TRER - ECOLI - GREMLIN Contacts

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TRER - HTH-type transcriptional regulator TreR

UniProt:	P36673	Sequences: MQNRLTIKDIARLSGVGKSTVSRVLNNESGVSQLTRERVEAVMNQHGFSPSRSARAMRGQSDKVVAIIVTRLDSLSENLAVQTMLPAFYEQGYDPIMMESQFSPQLVAEHLGVLKRRNIDGVVLFGFTGITEEMLAHWQSSLVLLARDAKGFASVCYDDEGAIKILMQRLYDQGHRNISYLGVPHSDVTTGKRRHEAYLAFCKAHKLHPVAALPGLAMKQGYENVAKVITPETTALLCATDTLALGASKYLQEQRIDTLQLASVGNTPLMKFLHPEIVTVDPGYAEAGRQAACQLIAQVTGRSEPQQIIIPATLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12202
Length:	315 (301)
Sequences:	35891 (25728)
Seq/√Len:	1482.9

ECOLI - TRER LACI CYTR MALI GNTR YCJW GALS IDNR GALR ASCG CRA PURR RBSR EBGR TORT RBSB ALSB XYLF LSRB YTFQ YPHF ARAF DGAL XYLR
BACSU - KDGR CCPA RBSR DEGA NTDR YKVZ YVDE EXUR MSMR 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_E	200_A	3.347	1.00
13_L	45_Q	3.078	1.00
175_H	234_T	3.059	1.00
166_L	262_A	2.646	1.00
195_H	199_L	2.617	1.00
121_G	295_L	2.614	1.00
175_H	260_Q	2.517	1.00
153_A	298_Q	2.399	1.00
266_N	281_D	2.390	1.00
164_K	204_A	2.312	1.00
33_Q	37_E	2.281	1.00
41_A	45_Q	2.225	1.00
222_Y	253_E	2.209	1.00
226_A	254_Q	2.204	1.00
87_A	90_E	2.194	1.00
87_A	293_C	2.177	1.00
37_E	41_A	2.149	1.00
168_Q	201_F	2.128	1.00
171_Y	205_H	2.110	1.00
161_G	165_I	2.109	1.00
164_K	201_F	2.079	1.00
226_A	250_Y	2.053	1.00
164_K	200_A	2.047	1.00
290_Q	293_C	2.025	1.00
24_V	39_V	2.004	1.00
88_F	292_A	1.989	1.00
160_E	196_E	1.934	1.00
36_R	40_E	1.909	1.00
87_A	289_R	1.901	1.00
162_A	264_V	1.899	1.00
8_K	18_K	1.899	1.00
170_L	235_A	1.872	1.00
163_I	167_M	1.869	1.00
25_L	43_M	1.866	1.00
83_T	288_G	1.851	1.00
230_T	254_Q	1.843	1.00
168_Q	172_D	1.838	1.00
251_L	259_L	1.816	1.00
167_M	198_Y	1.814	1.00
297_A	302_R	1.811	1.00
163_I	237_L	1.785	1.00
168_Q	205_H	1.781	1.00
169_R	173_Q	1.781	1.00
13_L	42_V	1.770	1.00
86_P	285_A	1.766	1.00
221_G	246_G	1.736	1.00
14_S	42_V	1.733	1.00
164_K	168_Q	1.713	1.00
179_S	233_T	1.711	1.00
225_V	247_A	1.665	1.00
180_Y	239_A	1.660	1.00
87_A	91_Q	1.655	1.00
83_T	285_A	1.652	1.00
238_C	247_A	1.648	1.00
66_A	119_I	1.643	1.00
222_Y	250_Y	1.643	1.00
283_G	286_E	1.637	1.00
250_Y	254_Q	1.617	1.00
145_L	291_A	1.590	1.00
161_G	164_K	1.558	1.00
91_Q	296_I	1.544	1.00
177_N	232_E	1.528	1.00
169_R	172_D	1.519	1.00
40_E	44_N	1.516	1.00
250_Y	253_E	1.497	1.00
171_Y	201_F	1.494	1.00
286_E	290_Q	1.490	1.00
252_Q	274_H	1.487	1.00
196_E	200_A	1.487	1.00
24_V	43_M	1.457	1.00
262_A	278_V	1.456	1.00
63_K	120_D	1.438	1.00
10_I	42_V	1.429	1.00
40_E	43_M	1.427	1.00
286_E	289_R	1.412	1.00
199_L	203_K	1.412	1.00
193_R	196_E	1.411	1.00
201_F	204_A	1.402	1.00
158_D	161_G	1.392	1.00
133_E	137_H	1.375	1.00
87_A	292_A	1.372	1.00
177_N	234_T	1.364	1.00
222_Y	226_A	1.363	1.00
251_L	256_I	1.359	1.00
296_I	300_T	1.359	1.00
177_N	210_V	1.346	1.00
215_G	220_Q	1.344	1.00
8_K	12_R	1.339	1.00
222_Y	249_K	1.335	1.00
167_M	171_Y	1.326	1.00
13_L	46_H	1.323	1.00
226_A	253_E	1.322	1.00
167_M	201_F	1.321	1.00
179_S	228_V	1.311	1.00
9_D	12_R	1.311	1.00
38_R	42_V	1.298	1.00
225_V	236_L	1.294	1.00
226_A	230_T	1.286	1.00
42_V	45_Q	1.280	1.00
33_Q	36_R	1.279	1.00
123_V	291_A	1.261	1.00
63_K	93_Y	1.261	1.00
165_I	168_Q	1.256	1.00
167_M	197_A	1.252	1.00
225_V	251_L	1.250	1.00
65_V	88_F	1.248	1.00
293_C	297_A	1.246	1.00
160_E	164_K	1.246	1.00
32_S	35_T	1.235	1.00
163_I	197_A	1.231	1.00
23_R	28_E	1.228	1.00
197_A	201_F	1.224	1.00
98_M	110_H	1.220	1.00
248_S	261_L	1.215	1.00
176_R	234_T	1.213	1.00
7_I	18_K	1.209	1.00
42_V	46_H	1.209	1.00
168_Q	204_A	1.208	1.00
88_F	95_P	1.194	1.00
84_M	292_A	1.194	1.00
169_R	278_V	1.194	1.00
35_T	38_R	1.189	1.00
98_M	114_L	1.188	1.00
10_I	14_S	1.180	1.00
285_A	289_R	1.178	1.00
175_H	235_A	1.178	1.00
66_A	114_L	1.172	1.00
160_E	193_R	1.162	1.00
201_F	205_H	1.157	1.00
198_Y	202_C	1.155	1.00
10_I	46_H	1.150	1.00
84_M	123_V	1.148	1.00
67_I	84_M	1.136	1.00
160_E	197_A	1.130	1.00
64_V	94_D	1.125	1.00
181_L	247_A	1.124	1.00
171_Y	207_L	1.120	1.00
91_Q	293_C	1.116	1.00
290_Q	294_Q	1.109	1.00
41_A	44_N	1.107	1.00
241_D	279_T	1.107	1.00
24_V	31_V	1.105	1.00
37_E	40_E	1.101	1.00
178_I	202_C	1.100	1.00
224_N	227_K	1.097	1.00
85_L	89_Y	1.096	1.00
219_K	223_E	1.093	1.00
64_V	96_I	1.093	1.00
180_Y	195_H	1.089	1.00
166_L	237_L	1.089	1.00
217_A	220_Q	1.086	1.00
200_A	204_A	1.084	1.00
67_I	95_P	1.082	1.00
246_G	250_Y	1.080	1.00
89_Y	106_L	1.071	1.00
196_E	199_L	1.063	1.00
177_N	231_P	1.063	1.00
27_N	36_R	1.059	1.00
236_L	247_A	1.045	1.00
7_I	21_V	1.043	1.00
288_G	292_A	1.041	1.00
93_Y	296_I	1.040	1.00
248_S	273_L	1.037	1.00
153_A	294_Q	1.030	1.00
289_R	293_C	1.029	1.00
108_A	112_G	1.026	1.00
198_Y	237_L	1.014	1.00
91_Q	300_T	1.007	1.00
238_C	243_L	1.006	1.00
252_Q	276_E	1.003	1.00
51_S	57_M	1.002	1.00
192_K	196_E	1.002	1.00
53_S	56_A	1.000	1.00
223_E	227_K	0.998	1.00
178_I	235_A	0.997	1.00
189_T	193_R	0.995	1.00
112_G	134_M	0.994	1.00
43_M	46_H	0.991	1.00
241_D	263_S	0.990	1.00
173_Q	260_Q	0.989	1.00
295_L	299_V	0.987	1.00
172_D	205_H	0.982	1.00
238_C	244_A	0.979	1.00
220_Q	223_E	0.977	1.00
218_M	249_K	0.960	1.00
176_R	207_L	0.956	1.00
106_L	109_E	0.950	1.00
14_S	21_V	0.945	1.00
225_V	229_I	0.941	1.00
199_L	209_P	0.940	1.00
112_G	116_R	0.936	1.00
221_G	225_V	0.935	1.00
90_E	289_R	0.934	1.00
166_L	280_V	0.933	1.00
157_Y	283_G	0.931	1.00
123_V	295_L	0.919	1.00
171_Y	176_R	0.917	1.00
82_Q	86_P	0.916	1.00
167_M	202_C	0.914	1.00
51_S	54_A	0.914	1.00
81_V	85_L	0.910	1.00
236_L	259_L	0.907	1.00
27_N	40_E	0.903	1.00
272_F	275_P	0.901	1.00
155_V	294_Q	0.894	1.00
202_C	207_L	0.889	1.00
65_V	123_V	0.886	1.00
50_P	55_R	0.884	1.00
54_A	57_M	0.883	1.00
177_N	208_H	0.881	1.00
256_I	259_L	0.880	1.00
223_E	226_A	0.880	1.00
294_Q	297_A	0.876	1.00
86_P	289_R	0.876	1.00
273_L	276_E	0.874	1.00
103_S	106_L	0.870	1.00
182_G	195_H	0.863	1.00
266_N	270_M	0.859	1.00
24_V	40_E	0.857	1.00
229_I	250_Y	0.854	1.00
84_M	288_G	0.848	1.00
232_E	256_I	0.847	1.00
76_S	284_Y	0.840	1.00
220_Q	224_N	0.839	1.00
67_I	81_V	0.837	1.00
80_A	145_L	0.835	1.00
6_T	9_D	0.833	1.00
202_C	209_P	0.830	1.00
241_D	266_N	0.824	1.00
34_L	37_E	0.822	1.00
200_A	203_K	0.822	1.00
251_L	261_L	0.817	1.00
225_V	228_V	0.816	1.00
263_S	279_T	0.813	1.00
157_Y	282_P	0.809	1.00
16_V	39_V	0.808	1.00
179_S	236_L	0.808	1.00
183_V	216_L	0.808	1.00
170_L	262_A	0.806	1.00
83_T	87_A	0.805	1.00
52_R	55_R	0.800	1.00
134_M	137_H	0.797	1.00
292_A	296_I	0.797	1.00
225_V	250_Y	0.796	1.00
121_G	299_V	0.795	1.00
271_K	276_E	0.795	1.00
86_P	90_E	0.795	1.00
81_V	97_M	0.789	1.00
62_D	120_D	0.788	1.00
19_S	23_R	0.784	1.00
181_L	238_C	0.780	1.00
214_P	243_L	0.779	1.00
159_D	194_R	0.778	1.00
213_L	227_K	0.775	1.00
79_L	285_A	0.775	1.00
83_T	289_R	0.772	1.00
193_R	197_A	0.772	1.00
154_S	307_Q	0.771	1.00
20_T	23_R	0.770	1.00
64_V	117_R	0.768	1.00
84_M	95_P	0.766	1.00
61_S	120_D	0.765	1.00
34_L	38_R	0.763	1.00
115_K	138_W	0.762	1.00
133_E	136_A	0.760	1.00
165_I	169_R	0.760	1.00
85_L	95_P	0.759	1.00
249_K	252_Q	0.752	1.00
186_S	192_K	0.751	1.00
135_L	142_L	0.751	1.00
70_T	77_E	0.751	1.00
96_I	119_I	0.749	1.00
297_A	301_G	0.745	1.00
109_E	112_G	0.745	1.00
180_Y	237_L	0.741	1.00
229_I	254_Q	0.740	1.00
165_I	280_V	0.736	1.00
23_R	29_S	0.734	1.00
244_A	263_S	0.733	1.00
82_Q	85_L	0.729	1.00
214_P	220_Q	0.724	1.00
49_S	116_R	0.721	1.00
23_R	30_G	0.714	1.00
265_G	282_P	0.712	1.00
136_A	142_L	0.710	1.00
144_L	149_A	0.709	1.00
65_V	292_A	0.707	1.00
24_V	36_R	0.704	1.00
234_T	260_Q	0.703	1.00
207_L	210_V	0.703	1.00
106_L	110_H	0.702	1.00
249_K	253_E	0.702	1.00
249_K	276_E	0.702	1.00
142_L	152_F	0.698	1.00
101_Q	106_L	0.698	1.00
237_L	262_A	0.697	1.00
66_A	122_V	0.697	1.00
123_V	145_L	0.696	1.00
68_I	110_H	0.693	1.00
61_S	300_T	0.692	1.00
156_C	307_Q	0.690	1.00
164_K	197_A	0.689	1.00
221_G	224_N	0.687	1.00
241_D	244_A	0.686	1.00
171_Y	202_C	0.684	1.00
148_D	307_Q	0.682	1.00
178_I	234_T	0.681	1.00
105_Q	109_E	0.675	1.00
85_L	99_E	0.674	1.00
245_L	273_L	0.673	1.00
121_G	143_V	0.673	1.00
37_E	44_N	0.668	1.00
49_S	112_G	0.662	1.00
195_H	211_A	0.661	1.00
227_K	230_T	0.661	1.00
96_I	117_R	0.661	1.00
191_G	216_L	0.661	1.00
111_L	122_V	0.660	1.00
180_Y	198_Y	0.660	1.00
79_L	284_Y	0.660	1.00
16_V	35_T	0.659	1.00
143_V	298_Q	0.659	1.00
136_A	152_F	0.657	1.00
248_S	252_Q	0.657	1.00
198_Y	209_P	0.657	1.00
115_K	140_S	0.647	1.00
30_G	35_T	0.645	1.00
143_V	295_L	0.644	1.00
185_H	213_L	0.642	1.00
10_I	21_V	0.639	1.00
153_A	306_Q	0.638	1.00
178_I	198_Y	0.636	1.00
44_N	47_G	0.632	1.00
144_L	152_F	0.631	1.00
135_L	139_Q	0.631	1.00
143_V	155_V	0.630	1.00
146_A	190_T	0.629	1.00
216_L	239_A	0.623	1.00
148_D	154_S	0.622	1.00
245_L	269_L	0.621	1.00
38_R	41_A	0.621	1.00
82_Q	285_A	0.616	1.00
121_G	291_A	0.616	1.00
164_K	167_M	0.616	1.00
170_L	237_L	0.615	1.00
249_K	274_H	0.615	1.00
122_V	140_S	0.614	1.00
183_V	191_G	0.614	1.00
8_K	58_R	0.611	1.00
240_T	265_G	0.611	1.00
240_T	243_L	0.609	1.00
270_M	277_I	0.607	1.00
83_T	284_Y	0.605	1.00
104_P	108_A	0.604	1.00
21_V	43_M	0.601	1.00
251_L	254_Q	0.600	1.00
74_S	242_T	0.597	1.00
65_V	121_G	0.597	1.00
159_D	193_R	0.595	1.00
88_F	93_Y	0.594	1.00
65_V	93_Y	0.594	1.00
93_Y	299_V	0.593	1.00
98_M	113_V	0.592	1.00
270_M	279_T	0.591	1.00
80_A	284_Y	0.587	1.00
169_R	262_A	0.586	1.00
218_M	269_L	0.586	1.00
65_V	299_V	0.585	1.00
294_Q	298_Q	0.584	1.00
191_G	239_A	0.583	1.00
62_D	94_D	0.583	1.00
146_A	159_D	0.582	1.00
177_N	233_T	0.582	1.00
49_S	53_S	0.581	1.00
195_H	213_L	0.578	1.00
155_V	290_Q	0.575	1.00
225_V	246_G	0.573	1.00
219_K	222_Y	0.573	1.00
23_R	31_V	0.573	1.00
245_L	267_T	0.572	1.00
93_Y	120_D	0.571	1.00
76_S	80_A	0.570	1.00
212_A	228_V	0.569	1.00
143_V	291_A	0.569	1.00
21_V	24_V	0.568	1.00
222_Y	225_V	0.568	1.00
143_V	294_Q	0.564	1.00
237_L	264_V	0.562	1.00
272_F	276_E	0.556	1.00
218_M	246_G	0.555	1.00
181_L	224_N	0.555	1.00
64_V	120_D	0.554	1.00
297_A	306_Q	0.554	1.00
166_L	235_A	0.552	1.00
134_M	138_W	0.551	1.00
84_M	88_F	0.548	1.00
290_Q	297_A	0.547	1.00
31_V	36_R	0.546	1.00
285_A	288_G	0.546	1.00
144_L	154_S	0.545	1.00
233_T	236_L	0.544	1.00
159_D	190_T	0.543	1.00
28_E	31_V	0.542	1.00
247_A	251_L	0.541	1.00
16_V	21_V	0.540	1.00
224_N	228_V	0.540	1.00
157_Y	162_A	0.539	1.00
114_L	119_I	0.539	1.00
112_G	115_K	0.539	1.00
264_V	282_P	0.538	1.00
252_Q	275_P	0.537	1.00
82_Q	101_Q	0.535	1.00
249_K	271_K	0.531	1.00
55_R	59_G	0.531	1.00
167_M	205_H	0.529	1.00
182_G	213_L	0.529	1.00
19_S	28_E	0.528	1.00
119_I	122_V	0.526	1.00
87_A	296_I	0.525	1.00
27_N	30_G	0.525	1.00
214_P	221_G	0.525	1.00
14_S	24_V	0.524	1.00
168_Q	171_Y	0.524	1.00
298_Q	301_G	0.523	1.00
21_V	39_V	0.520	1.00
9_D	13_L	0.520	1.00
160_E	163_I	0.518	1.00
36_R	39_V	0.518	1.00
222_Y	246_G	0.518	1.00
113_V	116_R	0.518	1.00
216_L	243_L	0.516	1.00
74_S	77_E	0.516	1.00
75_L	242_T	0.515	1.00
238_C	263_S	0.515	1.00
232_E	258_T	0.515	1.00
271_K	275_P	0.515	1.00
229_I	251_L	0.514	1.00
77_E	125_F	0.511	1.00
233_T	256_I	0.511	1.00
109_E	113_V	0.509	1.00
156_C	159_D	0.507	1.00
73_D	79_L	0.507	1.00
62_D	93_Y	0.506	1.00
88_F	296_I	0.506	1.00
212_A	224_N	0.505	1.00
253_E	274_H	0.505	1.00
235_A	260_Q	0.503	1.00
267_T	270_M	0.503	1.00
56_A	59_G	0.502	1.00
182_G	239_A	0.501	1.00
133_E	138_W	0.501	1.00
29_S	36_R	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
3bilA	2	0.7619	100	0.088	Contact Map
2o20A	2	0.819	100	0.096	Contact Map
3dbiA	2	0.8095	100	0.097	Contact Map
4o5aA	2	0.7968	100	0.103	Contact Map
3jvdA	2	0.7841	100	0.107	Contact Map
3ctpA	2	0.7968	100	0.109	Contact Map
1qpzA	2	0.9841	100	0.112	Contact Map
3e3mA	2	0.7873	100	0.113	Contact Map
2hsgA	1	0.9778	100	0.115	Contact Map
3h5oA	2	0.7968	100	0.116	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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