RHAR - ECOLI - GREMLIN Contacts

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RHAR - HTH-type transcriptional activator RhaR

UniProt:	P09378	Sequences: MAHQLKLLKDDFFASDQQAVAVADRYPQDVFAEHTHDFCELVIVWRGNGLHVLNDRPYRITRGDLFYIHADDKHSYASVNDLVLQNIIYCPERLKLNLDWQGAIPGFNASAGQPHWRLGSMGMAQARQVIGQLEHESSQHVPFANEMAELLFGQLVMLLNRHRYTSDSLPPTSSETLLDKLITRLAASLKSPFALDKFCDEASCSERVLRQQFRQQTGMTINQYLRQVRVCHAQYLLQHSRLLISDISTECGFEDSNYFSVVFTRETGMTPSQWRHLNSQKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10842
Length:	282 (240)
Sequences:	35067 (29677)
Seq/√Len:	1915.6

ECOLI - RHAR RHAS MELR YPDC YQHC ARAC YDIP CHBR YIDL YEAM RCLR YIJO YBCM ENVY FEAR GADX ADIY EUTR GADW APPY YDEO MARA SOXS ROB YKGA XYLR
BACSU - YDEC YISR YFIF YBFI 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
219_M	227_Q	3.213	1.00
234_Q	267_T	3.212	1.00
186_A	228_V	3.036	1.00
230_V	267_T	3.032	1.00
242_L	250_E	2.986	1.00
232_H	235_Y	2.905	1.00
196_D	206_E	2.815	1.00
184_R	188_S	2.781	1.00
227_Q	266_E	2.627	1.00
188_S	191_S	2.616	1.00
263_F	274_W	2.441	1.00
233_A	259_F	2.292	1.00
236_L	250_E	2.276	1.00
213_F	224_Y	2.186	1.00
181_L	209_L	2.174	1.00
194_A	197_K	2.075	1.00
236_L	251_C	2.039	1.00
242_L	246_D	2.013	1.00
269_M	277_L	1.974	1.00
189_L	228_V	1.946	1.00
50_L	57_P	1.930	1.00
185_L	225_L	1.883	1.00
184_R	201_E	1.861	1.00
230_V	266_E	1.837	1.00
236_L	242_L	1.820	1.00
222_N	226_R	1.803	1.00
178_L	217_T	1.775	1.00
181_L	202_A	1.771	1.00
50_L	59_R	1.768	1.00
182_I	217_T	1.752	1.00
243_L	246_D	1.748	1.00
256_S	260_S	1.746	1.00
183_T	187_A	1.719	1.00
198_F	221_I	1.700	1.00
46_R	83_V	1.660	1.00
52_V	57_P	1.653	1.00
235_Y	239_H	1.651	1.00
195_L	210_R	1.621	1.00
151_L	154_Q	1.620	1.00
208_V	212_Q	1.610	1.00
262_V	265_R	1.602	1.00
232_H	236_L	1.594	1.00
234_Q	274_W	1.586	1.00
48_N	59_R	1.574	1.00
219_M	223_Q	1.569	1.00
127_R	131_G	1.559	1.00
184_R	193_F	1.541	1.00
258_Y	262_V	1.539	1.00
221_I	225_L	1.536	1.00
228_V	232_H	1.535	1.00
209_L	221_I	1.531	1.00
237_L	244_I	1.530	1.00
61_T	64_D	1.510	1.00
245_S	256_S	1.503	1.00
186_A	224_Y	1.498	1.00
175_E	216_Q	1.473	1.00
208_V	211_Q	1.470	1.00
206_E	210_R	1.470	1.00
45_W	85_Q	1.463	1.00
246_D	250_E	1.461	1.00
39_C	70_A	1.449	1.00
48_N	61_T	1.448	1.00
246_D	249_T	1.441	1.00
245_S	249_T	1.440	1.00
269_M	273_Q	1.438	1.00
189_L	232_H	1.433	1.00
182_I	186_A	1.419	1.00
190_K	250_E	1.415	1.00
253_F	262_V	1.413	1.00
204_C	208_V	1.407	1.00
233_A	251_C	1.407	1.00
52_V	75_S	1.403	1.00
272_S	276_H	1.394	1.00
247_I	251_C	1.376	1.00
185_L	228_V	1.353	1.00
220_T	223_Q	1.350	1.00
232_H	251_C	1.347	1.00
150_L	154_Q	1.341	1.00
197_K	201_E	1.337	1.00
210_R	221_I	1.335	1.00
196_D	200_D	1.333	1.00
207_R	211_Q	1.323	1.00
181_L	198_F	1.320	1.00
227_Q	231_C	1.314	1.00
191_S	197_K	1.291	1.00
150_L	157_M	1.286	1.00
54_N	72_D	1.284	1.00
257_N	260_S	1.282	1.00
226_R	262_V	1.263	1.00
154_Q	158_L	1.256	1.00
260_S	270_T	1.252	1.00
69_H	72_D	1.242	1.00
260_S	272_S	1.218	1.00
240_S	275_R	1.215	1.00
228_V	231_C	1.213	1.00
150_L	153_G	1.211	1.00
234_Q	238_Q	1.205	1.00
205_S	208_V	1.202	1.00
204_C	209_L	1.200	1.00
177_L	204_C	1.185	1.00
46_R	62_R	1.167	1.00
140_H	144_A	1.151	1.00
261_V	265_R	1.144	1.00
40_E	74_H	1.119	1.00
36_H	74_H	1.118	1.00
193_F	198_F	1.108	1.00
242_L	247_I	1.106	1.00
192_P	254_E	1.103	1.00
128_Q	132_Q	1.103	1.00
231_C	234_Q	1.098	1.00
190_K	232_H	1.091	1.00
184_R	202_A	1.088	1.00
34_H	74_H	1.084	1.00
149_E	153_G	1.080	1.00
195_L	221_I	1.076	1.00
128_Q	131_G	1.069	1.00
273_Q	276_H	1.066	1.00
45_W	83_V	1.063	1.00
179_D	183_T	1.062	1.00
270_T	273_Q	1.059	1.00
176_T	180_K	1.057	1.00
199_C	206_E	1.048	1.00
226_R	265_R	1.046	1.00
212_Q	215_Q	1.045	1.00
244_I	247_I	1.032	1.00
50_L	77_A	1.027	1.00
131_G	135_H	0.996	1.00
223_Q	226_R	0.993	1.00
212_Q	216_Q	0.987	1.00
272_S	275_R	0.984	1.00
255_D	261_V	0.983	1.00
198_F	201_E	0.980	1.00
49_G	82_L	0.980	1.00
180_K	201_E	0.973	1.00
147_M	151_L	0.972	1.00
157_M	161_R	0.970	1.00
177_L	202_A	0.970	1.00
262_V	266_E	0.954	1.00
236_L	247_I	0.951	1.00
147_M	154_Q	0.950	1.00
182_I	224_Y	0.950	1.00
33_E	73_K	0.948	1.00
267_T	274_W	0.947	1.00
64_D	117_R	0.947	1.00
197_K	200_D	0.945	1.00
177_L	212_Q	0.938	1.00
260_S	264_T	0.936	1.00
202_A	209_L	0.929	1.00
185_L	221_I	0.927	1.00
207_R	210_R	0.913	1.00
230_V	262_V	0.909	1.00
154_Q	157_M	0.908	1.00
195_L	206_E	0.906	1.00
184_R	198_F	0.903	1.00
44_V	49_G	0.899	1.00
132_Q	136_E	0.894	1.00
222_N	258_Y	0.889	1.00
153_G	157_M	0.885	1.00
180_K	183_T	0.882	1.00
53_L	56_R	0.882	1.00
273_Q	277_L	0.874	1.00
91_P	95_K	0.873	1.00
234_Q	263_F	0.867	1.00
229_R	251_C	0.858	1.00
178_L	181_L	0.858	1.00
258_Y	261_V	0.858	1.00
264_T	270_T	0.857	1.00
52_V	55_D	0.850	1.00
226_R	266_E	0.849	1.00
223_Q	227_Q	0.847	1.00
204_C	212_Q	0.840	1.00
178_L	212_Q	0.840	1.00
49_G	60_I	0.838	1.00
213_F	221_I	0.834	1.00
192_P	197_K	0.832	1.00
124_A	128_Q	0.829	1.00
49_G	59_R	0.828	1.00
180_K	202_A	0.826	1.00
237_L	247_I	0.823	1.00
222_N	225_L	0.822	1.00
125_Q	158_L	0.821	1.00
240_S	247_I	0.821	1.00
230_V	259_F	0.818	1.00
125_Q	128_Q	0.818	1.00
188_S	201_E	0.810	1.00
189_L	225_L	0.797	1.00
233_A	236_L	0.797	1.00
39_C	67_Y	0.796	1.00
224_Y	228_V	0.791	1.00
158_L	162_H	0.790	1.00
174_S	215_Q	0.786	1.00
237_L	275_R	0.786	1.00
213_F	217_T	0.785	1.00
189_L	193_F	0.784	1.00
178_L	216_Q	0.778	1.00
249_T	254_E	0.778	1.00
179_D	182_I	0.777	1.00
42_V	86_N	0.769	1.00
223_Q	266_E	0.767	1.00
181_L	213_F	0.765	1.00
40_E	88_I	0.764	1.00
182_I	213_F	0.762	1.00
43_I	65_L	0.758	1.00
185_L	224_Y	0.758	1.00
269_M	274_W	0.757	1.00
51_H	66_F	0.755	1.00
145_N	149_E	0.754	1.00
33_E	75_S	0.751	1.00
189_L	251_C	0.749	1.00
248_S	256_S	0.736	1.00
238_Q	274_W	0.732	1.00
210_R	214_R	0.730	1.00
146_E	149_E	0.729	1.00
36_H	40_E	0.729	1.00
188_S	197_K	0.726	1.00
46_R	81_D	0.725	1.00
181_L	184_R	0.725	1.00
134_E	138_S	0.724	1.00
198_F	209_L	0.720	1.00
177_L	180_K	0.719	1.00
68_I	74_H	0.713	1.00
210_R	220_T	0.710	1.00
264_T	273_Q	0.708	1.00
255_D	258_Y	0.708	1.00
124_A	127_R	0.707	1.00
211_Q	215_Q	0.700	1.00
141_V	144_A	0.696	1.00
193_F	197_K	0.695	1.00
178_L	182_I	0.694	1.00
147_M	157_M	0.694	1.00
175_E	212_Q	0.687	1.00
175_E	179_D	0.685	1.00
186_A	232_H	0.680	1.00
189_L	229_R	0.680	1.00
123_M	127_R	0.677	1.00
254_E	258_Y	0.676	1.00
44_V	84_L	0.676	1.00
60_I	66_F	0.675	1.00
132_Q	151_L	0.672	1.00
181_L	221_I	0.672	1.00
82_L	86_N	0.672	1.00
44_V	47_G	0.671	1.00
210_R	222_N	0.662	1.00
225_L	229_R	0.661	1.00
135_H	139_Q	0.661	1.00
214_R	220_T	0.661	1.00
230_V	253_F	0.661	1.00
132_Q	135_H	0.658	1.00
243_L	247_I	0.657	1.00
38_F	88_I	0.656	1.00
132_Q	154_Q	0.655	1.00
257_N	270_T	0.653	1.00
158_L	161_R	0.651	1.00
174_S	177_L	0.650	1.00
125_Q	132_Q	0.642	1.00
181_L	201_E	0.640	1.00
193_F	229_R	0.638	1.00
181_L	185_L	0.634	1.00
219_M	224_Y	0.633	1.00
44_V	60_I	0.627	1.00
263_F	269_M	0.626	1.00
42_V	68_I	0.624	1.00
256_S	259_F	0.624	1.00
129_V	132_Q	0.622	1.00
48_N	80_N	0.621	1.00
195_L	222_N	0.619	1.00
114_P	117_R	0.619	1.00
247_I	275_R	0.616	1.00
199_C	202_A	0.613	1.00
200_D	203_S	0.613	1.00
146_E	150_L	0.612	1.00
217_T	224_Y	0.611	1.00
95_K	99_D	0.610	1.00
172_T	175_E	0.609	1.00
128_Q	135_H	0.608	1.00
136_E	139_Q	0.607	1.00
259_F	263_F	0.607	1.00
44_V	82_L	0.605	1.00
116_W	119_G	0.605	1.00
35_T	73_K	0.601	1.00
49_G	76_Y	0.601	1.00
231_C	266_E	0.600	1.00
42_V	51_H	0.600	1.00
39_C	42_V	0.598	1.00
174_S	216_Q	0.598	1.00
231_C	267_T	0.597	1.00
119_G	122_G	0.597	1.00
198_F	202_A	0.596	1.00
226_R	258_Y	0.594	1.00
148_A	151_L	0.594	1.00
42_V	84_L	0.594	1.00
122_G	125_Q	0.591	1.00
236_L	239_H	0.588	1.00
183_T	186_A	0.586	1.00
225_L	228_V	0.582	1.00
184_R	197_K	0.582	1.00
147_M	150_L	0.580	1.00
41_L	65_L	0.580	1.00
257_N	261_V	0.580	1.00
178_L	209_L	0.579	1.00
233_A	247_I	0.579	1.00
54_N	73_K	0.578	1.00
125_Q	129_V	0.577	1.00
226_R	230_V	0.575	1.00
43_I	123_M	0.573	1.00
45_W	131_G	0.572	1.00
259_F	271_P	0.572	1.00
235_Y	238_Q	0.571	1.00
146_E	153_G	0.570	1.00
255_D	265_R	0.568	1.00
129_V	151_L	0.562	1.00
112_G	115_H	0.562	1.00
151_L	158_L	0.561	1.00
253_F	258_Y	0.557	1.00
192_P	229_R	0.556	1.00
193_F	225_L	0.554	1.00
214_R	217_T	0.552	1.00
114_P	118_L	0.550	1.00
42_V	66_F	0.548	1.00
244_I	272_S	0.548	1.00
120_S	123_M	0.547	1.00
93_R	96_L	0.546	1.00
237_L	274_W	0.546	1.00
92_E	95_K	0.546	1.00
185_L	193_F	0.545	1.00
234_Q	269_M	0.544	1.00
176_T	216_Q	0.544	1.00
43_I	130_I	0.543	1.00
195_L	207_R	0.542	1.00
91_P	94_L	0.538	1.00
96_L	100_W	0.537	1.00
115_H	118_L	0.533	1.00
198_F	229_R	0.532	1.00
232_H	250_E	0.528	1.00
209_L	217_T	0.526	1.00
41_L	67_Y	0.526	1.00
76_Y	86_N	0.526	1.00
244_I	256_S	0.525	1.00
248_S	253_F	0.522	1.00
76_Y	84_L	0.522	1.00
263_F	267_T	0.521	1.00
53_L	68_I	0.520	1.00
92_E	96_L	0.517	1.00
223_Q	265_R	0.517	1.00
51_H	76_Y	0.514	1.00
226_R	253_F	0.510	1.00
147_M	161_R	0.510	1.00
51_H	68_I	0.509	1.00
188_S	193_F	0.509	1.00
163_R	166_S	0.508	1.00
249_T	256_S	0.508	1.00
202_A	206_E	0.507	1.00
155_L	159_L	0.507	1.00
134_E	137_S	0.506	1.00
231_C	235_Y	0.503	1.00
65_L	68_I	0.503	1.00
144_A	148_A	0.503	1.00
160_N	164_Y	0.502	1.00
44_V	62_R	0.502	1.00
143_F	147_M	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	0.8936	100	0.219	Contact Map
3oioA	1	0.3972	100	0.463	Contact Map
1bl0A	1	0.3865	100	0.463	Contact Map
3oouA	1	0.3723	100	0.465	Contact Map
3mn2A	1	0.3759	100	0.47	Contact Map
3w6vA	1	0.383	100	0.476	Contact Map
3mklA	1	0.3936	100	0.477	Contact Map
2k9sA	1	0.3759	100	0.478	Contact Map
3lsgA	2	0.3617	100	0.487	Contact Map
1d5yA	1	0.3865	99.9	0.492	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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