EXUR - BACSU - GREMLIN Contacts

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EXUR - Probable HTH-type transcriptional repressor ExuR

UniProt:	Q9JMQ1	Sequences: MVTIKDIAKLANVSHTTVSRALNNSPYIKEHTKKKILELAEQLNYTPNVNAKSLAMQKSHTIGLFFTSITNGTSHSFFADTIKGVNQAISEDYNLYVRGIDDLKNYDSVTPMRYDGIILMSQSDIDNSFIYHIREKNIPLVVLNRDIDDRTITNILSNDKEGSQEAVEYFIQSGHQDIAIIEGIEGFKSSQQRKEGYLSALIQHHIPIKHEYSVKGQYDMESGFQAMERLLALPNPPTAVFCSNDDMAIGAMNAIFAKGLRVPDDISVIGFDDIGFSQYITPRLSTVKRPVEKISVLGAQKLLSLISEPETKAEKILENTEFMVRDSVRRLTT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	333 (319)
Sequences:	36647 (26582)
Seq/√Len:	1488.3

ECOLI - GALS GALR PURR ASCG RBSR CYTR CRA LACI MALI GNTR IDNR EBGR YCJW TRER TORT YTFQ ALSB XYLF RBSB ARAF LSRB YPHF DGAL XYLR
BACSU - EXUR MSMR NTDR DEGA KDGR CCPA RBSR YVDE YKVZ 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
160_K	199_S	3.338	1.00
175_H	238_T	3.125	1.00
10_L	42_Q	3.106	1.00
261_R	264_D	3.012	1.00
194_K	198_L	2.595	1.00
166_A	269_I	2.590	1.00
116_G	302_L	2.582	1.00
175_H	267_S	2.431	1.00
273_D	288_K	2.425	1.00
153_T	305_L	2.382	1.00
164_Q	203_Q	2.288	1.00
30_E	34_K	2.250	1.00
38_E	42_Q	2.221	1.00
224_F	257_A	2.208	1.00
228_E	258_K	2.148	1.00
34_K	38_E	2.146	1.00
88_A	91_E	2.126	1.00
168_E	200_A	2.061	1.00
164_Q	199_S	2.060	1.00
164_Q	200_A	2.042	1.00
171_I	204_H	2.038	1.00
161_E	165_E	2.035	1.00
228_E	254_A	2.024	1.00
297_L	300_Q	2.023	1.00
88_A	300_Q	1.983	1.00
21_A	36_I	1.975	1.00
89_I	299_A	1.941	1.00
160_K	195_E	1.897	1.00
33_K	37_L	1.890	1.00
162_G	271_F	1.876	1.00
22_L	40_A	1.874	1.00
5_K	15_H	1.867	1.00
84_G	295_S	1.849	1.00
173_S	328_V	1.833	1.00
168_E	172_Q	1.828	1.00
163_S	167_V	1.826	1.00
170_F	239_A	1.824	1.00
88_A	296_V	1.823	1.00
255_I	266_I	1.780	1.00
288_K	321_E	1.774	1.00
223_G	250_G	1.770	1.00
232_A	258_K	1.766	1.00
163_S	241_F	1.761	1.00
304_S	309_P	1.757	1.00
10_L	39_L	1.755	1.00
167_V	197_Y	1.739	1.00
297_L	316_I	1.725	1.00
11_A	39_L	1.715	1.00
87_Q	292_E	1.712	1.00
168_E	204_H	1.703	1.00
164_Q	168_E	1.686	1.00
224_F	254_A	1.686	1.00
260_L	265_D	1.647	1.00
290_P	293_K	1.644	1.00
179_A	237_P	1.639	1.00
177_D	209_K	1.622	1.00
227_M	251_A	1.619	1.00
63_G	114_Y	1.619	1.00
180_I	243_S	1.611	1.00
84_G	292_E	1.607	1.00
165_E	320_T	1.602	1.00
242_C	251_A	1.591	1.00
283_R	326_D	1.582	1.00
254_A	258_K	1.577	1.00
261_R	265_D	1.574	1.00
143_L	298_G	1.566	1.00
169_Y	173_S	1.550	1.00
37_L	41_E	1.541	1.00
256_F	281_T	1.539	1.00
161_E	164_Q	1.527	1.00
177_D	236_P	1.517	1.00
169_Y	172_Q	1.515	1.00
171_I	200_A	1.497	1.00
195_E	199_S	1.490	1.00
254_A	257_A	1.477	1.00
214_V	229_R	1.464	1.00
293_K	297_L	1.456	1.00
169_Y	324_V	1.447	1.00
158_N	161_E	1.442	1.00
7_I	39_L	1.424	1.00
21_A	40_A	1.422	1.00
37_L	40_A	1.417	1.00
198_L	202_I	1.416	1.00
60_H	115_D	1.399	1.00
192_Q	195_E	1.389	1.00
303_L	307_S	1.387	1.00
273_D	325_R	1.385	1.00
200_A	203_Q	1.381	1.00
293_K	296_V	1.370	1.00
162_G	320_T	1.362	1.00
88_A	299_A	1.360	1.00
10_L	43_L	1.338	1.00
255_I	260_L	1.332	1.00
224_F	253_N	1.327	1.00
177_D	238_T	1.314	1.00
224_F	228_E	1.314	1.00
167_V	171_I	1.308	1.00
228_E	257_A	1.301	1.00
30_E	33_K	1.297	1.00
5_K	9_K	1.288	1.00
179_A	230_L	1.287	1.00
227_M	240_V	1.284	1.00
209_K	212_Y	1.281	1.00
167_V	200_A	1.278	1.00
167_V	196_G	1.268	1.00
35_K	39_L	1.261	1.00
217_Q	222_S	1.251	1.00
39_L	42_Q	1.250	1.00
6_D	9_K	1.247	1.00
169_Y	328_V	1.245	1.00
228_E	232_A	1.242	1.00
60_H	93_Y	1.242	1.00
227_M	255_I	1.237	1.00
29_K	32_T	1.236	1.00
20_R	25_S	1.233	1.00
160_K	164_Q	1.232	1.00
163_S	196_G	1.229	1.00
165_E	168_E	1.227	1.00
62_I	89_I	1.217	1.00
131_Y	135_E	1.217	1.00
252_M	268_V	1.208	1.00
118_I	298_G	1.204	1.00
98_R	105_N	1.199	1.00
196_G	200_A	1.194	1.00
175_H	239_A	1.191	1.00
7_I	11_A	1.191	1.00
168_E	203_Q	1.187	1.00
39_L	43_L	1.187	1.00
300_Q	304_S	1.183	1.00
176_Q	238_T	1.179	1.00
85_V	299_A	1.176	1.00
89_I	95_L	1.171	1.00
229_R	233_L	1.163	1.00
7_I	43_L	1.159	1.00
197_Y	201_L	1.159	1.00
32_T	35_K	1.158	1.00
4_I	15_H	1.153	1.00
160_K	192_Q	1.150	1.00
292_E	296_V	1.142	1.00
98_R	109_V	1.137	1.00
107_D	132_H	1.125	1.00
200_A	204_H	1.125	1.00
21_A	28_I	1.118	1.00
63_G	109_V	1.116	1.00
64_L	85_V	1.115	1.00
269_I	285_S	1.114	1.00
301_K	316_I	1.103	1.00
226_A	229_R	1.096	1.00
34_K	37_L	1.091	1.00
180_I	194_K	1.091	1.00
85_V	118_I	1.089	1.00
267_S	328_V	1.088	1.00
234_P	237_P	1.086	1.00
181_I	251_A	1.082	1.00
178_I	201_L	1.078	1.00
297_L	301_K	1.078	1.00
61_T	96_Y	1.078	1.00
221_E	225_Q	1.076	1.00
166_A	241_F	1.076	1.00
38_E	41_E	1.073	1.00
295_S	299_A	1.063	1.00
160_K	196_G	1.062	1.00
199_S	203_Q	1.062	1.00
219_D	222_S	1.057	1.00
250_G	254_A	1.055	1.00
240_V	251_A	1.055	1.00
24_N	33_K	1.048	1.00
86_N	90_S	1.044	1.00
4_I	18_V	1.041	1.00
64_L	95_L	1.040	1.00
61_T	94_N	1.035	1.00
173_S	324_V	1.033	1.00
50_N	53_S	1.031	1.00
195_E	198_L	1.023	1.00
48_N	54_L	1.021	1.00
185_E	215_K	1.012	1.00
93_Y	303_L	1.008	1.00
288_K	323_M	1.004	1.00
103_L	107_D	1.003	1.00
172_Q	204_H	0.998	1.00
214_V	226_A	0.998	1.00
177_D	235_N	0.997	1.00
245_D	286_T	0.994	1.00
171_I	206_I	0.991	1.00
191_Q	195_E	0.986	1.00
201_L	206_I	0.984	1.00
161_E	319_N	0.983	1.00
197_Y	241_F	0.983	1.00
242_C	248_A	0.980	1.00
276_F	279_Y	0.979	1.00
173_S	267_S	0.979	1.00
242_C	247_M	0.976	1.00
225_Q	229_R	0.973	1.00
153_T	301_K	0.973	1.00
256_F	283_R	0.972	1.00
222_S	225_Q	0.971	1.00
40_A	43_L	0.970	1.00
296_V	300_Q	0.968	1.00
223_G	227_M	0.967	1.00
297_L	318_E	0.962	1.00
302_L	306_I	0.961	1.00
245_D	270_G	0.946	1.00
178_I	239_A	0.945	1.00
11_A	18_V	0.939	1.00
83_K	87_Q	0.938	1.00
220_M	253_N	0.935	1.00
290_P	321_E	0.934	1.00
154_N	315_K	0.931	1.00
188_K	192_Q	0.928	1.00
252_M	262_V	0.926	1.00
208_I	211_E	0.923	1.00
166_A	287_V	0.918	1.00
176_Q	206_I	0.914	1.00
227_M	231_L	0.913	1.00
48_N	51_A	0.911	1.00
321_E	324_V	0.906	1.00
118_I	302_L	0.904	1.00
24_N	37_L	0.899	1.00
82_I	86_N	0.898	1.00
91_E	296_V	0.896	1.00
167_V	201_L	0.894	1.00
252_M	280_I	0.893	1.00
198_L	208_I	0.891	1.00
47_P	52_K	0.885	1.00
127_N	131_Y	0.870	1.00
186_G	191_Q	0.867	1.00
87_Q	296_V	0.867	1.00
158_N	317_L	0.865	1.00
171_I	176_Q	0.863	1.00
225_Q	228_E	0.856	1.00
21_A	37_L	0.855	1.00
157_S	290_P	0.854	1.00
260_L	266_I	0.852	1.00
240_V	266_I	0.850	1.00
85_V	295_S	0.846	1.00
155_I	301_K	0.843	1.00
153_T	314_E	0.839	1.00
161_E	320_T	0.838	1.00
290_P	318_E	0.838	1.00
77_F	291_V	0.835	1.00
231_L	254_A	0.833	1.00
273_D	323_M	0.832	1.00
62_I	118_I	0.832	1.00
116_G	306_I	0.828	1.00
276_F	280_I	0.828	1.00
301_K	304_S	0.828	1.00
183_G	218_Y	0.825	1.00
156_L	317_L	0.824	1.00
64_L	82_I	0.822	1.00
157_S	320_T	0.819	1.00
156_L	315_K	0.817	1.00
177_D	212_Y	0.815	1.00
81_T	143_L	0.813	1.00
179_A	240_V	0.812	1.00
324_V	328_V	0.810	1.00
13_V	36_I	0.804	1.00
159_D	193_R	0.803	1.00
299_A	303_L	0.799	1.00
199_S	202_I	0.797	1.00
49_V	52_K	0.796	1.00
61_T	112_M	0.795	1.00
194_K	213_S	0.795	1.00
255_I	268_V	0.793	1.00
245_D	273_D	0.790	1.00
222_S	226_A	0.787	1.00
51_A	54_L	0.786	1.00
110_T	136_K	0.786	1.00
169_Y	322_F	0.783	1.00
31_H	34_K	0.782	1.00
157_S	289_R	0.782	1.00
170_F	269_I	0.781	1.00
227_M	254_A	0.774	1.00
236_P	260_L	0.774	1.00
80_D	292_E	0.772	1.00
182_E	194_K	0.771	1.00
16_T	20_R	0.770	1.00
87_Q	91_E	0.770	1.00
192_Q	196_G	0.766	1.00
231_L	258_K	0.764	1.00
59_S	115_D	0.763	1.00
85_V	95_L	0.763	1.00
132_H	135_E	0.761	1.00
84_G	296_V	0.760	1.00
58_K	115_D	0.760	1.00
181_I	242_C	0.759	1.00
158_N	319_N	0.758	1.00
83_K	86_N	0.758	1.00
201_L	208_I	0.757	1.00
146_D	315_K	0.756	1.00
104_K	107_D	0.752	1.00
253_N	256_F	0.751	1.00
216_G	247_M	0.751	1.00
31_H	35_K	0.751	1.00
84_G	88_A	0.748	1.00
285_S	328_V	0.746	1.00
227_M	230_L	0.745	1.00
17_T	20_R	0.745	1.00
20_R	27_Y	0.744	1.00
180_I	241_F	0.742	1.00
126_D	129_F	0.733	1.00
82_I	97_V	0.731	1.00
270_G	286_T	0.729	1.00
134_R	152_I	0.728	1.00
212_Y	233_L	0.726	1.00
20_R	26_P	0.725	1.00
248_A	270_G	0.717	1.00
165_E	287_V	0.714	1.00
249_I	280_I	0.707	1.00
46_T	111_P	0.705	1.00
67_T	78_F	0.703	1.00
86_N	99_G	0.699	1.00
86_N	95_L	0.694	1.00
21_A	33_K	0.693	1.00
273_D	277_S	0.691	1.00
164_Q	196_G	0.690	1.00
107_D	111_P	0.690	1.00
255_I	262_V	0.689	1.00
63_G	117_I	0.688	1.00
131_Y	134_R	0.688	1.00
253_N	283_R	0.686	1.00
169_Y	285_S	0.685	1.00
216_G	222_S	0.682	1.00
229_R	232_A	0.681	1.00
62_I	299_A	0.681	1.00
96_Y	114_Y	0.680	1.00
142_V	147_I	0.676	1.00
34_K	41_E	0.674	1.00
116_G	141_V	0.674	1.00
241_F	269_I	0.673	1.00
272_D	289_R	0.672	1.00
245_D	248_A	0.672	1.00
214_V	230_L	0.670	1.00
140_L	152_I	0.670	1.00
304_S	308_E	0.669	1.00
133_I	140_L	0.668	1.00
277_S	280_I	0.667	1.00
253_N	257_A	0.666	1.00
58_K	307_S	0.665	1.00
214_V	233_L	0.662	1.00
116_G	298_G	0.660	1.00
134_R	140_L	0.660	1.00
190_S	218_Y	0.658	1.00
118_I	143_L	0.653	1.00
141_V	302_L	0.652	1.00
165_E	169_Y	0.651	1.00
129_F	132_H	0.650	1.00
206_I	210_H	0.649	1.00
194_K	215_K	0.646	1.00
96_Y	112_M	0.645	1.00
110_T	138_I	0.645	1.00
13_V	32_T	0.642	1.00
233_L	237_P	0.639	1.00
178_I	238_T	0.639	1.00
171_I	201_L	0.638	1.00
65_F	105_N	0.638	1.00
170_F	241_F	0.637	1.00
180_I	197_Y	0.636	1.00
252_M	256_F	0.631	1.00
238_T	267_S	0.631	1.00
5_K	55_A	0.630	1.00
80_D	291_V	0.626	1.00
233_L	236_P	0.626	1.00
218_Y	243_S	0.626	1.00
18_V	40_A	0.626	1.00
142_V	152_I	0.623	1.00
223_G	226_A	0.622	1.00
198_L	213_S	0.620	1.00
141_V	305_L	0.620	1.00
144_N	159_D	0.620	1.00
134_R	151_T	0.619	1.00
283_R	325_R	0.618	1.00
117_I	138_I	0.614	1.00
27_Y	32_T	0.614	1.00
244_N	247_M	0.609	1.00
35_K	38_E	0.607	1.00
103_L	129_F	0.607	1.00
183_G	190_S	0.606	1.00
41_E	44_N	0.605	1.00
106_Y	117_I	0.603	1.00
84_G	291_V	0.598	1.00
83_K	292_E	0.598	1.00
227_M	250_G	0.597	1.00
141_V	155_I	0.596	1.00
159_D	192_Q	0.596	1.00
182_E	215_K	0.595	1.00
62_I	306_I	0.594	1.00
144_N	189_S	0.592	1.00
7_I	18_V	0.591	1.00
107_D	110_T	0.589	1.00
46_T	107_D	0.589	1.00
220_M	250_G	0.588	1.00
93_Y	306_I	0.586	1.00
104_K	108_S	0.585	1.00
18_V	21_A	0.585	1.00
164_Q	167_V	0.584	1.00
20_R	28_I	0.579	1.00
77_F	81_T	0.579	1.00
253_N	281_T	0.577	1.00
244_N	272_D	0.576	1.00
249_I	274_I	0.576	1.00
142_V	154_N	0.575	1.00
89_I	303_L	0.574	1.00
81_T	291_V	0.573	1.00
46_T	50_N	0.572	1.00
301_K	305_L	0.567	1.00
62_I	116_G	0.567	1.00
255_I	258_K	0.566	1.00
198_L	210_H	0.566	1.00
308_E	311_T	0.565	1.00
197_Y	208_I	0.562	1.00
110_T	113_R	0.560	1.00
141_V	298_G	0.559	1.00
285_S	322_F	0.559	1.00
280_I	283_R	0.558	1.00
146_D	154_N	0.558	1.00
218_Y	247_M	0.557	1.00
241_F	271_F	0.557	1.00
93_Y	115_D	0.554	1.00
179_A	212_Y	0.554	1.00
253_N	278_Q	0.553	1.00
221_E	224_F	0.553	1.00
178_I	197_Y	0.553	1.00
59_S	94_N	0.553	1.00
242_C	270_G	0.552	1.00
105_N	108_S	0.550	1.00
52_K	56_M	0.549	1.00
287_V	320_T	0.549	1.00
190_S	243_S	0.546	1.00
108_S	111_P	0.545	1.00
166_A	239_A	0.544	1.00
141_V	301_K	0.544	1.00
128_S	131_Y	0.544	1.00
256_F	261_R	0.541	1.00
182_E	213_S	0.541	1.00
109_V	114_Y	0.540	1.00
62_I	93_Y	0.540	1.00
224_F	250_G	0.540	1.00
278_Q	283_R	0.538	1.00
206_I	209_K	0.537	1.00
305_L	308_E	0.537	1.00
83_K	101_D	0.536	1.00
85_V	89_I	0.536	1.00
169_Y	269_I	0.534	1.00
294_I	318_E	0.533	1.00
25_S	28_I	0.531	1.00
89_I	93_Y	0.530	1.00
304_S	314_E	0.530	1.00
226_A	230_L	0.529	1.00
177_D	237_P	0.527	1.00
269_I	328_V	0.527	1.00
18_V	36_I	0.526	1.00
13_V	18_V	0.526	1.00
98_R	108_S	0.525	1.00
125_I	129_F	0.524	1.00
245_D	274_I	0.524	1.00
297_L	304_S	0.524	1.00
251_A	255_I	0.523	1.00
61_T	115_D	0.521	1.00
28_I	33_K	0.521	1.00
88_A	303_L	0.521	1.00
271_F	289_R	0.521	1.00
292_E	295_S	0.520	1.00
155_I	297_L	0.518	1.00
78_F	120_M	0.518	1.00
128_S	132_H	0.517	1.00
132_H	136_K	0.516	1.00
16_T	25_S	0.514	1.00
6_D	10_L	0.514	1.00
260_L	263_P	0.513	1.00
262_V	265_D	0.512	1.00
53_S	56_M	0.511	1.00
80_D	275_G	0.510	1.00
317_L	320_T	0.504	1.00
76_S	246_D	0.504	1.00
224_F	227_M	0.502	1.00
157_S	162_G	0.502	1.00
181_I	226_A	0.502	1.00
237_P	240_V	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	0.8138	100	0.087	Contact Map
2hsgA	1	0.964	100	0.092	Contact Map
2o20A	2	0.8078	100	0.098	Contact Map
1qpzA	2	0.982	100	0.101	Contact Map
4o5aA	2	0.7898	100	0.105	Contact Map
3bilA	2	0.7508	100	0.106	Contact Map
3ctpA	2	0.7778	100	0.107	Contact Map
3e3mA	2	0.7868	100	0.11	Contact Map
3h5tA	2	0.9339	100	0.113	Contact Map
3kjxA	2	0.976	100	0.113	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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