GALR - ECOLI - GREMLIN Contacts

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GALR - HTH-type transcriptional regulator GalR

UniProt:	P03024	Sequences: MATIKDVARLAGVSVATVSRVINNSPKASEASRLAVHSAMESLSYHPNANARALAQQTTETVGLVVGDVSDPFFGAMVKAVEQVAYHTGNFLLIGNGYHNEQKERQAIEQLIRHRCAALVVHAKMIPDADLASLMKQMPGMVLINRILPGFENRCIALDDRYGAWLATRHLIQQGHTRIGYLCSNHSISDAEDRLQGYYDALAESGIAANDRLVTFGEPDESGGEQAMTELLGRGRNFTAVACYNDSMAAGAMGVLNDNGIDVPGEISLIGFDDVLVSRYVRPRLTTVRYPIVTMATQAAELALALADNRPLPEITNVFSPTLVRRHSVSTPSLEASHHATSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10364
Length:	343 (325)
Sequences:	36411 (26549)
Seq/√Len:	1472.7

ECOLI - GALR GALS PURR ASCG RBSR CYTR LACI CRA GNTR MALI IDNR YCJW EBGR TRER TORT ALSB YTFQ XYLF RBSB YPHF LSRB ARAF DGAL XYLR
BACSU - KDGR NTDR CCPA RBSR DEGA EXUR YKVZ MSMR 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
161_R	200_D	3.455	1.00
176_H	239_T	3.259	1.00
10_L	42_S	3.218	1.00
262_D	265_G	3.127	1.00
167_A	270_I	2.633	1.00
118_A	303_A	2.565	1.00
274_D	289_R	2.557	1.00
195_L	199_Y	2.548	1.00
154_R	306_L	2.491	1.00
176_H	268_S	2.476	1.00
165_W	204_E	2.349	1.00
225_E	258_D	2.277	1.00
30_E	34_L	2.251	1.00
84_V	87_H	2.241	1.00
38_S	42_S	2.221	1.00
84_V	301_E	2.214	1.00
34_L	38_S	2.209	1.00
298_Q	301_E	2.104	1.00
165_W	200_D	2.072	1.00
229_T	259_N	2.068	1.00
172_I	205_S	2.057	1.00
165_W	201_A	1.986	1.00
174_Q	329_V	1.972	1.00
85_A	300_A	1.968	1.00
162_Y	166_L	1.965	1.00
169_R	201_A	1.952	1.00
80_A	296_A	1.949	1.00
169_R	173_Q	1.948	1.00
163_G	272_F	1.917	1.00
21_V	36_V	1.915	1.00
164_A	168_T	1.915	1.00
256_L	267_I	1.909	1.00
305_A	310_R	1.909	1.00
33_R	37_H	1.904	1.00
161_R	196_Q	1.904	1.00
229_T	255_V	1.902	1.00
233_G	259_N	1.889	1.00
224_G	251_G	1.876	1.00
22_I	40_M	1.852	1.00
171_L	240_A	1.812	1.00
83_Q	293_V	1.795	1.00
5_K	15_V	1.793	1.00
164_A	242_A	1.773	1.00
84_V	297_T	1.767	1.00
289_R	322_T	1.765	1.00
165_W	169_R	1.711	1.00
169_R	205_S	1.709	1.00
225_E	255_V	1.675	1.00
261_I	266_E	1.671	1.00
11_A	39_A	1.661	1.00
168_T	198_Y	1.660	1.00
291_P	294_T	1.643	1.00
63_G	116_C	1.635	1.00
166_L	321_P	1.620	1.00
228_M	252_A	1.620	1.00
178_R	210_N	1.616	1.00
298_Q	317_N	1.593	1.00
10_L	39_A	1.591	1.00
80_A	293_V	1.590	1.00
284_R	327_H	1.579	1.00
180_G	238_F	1.577	1.00
262_D	266_E	1.573	1.00
181_Y	244_Y	1.568	1.00
243_C	252_A	1.554	1.00
196_Q	200_D	1.526	1.00
178_R	237_N	1.522	1.00
84_V	88_T	1.517	1.00
37_H	41_E	1.516	1.00
144_I	299_A	1.513	1.00
257_N	282_R	1.512	1.00
159_D	162_Y	1.501	1.00
255_V	259_N	1.492	1.00
162_Y	165_W	1.489	1.00
21_V	40_M	1.476	1.00
172_I	201_A	1.466	1.00
274_D	326_R	1.457	1.00
7_V	39_A	1.449	1.00
88_T	304_L	1.445	1.00
215_T	230_E	1.438	1.00
294_T	298_Q	1.435	1.00
37_H	40_M	1.424	1.00
270_I	286_T	1.424	1.00
228_M	241_V	1.422	1.00
193_D	196_Q	1.410	1.00
170_H	173_Q	1.403	1.00
255_V	258_D	1.398	1.00
84_V	300_A	1.393	1.00
168_T	172_I	1.382	1.00
294_T	297_T	1.380	1.00
199_Y	203_A	1.379	1.00
163_G	321_P	1.364	1.00
60_E	117_A	1.361	1.00
170_H	174_Q	1.359	1.00
229_T	258_D	1.357	1.00
170_H	325_R	1.352	1.00
168_T	197_G	1.349	1.00
256_L	261_I	1.338	1.00
170_H	329_V	1.312	1.00
225_E	254_G	1.308	1.00
180_G	231_L	1.308	1.00
218_E	223_G	1.304	1.00
164_A	197_G	1.303	1.00
210_N	213_L	1.302	1.00
178_R	239_T	1.283	1.00
301_E	305_A	1.280	1.00
62_V	85_A	1.273	1.00
60_E	90_N	1.271	1.00
168_T	201_A	1.267	1.00
176_H	240_A	1.266	1.00
225_E	229_T	1.264	1.00
304_L	308_D	1.263	1.00
63_G	111_L	1.256	1.00
197_G	201_A	1.253	1.00
132_A	136_K	1.253	1.00
7_V	11_A	1.251	1.00
5_K	9_R	1.248	1.00
29_S	32_S	1.248	1.00
10_L	43_L	1.247	1.00
30_E	33_R	1.247	1.00
201_A	204_E	1.246	1.00
235_G	238_F	1.236	1.00
6_D	9_R	1.235	1.00
228_M	256_L	1.235	1.00
20_R	25_S	1.223	1.00
120_V	299_A	1.209	1.00
64_L	81_V	1.205	1.00
109_E	133_S	1.204	1.00
95_G	111_L	1.202	1.00
85_A	92_L	1.200	1.00
229_T	233_G	1.200	1.00
169_R	204_E	1.195	1.00
39_A	43_L	1.193	1.00
161_R	165_W	1.183	1.00
35_A	39_A	1.182	1.00
253_M	269_L	1.174	1.00
166_L	169_R	1.174	1.00
230_E	234_R	1.169	1.00
81_V	300_A	1.165	1.00
7_V	43_L	1.164	1.00
161_R	193_D	1.163	1.00
81_V	120_V	1.155	1.00
182_L	252_A	1.155	1.00
95_G	107_A	1.152	1.00
39_A	42_S	1.147	1.00
222_S	226_Q	1.134	1.00
198_Y	202_L	1.133	1.00
4_I	15_V	1.125	1.00
251_G	255_V	1.120	1.00
293_V	297_T	1.119	1.00
268_S	329_V	1.111	1.00
32_S	35_A	1.106	1.00
4_I	18_V	1.104	1.00
241_V	252_A	1.101	1.00
64_L	92_L	1.101	1.00
177_T	239_T	1.100	1.00
246_D	287_T	1.088	1.00
88_T	301_E	1.085	1.00
167_A	242_A	1.082	1.00
179_I	202_L	1.078	1.00
161_R	197_G	1.077	1.00
172_I	207_I	1.071	1.00
173_Q	205_S	1.069	1.00
302_L	317_N	1.065	1.00
82_E	86_Y	1.064	1.00
61_T	91_F	1.061	1.00
48_N	54_L	1.060	1.00
38_S	41_E	1.055	1.00
200_D	204_E	1.054	1.00
181_Y	195_L	1.050	1.00
21_V	28_A	1.046	1.00
226_Q	230_E	1.044	1.00
246_D	271_G	1.039	1.00
174_Q	325_R	1.034	1.00
298_Q	302_L	1.029	1.00
34_L	37_H	1.026	1.00
178_R	236_R	1.025	1.00
220_D	223_G	1.024	1.00
61_T	93_L	1.023	1.00
198_Y	242_A	1.022	1.00
296_A	300_A	1.022	1.00
88_T	308_D	1.012	1.00
201_A	205_S	1.010	1.00
24_N	33_R	1.009	1.00
48_N	51_A	1.009	1.00
224_G	228_M	1.004	1.00
105_R	109_E	1.000	1.00
50_N	53_A	0.989	1.00
243_C	249_A	0.989	1.00
227_A	230_E	0.988	1.00
215_T	227_A	0.985	1.00
86_Y	103_K	0.976	1.00
103_K	106_Q	0.972	1.00
202_L	207_I	0.972	1.00
243_C	248_M	0.967	1.00
223_G	226_Q	0.962	1.00
40_M	43_L	0.962	1.00
196_Q	199_Y	0.959	1.00
186_H	216_F	0.956	1.00
297_T	301_E	0.953	1.00
167_A	288_V	0.949	1.00
90_N	304_L	0.948	1.00
298_Q	319_F	0.945	1.00
174_Q	268_S	0.943	1.00
303_A	307_A	0.942	1.00
253_M	281_V	0.940	1.00
253_M	263_V	0.938	1.00
228_M	232_L	0.935	1.00
83_Q	297_T	0.927	1.00
289_R	324_V	0.925	1.00
11_A	18_V	0.925	1.00
162_Y	320_S	0.921	1.00
179_I	240_A	0.919	1.00
87_H	297_T	0.918	1.00
192_E	196_Q	0.916	1.00
51_A	54_L	0.914	1.00
109_E	113_R	0.904	1.00
158_L	291_P	0.904	1.00
291_P	319_F	0.904	1.00
187_S	192_E	0.902	1.00
170_H	286_T	0.901	1.00
184_S	219_P	0.901	1.00
120_V	303_A	0.900	1.00
168_T	202_L	0.897	1.00
221_E	254_G	0.893	1.00
64_L	78_V	0.890	1.00
159_D	318_V	0.890	1.00
81_V	296_A	0.885	1.00
189_S	193_D	0.877	1.00
322_T	325_R	0.875	1.00
62_V	120_V	0.875	1.00
172_I	177_T	0.873	1.00
271_G	287_T	0.867	1.00
199_Y	209_A	0.865	1.00
47_P	52_R	0.865	1.00
79_K	83_Q	0.864	1.00
154_R	302_L	0.862	1.00
232_L	255_V	0.857	1.00
246_D	274_D	0.857	1.00
156_I	302_L	0.856	1.00
291_P	322_T	0.852	1.00
256_L	269_L	0.846	1.00
155_C	316_T	0.841	1.00
180_G	241_V	0.840	1.00
24_N	37_H	0.838	1.00
162_Y	321_P	0.835	1.00
261_I	267_I	0.834	1.00
226_Q	229_T	0.828	1.00
325_R	329_V	0.826	1.00
200_D	203_A	0.822	1.00
73_F	292_I	0.822	1.00
118_A	307_A	0.820	1.00
217_G	248_M	0.818	1.00
250_A	281_V	0.818	1.00
59_T	117_A	0.815	1.00
274_D	324_V	0.811	1.00
158_L	321_P	0.809	1.00
31_A	34_L	0.808	1.00
21_V	37_H	0.808	1.00
76_A	293_V	0.808	1.00
241_V	267_I	0.806	1.00
159_D	320_S	0.806	1.00
178_R	213_L	0.805	1.00
112_I	137_Q	0.803	1.00
158_L	290_Y	0.802	1.00
202_L	209_A	0.801	1.00
170_H	323_L	0.800	1.00
223_G	227_A	0.799	1.00
81_V	92_L	0.793	1.00
133_S	136_K	0.793	1.00
78_V	82_E	0.792	1.00
237_N	261_I	0.785	1.00
160_D	194_R	0.785	1.00
80_A	297_T	0.781	1.00
209_A	212_R	0.778	1.00
157_A	318_V	0.778	1.00
273_D	290_Y	0.777	1.00
83_Q	87_H	0.772	1.00
300_A	304_L	0.772	1.00
302_L	305_A	0.767	1.00
195_L	214_V	0.767	1.00
17_T	20_R	0.766	1.00
177_T	207_I	0.765	1.00
257_N	284_R	0.765	1.00
77_M	144_I	0.764	1.00
228_M	231_L	0.761	1.00
100_N	103_K	0.760	1.00
171_L	270_I	0.759	1.00
182_L	243_C	0.758	1.00
67_G	74_F	0.758	1.00
13_V	36_V	0.757	1.00
49_A	52_R	0.757	1.00
181_Y	242_A	0.756	1.00
246_D	249_A	0.751	1.00
61_T	114_H	0.751	1.00
46_H	113_R	0.749	1.00
183_C	195_L	0.746	1.00
193_D	197_G	0.745	1.00
103_K	107_A	0.744	1.00
286_T	329_V	0.744	1.00
213_L	234_R	0.742	1.00
31_A	35_A	0.740	1.00
106_Q	109_E	0.735	1.00
228_M	255_V	0.735	1.00
215_T	231_L	0.732	1.00
239_T	268_S	0.730	1.00
63_G	119_L	0.729	1.00
58_T	117_A	0.728	1.00
78_V	94_I	0.727	1.00
80_A	84_V	0.726	1.00
20_R	26_P	0.723	1.00
232_L	259_N	0.722	1.00
274_D	278_S	0.722	1.00
79_K	82_E	0.719	1.00
166_L	288_V	0.719	1.00
134_L	141_M	0.719	1.00
62_V	300_A	0.717	1.00
16_A	20_R	0.715	1.00
286_T	323_L	0.714	1.00
20_R	27_K	0.713	1.00
147_I	316_T	0.705	1.00
118_A	142_V	0.705	1.00
154_R	314_E	0.701	1.00
254_G	257_N	0.699	1.00
305_A	309_N	0.699	1.00
249_A	271_G	0.697	1.00
165_W	197_G	0.694	1.00
157_A	316_T	0.692	1.00
120_V	144_I	0.687	1.00
93_L	116_C	0.686	1.00
58_T	308_D	0.686	1.00
242_A	270_I	0.686	1.00
143_L	153_N	0.685	1.00
234_R	238_F	0.682	1.00
34_L	41_E	0.680	1.00
234_R	237_N	0.679	1.00
230_E	233_G	0.677	1.00
217_G	223_G	0.676	1.00
224_G	227_A	0.676	1.00
143_L	148_L	0.676	1.00
135_M	152_E	0.674	1.00
98_Y	103_K	0.673	1.00
82_E	96_N	0.672	1.00
172_I	202_L	0.671	1.00
132_A	135_M	0.671	1.00
256_L	263_V	0.669	1.00
82_E	92_L	0.669	1.00
65_V	107_A	0.666	1.00
102_Q	106_Q	0.659	1.00
112_I	139_P	0.656	1.00
228_M	251_G	0.655	1.00
215_T	234_R	0.655	1.00
254_G	284_R	0.655	1.00
179_I	239_T	0.649	1.00
27_K	32_S	0.649	1.00
178_R	208_A	0.647	1.00
5_K	55_A	0.647	1.00
254_G	258_D	0.638	1.00
21_V	33_R	0.637	1.00
46_H	109_E	0.635	1.00
191_A	219_P	0.634	1.00
41_E	44_S	0.633	1.00
171_L	242_A	0.629	1.00
145_N	160_D	0.625	1.00
245_N	273_D	0.623	1.00
184_S	191_A	0.622	1.00
179_I	198_Y	0.620	1.00
18_V	21_V	0.617	1.00
35_A	38_S	0.616	1.00
142_V	156_I	0.616	1.00
108_I	119_L	0.613	1.00
160_D	193_D	0.613	1.00
145_N	190_D	0.613	1.00
181_Y	198_Y	0.613	1.00
71_D	247_S	0.611	1.00
118_A	299_A	0.608	1.00
135_M	141_M	0.607	1.00
219_P	244_Y	0.607	1.00
79_K	293_V	0.605	1.00
256_L	259_N	0.604	1.00
180_G	213_L	0.602	1.00
80_A	292_I	0.602	1.00
278_S	287_T	0.601	1.00
142_V	303_A	0.601	1.00
250_A	275_V	0.601	1.00
198_Y	209_A	0.599	1.00
270_I	329_V	0.593	1.00
7_V	18_V	0.592	1.00
90_N	117_A	0.592	1.00
284_R	326_R	0.592	1.00
93_L	114_H	0.591	1.00
77_M	292_I	0.591	1.00
62_V	90_N	0.591	1.00
97_G	104_E	0.590	1.00
165_W	168_T	0.590	1.00
293_V	296_A	0.588	1.00
129_A	132_A	0.588	1.00
20_R	28_A	0.587	1.00
62_V	118_A	0.587	1.00
242_A	272_F	0.587	1.00
62_V	307_A	0.586	1.00
245_N	248_M	0.585	1.00
142_V	306_L	0.584	1.00
167_A	240_A	0.582	1.00
90_N	307_A	0.582	1.00
178_R	238_F	0.582	1.00
166_L	170_H	0.581	1.00
130_D	133_S	0.581	1.00
18_V	40_M	0.580	1.00
278_S	285_L	0.576	1.00
76_A	292_I	0.576	1.00
243_C	271_G	0.575	1.00
141_M	153_N	0.575	1.00
309_N	312_L	0.574	1.00
295_M	319_F	0.573	1.00
286_T	325_R	0.572	1.00
85_A	304_L	0.571	1.00
13_V	32_S	0.570	1.00
222_S	225_E	0.569	1.00
73_F	77_M	0.569	1.00
105_R	130_D	0.568	1.00
18_V	36_V	0.567	1.00
135_M	153_N	0.565	1.00
253_M	257_N	0.563	1.00
257_N	283_P	0.562	1.00
250_A	277_V	0.560	1.00
257_N	262_D	0.554	1.00
199_Y	211_D	0.554	1.00
272_F	290_Y	0.552	1.00
221_E	251_G	0.552	1.00
111_L	116_C	0.551	1.00
232_L	256_L	0.548	1.00
142_V	302_L	0.547	1.00
212_R	234_R	0.546	1.00
46_H	50_N	0.546	1.00
25_S	28_A	0.545	1.00
195_L	216_F	0.543	1.00
283_P	328_S	0.543	1.00
254_G	282_R	0.543	1.00
274_D	279_R	0.542	1.00
119_L	139_P	0.540	1.00
306_L	309_N	0.540	1.00
142_V	299_A	0.539	1.00
170_H	270_I	0.538	1.00
225_E	251_G	0.538	1.00
302_L	306_L	0.537	1.00
221_E	277_V	0.537	1.00
116_C	119_L	0.536	1.00
227_A	231_L	0.536	1.00
191_A	244_Y	0.535	1.00
209_A	214_V	0.534	1.00
238_F	261_I	0.534	1.00
219_P	248_M	0.533	1.00
52_R	56_Q	0.532	1.00
207_I	211_D	0.531	1.00
13_V	18_V	0.528	1.00
281_V	284_R	0.526	1.00
79_K	98_Y	0.526	1.00
156_I	298_Q	0.525	1.00
71_D	74_F	0.524	1.00
183_C	216_F	0.523	1.00
158_L	163_G	0.522	1.00
199_Y	214_V	0.521	1.00
11_A	21_V	0.521	1.00
143_L	155_C	0.520	1.00
174_Q	239_T	0.519	1.00
28_A	33_R	0.518	1.00
72_P	247_S	0.518	1.00
110_Q	113_R	0.518	1.00
279_R	284_R	0.515	1.00
288_V	321_P	0.515	1.00
258_D	282_R	0.515	1.00
101_E	105_R	0.514	1.00
217_G	224_G	0.512	1.00
59_T	91_F	0.510	1.00
183_C	214_V	0.510	1.00
95_G	110_Q	0.507	1.00
254_G	279_R	0.507	1.00
223_G	248_M	0.507	1.00
74_F	122_H	0.506	1.00
84_V	304_L	0.505	1.00
16_A	25_S	0.504	1.00
246_D	275_V	0.504	1.00
109_E	112_I	0.503	1.00
11_A	36_V	0.502	1.00
26_P	33_R	0.502	1.00
252_A	256_L	0.502	1.00
81_V	85_A	0.501	1.00
263_V	266_E	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	0.8047	100	0.082	Contact Map
2hsgA	1	0.9534	100	0.083	Contact Map
1qpzA	2	0.9825	100	0.089	Contact Map
2o20A	2	0.8017	100	0.09	Contact Map
3e3mA	2	0.7813	100	0.096	Contact Map
3bilA	2	0.7464	100	0.097	Contact Map
4o5aA	2	0.7843	100	0.098	Contact Map
3kjxA	2	0.965	100	0.101	Contact Map
3h5oA	2	0.7872	100	0.102	Contact Map
3ctpA	2	0.7726	100	0.104	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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