.471	1.00
168_F	322_L	1.468	1.00
96_L	301_Y	1.463	1.00
39_L	42_A	1.458	1.00
21_V	42_A	1.448	1.00
160_R	163_K	1.446	1.00
176_R	234_Y	1.446	1.00
170_I	199_Y	1.442	1.00
271_D	323_R	1.439	1.00
7_I	41_I	1.437	1.00
194_V	198_E	1.436	1.00
267_I	283_S	1.424	1.00
64_H	116_T	1.401	1.00
291_M	294_S	1.388	1.00
191_I	194_V	1.386	1.00
168_F	171_N	1.375	1.00
161_I	318_S	1.360	1.00
92_Q	297_V	1.344	1.00
26_P	29_N	1.344	1.00
207_R	210_D	1.341	1.00
253_I	258_L	1.331	1.00
197_A	201_R	1.324	1.00
10_E	45_L	1.323	1.00
199_Y	202_L	1.317	1.00
166_I	199_Y	1.310	1.00
215_G	220_S	1.310	1.00
5_K	9_I	1.292	1.00
32_E	35_K	1.290	1.00
166_I	195_A	1.281	1.00
66_L	93_C	1.281	1.00
37_R	41_I	1.271	1.00
6_D	9_I	1.270	1.00
41_I	44_K	1.264	1.00
226_K	230_A	1.262	1.00
178_G	228_M	1.257	1.00
222_Y	226_K	1.252	1.00
20_R	25_D	1.248	1.00
176_R	236_K	1.244	1.00
64_H	98_I	1.242	1.00
225_A	253_I	1.240	1.00
174_V	237_A	1.238	1.00
162_S	195_A	1.235	1.00
166_I	170_I	1.232	1.00
31_K	34_T	1.230	1.00
226_K	255_E	1.227	1.00
222_Y	251_R	1.224	1.00
167_D	202_L	1.223	1.00
225_A	238_L	1.220	1.00
298_N	302_E	1.212	1.00
250_L	266_L	1.212	1.00
41_I	45_L	1.211	1.00
301_Y	305_R	1.209	1.00
195_A	199_Y	1.207	1.00
89_I	297_V	1.197	1.00
200_G	205_V	1.185	1.00
34_T	37_R	1.183	1.00
175_N	236_K	1.181	1.00
164_E	167_D	1.178	1.00
7_I	11_A	1.177	1.00
4_L	15_L	1.177	1.00
227_Q	231_R	1.177	1.00
159_A	191_I	1.176	1.00
7_I	45_L	1.162	1.00
130_A	134_A	1.161	1.00
93_C	100_L	1.161	1.00
89_I	119_L	1.156	1.00
119_L	296_G	1.152	1.00
68_I	89_I	1.148	1.00
159_A	163_K	1.145	1.00
21_V	30_V	1.120	1.00
50_S	55_L	1.118	1.00
36_H	39_L	1.117	1.00
232_E	235_P	1.117	1.00
196_F	200_G	1.115	1.00
177_I	200_G	1.114	1.00
295_Q	299_L	1.112	1.00
172_Q	322_L	1.095	1.00
180_I	249_V	1.095	1.00
290_E	294_S	1.092	1.00
199_Y	203_K	1.089	1.00
219_S	223_E	1.086	1.00
40_E	43_E	1.079	1.00
238_L	249_V	1.073	1.00
96_L	298_N	1.069	1.00
198_E	202_L	1.066	1.00
179_F	193_E	1.063	1.00
293_G	297_V	1.062	1.00
224_L	227_Q	1.062	1.00
68_I	100_L	1.061	1.00
24_D	35_K	1.058	1.00
299_L	314_V	1.057	1.00
165_I	239_F	1.056	1.00
248_G	252_A	1.054	1.00
243_D	284_T	1.054	1.00
159_A	195_A	1.050	1.00
171_N	203_K	1.036	1.00
176_R	233_D	1.034	1.00
243_D	268_S	1.026	1.00
160_R	317_P	1.025	1.00
65_I	101_T	1.024	1.00
59_A	64_H	1.015	1.00
96_L	305_R	1.013	1.00
4_L	18_V	1.008	1.00
42_A	45_L	1.008	1.00
294_S	298_N	1.005	1.00
295_Q	316_V	1.003	1.00
194_V	197_A	1.003	1.00
170_I	205_V	1.001	1.00
240_V	246_A	0.989	1.00
221_G	225_A	0.983	1.00
300_V	304_A	0.980	1.00
90_E	94_E	0.979	1.00
250_L	260_I	0.979	1.00
65_I	99_E	0.977	1.00
217_S	220_S	0.976	1.00
98_I	301_Y	0.971	1.00
175_N	205_V	0.962	1.00
172_Q	265_S	0.957	1.00
11_A	18_V	0.954	1.00
184_D	213_R	0.953	1.00
286_R	321_K	0.953	1.00
223_E	227_Q	0.947	1.00
240_V	245_I	0.938	1.00
177_I	237_A	0.933	1.00
165_I	285_V	0.932	1.00
250_L	278_T	0.931	1.00
168_F	283_S	0.930	1.00
220_S	223_E	0.929	1.00
153_A	313_L	0.924	1.00
212_W	224_L	0.923	1.00
94_E	111_D	0.922	1.00
166_I	200_G	0.922	1.00
170_I	175_N	0.920	1.00
190_D	194_V	0.919	1.00
24_D	39_L	0.916	1.00
319_K	322_L	0.915	1.00
299_L	302_E	0.910	1.00
225_A	229_L	0.902	1.00
238_L	264_I	0.894	1.00
95_K	294_S	0.893	1.00
176_R	210_D	0.891	1.00
91_T	294_S	0.878	1.00
288_H	316_V	0.877	1.00
288_H	319_K	0.877	1.00
187_G	191_I	0.876	1.00
152_D	299_L	0.874	1.00
156_I	288_H	0.867	1.00
206_V	209_E	0.867	1.00
196_F	239_F	0.864	1.00
154_V	299_L	0.864	1.00
218_S	251_R	0.862	1.00
89_I	293_G	0.862	1.00
21_V	39_L	0.861	1.00
160_R	318_S	0.859	1.00
119_L	300_V	0.857	1.00
155_D	313_L	0.853	1.00
66_L	119_L	0.853	1.00
157_D	315_F	0.852	1.00
68_I	86_R	0.849	1.00
156_I	318_S	0.846	1.00
155_D	315_F	0.845	1.00
152_D	312_L	0.843	1.00
258_L	264_I	0.842	1.00
271_D	321_K	0.841	1.00
85_I	142_I	0.841	1.00
87_H	91_T	0.836	1.00
157_D	317_P	0.836	1.00
229_L	252_A	0.835	1.00
49_T	53_R	0.833	1.00
297_V	301_Y	0.826	1.00
234_Y	258_L	0.825	1.00
210_D	231_R	0.823	1.00
197_A	206_V	0.817	1.00
223_E	226_K	0.810	1.00
181_G	193_E	0.810	1.00
81_Y	289_S	0.806	1.00
182_G	216_F	0.803	1.00
178_G	238_L	0.802	1.00
243_D	271_D	0.802	1.00
13_V	38_I	0.801	1.00
214_G	245_I	0.793	1.00
158_L	192_R	0.790	1.00
169_Y	267_I	0.787	1.00
198_E	201_R	0.787	1.00
33_E	36_H	0.786	1.00
126_P	130_A	0.783	1.00
180_I	240_V	0.782	1.00
88_G	92_Q	0.781	1.00
117_G	304_A	0.779	1.00
253_I	266_L	0.777	1.00
16_A	20_R	0.770	1.00
271_D	275_A	0.770	1.00
84_A	290_E	0.768	1.00
145_H	313_L	0.768	1.00
65_I	113_K	0.767	1.00
225_A	252_A	0.767	1.00
33_E	37_R	0.766	1.00
156_I	287_I	0.763	1.00
191_I	195_A	0.757	1.00
3_T	6_D	0.756	1.00
17_T	20_R	0.752	1.00
229_L	256_R	0.751	1.00
268_S	284_T	0.751	1.00
88_G	294_S	0.749	1.00
164_E	285_V	0.747	1.00
239_F	267_I	0.746	1.00
212_W	231_R	0.746	1.00
90_E	104_Y	0.744	1.00
254_H	281_P	0.743	1.00
20_R	26_P	0.742	1.00
220_S	224_L	0.742	1.00
206_V	211_I	0.741	1.00
168_F	320_L	0.740	1.00
275_A	278_T	0.736	1.00
193_E	211_I	0.735	1.00
20_R	29_N	0.731	1.00
236_K	265_S	0.728	1.00
253_I	260_I	0.728	1.00
243_D	246_A	0.728	1.00
86_R	102_N	0.726	1.00
133_S	150_G	0.725	1.00
179_F	239_F	0.724	1.00
251_R	254_H	0.724	1.00
89_I	100_L	0.723	1.00
67_A	118_I	0.722	1.00
251_R	281_P	0.718	1.00
185_E	190_D	0.718	1.00
274_T	278_T	0.717	1.00
131_A	134_A	0.710	1.00
247_I	278_T	0.709	1.00
66_L	297_V	0.707	1.00
52_A	55_L	0.704	1.00
90_E	100_L	0.695	1.00
101_T	115_V	0.695	1.00
225_A	228_M	0.694	1.00
170_I	200_G	0.692	1.00
86_R	90_E	0.691	1.00
60_V	116_T	0.691	1.00
139_I	151_Y	0.690	1.00
270_N	287_I	0.689	1.00
21_V	35_K	0.687	1.00
91_T	95_K	0.687	1.00
36_H	43_E	0.684	1.00
141_F	151_Y	0.684	1.00
133_S	139_I	0.681	1.00
108_G	111_D	0.680	1.00
177_I	236_K	0.679	1.00
302_E	306_D	0.676	1.00
13_V	34_T	0.674	1.00
164_E	168_F	0.673	1.00
141_F	146_E	0.672	1.00
130_A	133_S	0.671	1.00
251_R	255_E	0.671	1.00
87_H	90_E	0.670	1.00
227_Q	230_A	0.670	1.00
117_G	140_C	0.669	1.00
212_W	228_M	0.668	1.00
59_A	305_R	0.668	1.00
281_P	323_R	0.667	1.00
214_G	220_S	0.664	1.00
75_L	82_Y	0.660	1.00
251_R	279_F	0.657	1.00
231_R	234_Y	0.657	1.00
59_A	116_T	0.655	1.00
221_G	224_L	0.655	1.00
283_S	320_L	0.653	1.00
119_L	142_I	0.647	1.00
163_K	195_A	0.639	1.00
98_I	304_A	0.636	1.00
84_A	289_S	0.633	1.00
133_S	151_Y	0.631	1.00
225_A	248_G	0.631	1.00
87_H	290_E	0.628	1.00
302_E	312_L	0.628	1.00
179_F	196_F	0.628	1.00
231_R	235_P	0.623	1.00
246_A	268_S	0.621	1.00
177_I	196_F	0.621	1.00
20_R	30_V	0.619	1.00
250_L	254_H	0.618	1.00
189_A	216_F	0.618	1.00
37_R	40_E	0.617	1.00
303_K	306_D	0.616	1.00
140_C	300_V	0.615	1.00
79_D	244_S	0.615	1.00
140_C	303_K	0.614	1.00
85_I	289_S	0.613	1.00
132_A	139_I	0.610	1.00
43_E	46_E	0.608	1.00
106_H	111_D	0.607	1.00
5_K	56_Q	0.606	1.00
7_I	18_V	0.605	1.00
163_K	166_I	0.605	1.00
216_F	241_A	0.605	1.00
152_D	311_P	0.604	1.00
242_S	270_N	0.600	1.00
169_Y	239_F	0.597	1.00
279_F	324_G	0.595	1.00
81_Y	85_I	0.594	1.00
253_I	256_R	0.594	1.00
285_V	318_S	0.594	1.00
66_L	117_G	0.594	1.00
117_G	296_G	0.594	1.00
247_I	272_I	0.591	1.00
269_V	287_I	0.590	1.00
200_G	206_V	0.590	1.00
158_L	191_I	0.588	1.00
18_V	42_A	0.588	1.00
239_F	269_V	0.585	1.00
218_S	248_G	0.584	1.00
98_I	116_T	0.584	1.00
140_C	154_V	0.584	1.00
18_V	21_V	0.583	1.00
299_L	303_K	0.582	1.00
29_N	34_T	0.581	1.00
54_K	57_T	0.579	1.00
168_F	267_I	0.579	1.00
118_I	137_D	0.578	1.00
143_D	158_L	0.577	1.00
140_C	296_G	0.575	1.00
254_H	259_N	0.575	1.00
93_C	301_Y	0.574	1.00
254_H	280_P	0.571	1.00
140_C	299_L	0.570	1.00
128_L	131_A	0.568	1.00
181_G	213_R	0.568	1.00
66_L	304_A	0.565	1.00
178_G	210_D	0.564	1.00
88_G	289_S	0.564	1.00
197_A	211_I	0.563	1.00
65_I	116_T	0.562	1.00
242_S	245_I	0.559	1.00
295_Q	302_E	0.558	1.00
182_G	189_A	0.558	1.00
143_D	188_K	0.557	1.00
165_I	237_A	0.557	1.00
25_D	30_V	0.555	1.00
208_E	211_I	0.555	1.00
255_E	279_F	0.551	1.00
249_V	253_I	0.551	1.00
145_H	153_A	0.550	1.00
290_E	293_G	0.550	1.00
189_A	241_A	0.547	1.00
53_R	57_T	0.546	1.00
101_T	113_K	0.546	1.00
87_H	106_H	0.543	1.00
11_A	21_V	0.540	1.00
219_S	222_Y	0.540	1.00
76_E	87_H	0.540	1.00
276_R	281_P	0.540	1.00
155_D	158_L	0.539	1.00
220_S	245_I	0.538	1.00
274_T	277_F	0.538	1.00
260_I	263_D	0.535	1.00
201_R	204_Q	0.534	1.00
154_V	295_Q	0.531	1.00
13_V	18_V	0.531	1.00
6_D	10_E	0.530	1.00
67_A	103_C	0.530	1.00
229_L	253_I	0.530	1.00
89_I	93_C	0.529	1.00
258_L	261_P	0.529	1.00
275_A	282_L	0.528	1.00
193_E	213_R	0.527	1.00
222_Y	248_G	0.525	1.00
292_M	316_V	0.524	1.00
240_V	268_S	0.522	1.00
16_A	25_D	0.521	1.00
30_V	35_K	0.520	1.00
172_Q	236_K	0.519	1.00
249_V	266_L	0.518	1.00
176_R	235_P	0.517	1.00
82_Y	121_V	0.517	1.00
209_E	231_R	0.517	1.00
127_A	130_A	0.516	1.00
156_I	269_V	0.515	1.00
84_A	273_P	0.514	1.00
115_V	118_I	0.514	1.00
18_V	38_I	0.512	1.00
197_A	208_E	0.512	1.00
78_N	84_A	0.511	1.00
235_P	238_L	0.511	1.00
79_D	82_Y	0.510	1.00
243_D	272_I	0.509	1.00
251_R	276_R	0.508	1.00
92_Q	301_Y	0.507	1.00
234_Y	263_D	0.507	1.00
80_P	244_S	0.505	1.00
237_A	265_S	0.504	1.00
222_Y	225_A	0.504	1.00
278_T	281_P	0.504	1.00
24_D	29_N	0.504	1.00
131_A	135_L	0.503	1.00
38_I	41_I	0.502	1.00
117_G	138_N	0.502	1.00
200_G	203_K	0.501	1.00
181_G	211_I	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
3dbiA	2	0.8012	100	0.094	Contact Map
2hsgA	1	0.9633	100	0.097	Contact Map
2o20A	2	0.8073	100	0.101	Contact Map
3bilA	2	0.7462	100	0.104	Contact Map
1qpzA	2	0.9694	100	0.106	Contact Map
4o5aA	2	0.7829	100	0.106	Contact Map
3ctpA	2	0.7798	100	0.111	Contact Map
3jvdA	2	0.7676	100	0.113	Contact Map
3e3mA	2	0.7798	100	0.114	Contact Map
3h5oA	2	0.789	100	0.115	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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