GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MR_MLE_N - Mandelate racemase muconate lactonizing enzyme N-terminal domain
Pfam: PF02746 (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: CL0227
Length: 117
Sequences: 4957
Seq/Len: 42.37
HH_delta: 0.067 (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
70_Q81_E1.649823.402
31_V95_A1.460483.011
74_D77_D1.45583.002
34_E40_V1.327812.738
57_S61_D1.205462.485
37_D107_I1.18552.444
32_R42_W1.172192.417
35_T103_L1.147172.365
32_R40_V1.036992.138
78_I100_L1.012482.088
102_D106_K0.969371.999
70_Q77_D0.957961.975
62_Y87_K0.910371.877
105_G112_L0.883531.822
80_Q84_R0.872581.799
54_T57_S0.834371.720
39_V103_L0.815541.682
64_A68_I0.797131.644
97_D101_W0.78841.626
56_A60_E0.762541.572
35_T39_V0.76121.569
39_V106_K0.71651.477
111_P114_Q0.699191.442
30_L42_W0.698541.440
39_V107_I0.68841.419
45_A95_A0.670921.383
77_D81_E0.662691.366
110_Q114_Q0.615251.269
73_D108_A0.587421.211
33_L100_L0.585831.208
82_L93_K0.569951.175
105_G115_L0.56481.165
73_D107_I0.558971.153
60_E64_A0.532391.098
61_D65_P0.52371.080
76_E80_Q0.513791.059
75_I104_L0.507981.047
35_T107_I0.503521.038
108_A115_L0.502571.036
79_W97_D0.500121.031
63_L82_L0.499611.030
110_Q115_L0.495641.022
62_Y65_P0.489681.010
70_Q78_I0.489461.009
35_T72_P0.488261.007
41_G99_A0.485421.001
101_W116_L0.475510.980
78_I81_E0.466060.961
71_D74_D0.460830.950
59_L96_I0.450970.930
90_P94_A0.448030.924
41_G106_K0.445050.918
63_L96_I0.442620.913
66_L85_L0.442240.912
66_L81_E0.437740.903
81_E84_R0.437260.902
106_K109_G0.434550.896
41_G102_D0.424250.875
34_E42_W0.409310.844
104_L108_A0.396350.817
40_V106_K0.395570.816
72_P104_L0.389190.802
58_A62_Y0.385820.796
47_P91_A0.38550.795
72_P100_L0.381050.786
112_L116_L0.380640.785
46_F49_P0.378740.781
48_S91_A0.372630.768
44_E102_D0.369910.763
33_L67_L0.368430.760
79_W83_Y0.368030.759
28_F91_A0.366730.756
54_T58_A0.36470.752
59_L64_A0.361360.745
34_E39_V0.359850.742
43_G95_A0.356770.736
53_E57_S0.356120.734
55_V59_L0.354180.730
108_A117_G0.348680.719
94_A98_M0.347980.717
56_A59_L0.347940.717
29_V52_A0.347750.717
65_P68_I0.345030.711
36_D72_P0.336870.695
100_L104_L0.334640.690
72_P107_I0.334230.689
68_I71_D0.33420.689
108_A111_P0.331710.684
73_D104_L0.327510.675
28_F48_S0.325680.672
26_R44_E0.325250.671
29_V55_V0.320970.662
98_M116_L0.320590.661
55_V89_N0.317870.655
79_W93_K0.314530.649
46_F52_A0.314420.648
33_L41_G0.310190.640
43_G102_D0.310060.639
83_Y93_K0.309680.639
112_L115_L0.306780.633
47_P90_P0.305630.630
26_R48_S0.304930.629
104_L115_L0.304770.628
77_D80_Q0.303270.625
45_A91_A0.301030.621
89_N93_K0.29930.617
86_I89_N0.298820.616
70_Q74_D0.295050.608
36_D107_I0.294640.608
48_S52_A0.2930.604
67_L96_I0.292930.604
79_W82_L0.290020.598
32_R41_G0.289910.598
98_M101_W0.289070.596
101_W112_L0.287470.593
45_A92_A0.2870.592
63_L85_L0.286520.591
43_G98_M0.286240.590
57_S62_Y0.284390.586
54_T89_N0.279250.576
45_A49_P0.278810.575
48_S51_T0.276540.570
105_G108_A0.274910.567
91_A94_A0.272530.562
26_R51_T0.272270.561
83_Y90_P0.271580.560
46_F50_G0.269410.555
67_L70_Q0.269090.555
46_F91_A0.267690.552
96_I100_L0.26730.551
47_P94_A0.267270.551
45_A48_S0.26640.549
33_L99_A0.265870.548
37_D109_G0.263140.543
87_K91_A0.260710.538
70_Q100_L0.260250.537
27_E49_P0.25960.535
34_E37_D0.257610.531
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
3dgbA199.90.067
4h83A199.90.069
3fcpA199.90.073
3i4kA199.90.075
3i6eA199.90.08
3my9A199.90.081
4e8gA0.991599.90.086
3r0uA199.90.086
4j1oA0.991599.90.087
3tj4A199.90.088

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