XYLR - BACSU - GREMLIN Contacts

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XYLR - Xylose repressor

UniProt:	P94490	Sequences: MDIADQTFVKKVNQKLLLKEILKNSPISRAKLSEMTGLNKSTVSSQVNTLMKESMVFEIGQGQSSGGRRPVMLVFNKKAGYSVGIDVGVDYINGILTDLEGTIVLDQYRHLESNSPEITKDILIDMIHHFITQMPQSPYGLIGIGICVPGLIDKDQKIVFTPNSNWRDIDLKSSIQEKYNVPVFIENEANAGAYGEKVFGAAKNHDNIIYVSISTGIGIGVIINNHLYRGVSGFSGEMGHMTIDFNGPKCSCGNRGCWELYASEKALLKSLQTKEKKLSYQDIINLAHLNDIGTLNALQNFGFYLGIGLTNILNTFNPQAVILRNSIIESHPMVLNSMRSEVSSRVYSQLGNSYELLPSSLGQNAPALGMSSIVIDHFLDMITM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	384 (299)
Sequences:	9535 (7372)
Seq/√Len:	426.3

ECOLI - MLC NAGC YPHH MAK ALSK NAGK NANK
BACSU - XYLR GLK SCRK
HALSA - Q9HMA7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_D	102_T	3.256	1.00
170_D	173_S	3.223	1.00
186_E	229_R	3.181	1.00
106_D	364_N	3.118	1.00
210_Y	324_R	2.683	1.00
252_C	257_C	2.543	1.00
97_T	371_S	2.494	1.00
258_W	308_G	2.479	1.00
232_S	317_N	2.465	1.00
143_G	374_V	2.459	1.00
250_C	257_C	2.458	1.00
124_I	178_K	2.452	1.00
95_I	367_A	2.417	1.00
172_K	176_Q	2.375	1.00
320_A	357_L	2.332	1.00
209_I	312_I	2.315	1.00
205_H	320_A	2.282	1.00
270_S	300_N	2.276	1.00
303_F	341_E	2.237	1.00
94_G	126_M	2.219	1.00
83_V	127_I	2.218	1.00
202_A	208_I	2.147	1.00
107_Q	129_H	2.134	1.00
153_D	156_Q	2.128	1.00
193_A	220_G	2.107	1.00
144_I	179_Y	2.106	1.00
241_M	311_N	2.090	1.00
121_D	178_K	2.087	1.00
192_G	210_Y	2.015	1.00
94_G	130_F	1.958	1.00
223_I	228_Y	1.950	1.00
107_Q	133_Q	1.943	1.00
299_Q	337_S	1.902	1.00
302_G	306_G	1.898	1.00
173_S	177_E	1.896	1.00
306_G	341_E	1.863	1.00
193_A	222_I	1.857	1.00
207_N	319_Q	1.845	1.00
231_V	319_Q	1.842	1.00
174_S	177_E	1.822	1.00
186_E	190_N	1.819	1.00
128_H	178_K	1.813	1.00
105_L	133_Q	1.796	1.00
332_P	336_N	1.785	1.00
309_L	321_V	1.783	1.00
339_R	343_S	1.745	1.00
240_H	252_C	1.728	1.00
249_K	255_R	1.680	1.00
199_F	372_S	1.676	1.00
342_V	356_L	1.673	1.00
186_E	191_A	1.662	1.00
84_G	367_A	1.661	1.00
302_G	338_M	1.632	1.00
279_S	282_D	1.621	1.00
285_N	289_L	1.614	1.00
240_H	250_C	1.606	1.00
307_I	311_N	1.603	1.00
242_T	311_N	1.560	1.00
169_I	174_S	1.554	1.00
206_D	224_N	1.548	1.00
286_L	291_D	1.528	1.00
206_D	319_Q	1.517	1.00
335_L	339_R	1.509	1.00
146_I	175_I	1.506	1.00
147_C	191_A	1.502	1.00
288_H	333_M	1.465	1.00
240_H	257_C	1.453	1.00
250_C	253_G	1.438	1.00
281_Q	285_N	1.438	1.00
144_I	181_V	1.428	1.00
205_H	319_Q	1.410	1.00
267_L	301_F	1.401	1.00
320_A	355_E	1.396	1.00
82_S	375_I	1.395	1.00
198_V	376_D	1.387	1.00
195_G	361_L	1.377	1.00
211_V	309_L	1.375	1.00
340_S	344_S	1.373	1.00
128_H	179_Y	1.373	1.00
270_S	273_T	1.360	1.00
197_K	208_I	1.358	1.00
187_N	237_E	1.346	1.00
83_V	141_L	1.345	1.00
208_I	222_I	1.343	1.00
248_P	269_K	1.343	1.00
302_G	337_S	1.341	1.00
91_Y	108_Y	1.339	1.00
341_E	344_S	1.338	1.00
124_I	179_Y	1.332	1.00
331_H	335_L	1.330	1.00
81_Y	104_V	1.330	1.00
85_I	123_L	1.330	1.00
341_E	345_R	1.326	1.00
85_I	94_G	1.323	1.00
312_I	315_T	1.312	1.00
313_L	342_V	1.283	1.00
335_L	358_P	1.273	1.00
105_L	130_F	1.259	1.00
141_L	181_V	1.253	1.00
107_Q	126_M	1.246	1.00
147_C	366_P	1.245	1.00
80_G	142_I	1.237	1.00
95_I	103_I	1.236	1.00
121_D	125_D	1.226	1.00
282_D	285_N	1.221	1.00
337_S	340_S	1.211	1.00
274_K	296_N	1.204	1.00
191_A	370_M	1.200	1.00
271_L	297_A	1.180	1.00
287_A	298_L	1.177	1.00
137_S	140_G	1.176	1.00
186_E	373_I	1.175	1.00
313_L	321_V	1.166	1.00
208_I	322_I	1.165	1.00
85_I	127_I	1.156	1.00
115_S	118_I	1.154	1.00
170_D	174_S	1.154	1.00
196_E	200_G	1.153	1.00
271_L	294_T	1.149	1.00
217_I	262_A	1.148	1.00
109_R	126_M	1.146	1.00
117_E	174_S	1.145	1.00
248_P	260_L	1.144	1.00
120_K	174_S	1.140	1.00
129_H	133_Q	1.136	1.00
97_T	103_I	1.130	1.00
84_G	370_M	1.126	1.00
248_P	261_Y	1.126	1.00
245_F	307_I	1.125	1.00
205_H	208_I	1.121	1.00
112_E	122_I	1.115	1.00
109_R	125_D	1.115	1.00
213_I	305_L	1.113	1.00
193_A	208_I	1.103	1.00
93_N	108_Y	1.102	1.00
109_R	129_H	1.101	1.00
209_I	219_I	1.097	1.00
128_H	138_P	1.083	1.00
174_S	178_K	1.082	1.00
270_S	297_A	1.075	1.00
337_S	341_E	1.067	1.00
96_L	130_F	1.063	1.00
176_Q	183_V	1.052	1.00
96_L	134_M	1.044	1.00
299_Q	341_E	1.038	1.00
184_F	374_V	1.034	1.00
270_S	274_K	1.019	1.00
295_L	299_Q	1.019	1.00
198_V	372_S	1.018	1.00
216_G	237_E	1.015	1.00
190_N	227_L	1.013	1.00
175_I	183_V	1.013	1.00
332_P	358_P	1.011	1.00
253_G	257_C	1.004	1.00
207_N	223_I	1.003	1.00
299_Q	340_S	0.994	1.00
151_L	161_T	0.993	1.00
248_P	270_S	0.992	1.00
248_P	273_T	0.985	1.00
282_D	286_L	0.980	1.00
128_H	132_T	0.974	1.00
287_A	295_L	0.972	1.00
91_Y	264_E	0.971	1.00
161_T	164_S	0.961	1.00
109_R	122_I	0.958	1.00
244_D	261_Y	0.954	1.00
285_N	288_H	0.952	1.00
189_A	212_S	0.945	1.00
126_M	129_H	0.943	1.00
193_A	210_Y	0.941	1.00
105_L	134_M	0.940	1.00
78_K	98_D	0.932	1.00
197_K	222_I	0.932	1.00
124_I	128_H	0.931	1.00
158_I	168_D	0.931	1.00
84_G	145_G	0.931	1.00
230_G	235_S	0.930	1.00
336_N	339_R	0.930	1.00
284_I	298_L	0.930	1.00
82_S	374_V	0.929	1.00
119_T	166_W	0.921	1.00
92_I	111_L	0.919	1.00
224_N	228_Y	0.919	1.00
221_V	228_Y	0.918	1.00
207_N	231_V	0.912	1.00
307_I	345_R	0.912	1.00
158_I	170_D	0.910	1.00
203_K	360_S	0.910	1.00
125_D	129_H	0.907	1.00
302_G	341_E	0.906	1.00
244_D	247_G	0.897	1.00
89_V	215_T	0.896	1.00
83_V	131_I	0.895	1.00
244_D	248_P	0.895	1.00
192_G	366_P	0.893	1.00
230_G	317_N	0.888	1.00
254_N	345_R	0.887	1.00
287_A	333_M	0.883	1.00
336_N	340_S	0.882	1.00
331_H	336_N	0.880	1.00
187_N	216_G	0.879	1.00
209_I	321_V	0.876	1.00
221_V	316_F	0.860	1.00
209_I	221_V	0.860	1.00
306_G	342_V	0.859	1.00
272_Q	276_K	0.859	1.00
230_G	236_G	0.859	1.00
207_N	228_Y	0.856	1.00
270_S	301_F	0.855	1.00
207_N	224_N	0.853	1.00
172_K	185_I	0.850	1.00
271_L	283_I	0.847	1.00
197_K	225_N	0.845	1.00
274_K	297_A	0.841	1.00
314_N	347_Y	0.841	1.00
98_D	104_V	0.836	1.00
122_I	125_D	0.832	1.00
191_A	373_I	0.829	1.00
288_H	332_P	0.827	1.00
228_Y	316_F	0.827	1.00
206_D	225_N	0.823	1.00
103_I	106_D	0.822	1.00
291_D	294_T	0.820	1.00
278_L	282_D	0.819	1.00
284_I	288_H	0.815	1.00
313_L	354_Y	0.812	1.00
116_P	169_I	0.810	1.00
189_A	220_G	0.808	1.00
267_L	283_I	0.805	1.00
176_Q	180_N	0.805	1.00
190_N	237_E	0.804	1.00
322_I	357_L	0.803	1.00
81_Y	140_G	0.799	1.00
362_G	365_A	0.798	1.00
329_E	358_P	0.798	1.00
199_F	368_L	0.796	1.00
250_C	256_G	0.795	1.00
257_C	260_L	0.795	1.00
258_W	301_F	0.793	1.00
145_G	374_V	0.789	1.00
303_F	307_I	0.789	1.00
93_N	106_D	0.788	1.00
331_H	358_P	0.788	1.00
323_L	328_I	0.786	1.00
176_Q	182_P	0.785	1.00
97_T	101_G	0.784	1.00
145_G	191_A	0.780	1.00
200_G	204_N	0.778	1.00
116_P	174_S	0.776	1.00
286_L	294_T	0.775	1.00
117_E	121_D	0.775	1.00
184_F	377_H	0.774	1.00
107_Q	130_F	0.772	1.00
242_T	245_F	0.772	1.00
85_I	144_I	0.772	1.00
322_I	359_S	0.770	1.00
87_V	123_L	0.768	1.00
240_H	253_G	0.764	1.00
180_N	183_V	0.763	1.00
335_L	338_M	0.761	1.00
118_I	121_D	0.760	1.00
205_H	355_E	0.758	1.00
188_E	218_G	0.758	1.00
293_G	296_N	0.752	1.00
274_K	293_G	0.745	1.00
221_V	236_G	0.745	1.00
287_A	294_T	0.742	1.00
242_T	254_N	0.739	1.00
88_G	215_T	0.737	1.00
200_G	203_K	0.735	1.00
83_V	96_L	0.735	1.00
116_P	166_W	0.735	1.00
343_S	353_S	0.734	1.00
196_E	361_L	0.730	1.00
303_F	337_S	0.728	1.00
214_S	326_S	0.726	1.00
268_L	272_Q	0.719	1.00
157_K	170_D	0.719	1.00
128_H	131_I	0.718	1.00
267_L	327_I	0.718	1.00
261_Y	304_Y	0.717	1.00
241_M	308_G	0.717	1.00
208_I	320_A	0.716	1.00
130_F	134_M	0.714	1.00
135_P	138_P	0.712	1.00
309_L	323_L	0.711	1.00
131_I	141_L	0.708	1.00
292_I	296_N	0.707	1.00
254_N	257_C	0.706	1.00
303_F	344_S	0.704	1.00
95_I	106_D	0.704	1.00
331_H	337_S	0.702	1.00
300_N	304_Y	0.702	1.00
157_K	172_K	0.697	1.00
148_V	152_I	0.696	1.00
81_Y	96_L	0.694	1.00
216_G	259_E	0.693	1.00
296_N	300_N	0.693	1.00
209_I	318_P	0.690	1.00
357_L	360_S	0.690	1.00
329_E	363_Q	0.688	1.00
287_A	290_N	0.686	1.00
242_T	307_I	0.686	1.00
213_I	327_I	0.686	1.00
309_L	342_V	0.683	1.00
211_V	238_M	0.682	1.00
243_I	304_Y	0.679	1.00
306_G	345_R	0.679	1.00
219_I	238_M	0.679	1.00
334_V	337_S	0.678	1.00
361_L	365_A	0.677	1.00
94_G	109_R	0.677	1.00
93_N	367_A	0.676	1.00
306_G	310_T	0.676	1.00
275_E	278_L	0.676	1.00
97_T	368_L	0.674	1.00
268_L	283_I	0.672	1.00
250_C	260_L	0.671	1.00
305_L	338_M	0.670	1.00
235_S	317_N	0.669	1.00
125_D	128_H	0.669	1.00
286_L	289_L	0.668	1.00
194_Y	197_K	0.667	1.00
192_G	324_R	0.666	1.00
173_S	176_Q	0.666	1.00
269_K	273_T	0.664	1.00
120_K	169_I	0.664	1.00
310_T	345_R	0.659	0.99
86_D	366_P	0.657	0.99
259_E	263_S	0.655	0.99
122_I	126_M	0.654	0.99
297_A	301_F	0.652	0.99
340_S	343_S	0.652	0.99
247_G	261_Y	0.650	0.99
361_L	368_L	0.647	0.99
124_I	175_I	0.647	0.99
187_N	190_N	0.647	0.99
267_L	297_A	0.647	0.99
163_N	251_S	0.645	0.99
284_I	330_S	0.642	0.99
131_I	138_P	0.639	0.99
196_E	359_S	0.635	0.99
271_L	286_L	0.634	0.99
218_G	237_E	0.634	0.99
82_S	142_I	0.631	0.99
88_G	326_S	0.628	0.99
84_G	371_S	0.627	0.99
82_S	97_T	0.626	0.99
231_V	317_N	0.626	0.99
245_F	303_F	0.626	0.99
148_V	159_V	0.620	0.99
177_E	180_N	0.619	0.99
92_I	109_R	0.619	0.99
354_Y	358_P	0.617	0.99
190_N	220_G	0.617	0.99
103_I	368_L	0.616	0.99
87_V	148_V	0.614	0.99
151_L	234_F	0.614	0.99
94_G	107_Q	0.614	0.99
90_D	215_T	0.613	0.99
84_G	147_C	0.612	0.99
323_L	356_L	0.612	0.99
244_D	307_I	0.612	0.99
292_I	295_L	0.612	0.99
87_V	92_I	0.611	0.99
83_V	144_I	0.609	0.99
129_H	132_T	0.602	0.99
86_D	326_S	0.602	0.99
332_P	339_R	0.599	0.99
120_K	171_L	0.598	0.99
175_I	179_Y	0.596	0.99
201_A	357_L	0.595	0.99
188_E	212_S	0.594	0.99
143_G	182_P	0.593	0.99
124_I	174_S	0.592	0.99
310_T	314_N	0.591	0.99
187_N	218_G	0.591	0.99
274_K	300_N	0.588	0.99
198_V	375_I	0.586	0.99
243_I	261_Y	0.583	0.99
266_A	269_K	0.581	0.99
216_G	239_G	0.579	0.99
162_P	251_S	0.578	0.99
250_C	254_N	0.578	0.99
96_L	141_L	0.578	0.99
192_G	212_S	0.577	0.99
254_N	260_L	0.575	0.99
276_K	282_D	0.574	0.99
302_G	334_V	0.572	0.99
202_A	322_I	0.566	0.98
231_V	318_P	0.564	0.98
211_V	219_I	0.561	0.98
309_L	338_M	0.561	0.98
126_M	130_F	0.559	0.98
243_I	308_G	0.557	0.98
264_E	268_L	0.557	0.98
127_I	179_Y	0.555	0.98
157_K	176_Q	0.551	0.98
127_I	144_I	0.550	0.98
283_I	287_A	0.550	0.98
295_L	333_M	0.548	0.98
278_L	283_I	0.546	0.98
154_K	229_R	0.545	0.98
296_N	299_Q	0.544	0.98
89_V	188_E	0.543	0.98
196_E	360_S	0.543	0.98
339_R	355_E	0.542	0.98
212_S	366_P	0.541	0.98
87_V	119_T	0.540	0.98
287_A	302_G	0.539	0.98
324_R	359_S	0.539	0.98
238_M	258_W	0.538	0.98
264_E	327_I	0.538	0.98
244_D	304_Y	0.538	0.98
268_L	280_Y	0.534	0.98
284_I	287_A	0.533	0.98
317_N	354_Y	0.532	0.98
201_A	360_S	0.532	0.98
262_A	301_F	0.531	0.98
111_L	119_T	0.530	0.98
280_Y	283_I	0.529	0.98
262_A	305_L	0.528	0.98
160_F	167_R	0.528	0.98
118_I	122_I	0.524	0.97
138_P	181_V	0.524	0.97
153_D	157_K	0.523	0.97
112_E	118_I	0.523	0.97
123_L	175_I	0.521	0.97
332_P	335_L	0.521	0.97
265_K	269_K	0.521	0.97
166_W	169_I	0.519	0.97
252_C	256_G	0.518	0.97
223_I	318_P	0.517	0.97
244_D	255_R	0.514	0.97
82_S	143_G	0.514	0.97
253_G	256_G	0.514	0.97
298_L	302_G	0.512	0.97
146_I	171_L	0.510	0.97
252_C	260_L	0.508	0.97
343_S	351_G	0.508	0.97
264_E	326_S	0.507	0.97
331_H	334_V	0.506	0.97
86_D	187_N	0.504	0.97
280_Y	284_I	0.504	0.97
210_Y	322_I	0.504	0.97
187_N	212_S	0.501	0.97
246_N	303_F	0.501	0.97
333_M	336_N	0.500	0.97

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
1z05A	2	0.9818	100	0.148	Contact Map
1z6rA	3	0.9479	100	0.156	Contact Map
2hoeA	2	0.9141	100	0.209	Contact Map
4ijaA	2	0.9453	100	0.238	Contact Map
3o8mA	1	0.9245	100	0.355	Contact Map
2ap1A	2	0.763	100	0.37	Contact Map
1bdgA	1	0.888	100	0.371	Contact Map
4db3A	2	0.7786	100	0.374	Contact Map
2yhwA	2	0.763	100	0.378	Contact Map
3f9mA	1	0.8932	100	0.383	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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