LSRB - ECOLI - GREMLIN Contacts

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LSRB - Autoinducer 2-binding protein LsrB

UniProt:	P76142	Sequences: MTLHRFKKIALLSALGIAAISMNVQAAERIAFIPKLVGVGFFTSGGNGAQQAGKELGVDVTYDGPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVRVLTWDSDTKPECRSYYINQGTPAQLGGMLVDMAARQVNKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAKEHPGWEIVTTQFGYNDATKSLQTAEGILKAYSDLDAIIAPDANALPAAAQAAENLKNDKVAIVGFSTPNVMRPYVERGTVKEFGLWDVVQQGKISVYVADALLKKGSMKTGDKLDIKGVGQVEVSPNSVQGYDYEADGNGIVLLPERVIFNKENIGKYDF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13809
Length:	340 (287)
Sequences:	38007 (28792)
Seq/√Len:	1699.5

ECOLI - LSRB XYLF DGAL RBSB ARAF TORT ALSB GALR ASCG GALS LACI CYTR YTFQ YPHF PURR MALI IDNR CRA YCJW RBSR GNTR TRER EBGR XYLR
BACSU - RBSB CCPA KDGR DEGA MSMR RBSR YKVZ NTDR ARAR EXUR GANR YVDE CCPB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_A	176_A	3.487	1.00
152_K	215_D	3.307	1.00
87_A	279_A	2.810	1.00
171_V	175_K	2.669	1.00
140_L	243_V	2.659	1.00
247_T	265_L	2.529	1.00
152_K	241_A	2.516	1.00
126_Y	282_L	2.426	1.00
138_G	180_K	2.356	1.00
52_A	55_E	2.278	1.00
205_E	235_L	2.272	1.00
201_L	234_N	2.240	1.00
142_D	177_K	2.206	1.00
138_G	177_K	2.181	1.00
138_G	176_A	2.177	1.00
52_A	277_Y	2.160	1.00
205_E	231_A	2.133	1.00
135_Q	139_M	2.113	1.00
274_I	277_Y	2.073	1.00
53_G	276_V	2.050	1.00
134_A	172_K	2.029	1.00
52_A	273_K	2.026	1.00
144_A	216_A	2.015	1.00
136_L	245_F	2.000	1.00
137_G	141_V	1.956	1.00
154_K	186_E	1.921	1.00
48_G	272_G	1.897	1.00
281_A	286_G	1.890	1.00
200_S	227_A	1.887	1.00
156_A	214_L	1.828	1.00
142_D	146_R	1.821	1.00
141_V	174_A	1.812	1.00
31_A	85_Y	1.801	1.00
265_L	297_K	1.779	1.00
137_G	218_I	1.777	1.00
147_Q	304_V	1.772	1.00
209_K	235_L	1.764	1.00
157_F	220_P	1.763	1.00
51_Q	269_V	1.759	1.00
138_G	142_D	1.734	1.00
232_A	240_V	1.729	1.00
219_A	228_A	1.727	1.00
204_A	228_A	1.717	1.00
201_L	231_A	1.691	1.00
267_D	270_Q	1.688	1.00
115_W	275_S	1.674	1.00
231_A	235_L	1.665	1.00
52_A	56_L	1.662	1.00
142_D	181_E	1.660	1.00
135_Q	138_G	1.635	1.00
172_K	176_A	1.628	1.00
127_Y	130_Q	1.628	1.00
48_G	269_V	1.624	1.00
143_M	147_Q	1.615	1.00
145_A	181_E	1.599	1.00
143_M	146_R	1.585	1.00
280_D	284_K	1.579	1.00
139_M	296_I	1.576	1.00
274_I	292_D	1.575	1.00
56_L	280_D	1.540	1.00
145_A	177_K	1.527	1.00
154_K	213_D	1.517	1.00
191_Q	206_G	1.506	1.00
231_A	234_N	1.493	1.00
270_Q	274_I	1.492	1.00
175_K	179_A	1.492	1.00
243_V	262_E	1.483	1.00
194_Y	199_K	1.456	1.00
28_E	86_N	1.453	1.00
201_L	230_Q	1.447	1.00
169_Q	172_K	1.441	1.00
143_M	300_G	1.427	1.00
132_T	135_Q	1.411	1.00
270_Q	273_K	1.410	1.00
154_K	215_D	1.410	1.00
52_A	276_V	1.403	1.00
233_E	256_E	1.372	1.00
236_K	239_K	1.369	1.00
156_A	207_I	1.350	1.00
16_G	19_A	1.347	1.00
137_G	173_E	1.333	1.00
141_V	145_A	1.331	1.00
201_L	205_E	1.327	1.00
136_L	296_I	1.325	1.00
31_A	80_F	1.325	1.00
134_A	138_G	1.325	1.00
211_Y	214_L	1.323	1.00
247_T	301_Q	1.319	1.00
89_I	275_S	1.317	1.00
253_P	256_E	1.311	1.00
177_K	180_K	1.306	1.00
29_R	59_D	1.302	1.00
141_V	173_E	1.295	1.00
53_G	60_V	1.289	1.00
173_E	177_K	1.282	1.00
205_E	234_N	1.281	1.00
277_Y	281_A	1.276	1.00
103_K	107_Q	1.276	1.00
141_V	177_K	1.275	1.00
28_E	58_V	1.268	1.00
204_A	232_A	1.260	1.00
205_E	209_K	1.258	1.00
260_V	302_V	1.258	1.00
78_N	104_R	1.256	1.00
63_D	76_L	1.254	1.00
152_K	216_A	1.249	1.00
139_M	142_D	1.247	1.00
30_I	53_G	1.228	1.00
204_A	217_I	1.227	1.00
186_E	189_T	1.224	1.00
153_A	215_D	1.217	1.00
63_D	80_F	1.216	1.00
49_A	276_V	1.214	1.00
29_R	61_T	1.206	1.00
269_V	273_K	1.201	1.00
32_F	49_A	1.184	1.00
56_L	277_Y	1.175	1.00
227_A	231_A	1.167	1.00
50_Q	54_K	1.159	1.00
174_A	178_I	1.152	1.00
196_D	199_K	1.135	1.00
198_T	202_Q	1.128	1.00
157_F	171_V	1.126	1.00
203_T	206_G	1.122	1.00
134_A	173_E	1.120	1.00
229_A	242_I	1.119	1.00
134_A	169_Q	1.117	1.00
142_D	180_K	1.116	1.00
168_N	172_K	1.110	1.00
206_G	210_A	1.108	1.00
199_K	202_Q	1.081	1.00
274_I	278_V	1.075	1.00
176_A	180_K	1.073	1.00
278_V	292_D	1.073	1.00
49_A	89_I	1.069	1.00
217_I	228_A	1.067	1.00
32_F	60_V	1.066	1.00
8_K	11_L	1.065	1.00
174_A	218_I	1.065	1.00
155_V	178_I	1.063	1.00
46_G	50_Q	1.063	1.00
72_G	75_Q	1.054	1.00
253_P	257_R	1.052	1.00
158_F	228_A	1.048	1.00
147_Q	241_A	1.046	1.00
272_G	276_V	1.042	1.00
172_K	175_K	1.042	1.00
222_A	244_G	1.038	1.00
222_A	263_F	1.036	1.00
197_A	230_Q	1.033	1.00
74_V	78_N	1.023	1.00
241_A	304_V	1.020	1.00
140_L	218_I	1.019	1.00
204_A	208_L	1.019	1.00
273_K	277_Y	1.018	1.00
54_K	72_G	1.017	1.00
219_A	224_A	1.013	1.00
99_C	103_K	1.000	1.00
147_Q	300_G	0.995	1.00
202_Q	206_G	0.992	1.00
256_E	260_V	0.991	1.00
146_R	181_E	0.988	1.00
165_T	169_Q	0.987	1.00
135_Q	295_D	0.987	1.00
58_V	280_D	0.986	1.00
279_A	283_L	0.984	1.00
200_S	204_A	0.981	1.00
78_N	82_N	0.975	1.00
47_N	51_Q	0.968	1.00
69_S	72_G	0.967	1.00
191_Q	203_T	0.967	1.00
140_L	264_G	0.962	1.00
141_V	178_I	0.961	1.00
55_E	273_K	0.958	1.00
143_M	304_V	0.957	1.00
143_M	262_E	0.956	1.00
155_V	216_A	0.955	1.00
16_G	22_M	0.955	1.00
17_I	20_I	0.951	1.00
56_L	284_K	0.951	1.00
126_Y	278_V	0.950	1.00
145_A	183_P	0.949	1.00
162_P	192_F	0.946	1.00
257_R	260_V	0.943	1.00
297_K	300_G	0.942	1.00
219_A	225_L	0.941	1.00
41_F	268_V	0.940	1.00
7_K	11_L	0.937	1.00
267_D	297_K	0.927	1.00
274_I	294_L	0.927	1.00
160_S	195_N	0.924	1.00
177_K	181_E	0.910	1.00
89_I	279_A	0.897	1.00
30_I	89_I	0.895	1.00
49_A	272_G	0.884	1.00
51_Q	55_E	0.882	1.00
265_L	299_V	0.879	1.00
87_A	283_L	0.878	1.00
199_K	203_T	0.874	1.00
29_R	83_Q	0.872	1.00
202_Q	205_E	0.869	1.00
222_A	247_T	0.865	1.00
147_Q	152_K	0.861	1.00
217_I	240_V	0.852	1.00
15_L	20_I	0.852	1.00
131_G	267_D	0.849	1.00
175_K	190_T	0.846	1.00
51_Q	273_K	0.844	1.00
225_L	244_G	0.842	1.00
193_G	224_A	0.842	1.00
132_T	293_K	0.841	1.00
156_A	217_I	0.841	1.00
176_A	179_A	0.840	1.00
208_L	231_A	0.835	1.00
278_V	281_A	0.835	1.00
61_T	83_Q	0.835	1.00
32_F	46_G	0.833	1.00
18_A	21_S	0.830	1.00
232_A	242_I	0.827	1.00
45_G	115_W	0.827	1.00
133_P	170_W	0.826	1.00
33_I	76_L	0.819	1.00
61_T	85_Y	0.817	1.00
189_T	210_A	0.817	1.00
49_A	60_V	0.816	1.00
144_A	243_V	0.809	1.00
276_V	280_D	0.809	1.00
13_S	16_G	0.807	1.00
145_A	153_A	0.806	1.00
131_G	266_W	0.805	1.00
163_T	168_N	0.802	1.00
67_E	72_G	0.797	1.00
46_G	62_Y	0.797	1.00
14_A	82_N	0.795	1.00
75_Q	78_N	0.791	1.00
130_Q	293_K	0.789	1.00
47_N	50_Q	0.788	1.00
127_Y	291_G	0.788	1.00
244_G	263_F	0.784	1.00
178_I	183_P	0.782	1.00
48_G	273_K	0.774	1.00
159_Y	171_V	0.773	1.00
204_A	231_A	0.773	1.00
7_K	10_A	0.773	1.00
154_K	189_T	0.770	1.00
154_K	212_S	0.769	1.00
208_L	235_L	0.768	1.00
153_A	183_P	0.768	1.00
104_R	107_Q	0.767	1.00
131_G	296_I	0.766	1.00
72_G	76_L	0.766	1.00
135_Q	296_I	0.763	1.00
101_A	104_R	0.759	1.00
246_S	266_W	0.758	1.00
157_F	218_I	0.753	1.00
130_Q	291_G	0.752	1.00
35_K	42_F	0.752	1.00
204_A	207_I	0.752	1.00
230_Q	233_E	0.752	1.00
143_M	298_G	0.750	1.00
27_A	86_N	0.745	1.00
118_D	291_G	0.745	1.00
138_G	173_E	0.741	1.00
262_E	298_G	0.738	1.00
19_A	22_M	0.736	1.00
267_D	294_L	0.735	1.00
128_I	278_V	0.734	1.00
158_F	219_A	0.730	1.00
87_A	113_L	0.730	1.00
27_A	59_D	0.729	1.00
89_I	115_W	0.728	1.00
31_A	88_I	0.727	1.00
9_I	12_L	0.726	1.00
169_Q	173_E	0.720	1.00
247_T	299_V	0.719	1.00
171_V	190_T	0.719	1.00
48_G	52_A	0.717	1.00
105_A	112_V	0.717	1.00
106_M	125_S	0.715	1.00
132_T	295_D	0.715	1.00
185_W	188_V	0.714	1.00
175_K	185_W	0.712	1.00
44_S	269_V	0.704	1.00
167_Q	195_N	0.700	1.00
222_A	225_L	0.700	1.00
103_K	106_M	0.697	1.00
145_A	182_H	0.695	1.00
126_Y	290_T	0.691	1.00
74_V	101_A	0.690	1.00
206_G	209_K	0.690	1.00
26_A	86_N	0.689	1.00
39_V	223_N	0.688	1.00
195_N	220_P	0.685	1.00
30_I	276_V	0.684	1.00
197_A	250_V	0.683	1.00
281_A	285_K	0.682	1.00
187_I	190_T	0.680	1.00
152_K	184_G	0.680	1.00
113_L	282_L	0.676	1.00
14_A	78_N	0.676	1.00
139_M	264_G	0.675	1.00
81_V	108_R	0.674	1.00
106_M	123_C	0.674	1.00
50_Q	60_V	0.673	1.00
221_D	246_S	0.672	1.00
191_Q	210_A	0.670	1.00
175_K	187_I	0.668	1.00
193_G	199_K	0.667	1.00
230_Q	234_N	0.664	1.00
200_S	203_T	0.658	1.00
114_T	119_T	0.658	1.00
247_T	251_M	0.655	1.00
77_I	88_I	0.654	1.00
116_D	166_D	0.653	1.00
191_Q	207_I	0.650	1.00
232_A	235_L	0.644	1.00
70_V	74_V	0.641	1.00
14_A	18_A	0.641	1.00
157_F	174_A	0.640	1.00
122_E	125_S	0.640	1.00
226_P	250_V	0.639	1.00
218_I	243_V	0.635	1.00
210_A	214_L	0.635	1.00
87_A	275_S	0.635	1.00
81_V	110_V	0.634	1.00
71_S	75_Q	0.630	1.00
145_A	178_I	0.630	1.00
20_I	24_V	0.627	1.00
79_N	83_Q	0.626	1.00
26_A	284_K	0.625	1.00
221_D	224_A	0.624	1.00
50_Q	65_P	0.622	1.00
30_I	87_A	0.621	1.00
53_G	58_V	0.621	1.00
44_S	268_V	0.618	1.00
114_T	127_Y	0.617	1.00
230_Q	256_E	0.616	1.00
251_M	263_F	0.615	1.00
12_L	15_L	0.614	1.00
300_G	304_V	0.614	1.00
254_Y	257_R	0.610	1.00
116_D	133_P	0.610	1.00
144_A	218_I	0.604	1.00
229_A	233_E	0.604	1.00
229_A	236_K	0.601	1.00
218_I	245_F	0.596	1.00
106_M	112_V	0.596	1.00
262_E	304_V	0.596	1.00
160_S	167_Q	0.592	1.00
42_F	91_S	0.591	1.00
30_I	283_L	0.588	1.00
76_L	79_N	0.587	1.00
198_T	201_L	0.585	1.00
251_M	260_V	0.585	1.00
29_R	86_N	0.583	1.00
230_Q	260_V	0.579	1.00
143_M	243_V	0.579	1.00
88_I	110_V	0.578	1.00
204_A	227_A	0.578	1.00
45_G	268_V	0.576	1.00
47_N	269_V	0.575	1.00
63_D	79_N	0.574	1.00
100_P	103_K	0.574	1.00
30_I	58_V	0.572	1.00
48_G	268_V	0.571	1.00
222_A	248_P	0.571	1.00
185_W	190_T	0.571	1.00
154_K	214_L	0.569	1.00
113_L	128_I	0.569	1.00
133_P	166_D	0.568	1.00
75_Q	79_N	0.567	1.00
154_K	211_Y	0.565	1.00
113_L	279_A	0.565	1.00
118_D	127_Y	0.562	1.00
215_D	241_A	0.560	1.00
155_V	215_D	0.560	1.00
167_Q	220_P	0.559	1.00
104_R	108_R	0.558	1.00
170_W	266_W	0.558	1.00
58_V	86_N	0.557	1.00
278_V	282_L	0.556	1.00
21_S	24_V	0.555	1.00
133_P	169_Q	0.554	1.00
293_K	296_I	0.553	1.00
269_V	272_G	0.553	1.00
216_A	241_A	0.551	1.00
156_A	189_T	0.551	1.00
245_F	266_W	0.550	1.00
79_N	82_N	0.550	1.00
282_L	285_K	0.550	1.00
197_A	227_A	0.549	1.00
41_F	45_G	0.549	1.00
140_L	216_A	0.548	1.00
195_N	224_A	0.548	1.00
188_V	191_Q	0.545	1.00
229_A	255_V	0.545	1.00
214_L	217_I	0.544	1.00
203_T	207_I	0.544	1.00
180_K	183_P	0.541	1.00
207_I	211_Y	0.541	1.00
113_L	278_V	0.541	1.00
130_Q	133_P	0.539	1.00
74_V	104_R	0.538	1.00
228_A	232_A	0.533	1.00
58_V	283_L	0.532	1.00
53_G	280_D	0.532	1.00
100_P	104_R	0.532	1.00
29_R	85_Y	0.531	1.00
139_M	143_M	0.527	1.00
28_E	283_L	0.527	1.00
193_G	200_S	0.526	1.00
116_D	271_Q	0.525	1.00
210_A	213_D	0.525	1.00
80_F	85_Y	0.523	1.00
201_L	204_A	0.523	1.00
138_G	141_V	0.521	1.00
28_E	284_K	0.517	1.00
271_Q	294_L	0.515	1.00
219_A	244_G	0.513	1.00
40_G	223_N	0.512	1.00
113_L	275_S	0.512	1.00
111_R	283_L	0.510	1.00
300_G	303_E	0.509	1.00
138_G	181_E	0.509	1.00
183_P	187_I	0.508	1.00
188_V	211_Y	0.507	1.00
178_I	185_W	0.506	1.00
226_P	248_P	0.502	1.00
208_L	232_A	0.500	1.00
164_V	167_Q	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
2hsgA	1	0.8559	100	0.268	Contact Map
2iksA	2	0.7971	100	0.272	Contact Map
3dbiA	2	0.8059	100	0.273	Contact Map
1qpzA	2	0.8912	100	0.274	Contact Map
3bilA	2	0.7471	100	0.275	Contact Map
3brqA	2	0.8	100	0.279	Contact Map
3kjxA	2	0.8676	100	0.28	Contact Map
3huuA	2	0.7706	100	0.281	Contact Map
4o5aA	2	0.7824	100	0.283	Contact Map
3e3mA	2	0.7794	100	0.284	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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