LSRC - ECOLI - GREMLIN Contacts

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LSRC - Autoinducer 2 import system permease protein LsrC

UniProt:	P77672	Sequences: MLKFIQNNREITALLAVVLLFVLPGFLDRQYLSVQTLTMVYSSAQILILLAMGATLVMLTRNIDVSVGSITGMCAVLLGMLLNAGYSLPVACVATLLLGLLAGFFNGVLVAWLKIPAIVATLGTLGLYRGIMLLWTGGKWIEGLPAELKQLSAPLLLGVSAIGWLTIILVAFMAWLLAKTAFGRSFYATGDNLQGARQLGVRTEAIRIVAFSLNGCMAALAGIVFASQIGFIPNQTGTGLEMKAIAACVLGGISLLGGSGAIIGAVLGAWFLTQIDSVLVLLRIPAWWNDFIAGLVLLAVLVFDGRLRCALERNLRRQKYARFMTPPPSVKPASSGKKREAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13807
Length:	342 (283)
Sequences:	30893 (19733)
Seq/√Len:	1173.0

ECOLI - LSRC LSRD YTFT YJFF LIVM YPHD XYLH ARAH ALSC RBSC MGLC LIVH
BACSU - RBSC YUFP YUFQ
HALSA - Q9HR22 Q9HR23
SULSO - Q97UZ8 Q97UZ9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_L	216_C	4.026	1.00
100_L	212_S	3.706	1.00
100_L	216_C	3.090	1.00
77_L	98_L	2.919	1.00
104_F	212_S	2.831	1.00
193_L	207_R	2.824	1.00
81_L	94_A	2.647	1.00
55_T	265_A	2.586	1.00
48_I	166_T	2.539	1.00
112_W	204_E	2.508	1.00
186_F	210_A	2.467	1.00
202_R	205_A	2.463	1.00
99_G	219_A	2.429	1.00
103_G	215_G	2.381	1.00
205_A	209_V	2.263	1.00
106_N	124_T	2.235	1.00
174_A	178_A	2.172	1.00
104_F	208_I	2.152	1.00
176_L	182_F	2.143	1.00
175_W	179_K	2.143	1.00
243_K	276_D	2.128	1.00
182_F	209_V	2.107	1.00
185_S	206_I	2.100	1.00
96_L	220_L	2.021	1.00
87_S	90_V	2.010	1.00
172_F	176_L	1.997	1.00
108_V	112_W	1.994	1.00
50_L	244_A	1.968	1.00
99_G	215_G	1.959	1.00
78_L	95_T	1.942	1.00
171_A	175_W	1.924	1.00
72_G	132_M	1.900	1.00
89_P	93_V	1.867	1.00
189_T	206_I	1.840	1.00
44_A	273_T	1.795	1.00
92_C	223_I	1.774	1.00
78_L	223_I	1.747	1.00
57_V	214_N	1.745	1.00
24_P	278_V	1.725	1.00
51_A	265_A	1.719	1.00
188_A	196_A	1.687	1.00
126_G	129_R	1.682	1.00
107_G	208_I	1.667	1.00
56_L	173_M	1.634	1.00
44_A	270_W	1.600	1.00
181_A	185_S	1.563	1.00
59_L	187_Y	1.563	1.00
102_A	128_Y	1.543	1.00
48_I	269_A	1.531	1.00
157_L	160_S	1.530	1.00
82_L	91_A	1.528	1.00
243_K	293_A	1.522	1.00
182_F	186_F	1.499	1.00
193_L	197_R	1.498	1.00
96_L	223_I	1.495	1.00
73_M	102_A	1.470	1.00
80_M	135_W	1.458	1.00
194_Q	197_R	1.451	1.00
69_S	129_R	1.447	1.00
50_L	71_T	1.441	1.00
81_L	84_A	1.433	1.00
71_T	225_F	1.433	1.00
170_V	266_V	1.430	1.00
251_G	264_G	1.425	1.00
60_T	210_A	1.415	1.00
185_S	196_A	1.401	1.00
124_T	128_Y	1.385	1.00
185_S	201_V	1.372	1.00
81_L	86_Y	1.372	1.00
209_V	212_S	1.359	1.00
112_W	208_I	1.356	1.00
150_Q	153_A	1.347	1.00
53_G	217_M	1.341	1.00
201_V	206_I	1.337	1.00
56_L	210_A	1.337	1.00
251_G	268_G	1.330	1.00
49_L	221_A	1.329	1.00
49_L	224_V	1.316	1.00
80_M	83_N	1.316	1.00
36_T	277_S	1.305	1.00
86_Y	94_A	1.297	1.00
196_A	201_V	1.290	1.00
90_V	93_V	1.286	1.00
62_N	117_A	1.284	1.00
108_V	208_I	1.278	1.00
86_Y	90_V	1.269	1.00
261_A	264_G	1.262	1.00
91_A	95_T	1.258	1.00
111_A	204_E	1.257	1.00
52_M	173_M	1.247	1.00
208_I	212_S	1.245	1.00
95_T	99_G	1.242	1.00
62_N	211_F	1.240	1.00
48_I	266_V	1.236	1.00
54_A	244_A	1.218	1.00
67_V	218_A	1.216	1.00
62_N	207_R	1.210	1.00
97_L	100_L	1.203	1.00
77_L	81_L	1.198	1.00
189_T	203_T	1.197	1.00
93_V	97_L	1.196	1.00
153_A	156_L	1.193	1.00
152_S	155_L	1.188	1.00
54_A	248_C	1.185	1.00
189_T	196_A	1.176	1.00
80_M	136_T	1.172	1.00
277_S	280_V	1.170	1.00
212_S	216_C	1.165	1.00
51_A	247_A	1.165	1.00
40_V	273_T	1.162	1.00
59_L	260_G	1.155	1.00
171_A	174_A	1.139	1.00
40_V	274_Q	1.139	1.00
197_R	204_E	1.125	1.00
78_L	227_S	1.119	1.00
164_W	168_I	1.116	1.00
178_A	187_Y	1.112	1.00
215_G	219_A	1.111	1.00
209_V	213_L	1.110	1.00
51_A	248_C	1.100	1.00
95_T	223_I	1.099	1.00
174_A	179_K	1.088	1.00
44_A	269_A	1.087	1.00
169_L	217_M	1.086	1.00
69_S	128_Y	1.078	1.00
111_A	121_T	1.069	1.00
100_L	219_A	1.068	1.00
76_V	234_N	1.053	1.00
101_L	104_F	1.047	1.00
109_L	120_A	1.042	1.00
53_G	67_V	1.038	1.00
70_I	102_A	1.037	1.00
276_D	293_A	1.031	1.00
144_L	147_E	1.030	1.00
186_F	206_I	1.023	1.00
76_V	132_M	1.019	1.00
157_L	164_W	1.006	1.00
272_L	293_A	1.004	1.00
240_L	243_K	1.000	1.00
247_A	268_G	0.996	1.00
161_A	164_W	0.992	1.00
81_L	91_A	0.989	1.00
50_L	221_A	0.989	1.00
288_W	291_F	0.988	1.00
173_M	213_L	0.985	1.00
222_G	226_A	0.984	1.00
68_G	241_E	0.983	1.00
168_I	172_F	0.982	1.00
25_G	29_R	0.982	1.00
213_L	217_M	0.980	1.00
206_I	209_V	0.979	1.00
247_A	269_A	0.978	1.00
58_M	248_C	0.975	1.00
156_L	160_S	0.971	1.00
170_V	217_M	0.971	1.00
182_F	206_I	0.971	1.00
108_V	113_L	0.967	1.00
46_I	221_A	0.965	1.00
45_Q	163_G	0.964	1.00
197_R	203_T	0.964	1.00
129_R	133_L	0.964	1.00
38_T	42_S	0.964	1.00
279_L	292_I	0.964	1.00
154_P	157_L	0.961	1.00
64_D	67_V	0.956	1.00
263_I	267_L	0.953	1.00
166_T	170_V	0.953	1.00
21_F	25_G	0.950	1.00
55_T	248_C	0.949	1.00
97_L	101_L	0.942	1.00
93_V	96_L	0.941	1.00
60_T	186_F	0.939	1.00
73_M	77_L	0.939	1.00
55_T	260_G	0.935	1.00
214_N	218_A	0.934	1.00
155_L	158_G	0.932	1.00
195_G	199_L	0.928	1.00
25_G	32_L	0.923	1.00
69_S	125_L	0.921	1.00
79_G	232_I	0.920	1.00
75_A	226_A	0.918	1.00
96_L	219_A	0.909	1.00
57_V	64_D	0.907	1.00
125_L	129_R	0.906	1.00
184_R	187_Y	0.903	1.00
299_A	303_F	0.903	1.00
114_K	193_L	0.899	1.00
59_L	178_A	0.893	1.00
54_A	67_V	0.890	1.00
51_A	269_A	0.889	1.00
149_K	153_A	0.887	1.00
109_L	113_L	0.886	1.00
142_E	145_P	0.884	1.00
110_V	120_A	0.879	1.00
267_L	309_C	0.878	1.00
261_A	265_A	0.870	1.00
205_A	208_I	0.870	1.00
106_N	120_A	0.869	1.00
68_G	239_G	0.867	1.00
76_V	136_T	0.866	1.00
167_I	171_A	0.865	1.00
152_S	156_L	0.863	1.00
74_C	222_G	0.859	1.00
259_S	263_I	0.858	1.00
48_I	170_V	0.856	1.00
149_K	152_S	0.856	1.00
90_V	94_A	0.855	1.00
306_R	310_A	0.853	1.00
70_I	218_A	0.852	1.00
162_I	224_V	0.851	1.00
71_T	237_G	0.848	1.00
218_A	222_G	0.848	1.00
78_L	82_L	0.842	1.00
192_N	195_G	0.842	1.00
28_D	32_L	0.840	1.00
43_S	47_L	0.838	1.00
21_F	274_Q	0.837	1.00
278_V	282_L	0.836	1.00
235_Q	238_T	0.833	1.00
71_T	240_L	0.831	1.00
143_G	146_A	0.830	1.00
37_L	278_V	0.828	1.00
189_T	210_A	0.828	1.00
176_L	179_K	0.827	1.00
203_T	207_R	0.827	1.00
49_L	166_T	0.825	1.00
20_L	24_P	0.824	1.00
52_M	265_A	0.823	1.00
177_L	186_F	0.823	1.00
74_C	99_G	0.821	1.00
35_Q	38_T	0.821	1.00
172_F	175_W	0.818	1.00
246_A	297_L	0.818	1.00
74_C	95_T	0.814	1.00
134_L	288_W	0.813	1.00
239_G	243_K	0.811	1.00
156_L	159_V	0.810	1.00
161_A	165_L	0.809	1.00
56_L	213_L	0.805	1.00
96_L	100_L	0.803	1.00
52_M	169_L	0.803	1.00
105_F	109_L	0.802	1.00
77_L	80_M	0.799	1.00
204_E	208_I	0.799	1.00
101_L	105_F	0.798	1.00
75_A	232_I	0.792	1.00
277_S	281_L	0.789	1.00
204_E	207_R	0.787	1.00
174_A	263_I	0.785	1.00
50_L	53_G	0.784	1.00
163_G	167_I	0.782	1.00
189_T	207_R	0.777	1.00
107_G	112_W	0.776	1.00
216_C	220_L	0.775	1.00
295_L	299_A	0.773	1.00
56_L	177_L	0.770	1.00
78_L	91_A	0.765	1.00
75_A	236_T	0.762	1.00
70_I	99_G	0.762	1.00
216_C	219_A	0.757	1.00
53_G	218_A	0.755	1.00
193_L	203_T	0.753	1.00
130_G	133_L	0.751	1.00
131_I	135_W	0.750	1.00
265_A	269_A	0.750	1.00
71_T	221_A	0.746	1.00
49_L	169_L	0.745	1.00
73_M	99_G	0.744	1.00
104_F	108_V	0.744	1.00
143_G	147_E	0.741	1.00
80_M	84_A	0.740	1.00
150_Q	154_P	0.740	1.00
129_R	241_E	0.736	1.00
107_G	111_A	0.734	1.00
50_L	67_V	0.734	1.00
99_G	103_G	0.731	1.00
117_A	211_F	0.731	1.00
270_W	274_Q	0.730	1.00
47_L	243_K	0.730	1.00
65_V	245_I	0.726	1.00
39_M	43_S	0.725	1.00
44_A	48_I	0.716	1.00
136_T	139_K	0.713	1.00
225_F	229_I	0.711	1.00
103_G	212_S	0.707	1.00
70_I	106_N	0.706	1.00
111_A	208_I	0.705	1.00
141_I	144_L	0.703	1.00
58_M	245_I	0.698	1.00
269_A	273_T	0.697	1.00
185_S	202_R	0.697	1.00
92_C	96_L	0.695	1.00
40_V	277_S	0.693	1.00
305_G	308_R	0.691	1.00
182_F	213_L	0.690	1.00
74_C	98_L	0.688	1.00
55_T	262_I	0.687	1.00
45_Q	166_T	0.683	1.00
47_L	247_A	0.671	1.00
150_Q	155_L	0.670	1.00
70_I	215_G	0.669	1.00
156_L	164_W	0.668	1.00
300_V	304_D	0.665	1.00
73_M	128_Y	0.663	1.00
36_T	281_L	0.662	1.00
110_V	211_F	0.658	1.00
60_T	189_T	0.658	1.00
276_D	289_N	0.656	1.00
41_Y	45_Q	0.655	1.00
34_V	37_L	0.654	1.00
247_A	265_A	0.652	1.00
70_I	74_C	0.646	1.00
82_L	227_S	0.645	1.00
219_A	223_I	0.643	1.00
24_P	28_D	0.641	1.00
74_C	218_A	0.640	1.00
39_M	277_S	0.640	1.00
42_S	228_Q	0.640	1.00
127_L	131_I	0.639	1.00
173_M	177_L	0.638	1.00
125_L	241_E	0.637	1.00
55_T	59_L	0.636	1.00
170_V	174_A	0.636	1.00
25_G	28_D	0.635	1.00
110_V	117_A	0.635	1.00
57_V	211_F	0.632	1.00
62_N	193_L	0.631	1.00
66_S	106_N	0.630	1.00
53_G	57_V	0.630	1.00
290_D	293_A	0.629	1.00
42_S	163_G	0.629	1.00
149_K	155_L	0.627	1.00
287_W	290_D	0.626	1.00
21_F	24_P	0.624	1.00
213_L	216_C	0.624	1.00
70_I	103_G	0.624	1.00
169_L	220_L	0.623	1.00
176_L	209_V	0.620	1.00
81_L	98_L	0.619	1.00
247_A	272_L	0.618	1.00
72_G	237_G	0.618	1.00
173_M	217_M	0.612	1.00
70_I	128_Y	0.611	1.00
225_F	240_L	0.607	1.00
77_L	94_A	0.605	1.00
57_V	62_N	0.605	1.00
175_W	178_A	0.603	1.00
212_S	215_G	0.602	1.00
47_L	269_A	0.600	1.00
56_L	176_L	0.597	1.00
207_R	210_A	0.594	1.00
46_I	228_Q	0.594	1.00
129_R	238_T	0.594	1.00
279_L	284_I	0.593	1.00
100_L	103_G	0.593	1.00
203_T	206_I	0.591	1.00
246_A	293_A	0.591	1.00
250_L	300_V	0.586	1.00
243_K	290_D	0.586	1.00
40_V	44_A	0.584	1.00
78_L	222_G	0.584	1.00
122_L	126_G	0.581	1.00
81_L	85_G	0.580	1.00
307_L	310_A	0.578	1.00
60_T	207_R	0.577	1.00
196_A	203_T	0.576	1.00
22_V	25_G	0.576	1.00
100_L	215_G	0.574	1.00
114_K	204_E	0.573	1.00
96_L	99_G	0.571	1.00
251_G	265_A	0.571	1.00
187_Y	260_G	0.571	1.00
86_Y	89_P	0.570	1.00
304_D	308_R	0.567	1.00
121_T	125_L	0.566	1.00
232_I	236_T	0.565	1.00
168_I	171_A	0.564	1.00
88_L	227_S	0.563	1.00
176_L	180_T	0.561	1.00
250_L	268_G	0.559	1.00
77_L	95_T	0.558	1.00
64_D	214_N	0.557	1.00
247_A	251_G	0.555	1.00
47_L	240_L	0.554	1.00
52_M	170_V	0.554	1.00
215_G	218_A	0.552	1.00
258_G	262_I	0.552	1.00
86_Y	91_A	0.551	1.00
194_Q	198_Q	0.550	1.00
29_R	32_L	0.545	1.00
188_A	195_G	0.544	1.00
155_L	159_V	0.543	1.00
187_Y	190_G	0.542	1.00
109_L	115_I	0.541	1.00
41_Y	44_A	0.539	1.00
122_L	125_L	0.539	1.00
52_M	174_A	0.534	1.00
248_C	265_A	0.533	1.00
126_G	130_G	0.532	1.00
22_V	26_F	0.532	1.00
67_V	214_N	0.531	1.00
61_R	207_R	0.531	1.00
46_I	225_F	0.531	1.00
36_T	39_M	0.528	1.00
233_P	236_T	0.526	1.00
174_A	261_A	0.526	1.00
291_F	295_L	0.524	1.00
73_M	98_L	0.524	1.00
178_A	181_A	0.520	1.00
165_L	220_L	0.518	1.00
264_G	268_G	0.518	1.00
165_L	168_I	0.516	1.00
37_L	41_Y	0.515	1.00
306_R	309_C	0.514	1.00
43_S	277_S	0.514	1.00
132_M	136_T	0.513	1.00
128_Y	132_M	0.512	1.00
77_L	99_G	0.511	1.00
165_L	169_L	0.510	1.00
26_F	29_R	0.509	1.00
57_V	210_A	0.509	1.00
238_T	241_E	0.506	1.00
45_Q	49_L	0.504	1.00
169_L	173_M	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
2qi9A	2	0.8216	97.4	0.881	Contact Map
4g1uA	2	0.7661	97	0.888	Contact Map
2nq2A	2	0.7953	96.9	0.889	Contact Map
4ldsA	2	0.6023	74.7	0.934	Contact Map
3wdoA	1	0.9123	74	0.934	Contact Map
4pypA	1	0.8099	52.9	0.943	Contact Map
2cfqA	1	0.6257	45.4	0.945	Contact Map
4zw9A	1	0.8509	44.7	0.945	Contact Map
2l16A	1	0.1228	30	0.95	Contact Map
1pw4A	1	0.6345	27.2	0.951	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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