RHAS - ECOLI - GREMLIN Contacts

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RHAS - HTH-type transcriptional activator RhaS

UniProt:	P09377	Sequences: MTVLHSVDFFPSGNASVAIEPRLPQADFPEHHHDFHEIVIVEHGTGIHVFNGQPYTITGGTVCFVRDHDRHLYEHTDNLCLTNVLYRSPDRFQFLAGLNQLLPQELDGQYPSHWRVNHSVLQQVRQLVAQMEQQEGENDLPSTASREILFMQLLLLLRKSSLQENLENSASRLNLLLAWLEDHFADEVNWDAVADQFSLSLRTLHRQLKQQTGLTPQRYLNRLRLMKARHLLRHSEASVTDIAYRCGFSDSNHFSTLFRREFNWSPRDIRQGRDGFLQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10843
Length:	278 (241)
Sequences:	33861 (29000)
Seq/√Len:	1868.0

ECOLI - RHAS RHAR YQHC MELR ARAC YPDC CHBR YDIP YIDL RCLR YIJO YBCM FEAR YEAM GADX GADW ENVY APPY EUTR ADIY YDEO MARA YKGA SOXS ROB XYLR
BACSU - YISR YDEC YFIF BTR YBFI YOBQ YTDP YESS ADAA 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
229_R	262_F	3.284	1.00
214_L	222_R	3.282	1.00
181_E	223_L	3.038	1.00
237_A	245_R	3.011	1.00
225_L	262_F	2.973	1.00
191_D	201_L	2.862	1.00
227_K	230_H	2.832	1.00
179_W	183_H	2.798	1.00
183_H	186_D	2.681	1.00
222_R	261_E	2.621	1.00
258_F	269_I	2.543	1.00
176_L	204_L	2.376	1.00
231_L	245_R	2.360	1.00
228_A	254_F	2.330	1.00
208_L	219_Y	2.209	1.00
231_L	246_C	2.095	1.00
189_N	192_A	2.083	1.00
237_A	241_D	2.006	1.00
184_F	223_L	1.968	1.00
47_I	54_P	1.927	1.00
264_W	272_G	1.920	1.00
217_Q	221_N	1.896	1.00
179_W	196_Q	1.890	1.00
176_L	197_F	1.863	1.00
180_L	220_L	1.849	1.00
231_L	237_A	1.842	1.00
177_L	212_T	1.819	1.00
47_I	56_T	1.818	1.00
173_L	212_T	1.780	1.00
251_S	255_S	1.758	1.00
225_L	261_E	1.739	1.00
238_S	241_D	1.736	1.00
49_V	54_P	1.734	1.00
257_L	260_R	1.699	1.00
229_R	269_I	1.689	1.00
190_W	205_H	1.669	1.00
149_L	152_Q	1.662	1.00
203_T	207_Q	1.649	1.00
193_V	216_P	1.648	1.00
227_K	231_L	1.621	1.00
178_A	182_D	1.615	1.00
58_T	61_T	1.595	1.00
42_E	82_T	1.583	1.00
45_T	56_T	1.561	1.00
223_L	227_K	1.556	1.00
214_L	218_R	1.554	1.00
43_H	80_C	1.525	1.00
240_T	251_S	1.523	1.00
216_P	220_L	1.516	1.00
201_L	205_H	1.509	1.00
232_L	239_V	1.507	1.00
204_L	216_P	1.504	1.00
170_A	211_Q	1.495	1.00
181_E	219_Y	1.492	1.00
264_W	268_D	1.485	1.00
179_W	188_V	1.476	1.00
184_F	227_K	1.476	1.00
241_D	244_Y	1.474	1.00
241_D	245_R	1.463	1.00
230_H	234_H	1.459	1.00
228_A	246_C	1.442	1.00
203_T	206_R	1.438	1.00
125_R	129_A	1.433	1.00
253_H	257_L	1.430	1.00
177_L	181_E	1.423	1.00
248_F	257_L	1.411	1.00
240_T	244_Y	1.404	1.00
45_T	58_T	1.397	1.00
199_L	203_T	1.391	1.00
185_A	245_R	1.390	1.00
180_L	223_L	1.386	1.00
49_V	72_L	1.384	1.00
267_R	271_Q	1.380	1.00
205_H	216_P	1.378	1.00
227_K	246_C	1.361	1.00
36_H	67_D	1.356	1.00
176_L	193_V	1.346	1.00
242_I	246_C	1.346	1.00
47_I	74_E	1.338	1.00
192_A	196_Q	1.334	1.00
148_I	152_Q	1.331	1.00
202_R	206_R	1.316	1.00
222_R	226_M	1.298	1.00
51_N	69_D	1.298	1.00
252_N	255_S	1.294	1.00
152_Q	156_L	1.287	1.00
215_T	218_R	1.277	1.00
221_N	257_L	1.247	1.00
199_L	204_L	1.234	1.00
186_D	192_A	1.229	1.00
148_I	151_M	1.227	1.00
191_D	195_D	1.225	1.00
255_S	265_S	1.220	1.00
126_Q	130_Q	1.212	1.00
223_L	226_M	1.212	1.00
235_S	270_R	1.207	1.00
255_S	267_R	1.192	1.00
200_S	203_T	1.191	1.00
172_R	199_L	1.188	1.00
148_I	155_L	1.183	1.00
42_E	80_C	1.166	1.00
229_R	233_R	1.163	1.00
66_R	69_D	1.163	1.00
256_T	260_R	1.130	1.00
43_H	59_G	1.113	1.00
207_Q	210_Q	1.103	1.00
185_A	227_K	1.102	1.00
237_A	242_I	1.091	1.00
268_D	271_Q	1.087	1.00
207_Q	211_Q	1.077	1.00
190_W	216_P	1.074	1.00
226_M	229_R	1.070	1.00
37_E	71_H	1.070	1.00
145_S	152_Q	1.068	1.00
126_Q	129_A	1.060	1.00
145_S	149_L	1.055	1.00
179_W	197_F	1.054	1.00
31_H	71_H	1.049	1.00
194_A	201_L	1.049	1.00
188_V	193_V	1.044	1.00
171_S	175_L	1.044	1.00
151_M	155_L	1.032	1.00
265_S	268_D	1.030	1.00
250_D	256_T	1.023	1.00
174_N	178_A	1.021	1.00
267_R	270_R	1.017	1.00
172_R	207_Q	1.015	1.00
138_N	142_S	1.009	1.00
147_E	151_M	1.001	1.00
30_E	70_R	0.995	1.00
221_N	260_R	0.994	1.00
33_H	71_H	0.991	1.00
187_E	249_S	0.982	1.00
180_L	216_P	0.980	1.00
231_L	242_I	0.975	1.00
193_V	196_Q	0.975	1.00
46_G	79_L	0.970	1.00
175_L	196_Q	0.961	1.00
152_Q	155_L	0.957	1.00
192_A	195_D	0.955	1.00
172_R	197_F	0.955	1.00
202_R	205_H	0.951	1.00
187_E	192_A	0.948	1.00
177_L	219_Y	0.944	1.00
129_A	133_Q	0.943	1.00
61_T	115_R	0.940	1.00
257_L	261_E	0.935	1.00
218_R	221_N	0.934	1.00
255_S	259_R	0.928	1.00
190_W	201_L	0.919	1.00
262_F	269_I	0.914	1.00
130_Q	134_Q	0.913	1.00
239_V	242_I	0.911	1.00
179_W	193_V	0.909	1.00
197_F	204_L	0.903	1.00
229_R	258_F	0.902	1.00
156_L	160_S	0.897	1.00
41_V	46_G	0.891	1.00
218_R	222_R	0.885	1.00
46_G	57_I	0.884	1.00
224_R	246_C	0.884	1.00
268_D	272_G	0.884	1.00
123_Q	126_Q	0.879	1.00
175_L	178_A	0.875	1.00
217_Q	253_H	0.867	1.00
50_F	53_Q	0.867	1.00
87_R	90_D	0.856	1.00
253_H	256_T	0.854	1.00
235_S	242_I	0.839	1.00
225_L	257_L	0.832	1.00
232_L	242_I	0.831	1.00
199_L	207_Q	0.830	1.00
174_N	177_L	0.829	1.00
175_L	197_F	0.828	1.00
155_L	159_K	0.825	1.00
30_E	72_L	0.825	1.00
221_N	261_E	0.822	1.00
173_L	176_L	0.814	1.00
37_E	85_L	0.814	1.00
232_L	270_R	0.813	1.00
173_L	207_Q	0.813	1.00
217_Q	220_L	0.812	1.00
259_R	265_S	0.812	1.00
184_F	220_L	0.812	1.00
144_A	147_E	0.812	1.00
49_V	52_G	0.812	1.00
208_L	216_P	0.810	1.00
89_P	93_Q	0.809	1.00
47_I	76_T	0.807	1.00
122_Q	126_Q	0.807	1.00
49_V	74_E	0.802	1.00
225_L	254_F	0.794	1.00
219_Y	223_L	0.794	1.00
183_H	196_Q	0.787	1.00
184_F	188_V	0.787	1.00
79_L	83_N	0.784	1.00
33_H	37_E	0.781	1.00
233_R	269_I	0.780	1.00
173_L	211_Q	0.779	1.00
183_H	192_A	0.775	1.00
208_L	212_T	0.773	1.00
36_H	64_F	0.772	1.00
206_R	210_Q	0.771	1.00
264_W	269_I	0.769	1.00
130_Q	149_L	0.767	1.00
122_Q	125_R	0.767	1.00
244_Y	249_S	0.765	1.00
218_R	261_E	0.761	1.00
121_L	125_R	0.756	1.00
184_F	246_C	0.755	1.00
39_V	83_N	0.753	1.00
46_G	56_T	0.748	1.00
45_T	76_T	0.747	1.00
228_A	231_L	0.741	1.00
176_L	180_L	0.735	1.00
180_L	219_Y	0.726	1.00
205_H	209_K	0.725	1.00
193_V	204_L	0.724	1.00
205_H	217_Q	0.723	1.00
176_L	208_L	0.720	1.00
177_L	208_L	0.720	1.00
259_R	268_D	0.717	1.00
130_Q	152_Q	0.714	1.00
205_H	215_T	0.713	1.00
243_A	251_S	0.712	1.00
145_S	155_L	0.710	1.00
144_A	148_I	0.709	1.00
48_H	63_C	0.708	1.00
143_T	147_E	0.708	1.00
173_L	177_L	0.706	1.00
188_V	192_A	0.703	1.00
123_Q	156_L	0.702	1.00
249_S	253_H	0.698	1.00
90_D	93_Q	0.691	1.00
169_S	172_R	0.691	1.00
176_L	179_W	0.684	1.00
110_Y	113_H	0.683	1.00
170_A	207_Q	0.680	1.00
123_Q	130_Q	0.680	1.00
176_L	216_P	0.678	1.00
40_I	62_V	0.678	1.00
172_R	175_L	0.675	1.00
145_S	148_I	0.669	1.00
169_S	210_Q	0.668	1.00
209_K	215_T	0.667	1.00
32_H	70_R	0.665	1.00
250_D	253_H	0.664	1.00
35_F	85_L	0.663	1.00
252_N	265_S	0.662	1.00
184_F	224_R	0.657	1.00
238_S	242_I	0.657	1.00
57_I	63_C	0.655	1.00
111_P	115_R	0.655	1.00
251_S	254_F	0.654	1.00
123_Q	127_L	0.652	1.00
65_V	71_H	0.652	1.00
242_I	270_R	0.645	1.00
254_F	258_F	0.643	1.00
158_R	162_L	0.643	1.00
193_V	197_F	0.641	1.00
41_V	81_L	0.640	1.00
156_L	159_K	0.639	1.00
221_N	253_H	0.639	1.00
214_L	219_Y	0.636	1.00
236_E	242_I	0.633	1.00
41_V	44_G	0.633	1.00
112_S	115_R	0.627	1.00
90_D	94_F	0.625	1.00
170_A	174_N	0.621	1.00
139_D	142_S	0.621	1.00
234_H	237_A	0.619	1.00
181_E	227_K	0.617	1.00
225_L	248_F	0.615	1.00
228_A	242_I	0.614	1.00
144_A	151_M	0.614	1.00
258_F	264_W	0.613	1.00
169_S	211_Q	0.611	1.00
190_W	217_Q	0.611	1.00
118_H	121_L	0.608	1.00
226_M	262_F	0.603	1.00
39_V	65_V	0.602	1.00
51_N	70_R	0.602	1.00
130_Q	133_Q	0.602	1.00
41_V	57_I	0.600	1.00
252_N	256_T	0.595	1.00
220_L	224_R	0.592	1.00
43_H	78_N	0.592	1.00
39_V	63_C	0.589	1.00
194_A	197_F	0.586	1.00
226_M	261_E	0.585	1.00
221_N	225_L	0.585	1.00
108_G	111_P	0.584	1.00
113_H	116_V	0.580	1.00
179_W	192_A	0.579	1.00
195_D	198_S	0.577	1.00
126_Q	133_Q	0.575	1.00
39_V	48_H	0.574	1.00
176_L	196_Q	0.571	1.00
188_V	224_R	0.571	1.00
204_L	212_T	0.570	1.00
129_A	132_E	0.569	1.00
178_A	181_E	0.569	1.00
127_L	130_Q	0.569	1.00
38_I	62_V	0.568	1.00
127_L	149_L	0.568	1.00
188_V	220_L	0.560	1.00
101_L	104_Q	0.559	1.00
36_H	39_V	0.558	1.00
173_L	204_L	0.557	1.00
220_L	223_L	0.557	1.00
117_N	120_V	0.556	1.00
254_F	266_P	0.556	1.00
142_S	146_R	0.556	1.00
149_L	156_L	0.555	1.00
190_W	202_R	0.553	1.00
145_S	159_K	0.553	1.00
132_E	136_G	0.550	1.00
78_N	81_L	0.550	1.00
212_T	219_Y	0.550	1.00
180_L	188_V	0.549	1.00
109_Q	112_S	0.545	1.00
42_E	129_A	0.544	1.00
39_V	81_L	0.542	1.00
34_D	87_R	0.541	1.00
134_Q	159_K	0.541	1.00
80_C	83_N	0.536	1.00
221_N	248_F	0.536	1.00
231_L	234_H	0.536	1.00
77_D	80_C	0.536	1.00
232_L	269_I	0.536	1.00
50_F	65_V	0.536	1.00
229_R	264_W	0.536	1.00
41_V	79_L	0.536	1.00
142_S	145_S	0.535	1.00
45_T	77_D	0.533	1.00
230_H	233_R	0.530	1.00
73_Y	81_L	0.528	1.00
40_I	121_L	0.527	1.00
171_S	211_Q	0.526	1.00
239_V	267_R	0.525	1.00
159_K	163_Q	0.523	1.00
132_E	135_E	0.521	1.00
174_N	211_Q	0.521	1.00
135_E	138_N	0.521	1.00
114_W	117_N	0.521	1.00
157_L	161_S	0.519	1.00
141_P	145_S	0.519	1.00
46_G	73_Y	0.519	1.00
133_Q	137_E	0.518	1.00
209_K	212_T	0.514	1.00
248_F	253_H	0.513	1.00
108_G	112_S	0.513	1.00
204_L	207_Q	0.511	1.00
38_I	64_F	0.511	1.00
239_V	251_S	0.510	1.00
37_E	65_V	0.509	1.00
82_T	85_L	0.507	1.00
99_N	103_P	0.504	1.00
250_D	260_R	0.504	1.00
258_F	262_F	0.503	1.00
257_L	262_F	0.502	1.00
173_L	197_F	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	0.8993	100	0.213	Contact Map
3oouA	1	0.3777	100	0.468	Contact Map
1bl0A	1	0.3957	100	0.47	Contact Map
3oioA	1	0.4029	100	0.475	Contact Map
3mn2A	1	0.3813	100	0.476	Contact Map
3mklA	1	0.3993	100	0.477	Contact Map
3w6vA	1	0.3921	100	0.483	Contact Map
2k9sA	1	0.3813	100	0.484	Contact Map
3lsgA	2	0.3669	100	0.49	Contact Map
1d5yA	1	0.3957	99.9	0.498	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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