GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Biotin_lipoyl - Biotin-requiring enzyme
Pfam: PF00364 (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: CL0105
Length: 74
Sequences: 16412
Seq/Len: 221.78
HH_delta: -0.051 (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
27_K53_I3.128172.936
33_P45_E3.106112.916
29_K51_S2.637272.475
21_L36_E2.436912.287
56_E73_I2.251552.113
22_V32_D2.198432.064
21_L33_P2.180492.047
24_E56_E2.14032.009
58_L73_I2.06811.941
30_K51_S2.036991.912
33_P47_E2.023491.899
29_K32_D1.963111.843
23_E26_D1.846221.733
60_E63_D1.840521.728
36_E45_E1.77031.662
66_E69_Q1.647751.547
22_V26_D1.500771.409
55_K73_I1.459011.369
54_I72_A1.393031.308
58_L70_V1.302851.223
28_V48_A1.2941.215
20_W61_E1.283671.205
33_P36_E1.271231.193
20_W35_A1.197141.124
59_V69_Q1.161221.090
50_V74_I1.135671.066
24_E55_K1.101241.034
20_W57_I1.096921.030
22_V54_I1.074471.009
57_I60_E1.016250.954
27_K51_S0.996150.935
35_A71_L0.986570.926
36_E43_E0.978860.919
57_I72_A0.963050.904
59_V63_D0.941520.884
52_G74_I0.927070.870
23_E57_I0.918480.862
26_D32_D0.865030.812
24_E57_I0.859720.807
30_K49_P0.841170.790
39_T44_M0.835990.785
70_V73_I0.813780.764
35_A72_A0.798060.749
39_T42_M0.776330.729
59_V65_V0.76750.720
38_E41_K0.766590.720
38_E43_E0.753890.708
40_M43_E0.752710.707
38_E42_M0.737680.692
35_A46_V0.726870.682
31_G49_P0.714950.671
28_V34_L0.711880.668
37_I44_M0.68660.644
31_G47_E0.684880.643
35_A57_I0.671470.630
28_V54_I0.667480.627
22_V72_A0.655080.615
20_W59_V0.652580.613
30_K50_V0.646980.607
36_E39_T0.632980.594
34_L48_A0.630470.592
39_T43_E0.629280.591
28_V74_I0.628320.590
65_V71_L0.591880.556
22_V57_I0.583910.548
64_T67_V0.5680.533
63_D69_Q0.565030.530
46_V71_L0.562120.528
44_M64_T0.558290.524
40_M44_M0.552450.519
47_E67_V0.528270.496
49_P74_I0.515040.483
44_M67_V0.515010.483
30_K48_A0.508470.477
34_L72_A0.497430.467
48_A51_S0.490270.460
65_V69_Q0.484070.454
37_I46_V0.464860.436
46_V49_P0.463350.435
34_L49_P0.46230.434
59_V71_L0.456560.429
20_W60_E0.439310.412
48_A74_I0.435370.409
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
3va7A0.918999.3-0.051
3n6rA0.918999.3-0.045
3dvaI199.3-0.041
3u9tA0.918999.3-0.04
3hblA0.918999.3-0.039
4hr7B199.2-0.008
2qf7A0.918999.10.017
3bg3A0.918999.10.021
1zy8K199.10.025
1y8oB199.10.042

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