PLDB - ECOLI - GREMLIN Contacts

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PLDB - Lysophospholipase L2

UniProt:	P07000	Sequences: MFQQQKDWETRENAFAAFTMGPLTDFWRQRDEAEFTGVDDIPVRFVRFRAQHHDRVVVICPGRIESYVKYAELAYDLFHLGFDVLIIDHRGQGRSGRLLADPHLGHVNRFNDYVDDLAAFWQQEVQPGPWRKRYILAHSMGGAISTLFLQRHPGVCDAIALTAPMFGIVIRMPSFMARQILNWAEAHPRFRDGYAIGTGRWRALPFAINVLTHSRQRYRRNLRFYADDPTIRVGGPTYHWVRESILAGEQVLAGAGDDATPTLLLQAEEERVVDNRMHDRFCELRTAAGHPVEGGRPLVIKGAYHEILFEKDAMRSVALHAIVDFFNRHNSPSGNRSTEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10739
Length:	340 (273)
Sequences:	34467 (29192)
Seq/√Len:	1766.8

ECOLI - PLDB MHPC RUTD YBFF BIOH MENH YCJY YFHR
BACSU - YDJP NAP YBFK YISY YFHM YUGF RSBQ MENH YBAC YCGS YRAK PLBAC YBDG YCLE YVAM YQJL EST YQKD CAH
HALSA - Q9HPT9 Q9HHP4 Q9HRJ0
SULSO - PIP Q7LXY9 Q97WG0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_R	83_D	5.016	1.00
134_Y	158_A	4.772	1.00
90_R	116_D	4.323	1.00
268_E	301_K	3.245	1.00
73_L	319_L	3.190	1.00
300_I	321_A	2.928	1.00
298_L	321_A	2.927	1.00
118_A	148_F	2.925	1.00
263_L	325_F	2.666	1.00
132_K	157_D	2.665	1.00
134_Y	157_D	2.629	1.00
42_P	96_G	2.514	1.00
80_L	323_V	2.474	1.00
311_K	317_V	2.464	1.00
163_A	270_E	2.446	1.00
46_V	67_Y	2.407	1.00
121_W	133_R	2.238	1.00
282_C	295_G	2.214	1.00
118_A	152_H	2.201	1.00
162_T	318_A	2.199	1.00
148_F	152_H	2.171	1.00
118_A	122_Q	2.135	1.00
122_Q	155_V	2.118	1.00
44_R	94_R	2.086	1.00
268_E	299_V	2.079	1.00
45_F	120_F	2.069	1.00
142_G	164_P	2.035	1.00
296_R	328_R	2.015	1.00
135_I	145_S	1.980	1.00
76_D	319_L	1.969	1.00
118_A	155_V	1.969	1.00
149_L	159_I	1.929	1.00
134_Y	326_F	1.894	1.00
275_N	299_V	1.873	1.00
60_C	117_L	1.848	1.00
303_A	311_K	1.801	1.00
87_I	117_L	1.784	1.00
61_P	92_Q	1.777	1.00
115_D	151_R	1.761	1.00
145_S	159_I	1.718	1.00
56_V	85_L	1.702	1.00
321_A	324_D	1.686	1.00
44_R	67_Y	1.680	1.00
147_L	151_R	1.680	1.00
47_R	85_L	1.677	1.00
48_F	86_I	1.671	1.00
134_Y	160_A	1.638	1.00
292_V	295_G	1.628	1.00
56_V	83_D	1.619	1.00
38_V	119_A	1.609	1.00
117_L	148_F	1.602	1.00
60_C	89_H	1.589	1.00
89_H	144_I	1.568	1.00
263_L	298_L	1.562	1.00
160_A	322_I	1.553	1.00
56_V	126_Q	1.548	1.00
61_P	89_H	1.545	1.00
111_N	151_R	1.514	1.00
320_H	324_D	1.509	1.00
280_R	284_L	1.492	1.00
49_R	83_D	1.487	1.00
48_F	74_A	1.463	1.00
82_F	134_Y	1.454	1.00
148_F	156_C	1.405	1.00
64_I	139_S	1.399	1.00
60_C	145_S	1.396	1.00
160_A	263_L	1.346	1.00
300_I	303_A	1.344	1.00
65_E	69_K	1.338	1.00
76_D	323_V	1.332	1.00
43_V	116_D	1.322	1.00
279_D	283_E	1.313	1.00
161_L	164_P	1.309	1.00
114_V	147_L	1.297	1.00
59_I	136_L	1.291	1.00
109_R	112_D	1.290	1.00
275_N	279_D	1.288	1.00
41_I	90_R	1.286	1.00
317_V	321_A	1.280	1.00
234_G	237_T	1.280	1.00
59_I	84_V	1.276	1.00
44_R	88_D	1.273	1.00
148_F	155_V	1.256	1.00
147_L	150_Q	1.256	1.00
76_D	79_H	1.254	1.00
55_R	82_F	1.254	1.00
55_R	134_Y	1.246	1.00
74_A	86_I	1.236	1.00
85_L	120_F	1.236	1.00
37_G	42_P	1.229	1.00
296_R	321_A	1.227	1.00
146_T	161_L	1.217	1.00
67_Y	86_I	1.214	1.00
152_H	155_V	1.204	1.00
262_T	292_V	1.202	1.00
50_A	83_D	1.185	1.00
58_V	121_W	1.184	1.00
64_I	92_Q	1.179	1.00
317_V	320_H	1.179	1.00
88_D	93_G	1.161	1.00
43_V	95_S	1.159	1.00
87_I	120_F	1.159	1.00
57_V	82_F	1.156	1.00
82_F	326_F	1.149	1.00
280_R	283_E	1.148	1.00
121_W	148_F	1.143	1.00
36_T	42_P	1.139	1.00
62_G	139_S	1.137	1.00
139_S	305_H	1.116	1.00
76_D	316_S	1.103	1.00
136_L	162_T	1.099	1.00
85_L	124_E	1.092	1.00
266_Q	278_H	1.086	1.00
265_L	300_I	1.082	1.00
69_K	308_L	1.078	1.00
126_Q	133_R	1.077	1.00
218_Y	221_N	1.060	1.00
80_L	327_N	1.048	1.00
136_L	322_I	1.036	1.00
121_W	126_Q	1.033	1.00
312_D	316_S	1.032	1.00
137_A	145_S	1.031	1.00
236_P	240_W	1.025	1.00
223_R	226_A	1.018	1.00
316_S	320_H	1.014	1.00
138_H	308_L	1.013	1.00
82_F	327_N	1.011	1.00
78_F	84_V	1.010	1.00
237_T	240_W	1.009	1.00
120_F	124_E	1.008	1.00
239_H	242_R	1.004	1.00
279_D	282_C	1.003	1.00
39_D	119_A	0.995	1.00
318_A	322_I	0.989	1.00
235_G	239_H	0.988	1.00
220_R	224_F	0.986	1.00
67_Y	88_D	0.983	1.00
279_D	299_V	0.978	1.00
122_Q	152_H	0.976	1.00
268_E	302_G	0.973	1.00
323_V	327_N	0.971	1.00
239_H	243_E	0.970	1.00
238_Y	241_V	0.969	1.00
35_F	38_V	0.966	1.00
55_R	132_K	0.964	1.00
48_F	78_F	0.958	1.00
219_R	223_R	0.956	1.00
192_D	196_I	0.954	1.00
67_Y	94_R	0.948	1.00
254_G	257_D	0.947	1.00
55_R	157_D	0.945	1.00
50_A	53_H	0.944	1.00
221_N	224_F	0.943	1.00
112_D	115_D	0.929	1.00
114_V	144_I	0.929	1.00
263_L	296_R	0.927	1.00
51_Q	83_D	0.926	1.00
178_R	182_N	0.926	1.00
256_G	284_L	0.921	1.00
238_Y	242_R	0.920	1.00
266_Q	297_P	0.916	1.00
133_R	156_C	0.914	1.00
43_V	90_R	0.914	1.00
298_L	317_V	0.907	1.00
266_Q	299_V	0.896	1.00
266_Q	275_N	0.894	1.00
303_A	310_E	0.891	1.00
265_L	318_A	0.887	1.00
241_V	244_S	0.887	1.00
240_W	245_I	0.885	1.00
159_I	262_T	0.876	1.00
75_Y	79_H	0.876	1.00
250_Q	254_G	0.868	1.00
60_C	135_I	0.868	1.00
219_R	222_L	0.867	1.00
184_A	188_P	0.867	1.00
45_F	124_E	0.862	1.00
279_D	297_P	0.860	1.00
193_G	196_I	0.857	1.00
119_A	122_Q	0.854	1.00
41_I	96_G	0.851	1.00
119_A	123_Q	0.850	1.00
135_I	156_C	0.850	1.00
126_Q	132_K	0.850	1.00
58_V	117_L	0.847	1.00
89_H	140_M	0.842	1.00
58_V	133_R	0.841	1.00
265_L	321_A	0.841	1.00
72_E	75_Y	0.834	1.00
296_R	324_D	0.828	1.00
221_N	225_Y	0.828	1.00
181_L	185_E	0.827	1.00
303_A	307_I	0.821	1.00
282_C	297_P	0.821	1.00
236_P	239_H	0.819	1.00
223_R	227_D	0.817	1.00
81_G	323_V	0.816	1.00
57_V	84_V	0.812	1.00
237_T	241_V	0.812	1.00
118_A	151_R	0.811	1.00
235_G	238_Y	0.810	1.00
304_Y	310_E	0.809	1.00
60_C	87_I	0.809	1.00
158_A	325_F	0.809	1.00
138_H	306_E	0.807	1.00
149_L	156_C	0.806	1.00
125_V	131_R	0.805	1.00
88_D	94_R	0.801	1.00
114_V	151_R	0.799	1.00
137_A	142_G	0.794	1.00
220_R	223_R	0.793	1.00
160_A	326_F	0.785	1.00
300_I	317_V	0.783	1.00
240_W	243_E	0.782	1.00
181_L	184_A	0.780	1.00
71_A	86_I	0.777	1.00
46_V	71_A	0.775	1.00
71_A	75_Y	0.775	1.00
136_L	160_A	0.775	1.00
324_D	328_R	0.774	1.00
118_A	121_W	0.772	1.00
224_F	227_D	0.771	1.00
75_Y	78_F	0.771	1.00
182_N	185_E	0.769	1.00
192_D	197_G	0.765	1.00
78_F	81_G	0.763	1.00
133_R	155_V	0.763	1.00
298_L	324_D	0.761	1.00
177_A	181_L	0.760	1.00
74_A	84_V	0.755	1.00
276_R	279_D	0.755	1.00
135_I	148_F	0.749	1.00
234_G	241_V	0.749	1.00
56_V	133_R	0.749	1.00
278_H	297_P	0.746	1.00
259_A	293_E	0.746	1.00
57_V	136_L	0.746	1.00
39_D	112_D	0.744	1.00
156_C	260_T	0.739	1.00
241_V	245_I	0.738	1.00
58_V	135_I	0.737	1.00
139_S	306_E	0.733	1.00
55_R	158_A	0.729	1.00
235_G	240_W	0.729	1.00
113_Y	140_M	0.726	1.00
76_D	80_L	0.726	1.00
224_F	228_D	0.724	1.00
269_E	302_G	0.723	1.00
180_I	184_A	0.722	1.00
53_H	56_V	0.722	1.00
138_H	163_A	0.722	1.00
180_I	183_W	0.721	1.00
234_G	240_W	0.719	1.00
185_E	188_P	0.718	1.00
89_H	113_Y	0.716	1.00
58_V	87_I	0.716	1.00
115_D	119_A	0.714	1.00
56_V	82_F	0.712	1.00
65_E	309_F	0.707	1.00
178_R	181_L	0.705	1.00
162_T	308_L	0.704	1.00
300_I	311_K	0.702	1.00
179_Q	182_N	0.700	1.00
236_P	241_V	0.698	1.00
206_F	211_L	0.697	1.00
59_I	70_Y	0.697	1.00
162_T	307_I	0.696	1.00
59_I	86_I	0.695	1.00
267_A	307_I	0.694	1.00
222_L	225_Y	0.691	1.00
211_L	214_S	0.691	1.00
115_D	118_A	0.691	1.00
228_D	232_R	0.690	1.00
176_M	179_Q	0.686	1.00
249_E	253_A	0.686	1.00
193_G	197_G	0.685	1.00
64_I	140_M	0.684	1.00
240_W	244_S	0.679	1.00
250_Q	253_A	0.679	1.00
214_S	217_R	0.675	1.00
111_N	147_L	0.672	1.00
158_A	326_F	0.670	1.00
182_N	186_A	0.666	1.00
311_K	316_S	0.664	1.00
82_F	323_V	0.663	1.00
163_A	266_Q	0.663	1.00
61_P	87_I	0.658	1.00
146_T	166_F	0.656	1.00
302_G	311_K	0.655	1.00
63_R	140_M	0.655	1.00
225_Y	229_P	0.654	1.00
191_R	197_G	0.651	1.00
147_L	254_G	0.650	1.00
251_V	254_G	0.649	1.00
158_A	261_P	0.646	1.00
319_L	323_V	0.646	1.00
67_Y	87_I	0.645	1.00
149_L	260_T	0.641	1.00
111_N	115_D	0.640	1.00
208_I	212_T	0.639	1.00
68_V	71_A	0.639	1.00
229_P	232_R	0.637	1.00
222_L	226_A	0.634	1.00
74_A	78_F	0.634	1.00
107_V	112_D	0.634	1.00
208_I	211_L	0.634	1.00
163_A	267_A	0.632	1.00
191_R	194_Y	0.630	1.00
243_E	246_L	0.626	1.00
195_A	198_T	0.625	1.00
137_A	141_G	0.622	1.00
150_Q	257_D	0.615	1.00
57_V	134_Y	0.612	1.00
212_T	215_R	0.610	1.00
185_E	189_R	0.610	1.00
178_R	184_A	0.608	1.00
89_H	92_Q	0.607	1.00
88_D	95_S	0.601	1.00
143_A	165_M	0.600	1.00
70_Y	73_L	0.600	1.00
234_G	238_Y	0.599	1.00
242_R	245_I	0.598	1.00
184_A	190_F	0.597	1.00
57_V	326_F	0.596	1.00
120_F	123_Q	0.595	1.00
44_R	95_S	0.593	1.00
175_F	179_Q	0.590	1.00
194_Y	197_G	0.589	1.00
207_A	210_V	0.589	1.00
81_G	84_V	0.588	1.00
179_Q	183_W	0.588	1.00
59_I	77_L	0.584	1.00
204_L	207_A	0.583	1.00
72_E	319_L	0.583	1.00
37_G	119_A	0.582	1.00
180_I	185_E	0.582	1.00
235_G	241_V	0.580	1.00
264_L	295_G	0.579	1.00
186_A	189_R	0.576	1.00
133_R	157_D	0.574	1.00
183_W	187_H	0.574	1.00
266_Q	273_V	0.573	1.00
47_R	50_A	0.572	1.00
89_H	117_L	0.571	1.00
228_D	231_I	0.570	1.00
207_A	211_L	0.570	1.00
237_T	243_E	0.569	1.00
268_E	275_N	0.568	1.00
160_A	265_L	0.562	1.00
191_R	195_A	0.561	1.00
276_R	280_R	0.560	1.00
190_F	193_G	0.559	1.00
179_Q	187_H	0.558	1.00
176_M	182_N	0.557	1.00
57_V	77_L	0.557	1.00
49_R	53_H	0.556	1.00
236_P	243_E	0.556	1.00
159_I	260_T	0.553	1.00
131_R	155_V	0.550	1.00
236_P	244_S	0.546	1.00
187_H	190_F	0.545	1.00
270_E	305_H	0.545	1.00
46_V	68_V	0.544	1.00
182_N	188_P	0.543	1.00
264_L	297_P	0.542	1.00
62_G	138_H	0.542	1.00
202_R	205_P	0.540	1.00
175_F	178_R	0.539	1.00
217_R	221_N	0.539	1.00
114_V	148_F	0.539	1.00
177_A	180_I	0.535	1.00
306_E	309_F	0.534	1.00
121_W	155_V	0.533	1.00
142_G	163_A	0.532	1.00
277_M	280_R	0.532	1.00
126_Q	131_R	0.531	1.00
320_H	323_V	0.528	1.00
237_T	244_S	0.527	1.00
146_T	164_P	0.527	1.00
217_R	220_R	0.526	1.00
180_I	188_P	0.525	1.00
229_P	233_V	0.523	1.00
186_A	190_F	0.523	1.00
114_V	118_A	0.520	1.00
237_T	242_R	0.519	1.00
113_Y	144_I	0.518	1.00
121_W	156_C	0.517	1.00
160_A	325_F	0.517	1.00
39_D	116_D	0.517	1.00
255_A	258_D	0.516	1.00
192_D	195_A	0.515	1.00
238_Y	244_S	0.515	1.00
63_R	92_Q	0.513	1.00
278_H	282_C	0.513	1.00
206_F	209_N	0.512	1.00
68_V	94_R	0.512	1.00
163_A	307_I	0.511	1.00
194_Y	198_T	0.510	1.00
176_M	180_I	0.509	1.00
209_N	213_H	0.507	1.00
138_H	162_T	0.507	1.00
188_P	192_D	0.507	1.00
188_P	191_R	0.506	1.00
60_C	144_I	0.505	1.00
184_A	187_H	0.504	1.00
79_H	323_V	0.504	1.00
140_M	144_I	0.504	1.00
73_L	76_D	0.501	1.00
234_G	239_H	0.500	1.00
104_L	107_V	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
3om8A	4	0.7735	100	0.321	Contact Map
1zoiA	3	0.7971	100	0.325	Contact Map
3oosA	1	0.7912	100	0.329	Contact Map
4psuA	1	0.8294	100	0.333	Contact Map
2pujA	4	0.8088	100	0.333	Contact Map
1ehyA	1	0.7941	100	0.335	Contact Map
4inzA	1	0.7853	100	0.337	Contact Map
2wueA	4	0.7971	100	0.338	Contact Map
2xuaA	2	0.7618	100	0.338	Contact Map
1q0rA	1	0.8176	100	0.34	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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