Q9HPV3 - HALSA - GREMLIN Contacts

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Q9HPV3 - Phytoene synthase

UniProt:	Q9HPV3	Sequences: MVSPEHLRRSKAVQRRTGRTFHIATRFLPERVRYPTYVLYAFFRLTDEIVDDEAPGPPDEQRRRLAHVRAAALGDRDPDDPVLAAFAALREDHDIPREEVTTFIDAMQQDVDTARYRSHDDLAEYLRGSSVAVGYMMLSIMDAPEPERARPHAASLGEAFQLTNFLRDVREDVLDYDRIYLPSQTLAAHGASHDDIAALSATPQVRDAIRAELDRTERLYRHGVAGIEHLPADCQFPVLAAAVMYADQHRLIRAQDCDVLSQRPTLTLRRRLSVVARTWLRWRVSDDPTAVFHAVTGIGEPDAGGVPEQSFAVRESQPTRAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	322 (273)
Sequences:	3754 (2508)
Seq/√Len:	151.8

BACSU - YISP
HALSA - Q9HPV3 Q9HPE1 Q9HRI5
SULSO - Q97UT8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
118_S	121_D	5.019	1.00
217_E	253_R	4.782	1.00
189_H	211_A	4.550	1.00
66_A	108_Q	4.492	1.00
155_S	222_H	4.000	1.00
188_A	211_A	3.579	1.00
185_T	212_E	2.935	1.00
113_T	121_D	2.626	1.00
35_P	93_H	2.617	1.00
98_E	102_T	2.608	1.00
117_R	121_D	2.529	1.00
217_E	250_R	2.414	1.00
258_D	261_S	2.337	1.00
88_A	92_D	2.331	1.00
251_L	270_R	2.325	1.00
163_T	220_Y	2.324	1.00
118_S	184_Q	2.315	1.00
192_S	195_D	2.275	1.00
66_A	105_D	2.225	1.00
247_D	270_R	2.157	1.00
106_A	129_S	2.097	1.00
7_L	88_A	2.083	1.00
155_S	219_L	2.027	1.00
70_A	101_T	2.017	1.00
70_A	97_R	2.017	1.00
63_R	108_Q	1.986	1.00
96_P	139_S	1.960	1.00
117_R	187_A	1.932	1.00
35_P	92_D	1.922	1.00
38_V	89_L	1.896	1.00
36_T	137_M	1.879	1.00
124_E	128_G	1.859	1.00
189_H	207_D	1.854	1.00
63_R	67_H	1.802	1.00
127_R	154_A	1.784	1.00
206_R	256_D	1.750	1.00
117_R	183_S	1.731	1.00
276_A	280_L	1.726	1.00
9_R	12_A	1.703	1.00
119_H	215_R	1.657	1.00
185_T	211_A	1.626	1.00
120_D	123_A	1.618	1.00
59_D	112_D	1.617	1.00
185_T	189_H	1.581	1.00
97_R	101_T	1.576	1.00
183_S	187_A	1.524	1.00
115_R	193_H	1.522	1.00
39_L	136_M	1.520	1.00
213_L	249_H	1.518	1.00
129_S	165_F	1.516	1.00
39_L	140_I	1.506	1.00
195_D	200_S	1.492	1.00
224_V	246_A	1.486	1.00
106_A	128_G	1.474	1.00
64_R	68_V	1.462	1.00
219_L	222_H	1.460	1.00
109_Q	124_E	1.447	1.00
191_A	208_A	1.437	1.00
135_Y	154_A	1.434	1.00
170_R	175_D	1.426	1.00
47_D	51_D	1.426	1.00
58_P	61_Q	1.419	1.00
123_A	158_E	1.407	1.00
212_E	215_R	1.399	1.00
158_E	219_L	1.379	1.00
208_A	212_E	1.367	1.00
210_R	253_R	1.364	1.00
40_Y	44_R	1.358	1.00
205_V	209_I	1.351	1.00
32_V	140_I	1.350	1.00
95_I	136_M	1.342	1.00
161_Q	164_N	1.298	1.00
273_S	277_R	1.293	1.00
47_D	168_D	1.293	1.00
127_R	135_Y	1.285	1.00
213_L	253_R	1.276	1.00
66_A	101_T	1.272	1.00
130_S	134_G	1.268	1.00
65_L	69_R	1.267	1.00
185_T	208_A	1.256	1.00
86_F	100_V	1.239	1.00
39_L	100_V	1.235	1.00
206_R	258_D	1.223	1.00
110_D	180_Y	1.221	1.00
185_T	215_R	1.221	1.00
35_P	89_L	1.216	1.00
46_T	65_L	1.216	1.00
68_V	71_A	1.213	1.00
210_R	257_C	1.213	1.00
189_H	208_A	1.211	1.00
51_D	168_D	1.206	1.00
42_F	104_I	1.202	1.00
251_L	254_A	1.202	1.00
149_A	229_H	1.194	1.00
214_D	253_R	1.193	1.00
42_F	46_T	1.192	1.00
57_P	60_E	1.187	1.00
67_H	71_A	1.178	1.00
213_L	257_C	1.172	1.00
247_D	250_R	1.171	1.00
217_E	246_A	1.168	1.00
119_H	212_E	1.162	1.00
57_P	61_Q	1.161	1.00
277_R	281_R	1.159	1.00
195_D	204_Q	1.157	1.00
109_Q	128_G	1.154	1.00
148_R	229_H	1.154	1.00
32_V	233_D	1.152	1.00
47_D	172_D	1.151	1.00
166_L	252_I	1.149	1.00
46_T	104_I	1.147	1.00
20_T	244_M	1.146	1.00
14_Q	37_Y	1.139	1.00
203_P	207_D	1.139	1.00
159_A	163_T	1.132	1.00
119_H	211_A	1.118	0.99
95_I	100_V	1.113	0.99
73_L	97_R	1.099	0.99
117_R	184_Q	1.098	0.99
127_R	132_A	1.093	0.99
113_T	116_Y	1.093	0.99
255_Q	262_Q	1.088	0.99
81_P	85_A	1.085	0.99
183_S	193_H	1.065	0.99
133_V	164_N	1.065	0.99
29_P	32_V	1.053	0.99
70_A	74_G	1.052	0.99
247_D	274_V	1.050	0.99
185_T	188_A	1.049	0.99
105_D	124_E	1.046	0.99
164_N	167_R	1.045	0.99
87_A	91_E	1.041	0.99
44_R	134_G	1.037	0.99
99_E	135_Y	1.034	0.99
224_V	242_A	1.030	0.99
220_Y	245_Y	1.030	0.99
230_L	238_V	1.029	0.99
211_A	215_R	1.024	0.99
131_V	157_G	1.016	0.99
15_R	22_H	1.015	0.99
184_Q	188_A	1.005	0.99
93_H	140_I	1.000	0.99
69_R	73_L	0.995	0.99
122_L	162_L	0.993	0.99
210_R	214_D	0.979	0.99
32_V	35_P	0.978	0.99
99_E	139_S	0.976	0.99
194_D	197_A	0.974	0.99
152_H	226_G	0.968	0.99
64_R	67_H	0.968	0.99
119_H	185_T	0.963	0.98
60_E	63_R	0.959	0.98
171_E	176_Y	0.958	0.98
145_E	148_R	0.958	0.98
34_Y	85_A	0.955	0.98
44_R	51_D	0.954	0.98
90_R	100_V	0.950	0.98
44_R	168_D	0.947	0.98
12_A	16_R	0.941	0.98
170_R	260_L	0.940	0.98
217_E	249_H	0.934	0.98
71_A	76_R	0.932	0.98
110_D	178_R	0.929	0.98
69_R	100_V	0.925	0.98
167_R	245_Y	0.923	0.98
96_P	99_E	0.917	0.98
163_T	249_H	0.914	0.98
109_Q	116_Y	0.914	0.98
191_A	204_Q	0.912	0.98
61_Q	64_R	0.908	0.98
45_L	80_D	0.907	0.98
214_D	218_R	0.905	0.98
46_T	107_M	0.904	0.98
152_H	229_H	0.899	0.98
68_V	80_D	0.898	0.98
40_Y	134_G	0.895	0.98
106_A	165_F	0.890	0.97
17_T	48_E	0.890	0.97
47_D	164_N	0.883	0.97
47_D	161_Q	0.879	0.97
11_K	37_Y	0.876	0.97
218_R	222_H	0.875	0.97
269_R	273_S	0.870	0.97
191_A	202_T	0.870	0.97
130_S	161_Q	0.865	0.97
221_R	246_A	0.860	0.97
44_R	47_D	0.857	0.97
69_R	72_A	0.854	0.97
44_R	164_N	0.846	0.97
166_L	249_H	0.845	0.96
65_L	68_V	0.844	0.96
130_S	164_N	0.835	0.96
193_H	197_A	0.835	0.96
21_F	44_R	0.835	0.96
60_E	64_R	0.834	0.96
51_D	164_N	0.830	0.96
21_F	164_N	0.830	0.96
40_Y	130_S	0.825	0.96
7_L	34_Y	0.825	0.96
173_V	197_A	0.820	0.96
115_R	177_D	0.820	0.96
159_A	220_Y	0.816	0.96
40_Y	164_N	0.814	0.96
168_D	172_D	0.809	0.96
103_F	132_A	0.809	0.96
195_D	202_T	0.808	0.95
12_A	15_R	0.807	0.95
153_A	157_G	0.806	0.95
21_F	130_S	0.804	0.95
186_L	208_A	0.801	0.95
68_V	83_L	0.798	0.95
161_Q	168_D	0.798	0.95
28_L	36_T	0.795	0.95
115_R	183_S	0.791	0.95
269_R	276_A	0.787	0.95
85_A	88_A	0.784	0.95
21_F	40_Y	0.784	0.95
205_V	259_V	0.776	0.94
86_F	90_R	0.776	0.94
103_F	107_M	0.769	0.94
9_R	81_P	0.768	0.94
172_D	180_Y	0.767	0.94
44_R	48_E	0.766	0.94
137_M	141_M	0.763	0.94
197_A	200_S	0.763	0.94
141_M	234_C	0.759	0.94
225_A	228_E	0.754	0.93
268_L	271_R	0.749	0.93
139_S	150_R	0.748	0.93
247_D	251_L	0.743	0.93
250_R	253_R	0.743	0.93
59_D	108_Q	0.742	0.93
270_R	273_S	0.741	0.93
34_Y	38_V	0.737	0.93
43_F	129_S	0.736	0.93
252_I	259_V	0.736	0.93
132_A	157_G	0.735	0.93
11_K	15_R	0.735	0.93
21_F	133_V	0.735	0.93
131_V	158_E	0.734	0.93
103_F	160_F	0.731	0.92
266_L	271_R	0.729	0.92
179_I	193_H	0.728	0.92
179_I	186_L	0.727	0.92
21_F	134_G	0.727	0.92
234_C	237_P	0.726	0.92
253_R	257_C	0.725	0.92
134_G	161_Q	0.724	0.92
62_R	68_V	0.715	0.92
166_L	213_L	0.714	0.92
43_F	133_V	0.710	0.91
20_T	167_R	0.710	0.91
202_T	261_S	0.707	0.91
44_R	130_S	0.700	0.91
27_F	240_A	0.700	0.91
99_E	127_R	0.697	0.91
40_Y	47_D	0.695	0.90
191_A	195_D	0.694	0.90
200_S	204_Q	0.690	0.90
119_H	219_L	0.687	0.90
227_I	230_L	0.687	0.90
43_F	136_M	0.684	0.90
191_A	205_V	0.684	0.90
49_I	61_Q	0.684	0.90
108_Q	112_D	0.682	0.90
35_P	38_V	0.681	0.89
138_L	226_G	0.681	0.89
151_P	155_S	0.680	0.89
137_M	238_V	0.679	0.89
130_S	168_D	0.677	0.89
218_R	221_R	0.675	0.89
65_L	72_A	0.673	0.89
162_L	215_R	0.673	0.89
32_V	231_P	0.672	0.89
202_T	260_L	0.669	0.89
161_Q	172_D	0.664	0.88
248_Q	263_R	0.664	0.88
62_R	69_R	0.663	0.88
227_I	242_A	0.662	0.88
105_D	108_Q	0.659	0.88
223_G	242_A	0.658	0.88
69_R	101_T	0.658	0.88
167_R	178_R	0.658	0.88
19_R	23_I	0.656	0.88
44_R	161_Q	0.654	0.88
131_V	165_F	0.652	0.87
163_T	216_T	0.651	0.87
157_G	167_R	0.650	0.87
7_L	38_V	0.644	0.87
14_Q	18_G	0.643	0.87
66_A	70_A	0.642	0.87
44_R	172_D	0.641	0.86
164_N	168_D	0.641	0.86
251_L	255_Q	0.640	0.86
105_D	128_G	0.640	0.86
10_S	82_V	0.638	0.86
255_Q	258_D	0.637	0.86
44_R	133_V	0.634	0.86
190_G	198_A	0.629	0.85
236_F	240_A	0.628	0.85
222_H	225_A	0.628	0.85
151_P	222_H	0.624	0.85
130_S	180_Y	0.623	0.85
47_D	130_S	0.621	0.85
131_V	138_L	0.619	0.85
103_F	136_M	0.619	0.85
72_A	83_L	0.617	0.84
248_Q	265_T	0.617	0.84
68_V	72_A	0.616	0.84
163_T	248_Q	0.613	0.84
155_S	158_E	0.612	0.84
216_T	249_H	0.609	0.84
51_D	161_Q	0.607	0.83
226_G	230_L	0.607	0.83
207_D	210_R	0.605	0.83
130_S	133_V	0.603	0.83
102_T	127_R	0.602	0.83
30_E	34_Y	0.602	0.83
164_N	245_Y	0.596	0.82
171_E	175_D	0.595	0.82
119_H	123_A	0.592	0.82
182_P	212_E	0.590	0.82
102_T	105_D	0.590	0.82
10_S	38_V	0.589	0.82
208_A	211_A	0.586	0.81
156_L	167_R	0.584	0.81
135_Y	139_S	0.583	0.81
162_L	219_L	0.582	0.81
134_G	164_N	0.582	0.81
138_L	150_R	0.581	0.81
78_P	83_L	0.580	0.81
201_A	206_R	0.578	0.80
14_Q	24_A	0.578	0.80
127_R	219_L	0.575	0.80
213_L	217_E	0.575	0.80
110_D	125_Y	0.575	0.80
40_Y	51_D	0.574	0.80
31_R	92_D	0.573	0.80
129_S	133_V	0.571	0.80
67_H	70_A	0.571	0.80
69_R	97_R	0.571	0.80
246_A	250_R	0.569	0.79
66_A	69_R	0.568	0.79
40_Y	161_Q	0.567	0.79
25_T	36_T	0.567	0.79
134_G	160_F	0.564	0.79
89_L	93_H	0.564	0.79
164_N	172_D	0.559	0.78
61_Q	68_V	0.557	0.78
43_F	241_A	0.557	0.78
141_M	238_V	0.555	0.78
258_D	262_Q	0.555	0.78
21_F	51_D	0.555	0.78
76_R	84_A	0.555	0.78
20_T	23_I	0.554	0.77
85_A	89_L	0.554	0.77
44_R	160_F	0.551	0.77
220_Y	249_H	0.550	0.77
251_L	267_T	0.550	0.77
11_K	34_Y	0.550	0.77
165_F	172_D	0.550	0.77
58_P	68_V	0.549	0.77
17_T	25_T	0.548	0.77
48_E	52_D	0.548	0.77
46_T	141_M	0.547	0.77
82_V	89_L	0.547	0.77
154_A	158_E	0.545	0.76
20_T	156_L	0.542	0.76
263_R	266_L	0.538	0.75
59_D	63_R	0.537	0.75
7_L	89_L	0.536	0.75
205_V	208_A	0.536	0.75
59_D	69_R	0.535	0.75
51_D	125_Y	0.534	0.75
266_L	270_R	0.534	0.75
39_L	133_V	0.533	0.75
20_T	50_V	0.533	0.75
271_R	274_V	0.531	0.74
108_Q	111_V	0.531	0.74
228_E	239_L	0.529	0.74
107_M	129_S	0.528	0.74
100_V	136_M	0.527	0.74
129_S	164_N	0.526	0.74
161_Q	165_F	0.525	0.74
134_G	172_D	0.522	0.73
213_L	252_I	0.521	0.73
156_L	242_A	0.519	0.73
149_A	238_V	0.519	0.73
102_T	128_G	0.515	0.72
167_R	220_Y	0.514	0.72
150_R	154_A	0.512	0.72
79_D	87_A	0.512	0.72
227_I	239_L	0.512	0.72
64_R	80_D	0.512	0.72
214_D	228_E	0.512	0.72
206_R	210_R	0.511	0.72
238_V	241_A	0.511	0.72
165_F	245_Y	0.509	0.71
101_T	105_D	0.507	0.71
50_V	107_M	0.507	0.71
130_S	172_D	0.506	0.71
215_R	219_L	0.505	0.71
224_V	228_E	0.505	0.71
22_H	37_Y	0.504	0.71
201_A	205_V	0.504	0.71
106_A	109_Q	0.503	0.70
160_F	164_N	0.502	0.70
162_L	216_T	0.502	0.70
41_A	85_A	0.501	0.70
127_R	158_E	0.500	0.70

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
4hd1A	1	0.795	100	0.221	Contact Map
3wcaA	1	0.9845	100	0.222	Contact Map
3acxA	1	0.8602	100	0.227	Contact Map
3we9A	1	0.7453	100	0.25	Contact Map
3vj8A	1	0.9752	100	0.261	Contact Map
4dhdA	2	0.7516	95.3	0.921	Contact Map
1wy0A	2	0.7547	94.5	0.924	Contact Map
3mzvA	2	0.764	94.4	0.924	Contact Map
3oyrA	2	0.7609	94.1	0.925	Contact Map
4lfgA	2	0.6832	93.7	0.926	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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