GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MR_MLE - Mandelate racemase muconate lactonizing enzyme C-terminal domain
Pfam: PF01188 (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: CL0256
Length: 67
Sequences: 3747
Seq/Len: 55.93
HH_delta: 0.016 (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
32_A41_I1.330922.595
49_D52_G1.137792.219
16_M39_E1.086412.119
54_A58_Q1.082622.111
33_R36_E1.030782.010
14_D39_E1.030512.010
29_I59_Q1.005541.961
24_T27_E1.000921.952
36_E61_S0.924651.803
43_E67_D0.893771.743
31_L35_L0.871621.700
55_E59_Q0.819411.598
55_E58_Q0.796171.553
4_A7_E0.77431.510
32_A60_T0.773561.509
25_L55_E0.765071.492
16_M40_W0.760161.482
3_R7_E0.7411.445
36_E62_V0.74081.445
34_A37_D0.727341.418
3_R38_Y0.717761.400
25_L56_L0.694721.355
53_L66_A0.690141.346
45_L56_L0.671341.309
9_V13_I0.664181.295
19_A23_W0.643611.255
6_R15_L0.621871.213
4_A8_A0.616421.202
2_I17_V0.612391.194
29_I55_E0.612341.194
45_L52_G0.604591.179
19_A41_I0.578541.128
3_R37_D0.572231.116
9_V15_L0.556141.085
6_R10_G0.548391.069
40_W67_D0.537391.048
16_M67_D0.526091.026
30_R34_A0.520941.016
25_L52_G0.493520.962
33_R61_S0.48820.952
23_W31_L0.484550.945
2_I38_Y0.475590.927
5_V9_V0.458480.894
45_L53_L0.458370.894
20_N43_E0.457050.891
29_I33_R0.452710.883
23_W41_I0.448920.875
29_I56_L0.446020.870
53_L64_I0.441860.862
43_E66_A0.427240.833
44_P64_I0.419780.819
21_Q45_L0.405810.791
40_W43_E0.399720.780
33_R37_D0.396180.773
8_A11_P0.392660.766
20_N67_D0.386650.754
2_I35_L0.375150.732
35_L38_Y0.374530.730
52_G55_E0.369550.721
40_W65_A0.364620.711
25_L45_L0.360280.703
25_L29_I0.359570.701
23_W66_A0.358810.700
20_N44_P0.353390.689
16_M43_E0.351330.685
29_I60_T0.348150.679
26_E30_R0.347880.678
26_E29_I0.345680.674
51_D54_A0.344780.672
56_L64_I0.344560.672
47_P66_A0.343750.670
36_E60_T0.337650.658
28_A45_L0.330850.645
21_Q40_W0.324050.632
17_V35_L0.323840.632
21_Q43_E0.321320.627
3_R34_A0.315990.616
57_R64_I0.315330.615
6_R12_D0.30920.603
16_M65_A0.305140.595
27_E31_L0.302430.590
41_I44_P0.301570.588
22_A43_E0.298840.583
43_E53_L0.298140.581
30_R33_R0.295410.576
6_R38_Y0.291420.568
19_A67_D0.285920.558
16_M21_Q0.282120.550
57_R60_T0.280780.548
33_R59_Q0.279210.545
47_P52_G0.275260.537
27_E30_R0.273070.533
7_E14_D0.270490.527
17_V41_I0.269970.526
34_A38_Y0.269710.526
44_P56_L0.266710.520
7_E30_R0.266620.520
56_L60_T0.25980.507
39_E63_P0.256720.501
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
4hpnA199.60.016
4kemA199.60.026
4h1zA199.60.026
4a35A199.60.033
4hnlA199.60.034
2oztA199.60.035
3fcpA199.60.036
3fxgA199.60.036
3ekgA199.60.036
2chrA199.60.036

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