Q9HQI3 - HALSA - GREMLIN Contacts

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Q9HQI3 - Geranylgeranyl diphosphate synthase

UniProt:	Q9HQI3	Sequences: MSQEARERAVLAAVRERRQQVNDAIDDDLPVAEPERLYEASRYILEAGGKRLRPAVLLLTAEALADTSDTPPYREFPDCIGGHVDVMSAAVSIEVIQSFTLIHDDIMDDDDLRRGSPAVHREYDTETAILAGDTLYSKAFEIMLETGAPPERGLRAMRTLAETCTHICEGQAMDIDFETRGDVVTDEYLEMVELKTAVLYAAAATLPGLLLSADEETVEALYNYGLRVGQAFQIQDDVLDLTVPSAELGKQRGSDLVEDKTTIITLHAAEHGVDVDGLLDAEDPADVTEAAVQAAVQALQDAGSIQYASDLAEDLVEEGKAHLEVLPENEARHRLEQIADYLIERGY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	347 (312)
Sequences:	7842 (5217)
Seq/√Len:	295.4

ECOLI - ISPB ISPA
BACSU - HEPS2 ISPA COMQ
HALSA - Q9HQI3 Q9HND0
SULSO - GGPS HEXPP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
214_D	217_T	3.240	1.00
227_R	318_E	3.102	1.00
320_K	340_D	3.009	1.00
297_Q	301_D	2.976	1.00
61_A	86_V	2.952	1.00
227_R	315_L	2.919	1.00
271_H	307_Y	2.916	1.00
111_D	121_R	2.711	1.00
205_T	222_Y	2.671	1.00
288_T	291_A	2.615	1.00
311_L	314_D	2.607	1.00
267_H	307_Y	2.603	1.00
320_K	336_E	2.539	1.00
193_E	226_L	2.358	1.00
303_G	306_Q	2.328	1.00
205_T	218_V	2.309	1.00
317_E	321_A	2.273	1.00
267_H	304_S	2.271	1.00
324_E	336_E	2.243	1.00
278_L	281_A	2.238	1.00
223_N	322_H	2.212	1.00
276_D	301_D	2.208	1.00
238_V	308_A	2.068	1.00
107_M	171_Q	2.048	1.00
201_A	222_Y	2.047	1.00
159_T	205_T	2.028	1.00
60_T	221_L	1.973	1.00
219_E	223_N	1.958	1.00
306_Q	310_D	1.931	1.00
159_T	209_L	1.918	1.00
332_R	336_E	1.901	1.00
208_G	221_L	1.890	1.00
244_P	247_E	1.868	1.00
184_V	187_E	1.854	1.00
314_D	318_E	1.836	1.00
102_I	119_V	1.814	1.00
273_V	276_D	1.805	1.00
321_A	324_E	1.800	1.00
313_E	317_E	1.768	1.00
156_A	206_L	1.762	1.00
300_Q	305_I	1.729	1.00
17_R	62_E	1.718	1.00
306_Q	309_S	1.702	1.00
60_T	204_A	1.698	1.00
234_I	308_A	1.695	1.00
88_S	145_E	1.693	1.00
103_H	133_D	1.688	1.00
223_N	227_R	1.683	1.00
310_D	314_D	1.665	1.00
141_E	162_E	1.660	1.00
155_R	218_V	1.657	1.00
268_A	299_L	1.647	1.00
22_N	51_R	1.637	1.00
124_D	127_T	1.629	1.00
204_A	225_G	1.612	1.00
171_Q	174_D	1.597	1.00
103_H	132_G	1.590	1.00
106_I	125_T	1.575	1.00
24_A	27_D	1.573	1.00
294_A	297_Q	1.566	1.00
24_A	91_V	1.566	1.00
328_E	332_R	1.542	1.00
213_A	217_T	1.536	1.00
64_L	217_T	1.528	1.00
238_V	305_I	1.504	1.00
190_E	194_L	1.502	1.00
310_D	313_E	1.498	1.00
100_T	167_I	1.485	1.00
299_L	304_S	1.478	1.00
267_H	270_E	1.476	1.00
320_K	339_A	1.473	1.00
238_V	309_S	1.467	1.00
243_V	248_L	1.463	1.00
24_A	88_S	1.455	1.00
155_R	215_E	1.452	1.00
112_L	117_P	1.445	1.00
220_A	325_V	1.444	1.00
311_L	315_L	1.441	1.00
278_L	294_A	1.429	1.00
110_D	254_S	1.411	1.00
201_A	226_L	1.406	1.00
138_K	141_E	1.392	1.00
251_Q	254_S	1.392	1.00
329_N	332_R	1.384	1.00
207_P	211_L	1.379	1.00
208_G	213_A	1.375	1.00
327_P	332_R	1.374	1.00
166_H	194_L	1.373	1.00
322_H	325_V	1.372	1.00
155_R	158_R	1.364	1.00
64_L	207_P	1.357	1.00
230_Q	315_L	1.349	1.00
215_E	219_E	1.344	1.00
316_V	320_K	1.344	1.00
185_T	270_E	1.339	1.00
278_L	282_E	1.333	1.00
185_T	311_L	1.330	1.00
270_E	307_Y	1.327	1.00
294_A	298_A	1.325	1.00
188_Y	192_V	1.324	1.00
257_V	289_E	1.307	1.00
227_R	322_H	1.298	1.00
193_E	230_Q	1.291	1.00
145_E	158_R	1.284	1.00
267_H	271_H	1.281	1.00
224_Y	323_L	1.249	1.00
316_V	343_I	1.248	1.00
307_Y	310_D	1.246	1.00
199_L	203_A	1.242	1.00
22_N	25_I	1.230	1.00
268_A	304_S	1.230	1.00
180_R	187_E	1.216	1.00
296_V	300_Q	1.202	1.00
190_E	193_E	1.202	1.00
278_L	283_D	1.196	1.00
185_T	267_H	1.195	1.00
16_E	19_Q	1.187	1.00
290_A	293_Q	1.182	1.00
23_D	27_D	1.169	1.00
293_Q	297_Q	1.164	1.00
304_S	307_Y	1.162	1.00
89_A	206_L	1.153	1.00
107_M	130_L	1.152	1.00
333_H	337_Q	1.152	1.00
58_L	90_A	1.147	1.00
328_E	333_H	1.143	1.00
155_R	209_L	1.143	1.00
92_S	143_M	1.140	1.00
235_Q	309_S	1.137	1.00
333_H	336_E	1.136	1.00
185_T	307_Y	1.129	1.00
268_A	302_A	1.127	1.00
220_A	322_H	1.126	1.00
26_D	42_R	1.125	1.00
118_A	121_R	1.124	1.00
235_Q	312_A	1.121	1.00
242_T	305_I	1.121	1.00
141_E	165_T	1.119	1.00
173_M	190_E	1.118	1.00
205_T	219_E	1.112	1.00
48_G	51_R	1.107	1.00
64_L	211_L	1.107	1.00
42_R	46_E	1.105	1.00
272_G	276_D	1.104	1.00
47_A	116_S	1.102	1.00
253_G	292_V	1.100	1.00
192_V	230_Q	1.096	1.00
189_L	230_Q	1.088	1.00
224_Y	339_A	1.085	1.00
315_L	318_E	1.083	1.00
60_T	64_L	1.074	1.00
177_F	191_M	1.071	1.00
144_L	157_M	1.070	1.00
272_G	302_A	1.069	1.00
62_E	331_A	1.061	1.00
109_D	125_T	1.058	1.00
89_A	156_A	1.048	1.00
263_I	311_L	1.047	1.00
188_Y	266_L	1.045	1.00
272_G	298_A	1.043	1.00
120_H	125_T	1.043	1.00
63_A	326_L	1.037	1.00
61_A	66_D	1.031	1.00
263_I	308_A	1.027	1.00
324_E	332_R	1.026	1.00
191_M	260_K	1.024	1.00
336_E	340_D	1.024	1.00
57_L	93_I	1.022	1.00
340_D	344_E	1.011	1.00
208_G	218_V	1.011	1.00
317_E	320_K	1.007	1.00
106_I	129_I	1.005	1.00
56_V	204_A	0.999	1.00
297_Q	300_Q	0.998	1.00
21_V	25_I	0.988	1.00
63_A	221_L	0.987	1.00
66_D	83_H	0.986	1.00
64_L	213_A	0.984	1.00
274_D	277_G	0.982	1.00
291_A	294_A	0.975	1.00
174_D	260_K	0.974	1.00
239_L	248_L	0.972	1.00
279_L	283_D	0.971	1.00
268_A	298_A	0.969	1.00
56_V	228_V	0.964	1.00
189_L	315_L	0.956	1.00
143_M	156_A	0.954	1.00
313_E	344_E	0.951	1.00
41_S	135_L	0.951	1.00
318_E	321_A	0.949	1.00
216_E	220_A	0.945	1.00
59_L	62_E	0.943	1.00
329_N	333_H	0.942	1.00
224_Y	322_H	0.940	1.00
156_A	210_L	0.937	1.00
253_G	296_V	0.932	1.00
20_Q	23_D	0.931	1.00
20_Q	84_V	0.930	1.00
158_R	162_E	0.930	1.00
19_Q	22_N	0.926	1.00
15_R	19_Q	0.913	1.00
223_N	318_E	0.909	1.00
293_Q	296_V	0.900	1.00
245_S	251_Q	0.898	1.00
43_Y	122_E	0.898	1.00
38_Y	42_R	0.895	1.00
217_T	220_A	0.890	1.00
24_A	28_D	0.889	1.00
173_M	194_L	0.887	1.00
43_Y	123_Y	0.873	1.00
189_L	311_L	0.871	1.00
91_V	142_I	0.865	1.00
316_V	339_A	0.863	1.00
309_S	313_E	0.863	1.00
26_D	46_E	0.862	1.00
267_H	311_L	0.862	1.00
53_R	232_F	0.861	1.00
177_F	187_E	0.859	1.00
23_D	26_D	0.857	1.00
276_D	302_A	0.854	1.00
58_L	86_V	0.848	1.00
14_V	55_A	0.845	1.00
66_D	86_V	0.844	1.00
40_A	119_V	0.841	1.00
219_E	222_Y	0.832	1.00
238_V	242_T	0.829	1.00
300_Q	306_Q	0.829	1.00
28_D	145_E	0.829	1.00
35_E	39_E	0.828	1.00
226_L	230_Q	0.827	1.00
325_V	332_R	0.827	1.00
239_L	243_V	0.827	1.00
22_N	26_D	0.826	1.00
102_I	128_A	0.826	1.00
220_A	224_Y	0.825	1.00
254_S	258_E	0.824	1.00
289_E	293_Q	0.822	1.00
16_E	20_Q	0.810	1.00
57_L	90_A	0.808	1.00
97_Q	100_T	0.803	1.00
280_D	283_D	0.803	1.00
89_A	210_L	0.802	1.00
117_P	121_R	0.798	0.99
305_I	309_S	0.797	0.99
119_V	123_Y	0.796	0.99
159_T	202_A	0.795	0.99
337_Q	340_D	0.795	0.99
215_E	218_V	0.792	0.99
177_F	183_V	0.787	0.99
19_Q	23_D	0.786	0.99
314_D	317_E	0.786	0.99
52_L	342_L	0.785	0.99
100_T	199_L	0.784	0.99
20_Q	87_M	0.776	0.99
21_V	58_L	0.772	0.99
248_L	252_R	0.772	0.99
185_T	266_L	0.771	0.99
281_A	284_P	0.768	0.99
36_R	176_D	0.763	0.99
138_K	165_T	0.762	0.99
61_A	211_L	0.762	0.99
112_L	245_S	0.762	0.99
163_T	202_A	0.758	0.99
204_A	221_L	0.758	0.99
209_L	218_V	0.756	0.99
287_V	291_A	0.754	0.99
102_I	135_L	0.749	0.99
85_D	146_T	0.747	0.99
304_S	308_A	0.745	0.99
167_I	200_Y	0.745	0.99
140_F	161_A	0.740	0.99
278_L	295_A	0.739	0.99
14_V	18_R	0.734	0.99
241_L	264_I	0.732	0.99
110_D	240_D	0.731	0.99
127_T	172_A	0.728	0.99
281_A	285_A	0.728	0.99
238_V	312_A	0.727	0.99
232_F	236_D	0.726	0.99
196_T	232_F	0.726	0.99
51_R	54_P	0.718	0.99
307_Y	311_L	0.717	0.99
41_S	131_A	0.717	0.99
224_Y	335_L	0.714	0.99
201_A	205_T	0.713	0.99
313_E	343_I	0.712	0.99
203_A	207_P	0.708	0.99
59_L	334_R	0.707	0.99
242_T	309_S	0.704	0.99
159_T	163_T	0.702	0.99
299_L	302_A	0.701	0.99
295_A	299_L	0.700	0.99
67_T	85_D	0.698	0.99
107_M	168_C	0.698	0.99
53_R	97_Q	0.696	0.99
223_N	226_L	0.696	0.99
46_E	116_S	0.696	0.99
263_I	267_H	0.695	0.99
202_A	206_L	0.694	0.99
200_Y	203_A	0.689	0.99
280_D	284_P	0.687	0.98
84_V	88_S	0.685	0.98
189_L	193_E	0.684	0.98
204_A	224_Y	0.684	0.98
185_T	263_I	0.683	0.98
271_H	303_G	0.682	0.98
111_D	120_H	0.678	0.98
14_V	21_V	0.677	0.98
240_D	248_L	0.675	0.98
243_V	247_E	0.675	0.98
67_T	83_H	0.674	0.98
166_H	193_E	0.673	0.98
67_T	84_V	0.672	0.98
102_I	106_I	0.672	0.98
137_S	164_C	0.672	0.98
49_G	53_R	0.669	0.98
231_A	319_G	0.663	0.98
89_A	143_M	0.663	0.98
43_Y	116_S	0.663	0.98
163_T	198_V	0.660	0.98
85_D	147_G	0.658	0.98
292_V	296_V	0.657	0.98
141_E	145_E	0.657	0.98
93_I	206_L	0.653	0.98
197_A	230_Q	0.652	0.98
173_M	191_M	0.652	0.98
331_A	334_R	0.651	0.98
217_T	327_P	0.650	0.98
310_D	317_E	0.649	0.98
330_E	333_H	0.648	0.98
242_T	300_Q	0.648	0.98
50_K	236_D	0.648	0.98
141_E	158_R	0.646	0.98
275_V	278_L	0.645	0.98
218_V	222_Y	0.644	0.98
57_L	203_A	0.643	0.98
283_D	286_D	0.643	0.98
321_A	325_V	0.643	0.98
334_R	337_Q	0.641	0.98
198_V	201_A	0.638	0.98
185_T	189_L	0.638	0.98
89_A	146_T	0.636	0.98
30_P	38_Y	0.635	0.97
147_G	153_G	0.634	0.97
17_R	58_L	0.634	0.97
40_A	43_Y	0.632	0.97
86_V	210_L	0.632	0.97
272_G	275_V	0.632	0.97
206_L	210_L	0.631	0.97
268_A	295_A	0.631	0.97
88_S	146_T	0.631	0.97
92_S	160_L	0.629	0.97
220_A	223_N	0.628	0.97
60_T	207_P	0.628	0.97
265_T	295_A	0.627	0.97
99_F	107_M	0.625	0.97
17_R	20_Q	0.624	0.97
107_M	175_I	0.623	0.97
236_D	239_L	0.621	0.97
18_R	22_N	0.621	0.97
227_R	230_Q	0.621	0.97
36_R	39_E	0.620	0.97
30_P	42_R	0.619	0.97
194_L	198_V	0.618	0.97
24_A	87_M	0.617	0.97
40_A	131_A	0.616	0.97
160_L	206_L	0.616	0.97
106_I	126_E	0.614	0.97
92_S	146_T	0.613	0.97
41_S	134_T	0.612	0.97
231_A	312_A	0.612	0.97
290_A	294_A	0.610	0.97
144_L	158_R	0.609	0.97
136_Y	168_C	0.608	0.97
298_A	301_D	0.607	0.97
284_P	291_A	0.607	0.97
236_D	250_K	0.603	0.97
163_T	201_A	0.602	0.97
245_S	252_R	0.600	0.96
282_E	286_D	0.599	0.96
154_L	158_R	0.599	0.96
95_V	135_L	0.598	0.96
244_P	248_L	0.598	0.96
205_T	209_L	0.597	0.96
96_I	160_L	0.597	0.96
44_I	262_T	0.597	0.96
330_E	334_R	0.596	0.96
117_P	122_E	0.596	0.96
39_E	43_Y	0.595	0.96
41_S	44_I	0.594	0.96
186_D	190_E	0.594	0.96
99_F	136_Y	0.590	0.96
173_M	176_D	0.590	0.96
137_S	168_C	0.589	0.96
57_L	207_P	0.589	0.96
189_L	234_I	0.588	0.96
231_A	316_V	0.587	0.96
44_I	119_V	0.585	0.96
50_K	232_F	0.584	0.96
104_D	108_D	0.583	0.96
305_I	308_A	0.581	0.96
196_T	236_D	0.581	0.96
105_D	113_R	0.580	0.96
323_L	336_E	0.580	0.96
88_S	142_I	0.580	0.96
174_D	178_E	0.577	0.96
235_Q	238_V	0.576	0.96
178_E	258_E	0.576	0.96
328_E	336_E	0.574	0.95
63_A	331_A	0.573	0.95
174_D	261_T	0.573	0.95
45_L	98_S	0.572	0.95
142_I	145_E	0.572	0.95
245_S	248_L	0.571	0.95
20_Q	24_A	0.568	0.95
21_V	91_V	0.564	0.95
96_I	139_A	0.564	0.95
337_Q	341_Y	0.564	0.95
313_E	340_D	0.562	0.95
195_K	233_Q	0.561	0.95
13_A	334_R	0.559	0.95
273_V	277_G	0.557	0.95
288_T	293_Q	0.556	0.95
176_D	180_R	0.553	0.94
140_F	143_M	0.551	0.94
28_D	142_I	0.550	0.94
234_I	312_A	0.549	0.94
95_V	142_I	0.549	0.94
58_L	62_E	0.547	0.94
54_P	98_S	0.547	0.94
53_R	196_T	0.543	0.94
155_R	159_T	0.543	0.94
32_A	35_E	0.542	0.94
136_Y	164_C	0.540	0.94
96_I	99_F	0.538	0.94
198_V	202_A	0.538	0.94
281_A	291_A	0.538	0.94
254_S	257_V	0.537	0.94
18_R	55_A	0.536	0.94
313_E	316_V	0.535	0.93
279_L	282_E	0.535	0.93
44_I	98_S	0.533	0.93
187_E	190_E	0.533	0.93
271_H	302_A	0.532	0.93
303_G	307_Y	0.529	0.93
183_V	187_E	0.526	0.93
193_E	198_V	0.523	0.93
277_G	280_D	0.523	0.93
311_L	318_E	0.522	0.93
13_A	17_R	0.520	0.93
110_D	120_H	0.519	0.92
162_E	205_T	0.519	0.92
53_R	101_L	0.517	0.92
224_Y	228_V	0.517	0.92
21_V	87_M	0.517	0.92
100_T	196_T	0.512	0.92
87_M	91_V	0.512	0.92
101_L	114_R	0.508	0.92
26_D	30_P	0.507	0.92
277_G	294_A	0.507	0.92
52_L	200_Y	0.506	0.91
298_A	302_A	0.505	0.91
20_Q	27_D	0.503	0.91
58_L	87_M	0.503	0.91
250_K	255_D	0.502	0.91
242_T	248_L	0.501	0.91
52_L	338_I	0.500	0.91
30_P	33_E	0.500	0.91

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
1wy0A	2	0.9366	100	0.106	Contact Map
3oyrA	2	0.9366	100	0.118	Contact Map
4lobA	2	0.8905	100	0.118	Contact Map
4jxyA	5	0.8847	100	0.12	Contact Map
3wjkA	2	0.902	100	0.122	Contact Map
3mzvA	2	0.9308	100	0.123	Contact Map
3aqbB	1	0.9222	100	0.13	Contact Map
3pkoA	2	0.9366	100	0.13	Contact Map
3nf2A	2	0.9164	100	0.132	Contact Map
3rmgA	2	0.879	100	0.134	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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