CHBR - ECOLI - GREMLIN Contacts

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CHBR - HTH-type transcriptional regulator ChbR

UniProt:	P17410	Sequences: MMQPVINAPEIATAREQQLFNGKNFHVFIYNKTESISGLHQHDYYEFTLVLTGRYFQEINGKRVLLERGDFVFIPLGSHHQSFYEFGATRILNVGISKRFFEQHYLPLLPYCFVASQVYRTNNAFLTYVETVISSLNFRETGLEEFVEMVTFYVINRLRHYREEQVIDDVPQWLKSTVEKMHDKEQFSESALENMVALSAKSQEYLTRATQRYYGKTPMQIINEIRINFAKKQLEMTNYSVTDIAFEAGYSSPSLFIKTFKKLTSFTPKSYRKKLTEFNQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10143
Length:	280 (237)
Sequences:	34321 (29151)
Seq/√Len:	1893.5

ECOLI - CHBR YQHC YDIP RHAS RHAR ARAC MELR YIDL YPDC RCLR YEAM YBCM FEAR YIJO APPY ENVY GADX ADIY EUTR GADW YDEO MARA SOXS YKGA ROB XYLR
BACSU - YBFI YDEC YISR YFIF BTR YOBQ ADAA YTDP YESS YDEE YESN

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
216_K	224_E	3.280	1.00
231_K	264_T	3.249	1.00
239_Y	247_E	3.143	1.00
182_H	225_I	2.966	1.00
227_I	264_T	2.856	1.00
193_E	203_Q	2.852	1.00
180_K	184_K	2.773	1.00
229_F	232_K	2.657	1.00
184_K	187_F	2.654	1.00
224_E	263_L	2.595	1.00
260_F	271_Y	2.505	1.00
233_Q	247_E	2.436	1.00
230_A	256_F	2.348	1.00
177_T	206_L	2.285	1.00
239_Y	243_D	2.124	1.00
210_T	221_I	2.104	1.00
233_Q	248_A	2.102	1.00
191_A	194_N	2.101	1.00
56_F	63_R	2.054	1.00
266_F	274_K	2.020	1.00
180_K	198_L	1.953	1.00
185_E	225_I	1.942	1.00
233_Q	239_Y	1.901	1.00
56_F	65_L	1.863	1.00
219_M	223_N	1.840	1.00
178_V	214_Y	1.813	1.00
240_S	243_D	1.786	1.00
174_L	214_Y	1.785	1.00
181_M	222_I	1.774	1.00
177_T	199_S	1.762	1.00
253_P	257_I	1.755	1.00
58_E	63_R	1.752	1.00
227_I	263_L	1.721	1.00
259_T	262_K	1.701	1.00
231_K	271_Y	1.686	1.00
205_Y	209_A	1.679	1.00
67_E	70_D	1.657	1.00
192_L	207_T	1.647	1.00
54_R	65_L	1.624	1.00
242_T	253_P	1.620	1.00
229_F	233_Q	1.618	1.00
195_M	218_P	1.617	1.00
179_E	183_D	1.616	1.00
225_I	229_F	1.608	1.00
51_L	92_L	1.596	1.00
232_K	236_M	1.587	1.00
216_K	220_Q	1.577	1.00
266_F	270_S	1.573	1.00
203_Q	207_T	1.534	1.00
52_T	90_R	1.504	1.00
243_D	246_F	1.489	1.00
185_E	229_F	1.481	1.00
58_E	81_Q	1.465	1.00
56_F	83_F	1.464	1.00
206_L	218_P	1.459	1.00
243_D	247_E	1.459	1.00
242_T	246_F	1.445	1.00
205_Y	208_R	1.444	1.00
171_P	213_Y	1.435	1.00
182_H	221_I	1.434	1.00
234_L	241_V	1.432	1.00
178_V	182_H	1.431	1.00
244_I	248_A	1.408	1.00
230_A	248_A	1.405	1.00
201_K	205_Y	1.403	1.00
186_Q	247_E	1.403	1.00
229_F	248_A	1.398	1.00
255_L	259_T	1.395	1.00
250_Y	259_T	1.392	1.00
54_R	67_E	1.371	1.00
204_E	208_R	1.366	1.00
218_P	222_I	1.361	1.00
181_M	225_I	1.340	1.00
269_K	273_K	1.336	1.00
126_L	130_E	1.334	1.00
45_Y	76_L	1.332	1.00
217_T	220_Q	1.328	1.00
156_N	160_H	1.326	1.00
194_N	198_L	1.323	1.00
254_S	257_I	1.319	1.00
225_I	228_N	1.299	1.00
60_N	78_S	1.293	1.00
177_T	195_M	1.293	1.00
224_E	228_N	1.292	1.00
207_T	218_P	1.277	1.00
223_N	259_T	1.276	1.00
193_E	197_A	1.247	1.00
173_W	201_K	1.212	1.00
201_K	206_L	1.207	1.00
187_F	194_N	1.204	1.00
51_L	90_R	1.197	1.00
257_I	267_T	1.195	1.00
231_K	235_E	1.194	1.00
75_P	78_S	1.184	1.00
202_S	205_Y	1.178	1.00
237_T	272_R	1.170	1.00
180_K	190_S	1.165	1.00
52_T	68_R	1.150	1.00
209_A	212_R	1.133	1.00
258_K	262_K	1.124	1.00
257_I	269_K	1.119	1.00
186_Q	229_F	1.115	1.00
196_V	203_Q	1.115	1.00
172_Q	176_S	1.098	1.00
239_Y	244_I	1.096	1.00
127_T	130_E	1.094	1.00
228_N	231_K	1.091	1.00
127_T	131_T	1.083	1.00
267_T	270_S	1.081	1.00
152_F	156_N	1.068	1.00
209_A	213_Y	1.063	1.00
192_L	218_P	1.049	1.00
188_S	251_S	1.046	1.00
39_L	79_H	1.037	1.00
270_S	273_K	1.036	1.00
269_K	272_R	1.023	1.00
130_E	134_S	1.018	1.00
175_K	179_E	1.014	1.00
173_W	209_A	1.008	1.00
223_N	262_K	1.000	1.00
42_H	80_H	0.998	1.00
233_Q	244_I	0.997	1.00
151_T	157_R	0.996	1.00
178_V	221_I	0.996	1.00
220_Q	223_N	0.989	1.00
252_S	258_K	0.982	1.00
180_K	199_S	0.979	1.00
40_H	80_H	0.978	1.00
149_M	152_F	0.977	1.00
156_N	159_R	0.974	1.00
241_V	244_I	0.969	1.00
259_T	263_L	0.968	1.00
257_I	261_K	0.962	1.00
55_Y	89_T	0.959	1.00
264_T	271_Y	0.956	1.00
194_N	197_A	0.953	1.00
192_L	203_Q	0.952	1.00
139_R	143_L	0.950	1.00
180_K	195_M	0.948	1.00
173_W	199_S	0.947	1.00
181_M	218_P	0.943	1.00
176_S	198_L	0.938	1.00
42_H	46_E	0.937	1.00
153_Y	156_N	0.933	1.00
195_M	198_L	0.930	1.00
190_S	195_M	0.928	1.00
204_E	207_T	0.919	1.00
220_Q	224_E	0.909	1.00
176_S	179_E	0.904	1.00
199_S	206_L	0.903	1.00
124_A	127_T	0.903	1.00
115_A	118_V	0.903	1.00
46_E	80_H	0.902	1.00
220_Q	263_L	0.893	1.00
231_K	260_F	0.889	1.00
58_E	83_F	0.889	1.00
50_V	55_Y	0.885	1.00
174_L	177_T	0.878	1.00
144_E	148_E	0.871	1.00
223_N	263_L	0.867	1.00
227_I	259_T	0.862	1.00
153_Y	159_R	0.861	1.00
39_L	81_Q	0.858	1.00
174_L	209_A	0.846	1.00
145_E	149_M	0.844	1.00
270_S	274_K	0.843	1.00
255_L	258_K	0.842	1.00
210_T	214_Y	0.841	1.00
261_K	267_T	0.839	1.00
48_T	93_N	0.837	1.00
122_N	126_L	0.836	1.00
46_E	95_G	0.824	1.00
59_I	62_K	0.819	1.00
188_S	194_N	0.818	1.00
184_K	198_L	0.818	1.00
176_S	199_S	0.817	1.00
146_F	149_M	0.817	1.00
175_K	178_V	0.813	1.00
201_K	209_A	0.813	1.00
185_E	222_I	0.812	1.00
153_Y	157_R	0.810	1.00
234_L	244_I	0.809	1.00
45_Y	73_F	0.804	1.00
219_M	222_I	0.803	1.00
55_Y	66_L	0.803	1.00
210_T	218_P	0.796	1.00
89_T	93_N	0.794	1.00
237_T	244_I	0.793	1.00
123_N	127_T	0.793	1.00
226_R	248_A	0.790	1.00
98_K	102_E	0.789	1.00
185_E	248_A	0.788	1.00
174_L	178_V	0.788	1.00
246_F	251_S	0.785	1.00
124_A	131_T	0.776	1.00
54_R	85_E	0.774	1.00
234_L	272_R	0.772	1.00
208_R	212_R	0.769	1.00
187_F	190_S	0.769	1.00
221_I	225_I	0.768	1.00
207_T	211_Q	0.767	1.00
227_I	256_F	0.766	1.00
245_A	253_P	0.763	1.00
219_M	255_L	0.763	1.00
266_F	271_Y	0.760	1.00
174_L	213_Y	0.754	1.00
58_E	61_G	0.753	1.00
235_E	271_Y	0.752	1.00
178_V	210_T	0.750	1.00
184_K	194_N	0.749	1.00
207_T	219_M	0.749	1.00
177_T	180_K	0.748	1.00
145_E	148_E	0.745	1.00
49_L	71_F	0.745	1.00
148_E	151_T	0.741	1.00
155_I	159_R	0.737	1.00
170_V	212_R	0.733	1.00
230_A	233_Q	0.728	1.00
261_K	270_S	0.727	1.00
115_A	119_Y	0.726	1.00
157_R	161_Y	0.726	1.00
55_Y	65_L	0.720	1.00
121_T	124_A	0.710	1.00
185_E	226_R	0.708	1.00
116_S	119_Y	0.707	1.00
240_S	244_I	0.706	1.00
100_F	103_Q	0.706	1.00
153_Y	158_L	0.705	1.00
131_T	135_S	0.703	1.00
173_W	176_S	0.699	1.00
128_Y	131_T	0.697	1.00
171_P	209_A	0.697	1.00
256_F	260_F	0.695	1.00
181_M	221_I	0.693	1.00
57_Q	72_V	0.693	1.00
66_L	72_V	0.692	1.00
150_V	153_Y	0.692	1.00
195_M	206_L	0.688	1.00
133_I	137_N	0.681	1.00
251_S	255_L	0.681	1.00
188_S	191_A	0.675	1.00
157_R	160_H	0.674	1.00
253_P	256_F	0.672	1.00
177_T	218_P	0.672	1.00
134_S	138_F	0.672	1.00
207_T	217_T	0.671	1.00
44_Y	95_G	0.669	1.00
123_N	126_L	0.668	1.00
131_T	134_S	0.667	1.00
50_V	53_G	0.665	1.00
216_K	221_I	0.665	1.00
56_F	85_E	0.663	1.00
41_Q	79_H	0.660	1.00
177_T	210_T	0.660	1.00
170_V	173_W	0.657	1.00
252_S	255_L	0.652	1.00
48_T	74_I	0.648	1.00
211_Q	217_T	0.646	1.00
177_T	181_M	0.645	1.00
185_E	190_S	0.641	1.00
230_A	244_I	0.641	1.00
158_L	161_Y	0.641	1.00
228_N	263_L	0.640	1.00
113_F	117_Q	0.640	1.00
195_M	199_S	0.639	1.00
113_F	116_S	0.637	1.00
50_V	91_I	0.637	1.00
171_P	175_K	0.636	1.00
52_T	88_A	0.635	1.00
48_T	91_I	0.634	1.00
254_S	267_T	0.632	1.00
244_I	272_R	0.629	1.00
260_F	266_F	0.628	1.00
227_I	250_Y	0.623	1.00
190_S	194_N	0.622	1.00
182_H	229_F	0.620	1.00
155_I	158_L	0.619	1.00
180_K	194_N	0.617	1.00
74_I	80_H	0.615	1.00
196_V	199_S	0.613	1.00
151_T	155_I	0.613	1.00
124_A	128_Y	0.612	1.00
231_K	266_F	0.607	1.00
197_A	200_A	0.603	1.00
170_V	213_Y	0.595	1.00
50_V	66_L	0.595	1.00
127_T	134_S	0.594	1.00
60_N	79_H	0.593	1.00
114_V	119_Y	0.592	1.00
48_T	72_V	0.591	1.00
228_N	264_T	0.590	1.00
47_F	73_F	0.588	1.00
238_N	244_I	0.587	1.00
254_S	258_K	0.586	1.00
150_V	155_I	0.581	1.00
172_Q	213_Y	0.579	1.00
233_Q	236_M	0.576	1.00
256_F	268_P	0.575	1.00
236_M	239_Y	0.575	1.00
63_R	83_F	0.575	1.00
168_D	171_P	0.572	1.00
223_N	255_L	0.572	1.00
91_I	94_V	0.572	1.00
175_K	213_Y	0.566	1.00
135_S	139_R	0.565	1.00
214_Y	221_I	0.563	1.00
143_L	147_V	0.562	1.00
128_Y	132_V	0.561	1.00
46_E	74_I	0.560	1.00
222_I	226_R	0.556	1.00
142_G	145_E	0.555	1.00
223_N	227_I	0.552	1.00
49_L	129_V	0.552	1.00
45_Y	98_K	0.550	1.00
124_A	156_N	0.549	1.00
47_F	71_F	0.547	1.00
132_V	135_S	0.546	1.00
149_M	156_N	0.542	1.00
48_T	57_Q	0.538	1.00
177_T	198_L	0.537	1.00
232_K	235_E	0.537	1.00
192_L	219_M	0.537	1.00
45_Y	48_T	0.533	1.00
156_N	161_Y	0.530	1.00
55_Y	82_S	0.530	1.00
188_S	226_R	0.528	1.00
252_S	262_K	0.528	1.00
143_L	146_F	0.528	1.00
49_L	122_N	0.527	1.00
245_A	250_Y	0.524	1.00
211_Q	214_Y	0.523	1.00
241_V	269_K	0.520	1.00
220_Q	262_K	0.519	1.00
105_Y	108_L	0.519	1.00
228_N	232_K	0.519	1.00
229_F	247_E	0.517	1.00
54_R	86_F	0.516	1.00
192_L	204_E	0.515	1.00
199_S	203_Q	0.514	1.00
92_L	95_G	0.514	1.00
136_L	139_R	0.513	1.00
50_V	89_T	0.513	1.00
130_E	133_I	0.513	1.00
113_F	118_V	0.511	1.00
177_T	209_A	0.509	1.00
153_Y	160_H	0.508	1.00
190_S	226_R	0.508	1.00
107_P	111_Y	0.507	1.00
98_K	101_F	0.507	1.00
109_L	112_C	0.504	1.00
223_N	250_Y	0.504	1.00
174_L	206_L	0.503	1.00
106_L	110_P	0.503	1.00
93_N	96_I	0.502	1.00
259_T	264_T	0.502	1.00
181_M	190_S	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
3gbgA	1	0.8893	100	0.255	Contact Map
1bl0A	1	0.3929	100	0.491	Contact Map
3oouA	1	0.375	100	0.493	Contact Map
3oioA	1	0.4	100	0.495	Contact Map
3mn2A	1	0.3786	100	0.498	Contact Map
3w6vA	1	0.3893	100	0.502	Contact Map
3mklA	1	0.3964	100	0.503	Contact Map
2k9sA	1	0.3821	100	0.504	Contact Map
3lsgA	2	0.3643	99.9	0.513	Contact Map
1d5yA	1	0.3929	99.9	0.518	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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