IDI - HALSA - GREMLIN Contacts

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IDI - Isopentenyl-diphosphate Delta-isomerase

UniProt:	Q9HP40	Sequences: MRDSMSEADRSSPGSGKTDREDETAENATQDVIAVTPDDERTGLANRLDAHTGDGVRHRAFTCLLFDEDGRVLLAQRADRKRLWDTHWDGTVASHPIEGQSQVDATRQRLAEELGIEPHQYDKLEITDRFEYKRRYLDEGLEWEVCAVLQATLHDTSFDRDPEEVGGAMWVDYEDLYENPRYYRQLRLCPWFEIAMRRDFEGDADPVPDGTRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	213 (167)
Sequences:	2054 (1313)
Seq/√Len:	101.6

ECOLI - YFCD IDI
HALSA - IDI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_T	40_E	6.768	1.00
67_D	71_R	6.103	1.00
79_D	86_T	5.268	1.00
76_Q	167_G	3.720	1.00
68_E	155_D	3.382	1.00
111_A	117_E	3.011	1.00
76_Q	166_G	2.817	1.00
92_V	110_L	2.642	1.00
179_N	188_L	2.485	1.00
171_V	176_L	2.481	1.00
63_C	106_T	2.282	1.00
39_D	59_R	2.249	1.00
49_D	54_D	2.103	1.00
45_A	49_D	2.077	1.00
172_D	175_D	2.042	1.00
109_R	112_E	1.997	1.00
101_S	104_D	1.943	1.00
31_D	44_L	1.923	1.00
84_W	190_P	1.850	1.00
158_F	168_A	1.821	1.00
79_D	166_G	1.801	1.00
66_F	72_V	1.788	1.00
116_I	154_H	1.697	1.00
51_H	95_H	1.697	1.00
35_V	59_R	1.684	1.00
71_R	172_D	1.619	1.00
45_A	56_V	1.547	1.00
51_H	144_E	1.541	1.00
32_V	50_A	1.536	1.00
46_N	49_D	1.532	1.00
45_A	50_A	1.518	1.00
30_Q	108_Q	1.508	1.00
87_H	189_C	1.504	1.00
176_L	192_F	1.490	1.00
89_D	189_C	1.475	1.00
105_A	108_Q	1.459	1.00
100_Q	108_Q	1.437	1.00
73_L	168_A	1.434	1.00
31_D	46_N	1.433	1.00
116_I	158_F	1.400	1.00
88_W	169_M	1.390	1.00
65_L	116_I	1.387	1.00
86_T	166_G	1.345	0.99
72_V	91_T	1.338	0.99
30_Q	97_I	1.335	0.99
76_Q	86_T	1.323	0.99
131_E	145_V	1.315	0.99
73_L	170_W	1.246	0.99
169_M	179_N	1.241	0.99
90_G	93_A	1.223	0.99
180_P	196_M	1.211	0.99
95_H	144_E	1.195	0.99
68_E	152_T	1.195	0.99
29_T	46_N	1.163	0.98
112_E	161_D	1.159	0.98
62_T	90_G	1.156	0.98
47_R	109_R	1.123	0.98
133_K	141_L	1.112	0.98
89_D	93_A	1.111	0.98
128_D	148_V	1.110	0.98
82_R	140_G	1.100	0.98
64_L	195_A	1.088	0.97
88_W	167_G	1.086	0.97
114_L	168_A	1.083	0.97
72_V	176_L	1.078	0.97
44_L	98_E	1.076	0.97
71_R	175_D	1.067	0.97
110_L	118_P	1.057	0.97
67_D	170_W	1.049	0.97
57_R	131_E	1.047	0.97
102_Q	147_A	1.028	0.96
30_Q	47_R	1.022	0.96
34_A	50_A	1.020	0.96
102_Q	149_L	1.016	0.96
63_C	110_L	1.009	0.96
80_R	163_E	0.990	0.95
34_A	56_V	0.989	0.95
51_H	58_H	0.974	0.95
74_L	171_V	0.958	0.94
34_A	45_A	0.956	0.94
29_T	48_L	0.953	0.94
107_R	117_E	0.947	0.94
177_Y	200_F	0.940	0.94
178_E	181_R	0.934	0.94
160_R	165_V	0.925	0.93
106_T	149_L	0.925	0.93
160_R	168_A	0.922	0.93
67_D	152_T	0.918	0.93
62_T	93_A	0.917	0.93
129_R	147_A	0.902	0.93
96_P	109_R	0.898	0.92
154_H	158_F	0.897	0.92
37_P	131_E	0.897	0.92
33_I	98_E	0.897	0.92
175_D	178_E	0.894	0.92
65_L	151_A	0.884	0.92
75_A	89_D	0.879	0.92
74_L	188_L	0.877	0.91
146_C	195_A	0.875	0.91
124_L	151_A	0.866	0.91
39_D	145_V	0.865	0.91
126_I	129_R	0.865	0.91
70_G	152_T	0.863	0.91
151_A	154_H	0.862	0.91
83_L	140_G	0.861	0.91
30_Q	109_R	0.854	0.90
60_A	132_Y	0.844	0.90
188_L	192_F	0.831	0.89
102_Q	106_T	0.829	0.89
103_V	106_T	0.807	0.88
62_T	146_C	0.790	0.87
65_L	110_L	0.790	0.87
41_R	98_E	0.790	0.87
34_A	43_G	0.788	0.86
64_L	192_F	0.788	0.86
114_L	165_V	0.784	0.86
154_H	157_S	0.778	0.86
90_G	191_W	0.776	0.86
66_F	150_Q	0.775	0.85
58_H	95_H	0.775	0.85
184_R	187_R	0.775	0.85
118_P	151_A	0.774	0.85
172_D	176_L	0.770	0.85
132_Y	142_E	0.761	0.84
94_S	109_R	0.757	0.84
133_K	143_W	0.749	0.83
33_I	59_R	0.748	0.83
128_D	195_A	0.747	0.83
132_Y	146_C	0.747	0.83
178_E	183_Y	0.747	0.83
84_W	140_G	0.744	0.83
132_Y	191_W	0.741	0.83
130_F	195_A	0.739	0.83
47_R	82_R	0.738	0.83
159_D	183_Y	0.737	0.83
103_V	149_L	0.736	0.82
107_R	111_A	0.733	0.82
169_M	175_D	0.732	0.82
30_Q	94_S	0.729	0.82
49_D	52_T	0.729	0.82
62_T	95_H	0.726	0.82
61_F	105_A	0.721	0.81
41_R	45_A	0.720	0.81
75_A	168_A	0.712	0.80
47_R	83_L	0.710	0.80
62_T	89_D	0.709	0.80
39_D	102_Q	0.708	0.80
51_H	142_E	0.707	0.80
36_T	42_T	0.707	0.80
124_L	159_D	0.706	0.80
47_R	97_I	0.701	0.79
51_H	62_T	0.694	0.79
66_F	127_T	0.689	0.78
111_A	118_P	0.688	0.78
50_A	95_H	0.686	0.78
39_D	129_R	0.684	0.78
157_S	178_E	0.684	0.78
176_L	181_R	0.680	0.77
32_V	82_R	0.678	0.77
62_T	144_E	0.676	0.77
90_G	132_Y	0.676	0.77
39_D	131_E	0.675	0.77
31_D	98_E	0.670	0.76
35_V	102_Q	0.667	0.76
33_I	99_G	0.667	0.76
173_Y	192_F	0.654	0.74
91_T	132_Y	0.653	0.74
62_T	191_W	0.652	0.74
33_I	73_L	0.650	0.74
30_Q	85_D	0.646	0.73
76_Q	88_W	0.639	0.73
74_L	169_M	0.629	0.72
173_Y	177_Y	0.623	0.71
103_V	177_Y	0.616	0.70
67_D	70_G	0.616	0.70
92_V	114_L	0.613	0.70
47_R	108_Q	0.611	0.69
61_F	95_H	0.607	0.69
72_V	173_Y	0.607	0.69
63_C	151_A	0.606	0.69
118_P	166_G	0.603	0.68
61_F	132_Y	0.599	0.68
74_L	172_D	0.598	0.68
185_Q	197_R	0.597	0.68
50_A	94_S	0.596	0.67
59_R	102_Q	0.595	0.67
57_R	143_W	0.592	0.67
60_A	93_A	0.591	0.67
100_Q	112_E	0.590	0.67
51_H	93_A	0.588	0.66
47_R	93_A	0.588	0.66
93_A	142_E	0.587	0.66
185_Q	188_L	0.586	0.66
177_Y	196_M	0.583	0.66
195_A	199_D	0.582	0.66
81_K	144_E	0.579	0.65
165_V	168_A	0.577	0.65
74_L	112_E	0.577	0.65
62_T	75_A	0.576	0.65
130_F	146_C	0.572	0.64
32_V	97_I	0.572	0.64
120_Q	157_S	0.571	0.64
142_E	191_W	0.571	0.64
126_I	145_V	0.569	0.64
180_P	188_L	0.565	0.63
41_R	44_L	0.564	0.63
51_H	91_T	0.560	0.63
51_H	60_A	0.558	0.62
81_K	164_E	0.557	0.62
107_R	119_H	0.555	0.62
171_V	179_N	0.555	0.62
44_L	117_E	0.555	0.62
74_L	168_A	0.553	0.62
32_V	95_H	0.552	0.62
76_Q	79_D	0.550	0.61
104_D	124_L	0.546	0.61
93_A	144_E	0.546	0.61
92_V	192_F	0.544	0.60
114_L	118_P	0.543	0.60
65_L	91_T	0.542	0.60
93_A	191_W	0.539	0.60
62_T	96_P	0.536	0.59
71_R	174_E	0.536	0.59
59_R	64_L	0.535	0.59
74_L	184_R	0.533	0.59
62_T	142_E	0.530	0.58
33_I	39_D	0.527	0.58
54_D	170_W	0.526	0.58
84_W	146_C	0.525	0.58
35_V	39_D	0.523	0.57
127_T	150_Q	0.522	0.57
60_A	142_E	0.520	0.57
34_A	142_E	0.518	0.57
32_V	149_L	0.517	0.57
84_W	87_H	0.514	0.56
66_F	152_T	0.514	0.56
67_D	155_D	0.514	0.56
125_E	197_R	0.513	0.56
75_A	189_C	0.512	0.56
62_T	195_A	0.511	0.56
45_A	54_D	0.510	0.56
73_L	158_F	0.510	0.56
155_D	159_D	0.509	0.55
37_P	40_E	0.509	0.55
56_V	141_L	0.506	0.55
63_C	124_L	0.506	0.55
93_A	109_R	0.503	0.55
95_H	142_E	0.503	0.55
194_I	197_R	0.501	0.54
87_H	187_R	0.500	0.54

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
2pnyA	1	0.9577	100	0.378	Contact Map
2dhoA	1	0.8826	100	0.383	Contact Map
3dupA	2	0.9765	100	0.513	Contact Map
1hztA	1	0.7089	100	0.513	Contact Map
2fkbA	1	0.784	100	0.573	Contact Map
1q27A	1	0.8028	100	0.58	Contact Map
2xsqA	2	0.6995	99.9	0.654	Contact Map
3e57A	2	0.8122	99.8	0.681	Contact Map
1sjyA	2	0.7136	99.8	0.686	Contact Map
3q91A	2	0.6244	99.8	0.688	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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