GGGPS - HALSA - GREMLIN Contacts

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GGGPS - Geranylgeranylglyceryl phosphate synthase

UniProt:	Q9HSF8	Sequences: MTAPWADWDHVLKIDPDKSLVDGETFDDIAQTGTDAIEIGGTLDVTTEKMRRVIDACRTHEVPLYQEPSNPAVVVEDEALDGYLVPVVLNAGDPFWITGAHKEWVRIADLDWERTTTEAYIVMNPDASVAEYTGADCGLDADEVGAYATVAERLLGQEVVYVEYSGTLGDPAVVEAAAGGVDDAAVFYGGGIDGYDAAYRMGAHADTIVVGDLVHEAGVDAVRETVSGVRDAQAEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	236 (217)
Sequences:	641 (488)
Seq/√Len:	33.1

BACSU - PCRB
HALSA - GGGPS Q9HNW3
SULSO - GGGPS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
122_V	129_V	7.961	1.00
193_D	197_A	4.685	1.00
181_V	186_V	4.103	1.00
194_G	197_A	3.985	1.00
39_I	57_C	3.798	1.00
121_I	160_V	3.578	1.00
93_D	134_G	3.574	1.00
94_P	97_I	3.014	1.00
87_V	157_Q	2.950	1.00
185_A	207_T	2.748	1.00
11_V	209_V	2.671	1.00
193_D	216_E	2.444	1.00
14_I	53_V	2.401	0.99
106_R	143_E	2.316	0.99
95_F	100_A	2.295	0.99
68_P	85_V	2.266	0.99
152_E	184_A	2.264	0.99
38_E	84_L	2.249	0.99
74_V	83_Y	2.209	0.99
130_A	137_C	2.188	0.99
39_I	54_I	2.134	0.99
43_L	128_S	2.060	0.98
145_G	173_V	2.034	0.98
10_H	34_T	1.920	0.97
17_D	43_L	1.899	0.97
208_I	229_V	1.890	0.97
159_V	187_F	1.832	0.96
124_N	139_L	1.791	0.96
168_L	200_R	1.790	0.96
17_D	44_D	1.787	0.96
198_A	208_I	1.730	0.95
195_Y	199_Y	1.725	0.95
39_I	64_L	1.711	0.95
217_A	221_A	1.670	0.94
47_T	75_V	1.625	0.93
150_V	154_L	1.607	0.93
119_A	157_Q	1.583	0.92
25_T	219_V	1.566	0.92
171_P	201_M	1.555	0.91
29_I	37_I	1.550	0.91
51_R	75_V	1.537	0.91
94_P	99_G	1.530	0.91
70_N	73_V	1.504	0.90
50_M	66_Q	1.491	0.89
84_L	118_E	1.474	0.89
175_E	179_G	1.443	0.88
187_F	209_V	1.427	0.87
221_A	224_E	1.419	0.87
51_R	79_A	1.408	0.86
14_I	32_T	1.400	0.86
149_T	153_R	1.384	0.85
172_A	175_E	1.375	0.85
21_V	25_T	1.371	0.85
125_P	139_L	1.358	0.84
87_V	155_L	1.357	0.84
213_L	221_A	1.330	0.83
192_I	198_A	1.328	0.83
11_V	36_A	1.328	0.83
58_R	64_L	1.326	0.83
194_G	200_R	1.318	0.82
127_A	135_A	1.312	0.82
14_I	20_L	1.290	0.81
10_H	210_V	1.282	0.81
156_G	204_H	1.278	0.80
66_Q	177_A	1.271	0.80
150_V	182_D	1.271	0.80
168_L	201_M	1.268	0.80
11_V	38_E	1.254	0.79
109_D	153_R	1.254	0.79
82_G	116_T	1.253	0.79
144_V	177_A	1.250	0.79
55_D	79_A	1.245	0.79
65_Y	82_G	1.242	0.79
98_T	155_L	1.224	0.77
122_V	135_A	1.170	0.74
149_T	180_G	1.162	0.74
86_P	133_T	1.157	0.73
54_I	58_R	1.154	0.73
29_I	32_T	1.149	0.73
56_A	59_T	1.131	0.72
26_F	56_A	1.117	0.71
176_A	179_G	1.099	0.69
141_A	145_G	1.082	0.68
105_V	152_E	1.075	0.68
194_G	208_I	1.070	0.67
42_T	201_M	1.056	0.66
103_E	140_D	1.046	0.66
116_T	159_V	1.045	0.65
12_L	214_V	1.041	0.65
219_V	223_R	1.040	0.65
14_I	125_P	1.039	0.65
14_I	26_F	1.024	0.64
34_T	226_V	1.024	0.64
98_T	105_V	1.021	0.64
148_A	152_E	1.021	0.64
116_T	194_G	1.014	0.63
52_R	56_A	1.003	0.62
12_L	34_T	0.997	0.62
74_V	224_E	0.993	0.61
30_A	62_V	0.982	0.61
91_A	133_T	0.975	0.60
48_E	52_R	0.974	0.60
32_T	53_V	0.971	0.60
212_D	215_H	0.970	0.60
20_L	56_A	0.970	0.60
89_L	119_A	0.967	0.59
168_L	171_P	0.964	0.59
90_N	122_V	0.959	0.59
223_R	227_S	0.954	0.58
17_D	128_S	0.952	0.58
108_A	115_T	0.945	0.58
101_H	155_L	0.944	0.57
164_Y	169_G	0.942	0.57
101_H	145_G	0.942	0.57
60_H	64_L	0.938	0.57
98_T	102_K	0.928	0.56
139_L	170_D	0.927	0.56
76_E	79_A	0.925	0.56
94_P	137_C	0.923	0.56
119_A	160_V	0.923	0.56
109_D	149_T	0.904	0.54
106_R	147_Y	0.901	0.54
130_A	135_A	0.898	0.54
101_H	150_V	0.896	0.54
146_A	176_A	0.885	0.53
57_C	64_L	0.881	0.52
89_L	157_Q	0.871	0.51
42_T	97_I	0.865	0.51
67_E	88_V	0.859	0.50
117_T	151_A	0.855	0.50
161_Y	189_G	0.850	0.50
178_A	196_D	0.849	0.50
98_T	117_T	0.848	0.50
49_K	52_R	0.843	0.49
73_V	91_A	0.839	0.49
39_I	62_V	0.838	0.49
171_P	200_R	0.836	0.49
181_V	184_A	0.834	0.48
88_V	133_T	0.832	0.48
10_H	90_N	0.825	0.48
54_I	185_A	0.820	0.47
107_I	160_V	0.819	0.47
198_A	201_M	0.812	0.47
55_D	58_R	0.799	0.45
217_A	224_E	0.797	0.45
34_T	163_E	0.796	0.45
44_D	49_K	0.786	0.44
124_N	129_V	0.786	0.44
48_E	175_E	0.784	0.44
173_V	204_H	0.779	0.44
48_E	55_D	0.779	0.44
145_G	177_A	0.771	0.43
105_V	154_L	0.764	0.43
93_D	99_G	0.764	0.43
145_G	176_A	0.758	0.42
58_R	203_A	0.755	0.42
162_V	188_Y	0.755	0.42
121_I	177_A	0.754	0.42
62_V	116_T	0.754	0.42
116_T	184_A	0.750	0.41
152_E	160_V	0.748	0.41
87_V	173_V	0.747	0.41
18_K	128_S	0.747	0.41
131_E	144_V	0.743	0.41
122_V	127_A	0.742	0.41
34_T	210_V	0.738	0.40
143_E	158_E	0.738	0.40
138_G	173_V	0.738	0.40
89_L	155_L	0.736	0.40
87_V	97_I	0.732	0.40
119_A	206_D	0.732	0.40
58_R	160_V	0.731	0.40
90_N	148_A	0.729	0.40
36_A	163_E	0.722	0.39
138_G	167_T	0.719	0.39
63_P	127_A	0.716	0.39
47_T	173_V	0.713	0.38
126_D	167_T	0.712	0.38
85_V	101_H	0.709	0.38
97_I	126_D	0.707	0.38
74_V	109_D	0.704	0.38
73_V	122_V	0.702	0.38
30_A	60_H	0.700	0.37
101_H	117_T	0.700	0.37
34_T	62_V	0.698	0.37
11_V	127_A	0.698	0.37
12_L	222_V	0.697	0.37
141_A	176_A	0.695	0.37
50_M	119_A	0.694	0.37
8_W	206_D	0.694	0.37
91_A	135_A	0.693	0.37
130_A	139_L	0.693	0.37
117_T	154_L	0.692	0.37
144_V	164_Y	0.690	0.37
69_S	129_V	0.689	0.37
142_D	146_A	0.685	0.36
195_Y	221_A	0.685	0.36
9_D	45_V	0.684	0.36
17_D	49_K	0.681	0.36
199_Y	202_G	0.681	0.36
156_G	203_A	0.679	0.36
93_D	97_I	0.678	0.36
160_V	184_A	0.676	0.36
96_W	112_W	0.673	0.35
26_F	53_V	0.672	0.35
181_V	185_A	0.671	0.35
92_G	134_G	0.669	0.35
38_E	118_E	0.668	0.35
123_M	146_A	0.667	0.35
106_R	110_L	0.661	0.34
12_L	53_V	0.661	0.34
151_A	160_V	0.660	0.34
14_I	54_I	0.658	0.34
54_I	62_V	0.658	0.34
45_V	180_G	0.658	0.34
102_K	167_T	0.656	0.34
217_A	220_D	0.653	0.34
87_V	126_D	0.651	0.34
50_M	63_P	0.648	0.33
103_E	106_R	0.648	0.33
54_I	64_L	0.648	0.33
152_E	207_T	0.646	0.33
90_N	135_A	0.641	0.33
162_V	173_V	0.638	0.33
197_A	200_R	0.635	0.33
82_G	193_D	0.634	0.32
75_V	79_A	0.631	0.32
71_P	104_W	0.629	0.32
146_A	180_G	0.627	0.32
189_G	211_G	0.626	0.32
10_H	33_G	0.624	0.32
118_E	148_A	0.624	0.32
67_E	188_Y	0.622	0.32
146_A	178_A	0.619	0.31
42_T	116_T	0.616	0.31
174_V	206_D	0.616	0.31
71_P	100_A	0.614	0.31
105_V	207_T	0.613	0.31
46_T	169_G	0.612	0.31
50_M	109_D	0.611	0.31
32_T	158_E	0.609	0.31
7_D	182_D	0.606	0.30
31_Q	51_R	0.602	0.30
156_G	193_D	0.602	0.30
37_I	83_Y	0.602	0.30
54_I	82_G	0.601	0.30
32_T	79_A	0.599	0.30
173_V	176_A	0.597	0.30
68_P	126_D	0.592	0.29
28_D	74_V	0.589	0.29
71_P	127_A	0.588	0.29
80_L	83_Y	0.587	0.29
134_G	140_D	0.587	0.29
91_A	97_I	0.586	0.29
126_D	209_V	0.586	0.29
82_G	185_A	0.585	0.29
97_I	150_V	0.584	0.29
90_N	130_A	0.582	0.29
133_T	148_A	0.581	0.29
174_V	216_E	0.580	0.29
86_P	90_N	0.579	0.29
37_I	57_C	0.579	0.29
161_Y	166_G	0.576	0.28
140_D	209_V	0.571	0.28
134_G	173_V	0.571	0.28
21_V	206_D	0.571	0.28
121_I	181_V	0.570	0.28
26_F	186_V	0.569	0.28
115_T	135_A	0.569	0.28
97_I	102_K	0.568	0.28
39_I	175_E	0.567	0.28
29_I	203_A	0.566	0.28
141_A	173_V	0.566	0.28
54_I	75_V	0.563	0.27
9_D	134_G	0.561	0.27
113_E	116_T	0.561	0.27
55_D	220_D	0.557	0.27
84_L	87_V	0.557	0.27
164_Y	188_Y	0.557	0.27
131_E	134_G	0.556	0.27
7_D	115_T	0.554	0.27
54_I	66_Q	0.548	0.26
66_Q	80_L	0.546	0.26
122_V	172_A	0.546	0.26
94_P	98_T	0.545	0.26
36_A	65_Y	0.545	0.26
90_N	133_T	0.543	0.26
179_G	182_D	0.542	0.26
87_V	94_P	0.542	0.26
57_C	87_V	0.538	0.26
166_G	209_V	0.538	0.26
159_V	214_V	0.536	0.26
119_A	151_A	0.535	0.26
93_D	98_T	0.534	0.26
65_Y	84_L	0.533	0.26
123_M	173_V	0.531	0.25
100_A	103_E	0.528	0.25
90_N	125_P	0.527	0.25
38_E	213_L	0.527	0.25
17_D	105_V	0.527	0.25
29_I	57_C	0.525	0.25
152_E	181_V	0.525	0.25
104_W	160_V	0.523	0.25
58_R	62_V	0.522	0.25
213_L	216_E	0.521	0.25
14_I	75_V	0.520	0.25
132_Y	216_E	0.519	0.25
42_T	49_K	0.518	0.25
68_P	105_V	0.517	0.25
93_D	136_D	0.516	0.24
74_V	106_R	0.516	0.24
131_E	141_A	0.516	0.24
162_V	177_A	0.515	0.24
163_E	189_G	0.515	0.24
70_N	100_A	0.514	0.24
163_E	188_Y	0.514	0.24
101_H	112_W	0.513	0.24
97_I	101_H	0.512	0.24
17_D	55_D	0.510	0.24
122_V	133_T	0.508	0.24
86_P	148_A	0.505	0.24
204_H	217_A	0.504	0.24
10_H	198_A	0.504	0.24
81_D	178_A	0.501	0.24
92_G	213_L	0.500	0.23
93_D	209_V	0.500	0.23

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
2f6uA	2	0.9364	100	0.591	Contact Map
3vzxA	2	0.9576	100	0.599	Contact Map
3w01A	2	0.9619	100	0.605	Contact Map
4nafA	2	0.9364	100	0.659	Contact Map
3vk5A	2	0.9237	100	0.682	Contact Map
4mm1A	3	0.9449	100	0.686	Contact Map
3ktsA	1	0.7669	99.9	0.718	Contact Map
4jejA	2	0.9322	99.9	0.725	Contact Map
3thaA	2	0.8517	99.6	0.816	Contact Map
1ujpA	1	0.822	99.5	0.823	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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