LYEL - HALSA - GREMLIN Contacts

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LYEL - Lycopene elongase

UniProt:	Q9HPD9	Sequences: MFRYLFVLSRPRFWLYLAGPVLVGVSYGATTVGELFSAPAVVLFSYFLLPANIYLYGINDVFDRDVDETNPKKDGRESRYRGGAAVAVIVAVCGVFLGFVAAPLPAEAWPYLAAWFVLATEYSAPPLRFKTTPVLDSLSNGLYVLPAAAAYAGVSGTHPPLLAVAGGWLWAMGMHTFSAIPDIEPDRAAGIQTTATALGADRALAYCAGIWLLSAAVFALVDVRFGLLLLAYPVLVFGIRRLQVAVGRAYWWYPAVNTLVGMVFTLGGLWGVVHG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	275 (259)
Sequences:	9085 (6499)
Seq/√Len:	403.8

ECOLI - CYOE UBIA MENA
BACSU - COXX2 COXX1 MENA
HALSA - LYEL Q9HQN6 DGGGP COXX
SULSO - DGGGP Q980Z2 COXX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_R	83_G	3.785	1.00
61_V	83_G	3.719	1.00
54_Y	94_G	3.182	1.00
82_G	85_A	3.124	1.00
201_D	205_A	3.102	1.00
84_A	88_V	3.049	1.00
61_V	87_A	2.989	1.00
231_A	234_V	2.781	1.00
4_Y	80_Y	2.596	1.00
101_A	104_L	2.443	1.00
25_V	41_V	2.330	1.00
183_I	187_R	2.310	1.00
71_P	74_D	2.281	1.00
184_E	187_R	2.144	1.00
57_G	93_C	2.134	1.00
65_D	69_T	2.095	1.00
249_A	253_Y	2.094	1.00
202_R	205_A	2.074	1.00
237_F	241_R	2.020	1.00
97_L	101_A	2.015	1.00
106_A	110_P	1.986	1.00
105_P	108_A	1.967	1.00
66_V	191_I	1.951	1.00
62_F	124_A	1.940	1.00
14_W	49_L	1.918	1.00
91_A	95_V	1.917	1.00
256_V	260_V	1.892	1.00
108_A	152_A	1.845	1.00
205_A	209_G	1.829	1.00
251_W	255_A	1.818	1.00
43_L	100_V	1.795	1.00
198_L	202_R	1.734	1.00
236_V	240_R	1.712	1.00
187_R	196_T	1.702	1.00
232_Y	236_V	1.644	1.00
183_I	200_A	1.629	1.00
88_V	92_V	1.610	1.00
87_A	91_A	1.605	1.00
65_D	68_E	1.595	1.00
99_F	103_P	1.578	1.00
5_L	85_A	1.577	1.00
22_L	45_S	1.575	1.00
83_G	87_A	1.571	1.00
250_Y	253_Y	1.552	1.00
224_R	231_A	1.550	1.00
100_V	104_L	1.531	1.00
254_P	258_T	1.530	1.00
37_S	40_A	1.521	1.00
195_A	203_A	1.513	1.00
51_A	97_L	1.510	1.00
81_R	86_V	1.509	1.00
16_Y	174_M	1.499	1.00
57_G	89_I	1.473	1.00
61_V	86_V	1.467	1.00
133_P	197_A	1.466	1.00
257_N	261_G	1.443	1.00
234_V	238_G	1.434	1.00
246_V	249_A	1.428	1.00
215_A	232_Y	1.406	1.00
227_L	267_G	1.406	1.00
43_L	103_P	1.405	1.00
234_V	237_F	1.392	1.00
66_V	69_T	1.364	1.00
58_I	90_V	1.357	1.00
50_P	96_F	1.354	1.00
53_I	93_C	1.324	1.00
212_L	216_A	1.322	1.00
183_I	196_T	1.316	1.00
250_Y	254_P	1.312	1.00
200_A	204_L	1.295	1.00
102_A	109_W	1.288	1.00
9_S	53_I	1.287	1.00
202_R	206_Y	1.281	1.00
247_G	250_Y	1.277	1.00
24_G	28_G	1.273	1.00
21_V	48_L	1.273	1.00
50_P	93_C	1.271	1.00
230_L	234_V	1.268	1.00
129_F	139_S	1.267	1.00
228_L	232_Y	1.253	1.00
129_F	132_T	1.250	1.00
236_V	239_I	1.246	1.00
239_I	243_Q	1.240	1.00
94_G	116_F	1.239	1.00
192_Q	197_A	1.233	1.00
233_P	237_F	1.220	1.00
151_Y	155_S	1.220	1.00
247_G	251_W	1.210	1.00
68_E	77_E	1.205	1.00
248_R	252_W	1.204	1.00
110_P	114_A	1.200	1.00
227_L	231_A	1.191	1.00
238_G	242_L	1.186	1.00
57_G	90_V	1.185	1.00
224_R	232_Y	1.177	1.00
156_G	160_P	1.173	1.00
251_W	254_P	1.164	1.00
161_L	165_A	1.153	1.00
253_Y	257_N	1.151	1.00
252_W	255_A	1.150	1.00
239_I	242_L	1.149	1.00
84_A	87_A	1.148	1.00
5_L	89_I	1.147	1.00
76_R	86_V	1.140	1.00
136_D	193_T	1.133	1.00
50_P	97_L	1.128	1.00
240_R	243_Q	1.126	1.00
254_P	257_N	1.115	1.00
61_V	90_V	1.110	1.00
225_F	229_L	1.109	1.00
102_A	106_A	1.108	1.00
98_G	101_A	1.105	1.00
252_W	256_V	1.104	1.00
130_K	191_I	1.102	1.00
89_I	93_C	1.099	1.00
257_N	260_V	1.088	1.00
166_G	217_V	1.081	1.00
42_V	46_Y	1.081	1.00
90_V	94_G	1.077	1.00
253_Y	260_V	1.076	1.00
113_A	117_V	1.071	1.00
176_T	206_Y	1.070	1.00
8_L	57_G	1.068	1.00
63_D	131_T	1.068	1.00
201_D	204_L	1.067	1.00
233_P	236_V	1.063	1.00
64_R	68_E	1.058	1.00
9_S	93_C	1.057	1.00
241_R	245_A	1.055	1.00
67_D	71_P	1.054	1.00
182_D	186_D	1.050	1.00
249_A	252_W	1.048	1.00
254_P	261_G	1.037	1.00
180_I	203_A	1.019	1.00
121_E	139_S	1.015	1.00
65_D	70_N	1.007	1.00
250_Y	257_N	1.006	1.00
194_T	198_L	0.999	1.00
180_I	202_R	0.998	1.00
55_L	119_A	0.995	1.00
107_E	111_Y	0.994	1.00
246_V	250_Y	0.993	1.00
264_F	267_G	0.984	1.00
238_G	241_R	0.981	1.00
261_G	265_T	0.981	1.00
142_L	164_V	0.979	1.00
107_E	152_A	0.971	1.00
260_V	264_F	0.962	1.00
69_T	189_A	0.962	1.00
118_L	142_L	0.961	1.00
7_V	80_Y	0.959	1.00
232_Y	235_L	0.959	1.00
183_I	195_A	0.957	1.00
98_G	102_A	0.955	1.00
205_A	208_A	0.954	1.00
256_V	259_L	0.953	1.00
173_G	210_I	0.948	1.00
120_T	124_A	0.945	1.00
107_E	110_P	0.944	1.00
152_A	160_P	0.944	1.00
225_F	232_Y	0.943	1.00
70_N	185_P	0.943	1.00
156_G	161_L	0.943	1.00
143_Y	147_A	0.941	1.00
169_L	210_I	0.937	1.00
39_P	43_L	0.932	1.00
66_V	131_T	0.931	1.00
179_A	195_A	0.931	1.00
165_A	169_L	0.928	1.00
250_Y	255_A	0.926	1.00
228_L	231_A	0.920	1.00
81_R	89_I	0.913	1.00
69_T	72_K	0.911	1.00
18_A	22_L	0.908	1.00
157_T	160_P	0.904	1.00
258_T	262_M	0.892	1.00
6_F	9_S	0.891	1.00
255_A	259_L	0.889	1.00
43_L	104_L	0.882	1.00
184_E	188_A	0.877	1.00
64_R	76_R	0.877	1.00
8_L	86_V	0.877	1.00
259_L	263_V	0.876	1.00
27_Y	151_Y	0.874	1.00
21_V	44_F	0.873	1.00
38_A	42_V	0.872	1.00
77_E	86_V	0.867	1.00
236_V	243_Q	0.866	1.00
97_L	104_L	0.865	1.00
115_W	145_L	0.859	1.00
121_E	129_F	0.857	1.00
143_Y	146_P	0.854	1.00
26_S	265_T	0.853	1.00
39_P	42_V	0.852	1.00
67_D	72_K	0.851	1.00
85_A	89_I	0.843	1.00
144_V	168_W	0.841	1.00
256_V	261_G	0.840	1.00
117_V	120_T	0.831	1.00
148_A	160_P	0.831	1.00
232_Y	239_I	0.829	1.00
148_A	164_V	0.825	1.00
101_A	112_L	0.824	1.00
212_L	240_R	0.823	1.00
259_L	262_M	0.823	1.00
63_D	66_V	0.821	1.00
232_Y	243_Q	0.818	1.00
213_L	217_V	0.818	1.00
19_G	261_G	0.817	1.00
51_A	112_L	0.816	1.00
237_F	240_R	0.811	1.00
18_A	45_S	0.806	1.00
23_V	163_A	0.804	1.00
208_A	212_L	0.798	1.00
204_L	208_A	0.797	1.00
226_G	230_L	0.797	1.00
217_V	221_V	0.790	1.00
144_V	171_A	0.790	1.00
123_S	131_T	0.785	1.00
46_Y	100_V	0.784	1.00
240_R	244_V	0.783	1.00
234_V	241_R	0.780	1.00
133_P	139_S	0.779	1.00
16_Y	20_P	0.779	1.00
235_L	243_Q	0.779	1.00
165_A	217_V	0.777	1.00
218_F	221_V	0.772	1.00
77_E	80_Y	0.772	1.00
6_F	11_P	0.769	1.00
222_D	225_F	0.768	1.00
260_V	265_T	0.765	1.00
36_F	41_V	0.763	1.00
258_T	261_G	0.762	1.00
85_A	88_V	0.760	1.00
224_R	228_L	0.759	1.00
214_S	218_F	0.756	1.00
246_V	254_P	0.755	1.00
108_A	149_A	0.755	1.00
180_I	200_A	0.754	1.00
9_S	57_G	0.753	1.00
129_F	133_P	0.750	1.00
63_D	123_S	0.749	1.00
15_L	258_T	0.745	1.00
57_G	81_R	0.744	1.00
22_L	265_T	0.744	1.00
257_N	264_F	0.737	1.00
229_L	232_Y	0.734	1.00
58_I	120_T	0.734	1.00
112_L	149_A	0.726	1.00
229_L	233_P	0.724	1.00
47_F	100_V	0.724	1.00
17_L	52_N	0.723	1.00
75_G	79_R	0.720	1.00
66_V	72_K	0.717	1.00
241_R	244_V	0.715	1.00
53_I	89_I	0.715	1.00
25_V	44_F	0.713	1.00
76_R	81_R	0.712	1.00
198_L	206_Y	0.710	1.00
26_S	269_L	0.709	1.00
242_L	245_A	0.709	1.00
70_N	74_D	0.703	1.00
67_D	70_N	0.700	1.00
172_M	210_I	0.696	1.00
66_V	70_N	0.696	1.00
144_V	167_G	0.693	1.00
206_Y	209_G	0.692	1.00
5_L	9_S	0.690	1.00
65_D	71_P	0.689	1.00
7_V	12_R	0.688	1.00
257_N	265_T	0.688	1.00
57_G	86_V	0.682	1.00
46_Y	50_P	0.681	0.99
61_V	76_R	0.680	0.99
184_E	200_A	0.676	0.99
130_K	136_D	0.672	0.99
87_A	90_V	0.672	0.99
259_L	264_F	0.671	0.99
66_V	189_A	0.671	0.99
246_V	252_W	0.668	0.99
219_A	223_V	0.660	0.99
81_R	85_A	0.659	0.99
143_Y	150_A	0.658	0.99
247_G	253_Y	0.648	0.99
180_I	204_L	0.648	0.99
54_Y	93_C	0.646	0.99
52_N	56_Y	0.645	0.99
76_R	79_R	0.643	0.99
24_G	151_Y	0.642	0.99
95_V	99_F	0.640	0.99
179_A	193_T	0.639	0.99
186_D	193_T	0.638	0.99
248_R	251_W	0.638	0.99
157_T	161_L	0.636	0.99
253_Y	261_G	0.634	0.99
106_A	109_W	0.633	0.99
249_A	254_P	0.633	0.99
25_V	28_G	0.633	0.99
206_Y	210_I	0.632	0.99
96_F	100_V	0.627	0.99
143_Y	151_Y	0.627	0.99
54_Y	120_T	0.625	0.99
53_I	57_G	0.624	0.99
199_G	203_A	0.624	0.99
22_L	41_V	0.621	0.99
59_N	123_S	0.620	0.99
167_G	171_A	0.618	0.99
136_D	140_N	0.617	0.99
134_V	197_A	0.615	0.99
136_D	179_A	0.612	0.99
135_L	141_G	0.612	0.99
97_L	103_P	0.611	0.99
88_V	91_A	0.609	0.99
23_V	167_G	0.609	0.99
234_V	243_Q	0.608	0.99
70_N	73_K	0.602	0.99
248_R	255_A	0.600	0.99
62_F	123_S	0.599	0.99
79_R	85_A	0.598	0.99
28_G	154_V	0.598	0.99
98_G	109_W	0.598	0.99
250_Y	261_G	0.598	0.99
33_G	36_F	0.597	0.99
251_W	258_T	0.593	0.99
173_G	211_W	0.592	0.99
215_A	218_F	0.588	0.99
86_V	90_V	0.588	0.99
135_L	139_S	0.588	0.99
235_L	238_G	0.587	0.99
231_A	235_L	0.585	0.98
246_V	251_W	0.584	0.98
47_F	101_A	0.584	0.98
210_I	213_L	0.582	0.98
235_L	239_I	0.582	0.98
63_D	191_I	0.580	0.98
226_G	229_L	0.575	0.98
180_I	195_A	0.575	0.98
25_V	36_F	0.574	0.98
257_N	262_M	0.573	0.98
225_F	234_V	0.571	0.98
255_A	258_T	0.570	0.98
229_L	236_V	0.568	0.98
178_S	181_P	0.568	0.98
224_R	238_G	0.564	0.98
144_V	151_Y	0.563	0.98
204_L	207_C	0.561	0.98
247_G	258_T	0.560	0.98
149_A	164_V	0.560	0.98
28_G	151_Y	0.559	0.98
97_L	102_A	0.558	0.98
253_Y	259_L	0.558	0.98
13_F	181_P	0.558	0.98
143_Y	171_A	0.556	0.98
239_I	244_V	0.555	0.98
7_V	75_G	0.554	0.98
175_H	179_A	0.554	0.98
137_S	175_H	0.550	0.98
224_R	235_L	0.542	0.98
140_N	145_L	0.541	0.97
61_V	64_R	0.538	0.97
261_G	264_F	0.535	0.97
135_L	138_L	0.531	0.97
25_V	155_S	0.530	0.97
134_V	192_Q	0.530	0.97
6_F	89_I	0.526	0.97
111_Y	152_A	0.525	0.97
117_V	121_E	0.524	0.97
110_P	113_A	0.524	0.97
24_G	150_A	0.520	0.97
262_M	265_T	0.519	0.97
231_A	260_V	0.517	0.97
45_S	49_L	0.517	0.97
246_V	255_A	0.517	0.97
207_C	211_W	0.516	0.97
60_D	63_D	0.515	0.97
150_A	154_V	0.513	0.97
219_A	222_D	0.511	0.96
254_P	265_T	0.507	0.96
246_V	253_Y	0.507	0.96
174_M	178_S	0.507	0.96
13_F	52_N	0.505	0.96
97_L	112_L	0.505	0.96
40_A	154_V	0.505	0.96
92_V	96_F	0.504	0.96
111_Y	148_A	0.503	0.96
147_A	150_A	0.503	0.96
159_P	162_L	0.502	0.96
249_A	257_N	0.500	0.96

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
4od4A	1	0.9236	100	0.27	Contact Map
4tq3A	1	0.9673	100	0.315	Contact Map
2xq2A	2	0.8073	13.8	0.947	Contact Map
2onkC	2	0.24	10.8	0.949	Contact Map
3d31C	2	0.2291	5.8	0.955	Contact Map
3dh4A	3	0.7564	5.7	0.955	Contact Map
1qleC	1	0.5491	4.8	0.957	Contact Map
1v54C	1	0.5418	3.7	0.959	Contact Map
4px7A	1	0.6327	3	0.961	Contact Map
4llsA	2	0.8073	2.9	0.961	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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