ARAC - ECOLI - GREMLIN Contacts

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ARAC - Arabinose operon regulatory protein

UniProt:	P0A9E0	Sequences: MAEAQNDPLLPGYSFNAHLVAGLTPIEANGYLDFFIDRPLGMKGYILNLTIRGQGVVKNQGREFVCRPGDILLFPPGEIHHYGRHPEAREWYHQWVYFRPRAYWHEWLNWPSIFANTGFFRPDEAHQPHFSDLFGQIINAGQGEGRYSELLAINLLEQLLLRRMEAINESLHPPMDNRVREACQYISDHLADSNFDIASVAQHVCLSPSRLSHLFRQQLGISVLSWREDQRISQAKLLLSTTRMPIATVGRNVGFDDQLYFSRVFKKCTGASPSEFRAGCEEKVNDVAVKLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10054
Length:	292 (241)
Sequences:	32935 (27857)
Seq/√Len:	1794.4

ECOLI - ARAC RHAS RHAR YDIP YPDC YQHC CHBR YIDL MELR RCLR YIJO YBCM FEAR APPY YEAM GADX ENVY GADW ADIY EUTR YDEO MARA YKGA SOXS ROB 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
236_K	269_T	3.192	1.00
221_I	229_D	3.143	1.00
187_S	230_Q	3.046	1.00
244_M	252_N	2.990	1.00
232_I	269_T	2.969	1.00
198_A	208_P	2.888	1.00
234_Q	237_L	2.750	1.00
185_Y	189_H	2.705	1.00
229_D	268_C	2.582	1.00
265_F	276_F	2.532	1.00
235_A	261_F	2.381	1.00
238_L	252_N	2.368	1.00
182_A	211_L	2.261	1.00
215_F	226_W	2.133	1.00
238_L	253_V	2.128	1.00
189_H	192_D	2.117	1.00
196_D	199_S	2.014	1.00
271_A	279_G	1.966	1.00
244_M	248_T	1.958	1.00
56_V	63_E	1.952	1.00
190_L	230_Q	1.936	1.00
56_V	65_V	1.874	1.00
186_I	227_R	1.871	1.00
238_L	244_M	1.852	1.00
224_L	228_E	1.838	1.00
182_A	204_V	1.831	1.00
185_Y	203_H	1.827	1.00
183_C	219_L	1.797	1.00
232_I	268_C	1.753	1.00
245_P	248_T	1.743	1.00
258_Q	262_S	1.728	1.00
51_I	94_Q	1.714	1.00
179_V	219_L	1.709	1.00
58_K	63_E	1.684	1.00
67_R	70_D	1.682	1.00
264_V	267_K	1.664	1.00
236_K	276_F	1.664	1.00
197_I	212_S	1.661	1.00
200_V	223_V	1.653	1.00
54_Q	65_V	1.642	1.00
234_Q	238_L	1.628	1.00
210_R	214_L	1.621	1.00
52_R	92_Y	1.612	1.00
184_Q	188_D	1.586	1.00
155_L	158_Q	1.562	1.00
208_P	212_S	1.549	1.00
237_L	241_T	1.546	1.00
247_A	258_Q	1.545	1.00
239_L	246_I	1.539	1.00
221_I	225_S	1.533	1.00
185_Y	195_F	1.531	1.00
230_Q	234_Q	1.504	1.00
211_L	223_V	1.497	1.00
271_A	275_E	1.479	1.00
260_Y	264_V	1.465	1.00
210_R	213_H	1.462	1.00
190_L	234_Q	1.456	1.00
187_S	226_W	1.452	1.00
255_F	264_V	1.449	1.00
247_A	251_R	1.446	1.00
176_D	218_Q	1.435	1.00
58_K	81_H	1.432	1.00
223_V	227_R	1.431	1.00
131_S	135_G	1.429	1.00
248_T	252_N	1.426	1.00
154_N	158_Q	1.426	1.00
248_T	251_R	1.426	1.00
235_A	253_V	1.411	1.00
249_V	253_V	1.402	1.00
191_A	252_N	1.398	1.00
206_L	210_R	1.396	1.00
56_V	83_G	1.393	1.00
45_Y	76_P	1.389	1.00
54_Q	67_R	1.385	1.00
183_C	187_S	1.375	1.00
154_N	157_E	1.367	1.00
274_S	278_A	1.359	1.00
186_I	230_Q	1.342	1.00
212_S	223_V	1.341	1.00
234_Q	253_V	1.332	1.00
199_S	203_H	1.314	1.00
209_S	213_H	1.314	1.00
158_Q	162_R	1.305	1.00
182_A	200_V	1.302	1.00
228_E	264_V	1.294	1.00
229_D	233_S	1.289	1.00
60_Q	78_E	1.284	1.00
154_N	161_L	1.272	1.00
259_L	262_S	1.261	1.00
222_S	225_S	1.261	1.00
206_L	211_L	1.252	1.00
262_S	272_S	1.234	1.00
230_Q	233_S	1.234	1.00
198_A	202_Q	1.202	1.00
262_S	274_S	1.194	1.00
242_T	277_R	1.193	1.00
178_R	206_L	1.181	1.00
51_I	92_Y	1.181	1.00
144_E	148_S	1.175	1.00
207_S	210_R	1.167	1.00
75_P	78_E	1.155	1.00
52_R	68_P	1.143	1.00
42_M	80_H	1.124	1.00
46_I	80_H	1.124	1.00
236_K	240_S	1.123	1.00
201_A	208_P	1.103	1.00
244_M	249_V	1.098	1.00
151_L	155_L	1.095	1.00
263_R	267_K	1.087	1.00
132_D	135_G	1.086	1.00
40_L	80_H	1.071	1.00
233_S	236_K	1.070	1.00
214_L	217_Q	1.069	1.00
151_L	158_Q	1.063	1.00
272_S	275_E	1.061	1.00
275_E	278_A	1.058	1.00
197_I	223_V	1.052	1.00
195_F	200_V	1.048	1.00
153_I	157_E	1.046	1.00
157_E	161_L	1.040	1.00
39_P	79_I	1.037	1.00
191_A	234_Q	1.030	1.00
214_L	218_Q	1.029	1.00
178_R	214_L	1.018	1.00
228_E	267_K	1.012	1.00
132_D	136_Q	1.010	1.00
274_S	277_R	1.004	1.00
177_N	181_E	1.002	1.00
185_Y	204_V	0.993	1.00
115_A	118_G	0.992	1.00
262_S	266_K	0.986	1.00
55_G	91_W	0.982	1.00
238_L	249_V	0.977	1.00
194_N	199_S	0.977	1.00
135_G	139_N	0.971	1.00
186_I	223_V	0.966	1.00
180_R	184_Q	0.965	1.00
194_N	256_D	0.965	1.00
124_E	127_Q	0.963	1.00
181_E	203_H	0.952	1.00
183_C	226_W	0.948	1.00
246_I	249_V	0.947	1.00
197_I	208_P	0.947	1.00
209_S	212_S	0.943	1.00
158_Q	161_L	0.931	1.00
257_D	263_R	0.930	1.00
199_S	202_Q	0.920	1.00
200_V	203_H	0.918	1.00
225_S	228_E	0.918	1.00
136_Q	140_A	0.914	1.00
264_V	268_C	0.912	1.00
192_D	195_F	0.910	1.00
204_V	211_L	0.906	1.00
178_R	204_V	0.899	1.00
58_K	83_G	0.897	1.00
50_T	55_G	0.897	1.00
231_R	253_V	0.896	1.00
236_K	265_F	0.894	1.00
185_Y	200_V	0.891	1.00
275_E	279_G	0.887	1.00
269_T	276_F	0.883	1.00
225_S	229_D	0.877	1.00
232_I	264_V	0.875	1.00
56_V	85_H	0.874	1.00
260_Y	263_R	0.873	1.00
161_L	165_E	0.862	1.00
106_E	111_P	0.857	1.00
179_V	214_L	0.851	1.00
242_T	249_V	0.848	1.00
266_K	272_S	0.842	1.00
48_N	95_W	0.836	1.00
192_D	199_S	0.832	1.00
136_Q	155_L	0.823	1.00
181_E	204_V	0.822	1.00
215_F	219_L	0.821	1.00
39_P	81_H	0.821	1.00
206_L	214_L	0.812	1.00
55_G	66_C	0.812	1.00
224_L	260_Y	0.811	1.00
54_Q	85_H	0.808	1.00
150_L	154_N	0.808	1.00
224_L	227_R	0.808	1.00
189_H	203_H	0.807	1.00
228_E	268_C	0.807	1.00
180_R	183_C	0.800	1.00
190_L	227_R	0.800	1.00
190_L	195_F	0.799	1.00
226_W	230_Q	0.795	1.00
225_S	268_C	0.793	1.00
179_V	218_Q	0.792	1.00
239_L	249_V	0.789	1.00
129_H	162_R	0.786	1.00
235_A	238_L	0.783	1.00
162_R	166_A	0.783	1.00
181_E	184_Q	0.780	1.00
59_N	62_R	0.779	1.00
215_F	223_V	0.778	1.00
128_P	132_D	0.778	1.00
123_D	126_H	0.776	1.00
58_K	61_G	0.775	1.00
239_L	277_R	0.772	1.00
271_A	276_F	0.772	1.00
179_V	182_A	0.772	1.00
151_L	161_L	0.768	1.00
45_Y	73_L	0.768	1.00
150_L	157_E	0.766	1.00
57_V	72_L	0.762	1.00
190_L	253_V	0.761	1.00
150_L	153_I	0.758	1.00
250_G	258_Q	0.753	1.00
251_R	256_D	0.753	1.00
118_G	121_R	0.751	1.00
183_C	215_F	0.745	1.00
129_H	132_D	0.744	1.00
212_S	216_R	0.742	1.00
52_R	90_E	0.739	1.00
213_H	217_Q	0.739	1.00
55_G	65_V	0.734	1.00
212_S	222_S	0.732	1.00
46_I	97_Y	0.732	1.00
175_M	217_Q	0.732	1.00
232_I	261_F	0.732	1.00
149_E	153_I	0.732	1.00
195_F	199_S	0.732	1.00
123_D	127_Q	0.730	1.00
136_Q	158_Q	0.729	1.00
128_P	131_S	0.726	1.00
179_V	183_C	0.722	1.00
182_A	185_Y	0.719	1.00
74_F	80_H	0.716	1.00
186_I	226_W	0.715	1.00
240_S	276_F	0.714	1.00
117_T	121_R	0.713	1.00
200_V	211_L	0.712	1.00
189_H	199_S	0.711	1.00
182_A	215_F	0.707	1.00
257_D	260_Y	0.706	1.00
49_L	71_I	0.706	1.00
145_G	148_S	0.706	1.00
42_M	46_I	0.704	1.00
212_S	224_L	0.704	1.00
266_K	275_E	0.702	1.00
50_T	53_G	0.700	1.00
106_E	109_N	0.699	1.00
138_I	142_Q	0.695	1.00
66_C	72_L	0.689	1.00
182_A	186_I	0.685	1.00
182_A	223_V	0.680	1.00
129_H	136_Q	0.680	1.00
91_W	95_W	0.676	1.00
190_L	231_R	0.676	1.00
122_P	126_H	0.675	1.00
245_P	249_V	0.675	1.00
176_D	214_L	0.672	1.00
50_T	93_H	0.672	1.00
178_R	181_E	0.668	1.00
41_G	79_I	0.667	1.00
44_G	97_Y	0.665	1.00
48_N	93_H	0.656	1.00
133_L	155_L	0.651	1.00
259_L	272_S	0.647	1.00
233_S	268_C	0.644	1.00
249_V	277_R	0.643	1.00
221_I	226_W	0.639	1.00
258_Q	261_F	0.639	1.00
175_M	178_R	0.637	1.00
140_A	165_E	0.634	1.00
232_I	255_F	0.634	1.00
132_D	139_N	0.630	1.00
127_Q	131_S	0.629	1.00
114_F	118_G	0.626	1.00
50_T	66_C	0.623	1.00
48_N	74_F	0.623	1.00
148_S	152_A	0.622	1.00
162_R	165_E	0.622	1.00
235_A	249_V	0.622	1.00
256_D	260_Y	0.618	1.00
133_L	136_Q	0.618	1.00
227_R	231_R	0.616	1.00
49_L	127_Q	0.613	1.00
60_Q	79_I	0.606	1.00
151_L	154_N	0.604	1.00
47_L	71_I	0.604	1.00
55_G	82_Y	0.604	1.00
195_F	231_R	0.602	1.00
243_R	249_V	0.602	1.00
259_L	263_R	0.601	1.00
265_F	271_A	0.601	1.00
126_H	129_H	0.599	1.00
43_K	99_R	0.599	1.00
261_F	265_F	0.599	1.00
261_F	273_P	0.598	1.00
200_V	204_V	0.597	1.00
47_L	73_L	0.597	1.00
159_L	163_R	0.593	1.00
186_I	195_F	0.593	1.00
228_E	260_Y	0.592	1.00
197_I	224_L	0.591	1.00
50_T	91_W	0.587	1.00
106_E	110_W	0.586	1.00
122_P	125_A	0.583	1.00
187_S	234_Q	0.582	1.00
48_N	72_L	0.582	1.00
105_H	109_N	0.581	1.00
233_S	269_T	0.581	1.00
201_A	204_V	0.577	1.00
176_D	180_R	0.572	1.00
246_I	274_S	0.572	1.00
155_L	162_R	0.570	1.00
236_K	271_A	0.569	1.00
100_P	103_Y	0.568	1.00
216_R	222_S	0.566	1.00
129_H	133_L	0.565	1.00
185_Y	199_S	0.564	1.00
108_L	111_P	0.561	1.00
219_L	226_W	0.559	1.00
239_L	276_F	0.559	1.00
48_N	57_V	0.558	1.00
228_E	232_I	0.558	1.00
184_Q	187_S	0.556	1.00
179_V	211_L	0.556	1.00
238_L	241_T	0.554	1.00
182_A	203_H	0.553	1.00
107_W	110_W	0.552	1.00
216_R	219_L	0.545	1.00
241_T	244_M	0.545	1.00
227_R	230_Q	0.545	1.00
255_F	260_Y	0.541	1.00
197_I	209_S	0.541	1.00
175_M	218_Q	0.540	1.00
92_Y	95_W	0.538	1.00
136_Q	139_N	0.535	1.00
57_V	82_Y	0.533	1.00
173_P	176_D	0.532	1.00
141_G	144_E	0.532	1.00
51_I	135_G	0.530	1.00
195_F	227_R	0.529	1.00
151_L	165_E	0.528	1.00
59_N	74_F	0.528	1.00
140_A	143_G	0.526	1.00
204_V	208_P	0.524	1.00
257_D	267_K	0.523	1.00
138_I	141_G	0.522	1.00
211_L	219_L	0.522	1.00
49_L	134_F	0.521	1.00
237_L	240_S	0.521	1.00
45_Y	48_N	0.521	1.00
139_N	143_G	0.521	1.00
54_Q	89_R	0.520	1.00
264_V	269_T	0.519	1.00
57_V	66_C	0.518	1.00
189_H	195_F	0.516	1.00
234_Q	252_N	0.515	1.00
36_I	83_G	0.515	1.00
185_Y	190_L	0.511	1.00
246_I	258_Q	0.510	1.00
255_F	261_F	0.506	1.00
84_R	91_W	0.506	1.00
55_G	84_R	0.504	1.00
82_Y	93_H	0.504	1.00
202_Q	205_C	0.501	1.00
160_L	163_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
3gbgA	1	0.863	100	0.235	Contact Map
3oouA	1	0.3596	100	0.472	Contact Map
1bl0A	1	0.3973	100	0.473	Contact Map
3oioA	1	0.3836	100	0.474	Contact Map
3mklA	1	0.3801	100	0.477	Contact Map
3mn2A	1	0.363	100	0.477	Contact Map
3w6vA	1	0.3801	100	0.478	Contact Map
2k9sA	1	0.3664	100	0.478	Contact Map
3lsgA	2	0.3527	100	0.488	Contact Map
1d5yA	1	0.4007	99.9	0.497	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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