GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
UBX - UBX domain
Pfam: PF00789 (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: CL0072
Length: 82
Sequences: 4709
Seq/Len: 57.43
HH_delta: 0.095 (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_D31_D1.020072.602
24_P27_D0.896232.286
25_K68_E0.835572.132
10_Q18_R0.805972.056
30_Q34_D0.801672.045
33_Y61_D0.788882.012
65_K69_E0.783041.998
66_T69_E0.762891.946
37_E48_F0.734151.873
31_D34_D0.648961.655
7_V74_P0.627251.600
8_R20_Q0.622971.589
36_V50_L0.610341.557
65_K70_A0.608771.553
73_L76_A0.600281.531
26_S68_E0.598211.526
32_L67_L0.595251.518
10_Q20_Q0.581731.484
8_R22_R0.574151.465
27_D35_F0.572151.460
7_V25_K0.539121.375
28_T31_D0.516821.318
9_I23_F0.515981.316
23_F27_D0.515371.315
33_Y48_F0.504521.287
66_T70_A0.491081.253
34_D38_S0.479851.224
23_F35_F0.422151.077
35_F38_S0.413881.056
23_F32_L0.413251.054
49_E58_E0.403581.030
15_D40_L0.396561.012
34_D37_E0.396131.011
44_E48_F0.392181.000
7_V22_R0.386670.986
23_F67_L0.381650.974
54_F57_R0.375450.958
12_R77_T0.37150.948
59_L78_L0.365280.932
37_E44_E0.361910.923
51_I56_R0.357060.911
19_L36_V0.35330.901
40_L43_P0.352680.900
11_V19_L0.351960.898
43_P48_F0.349160.891
51_I58_E0.348210.888
12_R18_R0.347550.887
21_R35_F0.343840.877
49_E79_I0.3420.872
26_S66_T0.337870.862
29_L59_L0.335440.856
50_L78_L0.334460.853
51_I54_F0.332720.849
11_V80_V0.332050.847
51_I79_I0.329040.839
59_L76_A0.328180.837
72_L78_L0.320990.819
42_S48_F0.320980.819
12_R79_I0.319020.814
33_Y62_E0.311380.794
9_I32_L0.30690.783
13_L80_V0.305150.778
60_T65_K0.304850.778
19_L40_L0.302980.773
8_R75_S0.294570.751
9_I72_L0.290960.742
35_F39_Q0.290470.741
27_D32_L0.289780.739
48_F80_V0.285330.728
29_L70_A0.284210.725
24_P31_D0.282990.722
30_Q62_E0.271190.692
14_P49_E0.270720.691
36_V48_F0.269110.686
50_L80_V0.265480.677
42_S80_V0.264870.676
21_R27_D0.26130.667
13_L19_L0.258720.660
19_L55_P0.258380.659
7_V75_S0.254910.650
30_Q61_D0.252450.644
7_V73_L0.252340.644
29_L32_L0.25230.644
40_L80_V0.252130.643
28_T33_Y0.248880.635
8_R74_P0.248780.635
8_R71_G0.24780.632
21_R59_L0.244310.623
11_V36_V0.244270.623
7_V24_P0.244190.623
14_P80_V0.242260.618
37_E40_L0.241680.617
11_V32_L0.240390.613
34_D41_F0.2370.605
32_L78_L0.234350.598
19_L77_T0.226360.577
31_D35_F0.226170.577
22_R34_D0.225960.576
43_P46_S0.225150.574
62_E70_A0.224480.573
29_L50_L0.22270.568
10_Q77_T0.222630.568
54_F59_L0.220140.562
13_L20_Q0.219490.560
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
2dzkA0.987899.10.095
1wj4A0.975699.10.105
3qx1A0.975699.10.109
4k95A0.9268990.112
3pluA0.939990.117
1uh6A0.939990.128
2cr5A0.9756990.135
1s3sG0.9634990.144
2kzrA0.902498.90.155
3v6cB0.93998.90.158

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