GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LEH - Limonene-12-epoxide hydrolase catalytic domain
Pfam: PF07858 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0051
Length: 125
Sequences: 8298
Seq/Len: 66.38
HH_delta: -0.02 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
31_A47_I1.526523.022
28_D108_T1.427822.827
101_E109_L1.39782.767
103_R108_T1.374432.721
24_A48_R1.33272.638
29_D44_R1.293132.560
79_R96_V1.125472.228
20_D48_R1.103822.185
6_V102_V0.999011.978
12_A16_D0.993041.966
5_E9_A0.99211.964
18_D22_A0.969011.918
8_R12_A0.823621.631
48_R52_R0.803871.592
32_V109_L0.798381.581
27_F31_A0.793931.572
43_G46_A0.792051.568
101_E108_T0.790451.565
98_G112_D0.763091.511
32_V42_R0.762151.509
34_H111_R0.74961.484
74_V101_E0.717451.420
17_R55_L0.702671.391
20_D24_A0.699481.385
27_F110_W0.694281.375
45_D49_A0.680891.348
22_A25_S0.667411.321
24_A44_R0.662491.312
7_V100_F0.656351.299
80_T93_Q0.634861.257
67_R78_E0.633721.255
9_A26_L0.631091.249
73_D101_E0.628161.244
45_D48_R0.622571.233
28_D103_R0.621151.230
49_A53_G0.618811.225
66_H80_T0.617081.222
9_A12_A0.612391.212
49_A52_R0.607311.202
27_F47_I0.600551.189
76_L99_V0.592071.172
34_H109_L0.591631.171
103_R106_K0.589381.167
9_A13_A0.570861.130
69_A76_L0.55081.090
19_V52_R0.550781.090
70_A75_V0.539081.067
9_A25_S0.538171.065
98_G110_W0.537281.064
12_A15_E0.530941.051
100_F107_I0.527361.044
29_D106_K0.522751.035
11_L15_E0.519361.028
19_V24_A0.511321.012
44_R48_R0.510911.012
67_R74_V0.50551.001
6_V26_L0.500790.991
13_A22_A0.492520.975
79_R98_G0.491890.974
13_A18_D0.485870.962
30_D108_T0.483070.956
44_R106_K0.476770.944
80_T95_P0.473860.938
28_D106_K0.469810.930
97_C113_Y0.46910.929
35_N112_D0.463910.918
33_Y112_D0.461280.913
102_V107_I0.459170.909
75_V102_V0.458060.907
73_D103_R0.457580.906
64_D80_T0.457220.905
53_G57_S0.454180.899
9_A22_A0.45260.896
7_V75_V0.44710.885
30_D103_R0.441950.875
52_R56_D0.437040.865
66_H78_E0.436080.863
33_Y47_I0.4350.861
13_A25_S0.432510.856
41_I46_A0.42890.849
6_V9_A0.424780.841
13_A26_L0.423990.839
13_A16_D0.422750.837
10_F14_L0.419040.830
10_F110_W0.410870.813
83_L94_F0.408590.809
76_L97_C0.398960.790
15_E63_F0.397890.788
6_V107_I0.391150.774
10_F107_I0.391150.774
42_R46_A0.389880.772
74_V99_V0.387560.767
65_I68_I0.384870.762
83_L92_I0.383480.759
46_A49_A0.382030.756
53_G56_D0.379740.752
5_E8_R0.378620.750
8_R68_I0.376820.746
84_R91_R0.374910.742
20_D25_S0.370470.733
59_S84_R0.370240.733
78_E113_Y0.369260.731
78_E111_R0.368390.729
31_A43_G0.365220.723
79_R83_L0.363980.721
68_I75_V0.359970.713
60_G84_R0.356350.706
31_A44_R0.352290.697
11_L98_G0.350140.693
10_F27_F0.345860.685
15_E62_E0.342710.679
71_D74_V0.342530.678
47_I51_L0.340140.673
16_D22_A0.332530.658
8_R65_I0.330270.654
31_A110_W0.32810.650
19_V23_L0.327430.648
28_D104_D0.322030.638
19_V55_L0.320250.634
85_F90_L0.316030.626
29_D45_D0.316010.626
69_A74_V0.310930.616
101_E111_R0.310770.615
58_L83_L0.309390.613
23_L51_L0.30860.611
34_H40_P0.30860.611
78_E96_V0.307160.608
24_A45_D0.304020.602
41_I50_F0.301390.597
11_L63_F0.301370.597
77_T100_F0.299270.592
96_V114_F0.299080.592
33_Y110_W0.298150.590
33_Y100_F0.297980.590
65_I77_T0.29250.579
66_H95_P0.288180.571
7_V102_V0.286460.567
55_L59_S0.28520.565
68_I77_T0.285010.564
28_D31_A0.284660.564
7_V11_L0.283180.561
33_Y38_L0.282960.560
99_V113_Y0.281370.557
81_D94_F0.280750.556
33_Y98_G0.276090.547
99_V111_R0.269120.533
100_F110_W0.267330.529
38_L114_F0.266630.528
51_L55_L0.26630.527
98_G114_F0.266260.527
10_F26_L0.266140.527
30_D43_G0.265760.526
57_S85_F0.265450.526
19_V48_R0.263490.522
25_S106_K0.262850.520
23_L26_L0.260620.516
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
4h3uA0.99299.8-0.02
3kkgA0.99299.80.052
3ebtA0.98499.70.055
3k0zA0.97699.70.058
2f99A0.99299.70.063
1sjwA0.99299.70.065
3dm8A0.99299.70.065
3fgyA0.99299.70.074
3f9sA0.99299.70.08
2gexA0.98499.70.083

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