YVRE - BACSU - GREMLIN Contacts

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YVRE - Putative sugar lactone lactonase YvrE

UniProt:	O34940	Sequences: MDAVLEADTRAVIGEGPLWDEENGRLYWVDILGSELHIFDPEEKINRSIKFKSFVTALAKYSKDELIMTMKDGFYLYHLRDDSLEKIKQPKDMHESLRFNDAKCDPYGRLWAGTTSMEGEQKQASLYRLNLDGSLVKIKDQVSTSNGLDWDRERNLMYYIDTPTQEIVRYSYDPQSGDVSNPEPVYRFDQSDGLPDGMTIDQNGMLWVALFGGSRVVHIDPFQKKEINSISVPAKYVTCCAFGGRDLKTLYITTATEQMTEKERYEQPHAGGLFSAQLETGGYQPVPFAGDV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	292 (231)
Sequences:	18880 (15271)
Seq/√Len:	1004.8

ECOLI - YNCE 6PGL TOLB BAMB
BACSU - YVRE YWHL 6PGL YWHK YXAL
HALSA - Q9HHP3 Q9HS46
SULSO - Q97VC7 Q97UH7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
124_A	128_R	3.771	1.00
147_G	161_D	3.036	1.00
197_G	210_L	2.880	1.00
239_C	253_T	2.834	1.00
101_D	114_T	2.743	1.00
16_G	30_D	2.613	1.00
28_W	38_I	2.603	1.00
209_A	219_I	2.475	1.00
243_G	246_D	2.459	1.00
103_K	149_D	2.391	1.00
29_V	39_F	2.382	1.00
217_V	226_E	2.361	1.00
251_Y	261_E	2.353	1.00
75_Y	84_L	2.304	1.00
233_P	252_I	2.296	1.00
159_Y	169_R	2.198	1.00
124_A	127_Y	2.187	1.00
208_V	218_H	2.179	1.00
191_S	209_A	2.141	1.00
216_V	252_I	2.114	1.00
167_I	209_A	2.087	1.00
208_V	242_F	2.074	1.00
252_I	262_K	1.996	1.00
112_A	150_W	1.993	1.00
159_Y	200_I	1.982	1.00
141_Q	160_I	1.928	1.00
59_A	103_K	1.917	1.00
160_I	170_Y	1.914	1.00
217_V	229_S	1.900	1.00
159_Y	207_W	1.843	1.00
220_D	223_Q	1.833	1.00
20_D	23_N	1.815	1.00
28_W	60_K	1.813	1.00
149_D	199_T	1.772	1.00
171_S	174_P	1.734	1.00
105_D	150_W	1.720	1.00
61_Y	104_C	1.703	1.00
113_G	129_L	1.688	1.00
161_D	195_P	1.679	1.00
146_N	163_P	1.656	1.00
199_T	241_A	1.628	1.00
78_H	81_D	1.626	1.00
56_T	70_M	1.595	1.00
124_A	129_L	1.587	1.00
40_D	43_E	1.551	1.00
196_D	212_G	1.540	1.00
219_I	226_E	1.536	1.00
20_D	60_K	1.527	1.00
91_K	113_G	1.506	1.00
112_A	158_Y	1.495	1.00
105_D	109_R	1.486	1.00
184_P	187_R	1.478	1.00
151_D	200_I	1.468	1.00
141_Q	162_T	1.438	1.00
208_V	250_L	1.421	1.00
75_Y	87_I	1.407	1.00
36_L	69_T	1.396	1.00
233_P	254_T	1.388	1.00
210_L	237_V	1.385	1.00
201_D	242_F	1.384	1.00
18_L	59_A	1.359	1.00
238_T	255_A	1.328	1.00
68_M	76_L	1.328	1.00
84_L	87_I	1.326	1.00
215_R	229_S	1.323	1.00
18_L	58_L	1.322	1.00
74_F	113_G	1.311	1.00
29_V	37_H	1.296	1.00
112_A	148_L	1.293	1.00
31_I	35_E	1.292	1.00
201_D	205_M	1.282	1.00
51_F	69_T	1.278	1.00
115_T	123_Q	1.273	1.00
208_V	240_C	1.269	1.00
68_M	104_C	1.266	1.00
112_A	128_R	1.263	1.00
161_D	198_M	1.258	1.00
114_T	145_S	1.255	1.00
252_I	260_T	1.252	1.00
226_E	229_S	1.249	1.00
28_W	58_L	1.237	1.00
210_L	240_C	1.236	1.00
31_I	34_S	1.218	1.00
123_Q	127_Y	1.202	1.00
69_T	77_Y	1.193	1.00
103_K	148_L	1.193	1.00
211_F	217_V	1.188	1.00
254_T	258_Q	1.185	1.00
201_D	204_G	1.183	1.00
149_D	198_M	1.183	1.00
77_Y	84_L	1.165	1.00
168_V	184_P	1.163	1.00
20_D	25_R	1.153	1.00
62_S	108_G	1.143	1.00
243_G	251_Y	1.125	1.00
162_T	166_E	1.111	1.00
243_G	248_K	1.110	1.00
159_Y	198_M	1.106	1.00
232_V	260_T	1.105	1.00
232_V	262_K	1.095	1.00
209_A	217_V	1.091	1.00
124_A	131_L	1.087	1.00
146_N	196_D	1.087	1.00
199_T	240_C	1.075	1.00
125_S	137_K	1.074	1.00
28_W	67_I	1.070	1.00
19_W	27_Y	1.058	1.00
51_F	77_Y	1.039	1.00
151_D	155_N	1.037	1.00
190_Q	219_I	1.034	1.00
62_S	104_C	1.034	1.00
221_P	224_K	1.031	1.00
243_G	249_T	1.025	1.00
202_Q	247_L	1.023	1.00
148_L	160_I	1.021	1.00
249_T	263_E	1.015	1.00
206_L	218_H	1.015	1.00
30_D	55_V	1.013	1.00
242_F	250_L	1.013	1.00
243_G	247_L	1.012	1.00
66_L	69_T	1.012	1.00
68_M	111_W	1.005	1.00
147_G	197_G	1.003	1.00
31_I	37_H	1.002	1.00
160_I	168_V	0.996	1.00
206_L	227_I	0.991	1.00
194_L	212_G	0.983	1.00
168_V	187_R	0.983	1.00
191_S	211_F	0.977	1.00
152_R	200_I	0.975	1.00
141_Q	145_S	0.972	1.00
61_Y	65_E	0.969	1.00
144_T	163_P	0.967	1.00
241_A	251_Y	0.960	1.00
202_Q	242_F	0.960	1.00
254_T	257_E	0.958	1.00
59_A	102_A	0.958	1.00
51_F	55_V	0.955	1.00
15_E	32_L	0.954	1.00
100_N	146_N	0.936	1.00
151_D	157_M	0.933	1.00
200_I	207_W	0.928	1.00
102_A	113_G	0.913	1.00
25_R	40_D	0.911	1.00
20_D	24_G	0.908	1.00
150_W	158_Y	0.908	1.00
113_G	127_Y	0.898	1.00
26_L	38_I	0.894	1.00
105_D	110_L	0.893	1.00
65_E	68_M	0.889	1.00
216_V	240_C	0.879	1.00
104_C	111_W	0.878	1.00
59_A	104_C	0.878	1.00
57_A	101_D	0.876	1.00
73_G	89_Q	0.873	1.00
106_P	150_W	0.873	1.00
36_L	58_L	0.869	1.00
37_H	46_N	0.865	1.00
196_D	238_T	0.864	1.00
123_Q	128_R	0.858	1.00
220_D	227_I	0.854	1.00
249_T	261_E	0.846	1.00
41_P	44_K	0.846	1.00
74_F	102_A	0.845	1.00
197_G	239_C	0.845	1.00
233_P	237_V	0.844	1.00
215_R	231_S	0.844	1.00
32_L	54_F	0.843	1.00
101_D	148_L	0.842	1.00
101_D	147_G	0.836	1.00
114_T	148_L	0.834	1.00
127_Y	131_L	0.822	1.00
37_H	47_R	0.820	1.00
128_R	131_L	0.817	1.00
191_S	195_P	0.807	1.00
73_G	87_I	0.806	1.00
207_W	221_P	0.804	1.00
19_W	41_P	0.799	1.00
200_I	221_P	0.797	1.00
152_R	204_G	0.797	1.00
126_L	160_I	0.793	1.00
151_D	154_R	0.791	1.00
79_L	82_D	0.787	1.00
199_T	242_F	0.785	1.00
218_H	230_I	0.780	1.00
211_F	215_R	0.780	1.00
201_D	206_L	0.780	1.00
169_R	200_I	0.777	1.00
240_C	252_I	0.775	1.00
65_E	78_H	0.775	1.00
201_D	208_V	0.774	1.00
145_S	160_I	0.773	1.00
162_T	165_Q	0.772	1.00
182_P	185_V	0.769	1.00
141_Q	164_T	0.766	1.00
78_H	85_E	0.765	1.00
240_C	250_L	0.765	1.00
213_G	217_V	0.764	1.00
150_W	172_Y	0.764	1.00
57_A	102_A	0.764	1.00
135_L	138_I	0.762	1.00
30_D	58_L	0.756	1.00
68_M	77_Y	0.750	1.00
197_G	240_C	0.746	1.00
205_M	220_D	0.742	1.00
30_D	34_S	0.736	1.00
232_V	252_I	0.736	1.00
48_S	51_F	0.735	1.00
148_L	158_Y	0.732	1.00
143_S	163_P	0.728	1.00
140_D	170_Y	0.721	1.00
50_K	75_Y	0.721	1.00
61_Y	64_D	0.718	1.00
195_P	209_A	0.717	1.00
68_M	102_A	0.715	1.00
205_M	222_F	0.710	1.00
17_P	29_V	0.706	1.00
233_P	256_T	0.705	1.00
184_P	188_F	0.705	1.00
33_G	37_H	0.702	1.00
212_G	236_Y	0.701	1.00
147_G	198_M	0.700	1.00
203_N	206_L	0.694	1.00
235_K	255_A	0.694	1.00
104_C	150_W	0.694	1.00
60_K	79_L	0.693	1.00
210_L	214_S	0.691	1.00
18_L	60_K	0.689	1.00
155_N	173_D	0.686	1.00
128_R	136_V	0.685	1.00
141_Q	168_V	0.678	1.00
84_L	226_E	0.676	1.00
164_T	168_V	0.675	1.00
29_V	33_G	0.673	1.00
198_M	209_A	0.668	1.00
185_V	188_F	0.667	1.00
28_W	36_L	0.665	1.00
91_K	99_F	0.659	1.00
14_G	17_P	0.658	1.00
162_T	168_V	0.657	1.00
76_L	104_C	0.655	1.00
61_Y	66_L	0.655	1.00
233_P	260_T	0.655	1.00
99_F	115_T	0.653	1.00
50_K	77_Y	0.653	1.00
220_D	225_K	0.653	1.00
99_F	102_A	0.650	1.00
69_T	75_Y	0.645	1.00
210_L	252_I	0.643	1.00
38_I	60_K	0.642	1.00
25_R	42_E	0.639	1.00
193_G	212_G	0.639	1.00
186_Y	189_D	0.637	1.00
58_L	69_T	0.637	1.00
127_Y	137_K	0.635	1.00
167_I	198_M	0.633	1.00
19_W	104_C	0.632	1.00
74_F	88_K	0.630	1.00
60_K	67_I	0.629	1.00
99_F	113_G	0.628	1.00
237_V	252_I	0.627	1.00
103_K	150_W	0.626	1.00
158_Y	172_Y	0.626	1.00
163_P	194_L	0.624	1.00
110_L	114_T	0.624	1.00
110_L	172_Y	0.622	1.00
20_D	28_W	0.621	1.00
211_F	214_S	0.620	1.00
246_D	249_T	0.619	1.00
78_H	83_S	0.619	1.00
232_V	254_T	0.610	1.00
150_W	200_I	0.607	1.00
53_S	70_M	0.606	1.00
123_Q	129_L	0.606	1.00
191_S	213_G	0.605	1.00
65_E	69_T	0.605	1.00
166_E	187_R	0.605	1.00
54_F	70_M	0.602	1.00
190_Q	217_V	0.599	1.00
27_Y	41_P	0.599	1.00
238_T	253_T	0.598	1.00
174_P	183_E	0.593	1.00
109_R	130_N	0.593	1.00
248_K	263_E	0.592	1.00
106_P	154_R	0.591	1.00
236_Y	255_A	0.588	1.00
256_T	260_T	0.583	1.00
211_F	219_I	0.582	1.00
216_V	237_V	0.581	1.00
103_K	112_A	0.580	1.00
160_I	164_T	0.578	1.00
122_K	128_R	0.578	1.00
40_D	44_K	0.577	1.00
242_F	264_R	0.577	1.00
162_T	170_Y	0.577	1.00
149_D	200_I	0.575	1.00
97_L	115_T	0.573	1.00
141_Q	170_Y	0.573	1.00
188_F	191_S	0.572	1.00
20_D	26_L	0.571	1.00
115_T	125_S	0.570	1.00
181_N	184_P	0.568	1.00
252_I	256_T	0.567	1.00
155_N	171_S	0.566	1.00
35_E	47_R	0.566	1.00
171_S	181_N	0.565	1.00
23_N	26_L	0.565	1.00
90_P	113_G	0.564	1.00
53_S	71_K	0.563	1.00
76_L	88_K	0.560	1.00
71_K	75_Y	0.558	1.00
112_A	126_L	0.551	1.00
171_S	183_E	0.549	1.00
163_P	196_D	0.548	1.00
122_K	144_T	0.548	1.00
169_R	183_E	0.548	1.00
51_F	68_M	0.543	1.00
105_D	112_A	0.542	1.00
140_D	168_V	0.541	1.00
104_C	131_L	0.539	1.00
51_F	75_Y	0.538	1.00
40_D	45_I	0.537	1.00
30_D	33_G	0.536	1.00
174_P	182_P	0.531	1.00
253_T	257_E	0.530	1.00
18_L	28_W	0.529	1.00
145_S	162_T	0.528	1.00
81_D	85_E	0.527	1.00
216_V	230_I	0.525	1.00
253_T	259_M	0.524	1.00
55_V	58_L	0.515	1.00
105_D	108_G	0.514	1.00
57_A	69_T	0.514	1.00
165_Q	194_L	0.512	1.00
91_K	115_T	0.512	1.00
51_F	71_K	0.511	1.00
125_S	128_R	0.511	1.00
135_L	139_K	0.510	1.00
100_N	122_K	0.509	1.00
206_L	242_F	0.509	1.00
56_T	100_N	0.509	1.00
161_D	209_A	0.508	1.00
63_K	66_L	0.508	1.00
66_L	85_E	0.501	1.00
67_I	76_L	0.500	1.00
70_M	100_N	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
1vyhC	1	0.8322	100	0.164	Contact Map
4u1eI	1	0.9178	100	0.185	Contact Map
1gotB	1	0.8322	100	0.194	Contact Map
4wjuA	1	0.8322	100	0.196	Contact Map
3ow8A	3	0.9247	100	0.199	Contact Map
4j73A	1	0.9178	100	0.199	Contact Map
3dm0A	1	0.9281	100	0.203	Contact Map
3sfzA	1	0.9486	100	0.206	Contact Map
3j60g	1	0.8733	100	0.206	Contact Map
4j87A	1	0.9384	100	0.209	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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