FEAR - ECOLI - GREMLIN Contacts

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FEAR - Transcriptional activator FeaR

UniProt:	Q47129	Sequences: MNPAVDNEFQQWLSQINQVCGNFTGRLLTERYTGVLDTHFAKGLKLSTVTTSGVNLSRTWQEVKGSDDAWFYTVFQLSGQAIMEQDERQVQIGAGDITLLDASRPCSLYWQESSKQISLLLPRTLLEQYFPHQKPICAERLDADLPMVQLSHRLLQESMNNPALSETESEAALQAMVCLLRPVLHQRESVQPRRERQFQKVVTLIDDNIREEILRPEWIAGETGMSVRSLYRMFADKGLVVAQYIRNRRLDFCADAIRHAADDEKLAGIGFHWGFSDQSHFSTVFKQRFGMTPGEYRRKFR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13422
Length:	301 (238)
Sequences:	27124 (23236)
Seq/√Len:	1506.2

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
254_A	289_F	3.187	1.00
206_D	248_R	3.108	1.00
264_E	272_H	3.085	1.00
250_L	289_F	3.033	1.00
239_L	247_N	2.996	1.00
217_E	227_V	2.756	1.00
252_F	255_D	2.716	1.00
247_N	288_R	2.642	1.00
208_N	211_E	2.573	1.00
204_L	208_N	2.553	1.00
285_F	296_Y	2.446	1.00
253_C	281_F	2.445	1.00
256_A	272_H	2.264	1.00
256_A	273_W	2.218	1.00
234_F	244_Y	2.167	1.00
201_V	230_L	2.039	1.00
201_V	223_T	1.959	1.00
215_R	218_W	1.936	1.00
82_I	89_Q	1.889	1.00
264_E	268_G	1.879	1.00
205_I	245_I	1.874	1.00
209_I	248_R	1.870	1.00
291_M	299_K	1.838	1.00
242_A	246_R	1.807	1.00
204_L	222_E	1.777	1.00
204_L	214_L	1.742	1.00
219_I	241_V	1.741	1.00
256_A	264_E	1.737	1.00
250_L	288_R	1.725	1.00
254_A	296_Y	1.721	1.00
82_I	91_Q	1.719	1.00
84_E	89_Q	1.717	1.00
278_Q	282_S	1.701	1.00
203_T	207_D	1.696	1.00
255_D	259_H	1.680	1.00
77_L	117_I	1.669	1.00
241_V	245_I	1.647	1.00
80_Q	91_Q	1.612	1.00
216_P	231_Y	1.608	1.00
257_I	266_L	1.606	1.00
284_V	287_Q	1.590	1.00
229_S	232_R	1.576	1.00
239_L	243_Q	1.571	1.00
248_R	252_F	1.559	1.00
265_K	268_G	1.557	1.00
252_F	256_A	1.551	1.00
178_C	182_P	1.541	1.00
78_S	115_K	1.523	1.00
229_S	233_M	1.498	1.00
205_I	248_R	1.487	1.00
195_E	237_K	1.480	1.00
280_H	284_V	1.479	1.00
225_M	229_S	1.463	1.00
171_A	174_Q	1.462	1.00
253_C	273_W	1.453	1.00
209_I	252_F	1.441	1.00
228_R	232_R	1.438	1.00
275_F	284_V	1.435	1.00
267_A	271_F	1.425	1.00
206_D	244_Y	1.420	1.00
279_S	282_S	1.419	1.00
202_V	206_D	1.417	1.00
267_A	278_Q	1.407	1.00
252_F	273_W	1.406	1.00
211_E	218_W	1.403	1.00
218_W	222_E	1.403	1.00
86_D	104_R	1.401	1.00
291_M	295_E	1.398	1.00
230_L	241_V	1.396	1.00
210_R	272_H	1.393	1.00
80_Q	93_G	1.389	1.00
231_Y	241_V	1.388	1.00
227_V	231_Y	1.386	1.00
82_I	109_Y	1.381	1.00
84_E	107_S	1.375	1.00
247_N	251_D	1.374	1.00
268_G	272_H	1.373	1.00
246_R	284_V	1.360	1.00
268_G	271_F	1.353	1.00
93_G	96_D	1.340	1.00
269_I	273_W	1.338	1.00
71_F	102_A	1.336	1.00
248_R	251_D	1.298	1.00
240_V	243_Q	1.292	1.00
148_V	152_H	1.282	1.00
217_E	221_G	1.280	1.00
294_G	298_R	1.280	1.00
201_V	219_I	1.271	1.00
282_S	292_T	1.262	1.00
282_S	294_G	1.257	1.00
225_M	230_L	1.255	1.00
197_Q	225_M	1.243	1.00
101_D	104_R	1.238	1.00
262_D	297_R	1.229	1.00
259_H	262_D	1.225	1.00
214_L	219_I	1.216	1.00
72_Y	106_C	1.208	1.00
226_S	229_S	1.196	1.00
254_A	258_R	1.193	1.00
170_E	174_Q	1.174	1.00
264_E	269_I	1.170	1.00
175_A	178_C	1.167	1.00
283_T	287_Q	1.151	1.00
202_V	244_Y	1.129	1.00
292_T	295_E	1.118	1.00
78_S	94_A	1.106	1.00
170_E	173_L	1.105	1.00
66_S	106_C	1.105	1.00
216_P	241_V	1.086	1.00
171_A	178_C	1.078	1.00
220_A	227_V	1.069	1.00
196_R	200_K	1.069	1.00
251_D	254_A	1.068	1.00
68_D	106_C	1.064	1.00
204_L	223_T	1.053	1.00
197_Q	223_T	1.048	1.00
295_E	298_R	1.048	1.00
199_Q	203_T	1.043	1.00
77_L	115_K	1.040	1.00
149_Q	153_R	1.039	1.00
233_M	236_D	1.033	1.00
246_R	287_Q	1.002	1.00
149_Q	152_H	1.002	1.00
233_M	237_K	0.989	1.00
266_L	269_I	0.978	1.00
294_G	297_R	0.976	1.00
197_Q	233_M	0.974	1.00
242_A	280_H	0.973	1.00
228_R	231_Y	0.970	1.00
81_A	92_I	0.968	1.00
65_G	105_P	0.965	1.00
218_W	221_G	0.965	1.00
152_H	156_Q	0.963	1.00
171_A	175_A	0.963	1.00
210_R	252_F	0.962	1.00
250_L	284_V	0.950	1.00
249_R	273_W	0.943	1.00
219_I	222_E	0.941	1.00
200_K	222_E	0.939	1.00
289_F	296_Y	0.933	1.00
204_L	219_I	0.932	1.00
282_S	286_K	0.920	1.00
234_F	241_V	0.919	1.00
277_D	283_T	0.918	1.00
284_V	288_R	0.918	1.00
200_K	203_T	0.905	1.00
76_Q	81_A	0.903	1.00
213_I	218_W	0.902	1.00
223_T	230_L	0.898	1.00
172_A	175_A	0.892	1.00
200_K	223_T	0.888	1.00
198_F	233_M	0.886	1.00
209_I	214_L	0.885	1.00
201_V	234_F	0.882	1.00
75_F	97_I	0.880	1.00
243_Q	247_N	0.877	1.00
81_A	114_S	0.874	1.00
291_M	296_Y	0.867	1.00
198_F	201_V	0.867	1.00
208_N	222_E	0.864	1.00
243_Q	246_R	0.862	1.00
213_I	276_S	0.857	1.00
286_K	292_T	0.851	1.00
216_P	227_V	0.851	1.00
137_C	141_L	0.850	1.00
198_F	202_V	0.849	1.00
254_A	285_F	0.847	1.00
205_I	241_V	0.847	1.00
256_A	269_I	0.847	1.00
280_H	283_T	0.837	1.00
225_M	233_M	0.836	1.00
199_Q	202_V	0.827	1.00
80_Q	111_Q	0.826	1.00
211_E	214_L	0.826	1.00
246_R	288_R	0.826	1.00
174_Q	178_C	0.823	1.00
85_Q	88_R	0.817	1.00
258_R	296_Y	0.817	1.00
198_F	237_K	0.816	1.00
242_A	245_I	0.815	1.00
270_G	278_Q	0.808	1.00
209_I	273_W	0.807	1.00
257_I	269_I	0.803	1.00
295_E	299_K	0.802	1.00
205_I	244_Y	0.799	1.00
194_R	236_D	0.795	1.00
250_L	281_F	0.795	1.00
257_I	297_R	0.795	1.00
262_D	269_I	0.794	1.00
83_M	98_T	0.794	1.00
84_E	87_E	0.790	1.00
156_Q	160_N	0.788	1.00
123_R	127_E	0.782	1.00
253_C	256_A	0.779	1.00
65_G	107_S	0.773	1.00
153_R	157_E	0.769	1.00
251_D	288_R	0.766	1.00
169_S	172_A	0.765	1.00
74_V	118_S	0.764	1.00
285_F	291_M	0.764	1.00
161_N	165_S	0.762	1.00
71_F	99_L	0.762	1.00
209_I	245_I	0.761	1.00
208_N	218_W	0.758	1.00
231_Y	235_A	0.754	1.00
271_F	276_S	0.752	1.00
166_E	169_S	0.749	1.00
253_C	269_I	0.746	1.00
140_R	143_A	0.745	1.00
219_I	223_T	0.745	1.00
195_E	199_Q	0.744	1.00
206_D	252_F	0.743	1.00
244_Y	248_R	0.742	1.00
195_E	233_M	0.739	1.00
214_L	218_W	0.732	1.00
231_Y	240_V	0.727	1.00
175_A	181_R	0.727	1.00
204_L	218_W	0.727	1.00
243_Q	288_R	0.725	1.00
72_Y	120_L	0.724	1.00
76_Q	79_G	0.723	1.00
84_E	109_Y	0.722	1.00
202_V	234_F	0.720	1.00
245_I	249_R	0.719	1.00
76_Q	100_L	0.713	1.00
173_L	179_L	0.712	1.00
201_V	204_L	0.712	1.00
92_I	98_T	0.710	1.00
145_L	149_Q	0.704	1.00
239_L	244_Y	0.703	1.00
219_I	230_L	0.700	1.00
279_S	292_T	0.699	1.00
150_L	153_R	0.698	1.00
168_E	171_A	0.697	1.00
165_S	169_S	0.694	1.00
216_P	242_A	0.688	1.00
231_Y	242_A	0.688	1.00
82_I	85_Q	0.686	1.00
76_Q	92_I	0.685	1.00
78_S	100_L	0.685	1.00
141_L	144_D	0.685	1.00
250_L	275_F	0.684	1.00
155_L	159_M	0.682	1.00
197_Q	200_K	0.681	1.00
137_C	140_R	0.681	1.00
81_A	91_Q	0.679	1.00
277_D	280_H	0.674	1.00
286_K	295_E	0.673	1.00
167_T	174_Q	0.671	1.00
178_C	181_R	0.670	1.00
265_K	269_I	0.667	1.00
201_V	205_I	0.667	1.00
68_D	72_Y	0.667	1.00
246_R	280_H	0.666	1.00
270_G	275_F	0.665	1.00
169_S	173_L	0.662	1.00
74_V	102_A	0.660	1.00
82_I	111_Q	0.658	1.00
201_V	241_V	0.654	1.00
232_R	236_D	0.652	1.00
157_E	161_N	0.652	1.00
269_I	297_R	0.652	1.00
100_L	106_C	0.651	1.00
125_L	128_Q	0.650	1.00
70_W	120_L	0.650	1.00
181_R	185_H	0.647	1.00
145_L	148_V	0.645	1.00
74_V	100_L	0.644	1.00
276_S	280_H	0.643	1.00
194_R	237_K	0.641	1.00
81_A	108_L	0.639	1.00
281_F	285_F	0.638	1.00
266_L	294_G	0.637	1.00
167_T	170_E	0.637	1.00
162_P	165_S	0.637	1.00
263_D	269_I	0.635	1.00
83_M	108_L	0.635	1.00
146_P	149_Q	0.632	1.00
235_A	240_V	0.631	1.00
214_L	249_R	0.629	1.00
150_L	155_L	0.627	1.00
140_R	144_D	0.626	1.00
196_R	237_K	0.621	1.00
114_S	118_S	0.618	1.00
175_A	182_P	0.613	1.00
123_R	126_L	0.608	1.00
78_S	113_S	0.608	1.00
221_G	224_G	0.607	1.00
177_V	181_R	0.606	1.00
74_V	116_Q	0.605	1.00
73_T	99_L	0.605	1.00
167_T	171_A	0.604	1.00
277_D	287_Q	0.603	1.00
124_T	127_E	0.601	1.00
175_A	179_L	0.601	1.00
86_D	105_P	0.600	1.00
271_F	278_Q	0.598	1.00
259_H	263_D	0.597	1.00
203_T	206_D	0.596	1.00
153_R	156_Q	0.596	1.00
71_F	74_V	0.593	1.00
256_A	259_H	0.590	1.00
281_F	293_P	0.588	1.00
168_E	172_A	0.587	1.00
251_D	255_D	0.584	1.00
254_A	291_M	0.583	1.00
279_S	283_T	0.582	1.00
155_L	158_S	0.578	1.00
80_Q	84_E	0.578	1.00
214_L	245_I	0.575	1.00
275_F	280_H	0.575	1.00
74_V	98_T	0.575	1.00
194_R	197_Q	0.572	1.00
201_V	222_E	0.566	1.00
251_D	289_F	0.566	1.00
153_R	175_A	0.563	1.00
166_E	170_E	0.561	1.00
85_Q	100_L	0.561	1.00
257_I	296_Y	0.560	1.00
246_R	250_L	0.559	1.00
219_I	249_R	0.559	1.00
100_L	114_S	0.557	1.00
175_A	180_L	0.557	1.00
76_Q	116_Q	0.557	1.00
220_A	223_T	0.552	1.00
146_P	153_R	0.552	1.00
96_D	138_A	0.546	1.00
146_P	150_L	0.545	1.00
216_P	228_R	0.544	1.00
198_F	230_L	0.543	1.00
266_L	278_Q	0.541	1.00
80_Q	83_M	0.541	1.00
136_I	139_E	0.540	1.00
284_V	289_F	0.540	1.00
138_A	141_L	0.538	1.00
205_I	214_L	0.534	1.00
154_L	158_S	0.534	1.00
209_I	249_R	0.533	1.00
255_D	258_R	0.532	1.00
147_M	150_L	0.532	1.00
124_T	128_Q	0.531	1.00
74_V	83_M	0.528	1.00
278_Q	281_F	0.527	1.00
201_V	233_M	0.521	1.00
259_H	264_E	0.512	1.00
115_K	118_S	0.512	1.00
228_R	235_A	0.511	1.00
168_E	175_A	0.510	1.00
129_Y	134_K	0.509	1.00
196_R	199_Q	0.509	1.00
198_F	223_T	0.509	1.00
149_Q	156_Q	0.508	1.00
139_E	142_D	0.504	1.00
108_L	116_Q	0.504	1.00
67_D	105_P	0.502	1.00
76_Q	80_Q	0.501	1.00
73_T	97_I	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	0.8239	100	0.312	Contact Map
3mklA	1	0.3621	100	0.516	Contact Map
3oouA	1	0.3455	100	0.517	Contact Map
3oioA	1	0.3588	100	0.521	Contact Map
1bl0A	1	0.3488	100	0.521	Contact Map
2k9sA	1	0.3522	100	0.522	Contact Map
3mn2A	1	0.3455	99.9	0.523	Contact Map
3w6vA	1	0.3455	99.9	0.528	Contact Map
3lsgA	2	0.3389	99.9	0.535	Contact Map
1d5yA	1	0.3488	99.9	0.546	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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