PSD - HALSA - GREMLIN Contacts

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PSD - Phosphatidylserine decarboxylase proenzyme

UniProt:	Q9HN46	Sequences: MLARGPWTWKYALPPAVVGVAALAASSPWGVVGVALAAFVVWFHRDPDRSPNGAGVVVPADGTVSVIRTRDDGRVRVGVFMNVHNVHVNRVPVAGRVESVVHEPGGHRPAFSKESAHNERVRIETAEWTVVLIAGAFARRIHPYVEAGEDLARGDRLGHISFGSRADVVLPPAYDRGDVVVESGQTVRAGETVLAR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	196 (189)
Sequences:	1392 (927)
Seq/√Len:	67.4

HALSA - PSD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_E	124_E	4.468	1.00
85_N	186_T	3.629	1.00
69_T	73_G	3.626	1.00
46_D	156_R	3.579	1.00
19_G	37_A	3.410	1.00
58_V	79_V	3.260	1.00
182_E	185_Q	3.001	1.00
59_P	79_V	2.874	1.00
75_V	179_V	2.647	1.00
124_E	127_E	2.645	1.00
91_V	151_L	2.447	1.00
67_I	183_S	2.361	1.00
98_E	127_E	2.226	1.00
96_R	150_D	2.179	1.00
146_E	149_E	2.161	1.00
168_V	194_L	2.112	1.00
12_A	41_V	2.111	1.00
59_P	168_V	2.099	1.00
106_G	117_H	2.084	1.00
44_H	162_F	2.080	1.00
145_V	151_L	2.036	1.00
81_M	166_A	2.002	1.00
94_A	152_A	1.913	1.00
56_V	93_V	1.893	1.00
60_A	89_N	1.871	1.00
58_V	187_V	1.852	1.00
15_P	40_V	1.802	1.00
56_V	195_A	1.772	1.00
81_M	189_A	1.733	1.00
16_A	37_A	1.684	0.99
131_V	169_V	1.670	0.99
123_I	130_V	1.652	0.99
4_R	12_A	1.641	0.99
83_V	136_A	1.607	0.99
188_R	191_E	1.593	0.99
76_R	169_V	1.589	0.99
48_D	156_R	1.561	0.99
93_V	128_W	1.541	0.99
141_I	163_G	1.532	0.99
23_L	33_G	1.526	0.99
23_L	30_G	1.520	0.99
11_Y	161_S	1.515	0.99
96_R	124_E	1.511	0.99
91_V	157_L	1.502	0.99
57_V	153_R	1.495	0.99
152_A	155_D	1.490	0.99
90_R	190_G	1.486	0.99
80_F	110_A	1.460	0.98
89_N	157_L	1.446	0.98
120_R	131_V	1.418	0.98
69_T	172_P	1.417	0.98
77_V	179_V	1.403	0.98
95_G	123_I	1.387	0.98
86_V	166_A	1.375	0.98
144_Y	159_H	1.366	0.98
91_V	145_V	1.364	0.98
142_H	161_S	1.335	0.97
49_R	61_D	1.320	0.97
110_A	138_A	1.316	0.97
130_V	157_L	1.315	0.97
99_S	147_A	1.302	0.97
99_S	122_R	1.298	0.97
13_L	17_V	1.260	0.96
122_R	127_E	1.205	0.95
81_M	89_N	1.181	0.94
46_D	90_R	1.179	0.94
174_Y	195_A	1.176	0.94
188_R	192_T	1.175	0.94
93_V	125_T	1.169	0.94
5_G	144_Y	1.149	0.94
72_D	129_T	1.140	0.93
75_V	173_A	1.131	0.93
69_T	75_V	1.130	0.93
121_V	145_V	1.126	0.93
173_A	179_V	1.126	0.93
19_G	23_L	1.119	0.93
100_V	146_E	1.109	0.92
11_Y	15_P	1.079	0.91
103_E	120_R	1.074	0.91
92_P	130_V	1.070	0.91
187_V	192_T	1.064	0.91
180_V	193_V	1.051	0.90
15_P	37_A	1.041	0.90
87_H	160_I	1.038	0.90
10_K	14_P	1.031	0.89
100_V	147_A	1.013	0.88
43_F	87_H	1.011	0.88
43_F	164_S	1.007	0.88
100_V	143_P	1.004	0.88
6_P	9_W	1.003	0.88
121_V	151_L	1.001	0.88
121_V	157_L	0.999	0.88
77_V	194_L	0.998	0.88
75_V	172_P	0.995	0.88
113_K	134_A	0.994	0.87
77_V	170_L	0.990	0.87
89_N	132_L	0.983	0.87
78_G	165_R	0.980	0.87
119_E	134_A	0.950	0.85
37_A	41_V	0.944	0.85
109_P	112_S	0.921	0.83
125_T	174_Y	0.921	0.83
39_F	84_H	0.916	0.83
80_F	138_A	0.915	0.83
81_M	160_I	0.915	0.83
126_A	173_A	0.912	0.83
12_A	15_P	0.910	0.82
123_I	128_W	0.907	0.82
102_H	119_E	0.905	0.82
21_A	25_A	0.901	0.82
66_V	76_R	0.898	0.82
36_L	40_V	0.896	0.81
110_A	135_G	0.883	0.80
105_G	139_R	0.882	0.80
47_P	86_V	0.872	0.80
28_P	32_V	0.870	0.79
56_V	128_W	0.867	0.79
91_V	94_A	0.865	0.79
12_A	37_A	0.863	0.79
51_P	191_E	0.862	0.79
74_R	127_E	0.857	0.78
64_V	179_V	0.854	0.78
7_W	81_M	0.850	0.78
80_F	135_G	0.849	0.78
4_R	8_T	0.834	0.77
39_F	42_W	0.828	0.76
57_V	190_G	0.825	0.76
34_V	38_A	0.817	0.75
70_R	169_V	0.809	0.74
143_P	157_L	0.808	0.74
43_F	80_F	0.795	0.73
27_S	31_V	0.789	0.72
19_G	33_G	0.788	0.72
81_M	87_H	0.780	0.72
55_G	94_A	0.779	0.71
124_E	184_G	0.778	0.71
53_G	180_V	0.776	0.71
9_W	13_L	0.775	0.71
56_V	168_V	0.773	0.71
35_A	39_F	0.772	0.71
9_W	24_A	0.768	0.70
88_V	156_R	0.768	0.70
88_V	190_G	0.762	0.70
81_M	134_A	0.747	0.68
149_E	155_D	0.747	0.68
97_V	145_V	0.745	0.68
135_G	139_R	0.745	0.68
79_V	194_L	0.740	0.68
140_R	162_F	0.737	0.67
135_G	140_R	0.736	0.67
87_H	164_S	0.735	0.67
43_F	81_M	0.734	0.67
25_A	28_P	0.733	0.67
78_G	167_D	0.733	0.67
57_V	192_T	0.731	0.67
43_F	160_I	0.730	0.66
87_H	138_A	0.725	0.66
32_V	84_H	0.724	0.66
80_F	87_H	0.718	0.65
12_A	19_G	0.718	0.65
5_G	72_D	0.718	0.65
22_A	26_S	0.716	0.65
160_I	164_S	0.714	0.65
61_D	189_A	0.714	0.65
22_A	28_P	0.698	0.63
123_I	151_L	0.697	0.63
122_R	129_T	0.696	0.63
51_P	153_R	0.694	0.63
134_A	160_I	0.691	0.62
16_A	57_V	0.688	0.62
121_V	143_P	0.687	0.62
9_W	142_H	0.686	0.62
5_G	74_R	0.685	0.62
111_F	115_S	0.679	0.61
90_R	189_A	0.679	0.61
54_A	73_G	0.676	0.61
4_R	89_N	0.670	0.60
50_S	191_E	0.668	0.60
17_V	50_S	0.665	0.59
135_G	138_A	0.662	0.59
119_E	133_I	0.661	0.59
22_A	33_G	0.659	0.59
110_A	140_R	0.658	0.58
8_T	166_A	0.658	0.58
75_V	174_Y	0.656	0.58
40_V	137_F	0.652	0.58
156_R	189_A	0.650	0.58
134_A	167_D	0.650	0.58
43_F	138_A	0.650	0.58
44_H	80_F	0.649	0.57
22_A	30_G	0.648	0.57
160_I	166_A	0.646	0.57
36_L	109_P	0.646	0.57
174_Y	179_V	0.645	0.57
115_S	133_I	0.644	0.57
185_Q	192_T	0.643	0.57
90_R	154_G	0.640	0.56
9_W	12_A	0.639	0.56
130_V	168_V	0.638	0.56
14_P	18_V	0.638	0.56
58_V	192_T	0.637	0.56
19_G	22_A	0.627	0.55
7_W	144_Y	0.625	0.55
57_V	191_E	0.622	0.54
6_P	10_K	0.621	0.54
65_S	76_R	0.620	0.54
32_V	54_A	0.618	0.54
83_V	109_P	0.618	0.54
20_V	24_A	0.617	0.54
26_S	29_W	0.617	0.54
36_L	84_H	0.617	0.54
109_P	136_A	0.614	0.53
147_A	192_T	0.610	0.53
113_K	167_D	0.610	0.53
106_G	194_L	0.609	0.53
74_R	122_R	0.608	0.53
78_G	82_N	0.608	0.53
81_M	164_S	0.602	0.52
76_R	167_D	0.601	0.52
120_R	167_D	0.601	0.52
63_T	82_N	0.599	0.52
44_H	161_S	0.594	0.51
73_G	172_P	0.590	0.50
105_G	135_G	0.589	0.50
53_G	153_R	0.587	0.50
121_V	130_V	0.586	0.50
17_V	24_A	0.581	0.49
109_P	129_T	0.578	0.49
23_L	34_V	0.578	0.49
30_G	34_V	0.577	0.49
10_K	23_L	0.575	0.49
115_S	120_R	0.574	0.49
152_A	179_V	0.573	0.48
56_V	174_Y	0.573	0.48
116_A	121_V	0.571	0.48
110_A	165_R	0.571	0.48
128_W	174_Y	0.569	0.48
25_A	35_A	0.569	0.48
17_V	52_N	0.563	0.47
81_M	113_K	0.563	0.47
87_H	140_R	0.562	0.47
97_V	121_V	0.560	0.47
43_F	135_G	0.559	0.47
60_A	143_P	0.556	0.46
22_A	29_W	0.555	0.46
96_R	100_V	0.553	0.46
12_A	17_V	0.550	0.46
15_P	64_V	0.550	0.46
145_V	149_E	0.550	0.46
22_A	34_V	0.547	0.45
43_F	132_L	0.547	0.45
30_G	39_F	0.545	0.45
75_V	122_R	0.543	0.45
4_R	9_W	0.543	0.45
10_K	24_A	0.542	0.45
15_P	36_L	0.539	0.44
68_R	76_R	0.539	0.44
37_A	57_V	0.538	0.44
17_V	146_E	0.533	0.44
7_W	187_V	0.532	0.44
43_F	133_I	0.531	0.43
122_R	147_A	0.531	0.43
77_V	168_V	0.530	0.43
113_K	120_R	0.529	0.43
43_F	139_R	0.527	0.43
43_F	89_N	0.526	0.43
43_F	110_A	0.525	0.43
55_G	93_V	0.524	0.43
16_A	23_L	0.523	0.43
43_F	140_R	0.522	0.42
107_H	134_A	0.521	0.42
81_M	144_Y	0.521	0.42
49_R	191_E	0.519	0.42
11_Y	18_V	0.519	0.42
90_R	156_R	0.518	0.42
27_S	173_A	0.515	0.42
100_V	122_R	0.514	0.42
126_A	174_Y	0.510	0.41
114_E	161_S	0.508	0.41
99_S	129_T	0.507	0.41
97_V	143_P	0.507	0.41
46_D	157_L	0.507	0.41
67_I	153_R	0.503	0.40
68_R	183_S	0.500	0.40

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
1f3zA	2	0.6684	97.6	0.883	Contact Map
1ax3A	1	0.7245	97.5	0.883	Contact Map
2gprA	1	0.7041	97.4	0.885	Contact Map
3ourB	1	0.6684	97	0.894	Contact Map
2d5dA	1	0.3418	94.9	0.911	Contact Map
1dczA	1	0.3776	93.9	0.915	Contact Map
4tkoB	1	0.7806	90.4	0.924	Contact Map
1z6hA	1	0.3469	88.3	0.927	Contact Map
2xhaA	1	0.6071	87.2	0.928	Contact Map
2jkuA	1	0.1786	86.7	0.929	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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