GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SLBB - SLBB domain
Pfam: PF10531 (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: 59
Sequences: 4934
Seq/Len: 83.63
HH_delta: 0.202 (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
4_V8_V1.168062.244
21_T24_D1.120632.153
4_V29_A1.085762.086
32_L36_A1.072862.061
16_L20_T1.022151.964
23_S27_A0.951191.827
1_T15_E0.893071.716
3_T13_T0.8531.639
2_V25_A0.794531.526
9_N33_T0.722081.387
1_T13_T0.721671.386
7_E33_T0.710651.365
10_R30_G0.706591.357
20_T24_D0.640451.230
17_P20_T0.620991.193
16_L25_A0.566241.088
7_E36_A0.559611.075
26_I32_L0.546571.050
33_T36_A0.544891.047
26_I29_A0.513210.986
5_S23_S0.50420.969
7_E35_R0.48830.938
5_S27_A0.476390.915
13_T17_P0.472880.908
20_T28_Q0.471150.905
26_I31_G0.448640.862
1_T5_S0.441560.848
2_V11_P0.435290.836
8_V29_A0.434850.835
1_T7_E0.432470.831
9_N34_P0.425940.818
2_V16_L0.422940.812
13_T24_D0.412350.792
8_V11_P0.408550.785
19_G23_S0.407840.783
1_T46_K0.40130.771
18_P46_K0.396270.761
23_S35_R0.395090.759
3_T25_A0.391460.752
14_Y28_Q0.390140.749
2_V17_P0.367310.706
10_R14_Y0.360670.693
13_T23_S0.359120.690
19_G46_K0.356310.684
15_E20_T0.350570.673
12_G28_Q0.344170.661
4_V22_L0.339270.652
11_P22_L0.335720.645
14_Y29_A0.333930.641
9_N30_G0.332750.639
11_P29_A0.32970.633
15_E28_Q0.319170.613
34_P37_D0.318880.613
13_T21_T0.3080.592
14_Y25_A0.30770.591
14_Y19_G0.298930.574
33_T46_K0.296450.569
1_T19_G0.29230.562
12_G16_L0.290520.558
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
2j58A198.60.202
2j58A0.949298.30.294
3i9v10.830597.90.382
3p42A0.898397.70.407
3p42A0.932284.30.682
3bzcA0.949228.20.781
2l32A0.881411.80.815
1tygB0.830510.90.817
1itwA1100.82
2b0tA1100.82

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