GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cupin_3 - Protein of unknown function (DUF861)
Pfam: PF05899 (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: CL0029
Length: 74
Sequences: 12198
Seq/Len: 164.84
HH_delta: 0.106 (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
37_T47_T2.585723.332
37_T45_T2.570053.312
37_T65_E2.112022.722
37_T67_R2.040732.630
39_T63_T2.037912.626
35_E49_K2.034042.621
49_K52_D1.940542.501
35_E47_T1.670452.153
39_T45_T1.50091.934
30_Y53_A1.378451.776
26_D55_F1.348951.738
33_E50_A1.312161.691
19_F65_E1.270851.638
28_F53_A1.206051.554
35_E67_R1.197111.543
39_T65_E1.180111.521
35_E68_E1.158881.493
40_D46_V1.085991.399
26_D58_K0.994931.282
40_D44_E0.994031.281
15_T18_K0.983181.267
47_T67_R0.884361.140
57_P60_W0.878371.132
23_Y62_G0.868251.119
26_D57_P0.854771.101
29_F54_F0.827061.066
38_I48_F0.81831.054
11_V32_L0.789821.018
36_V47_T0.772670.996
36_V48_F0.771390.994
29_F56_L0.767350.989
14_C66_V0.748070.964
10_G27_E0.741750.956
14_C18_K0.739070.952
21_W61_T0.729270.940
22_P62_G0.720220.928
19_F63_T0.708350.913
48_F52_D0.67980.876
31_V36_V0.67850.874
38_I64_W0.666650.859
31_V48_F0.640390.825
38_I56_L0.636830.821
29_F36_V0.634890.818
48_F54_F0.630130.812
38_I54_F0.622190.802
22_P61_T0.619710.799
16_P68_E0.616210.794
24_P59_G0.611950.789
21_W63_T0.60290.777
42_D60_W0.58910.759
27_E56_L0.587230.757
16_P66_V0.581360.749
28_F55_F0.568360.732
9_A28_F0.563390.726
29_F64_W0.54340.700
40_D60_W0.534760.689
36_V64_W0.530580.684
14_C36_V0.52370.675
29_F48_F0.502370.647
20_P63_T0.502060.647
36_V52_D0.497710.641
40_D43_G0.495360.638
29_F38_I0.489970.631
25_E29_F0.448990.579
46_V54_F0.440760.568
45_T65_E0.42420.547
10_G29_F0.418360.539
31_V52_D0.410120.528
12_W25_E0.408480.526
27_E64_W0.407270.525
12_W27_E0.406770.524
8_S25_E0.404520.521
9_A30_Y0.404370.521
33_E68_E0.386760.498
31_V51_G0.383360.494
27_E62_G0.383070.494
42_D61_T0.380570.490
56_L62_G0.380150.490
25_E58_K0.377280.486
28_F54_F0.374320.482
31_V34_G0.365010.470
10_G55_F0.362710.467
17_G66_V0.361240.466
11_V28_F0.360040.464
31_V50_A0.358840.462
48_F64_W0.347290.448
40_D56_L0.346590.447
56_L60_W0.344490.444
12_W59_G0.343010.442
10_G62_G0.336190.433
39_T44_E0.332160.428
34_G50_A0.324910.419
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
2pytA0.9865990.106
1o5uA0.9865990.114
3bcwA198.90.119
4axoA0.986598.90.136
3lwcA0.986598.80.183
1sq4A0.986598.70.187
4e2qA0.986598.70.189
1sfnA0.986598.70.201
1rc6A0.986598.70.208
1sfnA0.986598.70.214

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