LSRD - ECOLI - GREMLIN Contacts

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LSRD - Autoinducer 2 import system permease protein LsrD

UniProt:	P0AFS1	Sequences: MRIRYGWELALAALLVIEIVAFGAINPRMLDLNMLLFSTSDFICIGIVALPLTMVIVSGGIDISFGSTIGLCAIALGVLFQSGVPMPLAILLTLLLGALCGLINAGLIIYTKVNPLVITLGTLYLFAGSALLLSGMAGATGYEGIGGFPMAFTDFANLDVLGLPVPLIIFLICLLVFWLWLHKTHAGRNVFLIGQSPRVALYSAIPVNRTLCALYAMTGLASAVAAVLLVSYFGSARSDLGASFLMPAITAVVLGGANIYGGSGSIIGTAIAVLLVGYLQQGLQMAGVPNQVSSALSGALLIVVVVGRSVSLHRQQIKEWLARRANNPLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13808
Length:	330 (270)
Sequences:	31300 (20001)
Seq/√Len:	1217.2

ECOLI - LSRD LSRC YJFF YPHD YTFT ARAH XYLH MGLC ALSC RBSC LIVM 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
94_L	220_L	3.864	1.00
98_A	216_A	3.629	1.00
98_A	220_L	3.069	1.00
75_A	96_L	2.970	1.00
102_L	216_A	2.919	1.00
197_P	211_L	2.874	1.00
79_L	92_L	2.763	1.00
53_T	269_T	2.523	1.00
190_V	214_L	2.512	1.00
206_P	209_R	2.508	1.00
110_Y	208_N	2.421	1.00
180_W	186_A	2.359	1.00
46_G	170_F	2.352	1.00
209_R	213_A	2.341	1.00
97_G	223_A	2.299	1.00
179_L	183_K	2.279	1.00
101_G	219_G	2.274	1.00
178_W	182_H	2.272	1.00
102_L	212_C	2.233	1.00
189_N	210_T	2.166	1.00
104_N	122_T	2.142	1.00
106_G	110_Y	2.139	1.00
247_P	280_Q	2.118	1.00
186_A	213_A	2.082	1.00
176_V	180_W	2.079	1.00
70_G	130_A	1.951	1.00
76_L	93_T	1.951	1.00
48_V	248_A	1.950	1.00
87_P	91_L	1.907	1.00
94_L	224_V	1.899	1.00
85_P	88_L	1.830	1.00
76_L	227_V	1.819	1.00
175_L	179_L	1.792	1.00
97_G	219_G	1.787	1.00
193_I	210_T	1.759	1.00
49_A	269_T	1.750	1.00
42_F	277_G	1.743	1.00
90_I	227_V	1.723	1.00
55_V	218_T	1.686	1.00
124_Y	127_A	1.669	1.00
192_L	200_A	1.665	1.00
54_M	177_F	1.656	1.00
105_A	212_C	1.637	1.00
154_D	157_N	1.582	1.00
42_F	274_L	1.579	1.00
185_H	189_N	1.574	1.00
80_F	89_A	1.543	1.00
46_G	273_V	1.541	1.00
57_V	191_F	1.535	1.00
247_P	297_S	1.504	1.00
100_C	126_F	1.500	1.00
71_L	100_C	1.492	1.00
186_A	190_V	1.478	1.00
67_S	127_A	1.475	1.00
198_R	201_L	1.475	1.00
94_L	227_V	1.468	1.00
213_A	216_A	1.462	1.00
110_Y	212_C	1.460	1.00
122_T	126_F	1.429	1.00
145_I	148_F	1.429	1.00
78_V	81_Q	1.426	1.00
197_P	201_L	1.425	1.00
48_V	69_I	1.417	1.00
69_I	229_L	1.413	1.00
78_V	133_L	1.390	1.00
189_N	205_I	1.380	1.00
79_L	82_S	1.374	1.00
265_S	268_G	1.364	1.00
146_G	149_P	1.364	1.00
47_I	225_A	1.362	1.00
174_L	270_A	1.352	1.00
143_E	146_G	1.346	1.00
88_L	91_L	1.340	1.00
255_G	268_G	1.335	1.00
106_G	212_C	1.332	1.00
200_A	205_I	1.324	1.00
58_S	214_L	1.321	1.00
189_N	200_A	1.321	1.00
79_L	84_V	1.278	1.00
51_P	221_A	1.272	1.00
54_M	214_L	1.265	1.00
193_I	207_V	1.264	1.00
84_V	88_L	1.261	1.00
34_M	281_Q	1.250	1.00
84_V	92_L	1.232	1.00
255_G	272_A	1.231	1.00
212_C	216_A	1.229	1.00
158_L	161_L	1.228	1.00
109_I	208_N	1.224	1.00
46_G	270_A	1.222	1.00
47_I	228_L	1.222	1.00
52_L	252_V	1.218	1.00
89_A	93_T	1.217	1.00
65_F	222_S	1.217	1.00
91_L	95_L	1.211	1.00
50_L	177_F	1.203	1.00
60_G	211_L	1.198	1.00
93_T	97_G	1.193	1.00
205_I	210_T	1.189	1.00
38_S	278_Y	1.182	1.00
193_I	200_A	1.173	1.00
38_S	277_G	1.166	1.00
68_T	100_C	1.156	1.00
182_H	191_F	1.156	1.00
52_L	248_A	1.151	1.00
75_A	79_L	1.144	1.00
173_C	221_A	1.132	1.00
95_L	98_A	1.130	1.00
60_G	115_P	1.130	1.00
216_A	220_L	1.123	1.00
178_W	183_K	1.114	1.00
60_G	215_Y	1.111	1.00
42_F	273_V	1.110	1.00
49_A	251_A	1.103	1.00
156_A	159_D	1.099	1.00
67_S	126_F	1.088	1.00
201_L	207_V	1.074	1.00
281_Q	284_Q	1.074	1.00
201_L	208_N	1.061	1.00
74_I	130_A	1.058	1.00
244_F	247_P	1.057	1.00
127_A	131_L	1.052	1.00
213_A	217_M	1.049	1.00
99_L	102_L	1.047	1.00
210_T	213_A	1.039	1.00
219_G	223_A	1.038	1.00
51_P	65_F	1.032	1.00
177_F	217_M	1.027	1.00
280_Q	297_S	1.022	1.00
174_L	221_A	1.022	1.00
57_V	264_G	1.021	1.00
107_L	118_I	1.018	1.00
175_L	178_W	1.012	1.00
159_D	162_G	1.006	1.00
98_A	223_A	1.005	1.00
36_L	40_S	1.004	1.00
76_L	231_S	1.003	1.00
172_I	176_V	1.001	1.00
49_A	252_V	1.001	1.00
93_T	227_V	1.000	1.00
53_T	252_V	0.992	1.00
78_V	134_S	0.989	1.00
190_V	210_T	0.989	1.00
144_G	147_G	0.984	1.00
217_M	221_A	0.984	1.00
251_A	272_A	0.980	1.00
123_L	127_A	0.980	1.00
91_L	94_L	0.977	1.00
292_V	295_A	0.974	1.00
74_I	238_S	0.971	1.00
155_F	158_L	0.967	1.00
104_N	118_I	0.965	1.00
71_L	75_A	0.960	1.00
106_G	111_T	0.959	1.00
251_A	273_V	0.958	1.00
79_L	89_A	0.955	1.00
33_N	36_L	0.952	1.00
186_A	210_T	0.951	1.00
48_V	225_A	0.947	1.00
164_P	168_I	0.943	1.00
67_S	123_L	0.943	1.00
226_A	230_V	0.942	1.00
157_N	161_L	0.942	1.00
109_I	119_T	0.924	1.00
209_R	212_C	0.923	1.00
267_I	271_I	0.922	1.00
49_A	273_V	0.909	1.00
276_V	297_S	0.907	1.00
95_L	99_L	0.904	1.00
56_I	252_V	0.903	1.00
72_C	97_G	0.898	1.00
178_W	267_I	0.895	1.00
46_G	174_L	0.894	1.00
76_L	80_F	0.889	1.00
218_T	222_S	0.889	1.00
282_G	286_A	0.887	1.00
239_D	242_A	0.887	1.00
53_T	264_G	0.887	1.00
112_K	197_P	0.886	1.00
66_G	245_L	0.884	1.00
148_F	151_A	0.884	1.00
107_L	111_T	0.883	1.00
44_C	225_A	0.881	1.00
161_L	168_I	0.877	1.00
52_L	65_F	0.876	1.00
188_R	191_F	0.876	1.00
41_D	45_I	0.875	1.00
74_I	134_S	0.872	1.00
108_I	118_I	0.872	1.00
157_N	160_V	0.871	1.00
78_V	82_S	0.869	1.00
133_L	136_M	0.868	1.00
57_V	182_H	0.864	1.00
171_L	175_L	0.863	1.00
165_V	168_I	0.863	1.00
147_G	150_M	0.862	1.00
165_V	169_I	0.858	1.00
77_G	236_A	0.855	1.00
68_T	222_S	0.854	1.00
73_A	230_V	0.853	1.00
69_I	244_F	0.851	1.00
50_L	173_C	0.849	1.00
294_S	297_S	0.848	1.00
144_G	148_F	0.845	1.00
181_L	190_V	0.844	1.00
193_I	214_L	0.844	1.00
35_L	282_G	0.843	1.00
105_A	109_I	0.839	1.00
222_S	226_A	0.836	1.00
196_S	199_V	0.835	1.00
199_V	203_S	0.834	1.00
54_M	217_M	0.833	1.00
72_C	93_T	0.828	1.00
88_L	92_L	0.828	1.00
69_I	241_G	0.825	1.00
208_N	211_L	0.824	1.00
55_V	62_D	0.820	1.00
283_L	296_L	0.817	1.00
62_D	65_F	0.814	1.00
72_C	226_A	0.808	1.00
150_M	153_T	0.804	1.00
58_S	190_V	0.802	1.00
103_I	107_L	0.800	1.00
134_S	137_A	0.798	1.00
151_A	154_D	0.797	1.00
164_P	167_L	0.797	1.00
263_S	267_I	0.793	1.00
75_A	78_V	0.791	1.00
156_A	161_L	0.790	1.00
303_V	307_G	0.788	1.00
132_L	292_V	0.787	1.00
207_V	211_L	0.786	1.00
50_L	269_T	0.786	1.00
68_T	97_G	0.784	1.00
73_A	236_A	0.783	1.00
265_S	269_T	0.783	1.00
299_A	303_V	0.783	1.00
54_M	181_L	0.782	1.00
180_W	183_K	0.778	1.00
168_I	172_I	0.777	1.00
281_Q	285_M	0.777	1.00
208_N	212_C	0.776	1.00
250_T	301_L	0.772	1.00
193_I	211_L	0.772	1.00
220_L	223_A	0.769	1.00
66_G	243_S	0.769	1.00
166_P	228_L	0.767	1.00
163_L	168_I	0.765	1.00
99_L	103_I	0.759	1.00
197_P	207_V	0.758	1.00
150_M	154_D	0.754	1.00
129_S	133_L	0.751	1.00
102_L	106_G	0.749	1.00
48_V	65_F	0.748	1.00
128_G	131_L	0.747	1.00
94_L	223_A	0.743	1.00
73_A	240_L	0.743	1.00
220_L	224_V	0.742	1.00
269_T	273_V	0.740	1.00
51_P	222_S	0.733	1.00
143_E	147_G	0.726	1.00
94_L	98_A	0.722	1.00
48_V	51_P	0.720	1.00
63_I	249_I	0.719	1.00
37_F	41_D	0.717	1.00
115_P	215_Y	0.714	1.00
71_L	97_G	0.709	1.00
43_I	167_L	0.707	1.00
273_V	277_G	0.703	1.00
243_S	247_P	0.694	1.00
274_L	278_Y	0.694	1.00
176_V	179_L	0.691	1.00
47_I	173_C	0.691	1.00
125_L	129_S	0.690	1.00
76_L	89_A	0.687	1.00
229_L	233_F	0.687	1.00
55_V	215_Y	0.687	1.00
69_I	225_A	0.686	1.00
72_C	96_L	0.679	1.00
60_G	197_P	0.679	1.00
237_R	240_L	0.678	1.00
105_A	110_Y	0.678	1.00
291_Q	294_S	0.676	1.00
42_F	46_G	0.675	1.00
109_I	212_C	0.670	1.00
34_M	285_M	0.670	1.00
167_L	171_L	0.670	1.00
71_L	126_F	0.669	1.00
189_N	206_P	0.665	1.00
280_Q	293_S	0.663	1.00
127_A	242_A	0.663	1.00
68_T	72_C	0.663	1.00
45_I	247_P	0.663	1.00
68_T	104_N	0.662	1.00
38_S	281_Q	0.662	1.00
90_I	94_L	0.660	1.00
145_I	149_P	0.658	1.00
40_S	232_Y	0.658	1.00
47_I	170_F	0.655	1.00
156_A	160_V	0.654	1.00
80_F	231_S	0.651	1.00
217_M	220_L	0.646	1.00
56_I	249_I	0.643	1.00
170_F	174_L	0.642	1.00
37_F	281_Q	0.642	1.00
101_G	216_A	0.638	1.00
177_F	221_A	0.633	1.00
68_T	219_G	0.632	1.00
53_T	57_V	0.631	1.00
45_I	251_A	0.631	1.00
70_G	241_G	0.630	1.00
174_L	178_W	0.629	1.00
207_V	210_T	0.629	1.00
186_A	217_M	0.625	1.00
179_L	182_H	0.625	1.00
132_L	136_M	0.625	1.00
254_L	272_A	0.623	1.00
68_T	126_F	0.623	1.00
304_V	308_R	0.618	1.00
38_S	42_F	0.617	1.00
72_C	222_S	0.617	1.00
53_T	266_I	0.616	1.00
149_P	153_T	0.614	1.00
236_A	240_L	0.614	1.00
39_T	43_I	0.613	1.00
32_L	35_L	0.612	1.00
79_L	96_L	0.610	1.00
223_A	227_V	0.610	1.00
58_S	193_I	0.609	1.00
45_I	273_V	0.603	1.00
138_G	237_R	0.602	1.00
143_E	149_P	0.599	1.00
68_T	101_G	0.598	1.00
84_V	89_A	0.597	1.00
229_L	244_F	0.597	1.00
177_F	181_L	0.596	1.00
172_I	175_L	0.595	1.00
180_W	213_A	0.593	1.00
127_A	245_L	0.592	1.00
173_C	224_V	0.590	1.00
98_A	101_G	0.589	1.00
51_P	55_V	0.588	1.00
108_I	115_P	0.587	1.00
108_I	215_Y	0.584	1.00
97_G	101_G	0.581	1.00
112_K	208_N	0.577	1.00
45_I	244_F	0.577	1.00
58_S	211_L	0.577	1.00
75_A	92_L	0.573	1.00
295_A	299_A	0.570	1.00
76_L	226_A	0.565	1.00
50_L	174_L	0.565	1.00
306_V	310_V	0.563	1.00
160_V	168_I	0.562	1.00
64_S	104_N	0.562	1.00
180_W	184_T	0.561	1.00
247_P	294_S	0.560	1.00
268_G	272_A	0.558	1.00
283_L	288_V	0.557	1.00
290_N	293_S	0.556	1.00
143_E	148_F	0.556	1.00
154_D	159_D	0.555	1.00
44_C	229_L	0.553	1.00
144_G	149_P	0.552	1.00
219_G	222_S	0.551	1.00
50_L	178_W	0.548	1.00
211_L	214_L	0.548	1.00
120_L	124_Y	0.548	1.00
124_Y	128_G	0.547	1.00
130_A	134_S	0.546	1.00
200_A	207_V	0.545	1.00
252_V	269_T	0.543	1.00
135_G	138_G	0.543	1.00
178_W	265_S	0.543	1.00
198_R	202_Y	0.542	1.00
41_D	281_Q	0.542	1.00
54_M	180_W	0.541	1.00
251_A	269_T	0.540	1.00
236_A	241_G	0.537	1.00
123_L	245_L	0.532	1.00
35_L	39_T	0.532	1.00
33_N	37_F	0.530	1.00
216_A	219_G	0.528	1.00
75_A	97_G	0.526	1.00
158_L	165_V	0.526	1.00
94_L	97_G	0.525	1.00
149_P	152_F	0.524	1.00
297_S	301_L	0.524	1.00
254_L	304_V	0.522	1.00
71_L	96_L	0.522	1.00
92_L	95_L	0.520	1.00
251_A	276_V	0.519	1.00
134_S	138_G	0.518	1.00
39_T	42_F	0.517	1.00
255_G	269_T	0.514	1.00
160_V	165_V	0.511	1.00
98_A	219_G	0.508	1.00
120_L	123_L	0.508	1.00
153_T	157_N	0.508	1.00
132_L	137_A	0.507	1.00
55_V	60_G	0.506	1.00
75_A	93_T	0.506	1.00
32_L	36_L	0.504	1.00
34_M	37_F	0.502	1.00
79_L	93_T	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
2nq2A	2	0.8394	97.5	0.872	Contact Map
2qi9A	2	0.8667	97.5	0.873	Contact Map
4g1uA	2	0.8061	97.3	0.877	Contact Map
2cfqA	1	0.5879	60.2	0.937	Contact Map
2gfpA	2	0.5758	40.7	0.944	Contact Map
2kluA	1	0.1545	39.2	0.945	Contact Map
4m64A	1	0.6303	32.3	0.947	Contact Map
3wdoA	1	0.9182	31.6	0.947	Contact Map
1u7gA	3	0.5636	29.7	0.948	Contact Map
3d31C	2	0.7182	26	0.95	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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