GGPS - SULSO - GREMLIN Contacts

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GGPS - Geranylgeranyl diphosphate synthase

UniProt:	P95999	Sequences: MSSDDLSLYFNEIVNNVNFRIKNFVKSNFKTLEEASFHLFTAGGKRLRPLVLVSSSDLIGGDRERAYKAAAAVEILHNFTLVHDDIMDNDGLRRGLPTVHVKWGEPMAILAGDYLHAKAFEALNEALKGLDGNTFYKAFSIFITSIEIISEGQAMDMSFENRLDVTEEEYIQMIKGKTAMLFSCSAALGGIINKANDDVVKKLTEYGLNLGISFQIVDDILGIIGDEKELGKPIYSDIREGKKTILVIKTLSEATEDEKKILVSTLGNKEAKKEDLERASEIIRKHSLQYAYDLAKKYSDLAIENLREIPVSNKTAEKALKYLAQFTIQRRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	332 (301)
Sequences:	9598 (6337)
Seq/√Len:	365.3

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
56_S	66_A	3.368	1.00
196_N	199_V	3.300	1.00
187_A	204_T	3.045	1.00
91_G	101_V	2.870	1.00
183_S	204_T	2.772	1.00
261_I	278_R	2.621	1.00
209_N	301_L	2.537	1.00
253_E	290_Y	2.491	1.00
281_E	285_K	2.478	1.00
141_I	187_A	2.456	1.00
166_T	169_E	2.450	1.00
175_K	208_L	2.399	1.00
209_N	298_Y	2.399	1.00
187_A	200_V	2.348	1.00
303_I	321_K	2.339	1.00
272_K	275_D	2.298	1.00
226_D	229_E	2.281	1.00
294_L	297_K	2.277	1.00
141_I	191_I	2.272	1.00
183_S	208_L	2.257	1.00
92_L	97_P	2.196	1.00
249_K	290_Y	2.156	1.00
233_P	236_S	2.105	1.00
55_S	203_L	2.036	1.00
258_E	285_K	2.029	1.00
118_K	121_E	2.022	1.00
286_H	289_Q	1.988	1.00
138_A	188_L	1.940	1.00
87_M	153_Q	1.940	1.00
249_K	287_S	1.908	1.00
190_G	203_L	1.906	1.00
186_A	207_G	1.882	1.00
205_E	305_N	1.875	1.00
300_D	304_E	1.870	1.00
307_R	321_K	1.865	1.00
20_R	71_A	1.836	1.00
55_S	186_A	1.834	1.00
104_G	107_M	1.812	1.00
137_K	200_V	1.788	1.00
172_Q	176_G	1.772	1.00
13_I	57_D	1.729	1.00
20_R	68_K	1.727	1.00
220_I	291_A	1.688	1.00
259_K	263_V	1.681	1.00
59_I	199_V	1.666	1.00
201_K	205_E	1.649	1.00
121_E	144_T	1.620	1.00
289_Q	293_D	1.614	1.00
20_R	23_N	1.609	1.00
297_K	301_L	1.583	1.00
317_E	321_K	1.582	1.00
255_T	258_E	1.572	1.00
83_H	113_D	1.569	1.00
205_E	209_N	1.560	1.00
167_E	249_K	1.546	1.00
195_A	199_V	1.544	1.00
22_K	37_F	1.544	1.00
124_N	139_F	1.537	1.00
311_V	317_E	1.529	1.00
260_K	264_S	1.525	1.00
304_E	307_R	1.517	1.00
68_K	125_E	1.504	1.00
261_I	264_S	1.501	1.00
296_K	300_D	1.501	1.00
190_G	195_A	1.484	1.00
56_S	61_G	1.476	1.00
18_N	46_R	1.469	1.00
83_H	112_G	1.465	1.00
278_R	281_E	1.445	1.00
137_K	197_D	1.444	1.00
162_R	169_E	1.428	1.00
82_V	99_V	1.426	1.00
90_D	236_S	1.417	1.00
289_Q	292_Y	1.414	1.00
107_M	154_A	1.410	1.00
37_F	41_T	1.407	1.00
153_Q	156_D	1.402	1.00
137_K	140_S	1.395	1.00
225_G	230_L	1.387	1.00
284_R	288_L	1.385	1.00
293_D	297_K	1.384	1.00
155_M	172_Q	1.378	1.00
257_D	260_K	1.376	1.00
183_S	187_A	1.364	1.00
236_S	240_E	1.358	1.00
125_E	140_S	1.351	1.00
184_C	188_L	1.351	1.00
216_I	291_A	1.334	1.00
55_S	59_I	1.330	1.00
54_S	57_D	1.322	1.00
293_D	296_K	1.309	1.00
18_N	21_I	1.283	1.00
197_D	201_K	1.281	1.00
189_G	193_N	1.279	1.00
283_I	287_S	1.279	1.00
294_L	298_Y	1.278	1.00
227_E	234_I	1.276	1.00
86_I	105_E	1.268	1.00
220_I	292_Y	1.266	1.00
250_T	283_I	1.261	1.00
249_K	253_E	1.261	1.00
220_I	288_L	1.244	1.00
80_T	149_I	1.242	1.00
249_K	252_S	1.241	1.00
170_Y	174_I	1.232	1.00
53_V	70_A	1.221	1.00
227_E	233_P	1.217	1.00
19_F	23_N	1.208	1.00
42_A	96_L	1.206	1.00
140_S	144_T	1.199	1.00
75_I	122_A	1.196	1.00
59_I	193_N	1.194	1.00
299_S	303_I	1.184	1.00
15_N	18_N	1.178	1.00
137_K	191_I	1.173	1.00
202_K	308_E	1.168	1.00
305_N	308_E	1.167	1.00
181_L	185_S	1.158	1.00
221_L	230_L	1.152	1.00
310_P	317_E	1.148	1.00
261_I	265_T	1.148	1.00
180_M	183_S	1.140	1.00
278_R	282_I	1.131	1.00
175_K	212_I	1.131	1.00
253_E	256_E	1.120	1.00
252_S	290_Y	1.120	1.00
59_I	189_G	1.120	1.00
148_I	176_G	1.115	1.00
262_L	279_A	1.111	1.00
290_Y	293_D	1.108	1.00
280_S	284_R	1.099	1.00
38_H	102_K	1.098	1.00
212_I	298_Y	1.095	1.00
69_A	138_A	1.094	1.00
167_E	294_L	1.093	1.00
138_A	192_I	1.092	1.00
141_I	184_C	1.085	1.00
250_T	287_S	1.085	1.00
14_V	18_N	1.085	1.00
145_S	184_C	1.084	1.00
186_A	203_L	1.081	1.00
31_T	158_S	1.077	1.00
155_M	176_G	1.076	1.00
190_G	200_V	1.074	1.00
17_V	21_I	1.073	1.00
72_A	123_L	1.063	1.00
268_N	275_D	1.062	1.00
159_F	173_M	1.056	1.00
16_N	67_Y	1.053	1.00
31_T	104_G	1.046	1.00
311_V	318_K	1.044	1.00
318_K	322_Y	1.043	1.00
20_R	24_F	1.042	1.00
30_K	34_E	1.040	1.00
22_K	41_T	1.039	1.00
198_D	202_K	1.034	1.00
312_S	316_A	1.032	1.00
155_M	173_M	1.029	1.00
16_N	64_E	1.027	1.00
52_L	73_V	1.026	1.00
263_V	267_G	1.022	1.00
277_E	281_E	1.017	1.00
69_A	188_L	1.014	1.00
172_Q	175_K	1.011	1.00
209_N	305_N	1.008	1.00
33_E	37_F	1.000	1.00
167_E	252_S	0.998	1.00
53_V	67_Y	0.998	1.00
206_Y	306_L	0.987	1.00
159_F	165_V	0.986	1.00
318_K	321_K	0.984	1.00
12_E	16_N	0.976	1.00
199_V	202_K	0.970	1.00
51_V	186_A	0.966	1.00
174_I	212_I	0.966	1.00
277_E	280_S	0.963	1.00
287_S	290_Y	0.963	1.00
56_S	193_N	0.963	1.00
18_N	22_K	0.961	1.00
87_M	110_L	0.961	1.00
220_I	224_I	0.961	1.00
43_G	46_R	0.960	1.00
53_V	66_A	0.959	1.00
59_I	195_A	0.955	1.00
12_E	15_N	0.955	1.00
217_V	295_A	0.951	1.00
97_P	101_V	0.943	1.00
35_A	99_V	0.940	1.00
298_Y	301_L	0.934	1.00
98_T	101_V	0.931	1.00
89_N	105_E	0.930	1.00
239_R	273_K	0.930	1.00
170_Y	248_I	0.929	1.00
159_F	169_E	0.927	1.00
69_A	123_L	0.926	1.00
224_I	255_T	0.924	1.00
167_E	171_I	0.921	1.00
202_K	305_N	0.921	1.00
165_V	169_E	0.916	1.00
121_E	147_E	0.914	1.00
300_D	303_I	0.906	1.00
301_L	304_E	0.899	1.00
92_L	227_E	0.896	1.00
100_H	105_E	0.886	1.00
16_N	19_F	0.884	1.00
224_I	288_L	0.883	1.00
307_R	317_E	0.882	1.00
274_E	277_E	0.882	1.00
123_L	138_A	0.881	1.00
187_A	191_I	0.879	1.00
217_V	292_Y	0.875	1.00
86_I	109_I	0.872	1.00
17_V	71_A	0.868	1.00
186_A	206_Y	0.867	1.00
11_N	15_N	0.866	1.00
245_I	291_A	0.863	1.00
171_I	175_K	0.862	1.00
14_V	50_L	0.862	1.00
167_E	290_Y	0.855	1.00
69_A	192_I	0.853	1.00
183_S	207_G	0.853	1.00
223_I	246_L	0.851	1.00
39_L	99_V	0.849	1.00
24_F	68_K	0.849	1.00
24_F	125_E	0.844	1.00
171_I	212_I	0.843	1.00
31_T	34_E	0.842	1.00
187_A	201_K	0.834	1.00
275_D	278_R	0.833	1.00
245_I	294_L	0.833	1.00
62_D	65_R	0.831	1.00
205_E	208_L	0.831	1.00
281_E	284_R	0.829	1.00
160_E	243_K	0.827	1.00
124_N	140_S	0.822	1.00
185_S	189_G	0.820	1.00
223_I	238_I	0.819	1.00
136_Y	140_S	0.817	1.00
36_S	114_Y	0.809	1.00
173_M	242_K	0.806	1.00
156_D	242_K	0.803	1.00
19_F	22_K	0.799	1.00
206_Y	305_N	0.797	1.00
76_L	142_F	0.796	1.00
17_V	53_V	0.794	1.00
71_A	122_A	0.793	1.00
51_V	210_L	0.792	1.00
254_A	258_E	0.791	1.00
34_E	38_H	0.791	1.00
254_A	282_I	0.788	1.00
191_I	200_V	0.787	1.00
57_D	63_R	0.782	1.00
221_L	225_G	0.781	1.00
75_I	118_K	0.779	1.00
91_G	100_H	0.778	1.00
121_E	125_E	0.773	1.00
201_K	204_T	0.773	1.00
61_G	66_A	0.770	1.00
120_F	143_I	0.769	1.00
52_L	66_A	0.766	1.00
41_T	96_L	0.763	1.00
57_D	316_A	0.762	1.00
38_H	103_W	0.762	1.00
58_L	309_I	0.761	1.00
225_G	229_E	0.758	1.00
79_F	116_H	0.756	1.00
68_K	126_A	0.754	1.00
36_S	115_L	0.746	1.00
24_F	122_A	0.746	1.00
258_E	261_I	0.746	1.00
312_S	317_E	0.743	1.00
230_L	234_I	0.743	1.00
205_E	301_L	0.738	1.00
121_E	140_S	0.735	1.00
48_R	214_F	0.734	1.00
13_I	16_N	0.732	1.00
99_V	103_W	0.728	1.00
49_P	78_N	0.727	1.00
250_T	282_I	0.727	1.00
141_I	145_S	0.725	1.00
58_L	203_L	0.723	1.00
260_K	263_V	0.721	1.00
273_K	277_E	0.720	1.00
208_L	212_I	0.719	1.00
200_V	204_T	0.717	1.00
247_V	266_L	0.717	1.00
308_E	317_E	0.716	0.99
204_T	208_L	0.716	0.99
256_E	260_K	0.713	0.99
82_V	108_A	0.712	0.99
171_I	298_Y	0.712	0.99
292_Y	296_K	0.711	0.99
276_L	280_S	0.710	0.99
97_P	102_K	0.709	0.99
52_L	185_S	0.708	0.99
155_M	159_F	0.708	0.99
46_R	49_P	0.707	0.99
52_L	70_A	0.705	0.99
297_K	300_D	0.702	0.99
218_D	221_L	0.702	0.99
220_I	251_L	0.701	0.99
251_L	263_V	0.700	0.99
273_K	276_L	0.698	0.99
142_F	188_L	0.697	0.99
288_L	292_Y	0.697	0.99
39_L	82_V	0.697	0.99
15_N	19_F	0.694	0.99
256_E	259_K	0.689	0.99
52_L	189_G	0.689	0.99
99_V	102_K	0.688	0.99
290_Y	294_L	0.687	0.99
230_L	233_P	0.684	0.99
265_T	279_A	0.682	0.99
158_S	162_R	0.680	0.99
235_Y	276_L	0.680	0.99
66_A	192_I	0.678	0.99
80_T	181_L	0.677	0.99
202_K	206_Y	0.672	0.99
13_I	53_V	0.666	0.99
126_A	135_F	0.666	0.99
264_S	268_N	0.665	0.99
287_S	291_A	0.665	0.99
249_K	294_L	0.664	0.99
116_H	150_S	0.664	0.99
214_F	218_D	0.663	0.99
36_S	111_A	0.663	0.99
161_N	241_G	0.662	0.99
77_H	80_T	0.661	0.99
69_A	126_A	0.658	0.99
141_I	144_T	0.657	0.99
168_E	171_I	0.656	0.99
235_Y	280_S	0.656	0.99
167_E	245_I	0.655	0.99
257_D	261_I	0.654	0.99
188_L	192_I	0.651	0.99
48_R	77_H	0.648	0.99
16_N	20_R	0.648	0.99
217_V	258_E	0.648	0.99
137_K	141_I	0.647	0.99
206_Y	320_L	0.644	0.99
67_Y	71_A	0.642	0.99
141_I	204_T	0.641	0.99
168_E	172_Q	0.641	0.99
197_D	200_V	0.639	0.99
38_H	96_L	0.639	0.99
167_E	248_I	0.638	0.99
151_E	176_G	0.638	0.99
176_G	180_M	0.635	0.99
171_I	294_L	0.634	0.99
304_E	308_E	0.633	0.99
26_K	33_E	0.628	0.99
96_L	102_K	0.628	0.99
22_K	26_K	0.626	0.99
20_R	67_Y	0.626	0.99
217_V	220_I	0.625	0.99
272_K	276_L	0.624	0.99
117_A	150_S	0.623	0.99
68_K	122_A	0.622	0.99
202_K	205_E	0.622	0.99
279_A	283_I	0.622	0.99
218_D	232_K	0.620	0.99
220_I	295_A	0.616	0.98
106_P	157_M	0.616	0.98
136_Y	139_F	0.616	0.98
284_R	289_Q	0.614	0.98
293_D	300_D	0.609	0.98
31_T	107_M	0.608	0.98
59_I	203_L	0.603	0.98
16_N	63_R	0.603	0.98
29_F	33_E	0.601	0.98
35_A	111_A	0.601	0.98
11_N	14_V	0.599	0.98
73_V	185_S	0.596	0.98
274_E	278_R	0.595	0.98
65_R	126_A	0.594	0.98
36_S	39_L	0.589	0.98
165_V	243_K	0.587	0.98
178_T	214_F	0.584	0.98
64_E	68_K	0.582	0.98
316_A	319_A	0.580	0.98
82_V	115_L	0.580	0.98
319_A	322_Y	0.574	0.98
249_K	257_D	0.573	0.98
114_Y	150_S	0.573	0.98
17_V	67_Y	0.572	0.98
262_L	282_I	0.571	0.98
225_G	234_I	0.570	0.98
246_L	249_K	0.567	0.97
82_V	86_I	0.567	0.97
39_L	78_N	0.566	0.97
134_T	194_K	0.565	0.97
118_K	147_E	0.565	0.97
149_I	182_F	0.564	0.97
35_A	107_M	0.564	0.97
177_K	215_Q	0.561	0.97
87_M	150_S	0.558	0.97
68_K	71_A	0.557	0.97
206_Y	209_N	0.556	0.97
265_T	275_D	0.555	0.97
175_K	180_M	0.554	0.97
87_M	157_M	0.550	0.97
79_F	117_A	0.550	0.97
173_M	243_K	0.549	0.97
262_L	265_T	0.549	0.97
182_F	210_L	0.549	0.97
213_S	299_S	0.548	0.97
296_K	299_S	0.548	0.97
105_E	109_I	0.547	0.97
90_D	222_G	0.545	0.97
250_T	262_L	0.544	0.97
30_K	33_E	0.543	0.97
45_K	214_F	0.540	0.97
282_I	285_K	0.539	0.97
162_R	165_V	0.538	0.96
54_S	319_A	0.537	0.96
253_E	286_H	0.535	0.96
262_L	266_L	0.535	0.96
271_A	275_D	0.534	0.96
56_S	192_I	0.533	0.96
224_I	292_Y	0.532	0.96
180_M	208_L	0.531	0.96
245_I	249_K	0.531	0.96
236_S	239_R	0.530	0.96
250_T	279_A	0.530	0.96
209_N	212_I	0.529	0.96
84_D	88_D	0.529	0.96
171_I	216_I	0.524	0.96
222_G	230_L	0.523	0.96
160_E	240_E	0.521	0.96
170_Y	245_I	0.520	0.96
227_E	230_L	0.520	0.96
45_K	218_D	0.520	0.96
178_T	182_F	0.516	0.96
58_L	316_A	0.514	0.95
222_G	236_S	0.514	0.95
144_T	187_A	0.513	0.95
61_G	189_G	0.513	0.95
60_G	63_R	0.513	0.95
79_F	87_M	0.511	0.95
73_V	188_L	0.509	0.95
306_L	321_K	0.508	0.95
122_A	125_E	0.508	0.95
21_I	41_T	0.506	0.95
154_A	158_S	0.506	0.95
44_G	48_R	0.506	0.95
179_A	212_I	0.504	0.95
159_F	162_R	0.503	0.95
196_N	201_K	0.502	0.95
261_I	282_I	0.501	0.95
120_F	123_L	0.500	0.95
72_A	142_F	0.500	0.95
216_I	257_D	0.500	0.95

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
3oyrA	2	0.9729	100	0.048	Contact Map
4jxyA	5	0.9127	100	0.057	Contact Map
3aqbB	1	0.9699	100	0.063	Contact Map
3mzvA	2	0.9729	100	0.065	Contact Map
1wy0A	2	0.9759	100	0.072	Contact Map
3wjkA	2	0.9428	100	0.073	Contact Map
4lobA	2	0.9187	100	0.074	Contact Map
3rmgA	2	0.9127	100	0.08	Contact Map
3lmdA	2	0.9066	100	0.084	Contact Map
4dhdA	2	0.9398	100	0.095	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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