LYAT - BACSU - GREMLIN Contacts

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LYAT - Transcriptional regulator LytR

UniProt:	Q02115	Sequences: MRNERRKKKKTLLLTILTIIGLLVLGTGGYAYYLWHKAASTVASIHESIDKSKKRDKEVSINKKDPFSVLIMGVDERDGDKGRADTLIYMTVNPKTNTTDMVSIPRDTYTKIIGKGTMDKINHSYAFGGTQMTVDTVENFLDVPVDYFVKVNMESFRDVVDTLGGITVNSTFAFSYDGYSFGKGEITLNGKEALAYTRMRKEDPRGDFGRQDRQRQVIQGIINKGANISSITKFGDMFKVVENNVKTNLTFDNMWDIQSDYKGARKHIKQHELKGTGTKINGIYYYQADESALSDITKELKESLEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	306 (282)
Sequences:	6250 (4702)
Seq/√Len:	280.0

BACSU - LYAT YVHJ YWTF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
167_T	187_T	5.296	1.00
175_S	180_S	3.878	1.00
104_I	121_I	3.598	1.00
189_N	192_E	3.474	1.00
167_T	185_E	3.392	1.00
147_Y	248_N	3.390	1.00
88_I	101_M	3.116	1.00
197_T	217_V	3.077	1.00
205_R	212_D	2.880	1.00
68_S	91_T	2.750	1.00
173_A	182_G	2.700	1.00
173_A	183_K	2.675	1.00
169_N	185_E	2.599	1.00
89_Y	145_V	2.534	1.00
72_M	133_T	2.372	1.00
90_M	101_M	2.319	1.00
32_Y	36_H	2.299	1.00
87_L	121_I	2.267	1.00
196_Y	213_R	2.179	1.00
29_G	33_Y	2.141	1.00
187_T	224_K	2.102	1.00
111_K	118_M	2.057	1.00
182_G	186_I	2.038	1.00
72_M	87_L	2.010	1.00
104_I	137_V	1.993	1.00
128_G	132_M	1.992	1.00
89_Y	143_V	1.946	1.00
188_L	192_E	1.934	1.00
119_D	123_H	1.931	1.00
93_N	96_T	1.910	1.00
156_F	197_T	1.894	1.00
157_R	191_K	1.875	1.00
170_S	186_I	1.829	1.00
87_L	133_T	1.828	1.00
108_T	288_A	1.795	1.00
70_L	137_V	1.791	1.00
161_D	190_G	1.784	1.00
289_D	292_A	1.757	1.00
30_Y	34_L	1.740	1.00
156_F	194_L	1.726	1.00
163_L	221_I	1.692	1.00
67_F	92_V	1.660	1.00
66_P	94_P	1.627	1.00
12_L	15_T	1.621	1.00
71_I	90_M	1.614	1.00
138_E	144_P	1.611	1.00
84_A	133_T	1.602	1.00
250_T	253_N	1.602	1.00
162_T	240_V	1.600	1.00
293_L	297_T	1.554	1.00
166_I	217_V	1.541	1.00
112_I	124_S	1.531	1.00
15_T	19_I	1.530	1.00
28_G	32_Y	1.524	1.00
26_G	30_Y	1.520	1.00
173_A	180_S	1.505	1.00
111_K	139_N	1.493	1.00
292_A	295_D	1.486	1.00
134_V	248_N	1.479	1.00
109_Y	118_M	1.443	1.00
121_I	137_V	1.438	1.00
18_T	22_L	1.410	1.00
13_L	16_I	1.397	1.00
119_D	127_F	1.373	1.00
66_P	91_T	1.371	1.00
199_M	202_E	1.360	1.00
134_V	138_E	1.355	1.00
31_A	35_W	1.353	1.00
132_M	136_T	1.346	1.00
33_Y	37_K	1.345	1.00
294_S	298_K	1.334	1.00
124_S	133_T	1.321	1.00
113_I	132_M	1.320	1.00
205_R	209_G	1.313	1.00
171_T	216_Q	1.312	1.00
112_I	119_D	1.298	1.00
168_V	188_L	1.293	1.00
100_D	269_K	1.273	1.00
14_L	18_T	1.272	1.00
170_S	182_G	1.271	1.00
196_Y	216_Q	1.260	1.00
22_L	26_G	1.257	1.00
202_E	205_R	1.255	1.00
208_F	286_Y	1.255	1.00
158_D	244_N	1.250	1.00
11_T	14_L	1.242	1.00
160_V	217_V	1.238	1.00
169_N	186_I	1.232	1.00
101_M	270_Q	1.227	1.00
259_S	262_K	1.222	1.00
181_F	195_A	1.218	1.00
112_I	136_T	1.210	1.00
28_G	31_A	1.205	1.00
158_D	243_N	1.201	1.00
77_R	80_D	1.198	1.00
109_Y	285_Y	1.198	1.00
165_G	190_G	1.191	1.00
170_S	181_F	1.188	1.00
98_T	269_K	1.183	1.00
177_D	195_A	1.180	1.00
10_K	14_L	1.179	1.00
211_Q	215_R	1.177	1.00
17_L	21_G	1.175	1.00
166_I	193_A	1.167	1.00
84_A	87_L	1.167	1.00
11_T	15_T	1.162	1.00
209_G	212_D	1.154	1.00
12_L	16_I	1.148	1.00
282_G	285_Y	1.146	1.00
153_M	194_L	1.145	1.00
174_F	181_F	1.139	1.00
168_V	217_V	1.137	1.00
140_F	293_L	1.137	1.00
72_M	130_T	1.130	1.00
91_T	102_V	1.128	1.00
166_I	220_G	1.123	1.00
66_P	93_N	1.119	1.00
168_V	196_Y	1.118	1.00
83_R	123_H	1.116	1.00
31_A	34_L	1.116	1.00
110_T	136_T	1.113	1.00
290_E	294_S	1.112	1.00
275_G	286_Y	1.111	1.00
109_Y	120_K	1.106	1.00
192_E	195_A	1.100	1.00
124_S	128_G	1.096	1.00
174_F	199_M	1.095	1.00
67_F	147_Y	1.089	1.00
123_H	127_F	1.086	1.00
255_W	259_S	1.083	1.00
157_R	194_L	1.082	1.00
41_T	242_E	1.072	1.00
75_D	83_R	1.069	1.00
163_L	225_G	1.068	1.00
113_I	136_T	1.062	1.00
112_I	132_M	1.061	1.00
69_V	92_V	1.053	1.00
288_A	293_L	1.046	1.00
76_E	152_N	1.044	1.00
130_T	148_F	1.035	1.00
84_A	124_S	1.034	1.00
68_S	146_D	1.028	1.00
235_G	239_K	1.026	1.00
228_I	232_T	1.025	1.00
109_Y	283_I	1.019	1.00
224_K	227_N	1.015	1.00
110_T	121_I	1.009	1.00
83_R	127_F	1.008	1.00
89_Y	141_L	0.999	1.00
217_V	221_I	0.998	1.00
120_K	284_Y	0.991	1.00
114_G	132_M	0.991	1.00
134_V	148_F	0.988	1.00
89_Y	104_I	0.984	1.00
220_G	223_N	0.983	1.00
106_R	200_R	0.979	1.00
107_D	120_K	0.979	1.00
220_G	224_K	0.974	1.00
84_A	150_K	0.972	1.00
170_S	188_L	0.971	1.00
215_R	219_Q	0.970	1.00
25_L	28_G	0.967	1.00
170_S	173_A	0.967	1.00
132_M	135_D	0.964	1.00
215_R	270_Q	0.951	1.00
253_N	256_D	0.949	1.00
123_H	126_A	0.941	1.00
216_Q	220_G	0.941	1.00
227_N	230_S	0.938	1.00
104_I	108_T	0.936	1.00
176_Y	199_M	0.933	1.00
181_F	186_I	0.927	1.00
181_F	188_L	0.926	1.00
35_W	38_A	0.924	1.00
147_Y	253_N	0.921	1.00
211_Q	272_E	0.921	1.00
233_K	236_D	0.919	1.00
120_K	283_I	0.914	1.00
167_T	224_K	0.909	1.00
208_F	275_G	0.899	1.00
125_Y	150_K	0.897	1.00
215_R	272_E	0.895	1.00
65_D	95_K	0.890	1.00
104_I	141_L	0.888	1.00
67_F	94_P	0.882	1.00
69_V	90_M	0.882	1.00
77_R	153_M	0.880	1.00
228_I	231_I	0.872	1.00
120_K	285_Y	0.872	1.00
194_L	198_R	0.870	1.00
279_K	284_Y	0.868	1.00
208_F	211_Q	0.867	1.00
146_D	248_N	0.860	1.00
37_K	239_K	0.859	1.00
27_T	31_A	0.852	1.00
113_I	135_D	0.851	1.00
206_G	209_G	0.851	1.00
191_K	195_A	0.845	1.00
179_Y	195_A	0.840	1.00
278_T	287_Q	0.838	1.00
169_N	183_K	0.836	1.00
277_G	284_Y	0.835	1.00
113_I	139_N	0.834	1.00
112_I	115_K	0.826	1.00
119_D	282_G	0.825	1.00
236_D	240_V	0.822	1.00
21_G	24_V	0.820	0.99
21_G	25_L	0.816	0.99
161_D	189_N	0.814	0.99
168_V	220_G	0.812	0.99
83_R	119_D	0.806	0.99
169_N	216_Q	0.804	0.99
202_E	209_G	0.804	0.99
176_Y	202_E	0.804	0.99
134_V	145_V	0.802	0.99
151_V	155_S	0.802	0.99
160_V	189_N	0.800	0.99
147_Y	250_T	0.799	0.99
74_V	77_R	0.799	0.99
119_D	283_I	0.797	0.99
74_V	150_K	0.794	0.99
69_V	147_Y	0.793	0.99
100_D	271_H	0.793	0.99
72_M	84_A	0.791	0.99
212_D	215_R	0.790	0.99
88_I	218_I	0.786	0.99
230_S	233_K	0.785	0.99
35_W	39_A	0.783	0.99
13_L	17_L	0.782	0.99
249_L	253_N	0.781	0.99
85_D	200_R	0.777	0.99
15_T	18_T	0.776	0.99
69_V	249_L	0.776	0.99
30_Y	33_Y	0.774	0.99
103_S	211_Q	0.771	0.99
76_E	150_K	0.767	0.99
120_K	123_H	0.767	0.99
255_W	258_Q	0.763	0.99
171_T	196_Y	0.762	0.99
136_T	140_F	0.760	0.99
216_Q	219_Q	0.759	0.99
222_I	226_A	0.753	0.99
110_T	140_F	0.750	0.99
179_Y	192_E	0.750	0.99
159_V	237_M	0.745	0.99
176_Y	179_Y	0.745	0.99
172_F	183_K	0.736	0.99
93_N	98_T	0.726	0.99
103_S	215_R	0.726	0.99
70_L	87_L	0.724	0.99
260_D	264_A	0.724	0.99
293_L	296_I	0.721	0.99
109_Y	280_I	0.716	0.99
152_N	244_N	0.713	0.99
19_I	23_L	0.712	0.99
85_D	106_R	0.709	0.99
10_K	13_L	0.709	0.99
112_I	127_F	0.708	0.99
294_S	297_T	0.706	0.98
158_D	162_T	0.705	0.98
212_D	216_Q	0.703	0.98
33_Y	36_H	0.702	0.98
162_T	237_M	0.702	0.98
83_R	126_A	0.701	0.98
99_T	264_A	0.697	0.98
137_V	140_F	0.696	0.98
150_K	246_K	0.695	0.98
65_D	94_P	0.695	0.98
138_E	143_V	0.694	0.98
121_I	136_T	0.694	0.98
119_D	124_S	0.689	0.98
219_Q	223_N	0.686	0.98
239_K	242_E	0.685	0.98
131_Q	135_D	0.684	0.98
193_A	217_V	0.684	0.98
165_G	187_T	0.680	0.98
291_S	295_D	0.679	0.98
140_F	288_A	0.675	0.98
258_Q	262_K	0.673	0.98
25_L	29_G	0.672	0.98
162_T	236_D	0.669	0.98
39_A	44_S	0.669	0.98
44_S	47_E	0.668	0.98
202_E	213_R	0.667	0.98
41_T	44_S	0.666	0.98
34_L	38_A	0.666	0.98
252_D	256_D	0.664	0.98
168_V	216_Q	0.662	0.98
36_H	40_S	0.661	0.98
70_L	133_T	0.660	0.98
213_R	216_Q	0.659	0.98
71_I	151_V	0.658	0.98
280_I	285_Y	0.654	0.98
174_F	202_E	0.654	0.98
181_F	192_E	0.654	0.98
88_I	211_Q	0.652	0.97
238_F	242_E	0.651	0.97
155_S	159_V	0.649	0.97
14_L	25_L	0.645	0.97
170_S	216_Q	0.643	0.97
54_K	57_K	0.643	0.97
249_L	254_M	0.642	0.97
18_T	21_G	0.641	0.97
71_I	149_V	0.640	0.97
125_Y	130_T	0.638	0.97
85_D	210_R	0.637	0.97
276_T	289_D	0.635	0.97
19_I	26_G	0.635	0.97
142_D	297_T	0.635	0.97
287_Q	290_E	0.633	0.97
75_D	85_D	0.632	0.97
208_F	272_E	0.626	0.97
88_I	103_S	0.625	0.97
107_D	200_R	0.624	0.97
274_K	292_A	0.624	0.97
226_A	229_S	0.624	0.97
157_R	161_D	0.623	0.97
115_K	132_M	0.621	0.97
42_V	46_H	0.620	0.97
130_T	150_K	0.620	0.97
160_V	163_L	0.618	0.97
176_Y	201_K	0.617	0.96
148_F	248_N	0.616	0.96
44_S	48_S	0.615	0.96
159_V	163_L	0.614	0.96
34_L	37_K	0.610	0.96
277_G	286_Y	0.608	0.96
207_D	211_Q	0.607	0.96
280_I	287_Q	0.607	0.96
284_Y	287_Q	0.606	0.96
106_R	210_R	0.602	0.96
218_I	222_I	0.600	0.96
20_I	24_V	0.599	0.96
261_Y	264_A	0.597	0.96
72_M	148_F	0.597	0.96
138_E	145_V	0.596	0.96
291_S	294_S	0.596	0.96
154_E	158_D	0.595	0.96
179_Y	186_I	0.593	0.96
133_T	140_F	0.591	0.96
85_D	122_N	0.587	0.95
115_K	127_F	0.587	0.95
155_S	244_N	0.587	0.95
275_G	278_T	0.584	0.95
108_T	273_L	0.584	0.95
158_D	161_D	0.583	0.95
159_V	162_T	0.582	0.95
167_T	170_S	0.582	0.95
139_N	142_D	0.580	0.95
70_L	89_Y	0.579	0.95
105_P	272_E	0.579	0.95
18_T	25_L	0.578	0.95
196_Y	217_V	0.577	0.95
170_S	174_F	0.576	0.95
240_V	244_N	0.576	0.95
98_T	267_H	0.574	0.95
173_A	186_I	0.573	0.95
290_E	293_L	0.571	0.95
295_D	298_K	0.571	0.95
97_N	263_G	0.571	0.95
176_Y	181_F	0.569	0.95
66_P	96_T	0.568	0.94
96_T	99_T	0.567	0.94
137_V	141_L	0.567	0.94
236_D	239_K	0.565	0.94
93_N	97_N	0.564	0.94
209_G	213_R	0.561	0.94
194_L	197_T	0.561	0.94
138_E	146_D	0.560	0.94
252_D	255_W	0.559	0.94
65_D	146_D	0.559	0.94
124_S	136_T	0.558	0.94
110_T	113_I	0.555	0.94
281_N	285_Y	0.554	0.94
92_V	99_T	0.554	0.94
17_L	24_V	0.549	0.93
204_P	209_G	0.548	0.93
16_I	19_I	0.547	0.93
199_M	205_R	0.544	0.93
207_D	214_Q	0.544	0.93
170_S	185_E	0.544	0.93
102_V	271_H	0.543	0.93
105_P	211_Q	0.542	0.93
171_T	183_K	0.539	0.93
83_R	122_N	0.539	0.93
92_V	257_I	0.538	0.93
152_N	156_F	0.538	0.93
171_T	212_D	0.537	0.93
86_T	197_T	0.536	0.93
30_Y	38_A	0.535	0.93
170_S	196_Y	0.535	0.93
211_Q	270_Q	0.535	0.93
108_T	140_F	0.533	0.92
67_F	257_I	0.532	0.92
175_S	182_G	0.531	0.92
91_T	94_P	0.524	0.92
87_L	104_I	0.523	0.92
86_T	103_S	0.523	0.92
158_D	240_V	0.523	0.92
68_S	89_Y	0.522	0.92
109_Y	119_D	0.522	0.92
123_H	284_Y	0.521	0.92
61_I	65_D	0.519	0.91
219_Q	270_Q	0.519	0.91
161_D	165_G	0.519	0.91
172_F	204_P	0.519	0.91
29_G	32_Y	0.519	0.91
277_G	280_I	0.518	0.91
10_K	15_T	0.517	0.91
14_L	17_L	0.517	0.91
23_L	26_G	0.516	0.91
105_P	208_F	0.515	0.91
108_T	120_K	0.509	0.91
170_S	183_K	0.509	0.91
223_N	226_A	0.509	0.91
176_Y	195_A	0.508	0.91
151_V	245_V	0.506	0.90
174_F	180_S	0.505	0.90
260_D	263_G	0.503	0.90
226_A	265_R	0.502	0.90
109_Y	278_T	0.502	0.90
39_A	42_V	0.501	0.90
159_V	244_N	0.500	0.90

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
3owqA	1	0.7745	100	0.101	Contact Map
3pe5A	1	0.8039	100	0.155	Contact Map
3qfiA	1	0.7745	100	0.176	Contact Map
3nxhA	1	0.6928	100	0.177	Contact Map
4de9A	1	0.7516	100	0.195	Contact Map
3okzA	1	0.8203	100	0.208	Contact Map
2xxpA	1	0.9869	100	0.229	Contact Map
4obmA	1	0.8039	97.8	0.891	Contact Map
1rz2A	1	0.5131	64.6	0.948	Contact Map
2m8rA	1	0.1209	61.7	0.949	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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