GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
KH_1 - KH domain
Pfam: PF00013 (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: CL0007
Length: 60
Sequences: 4471
Seq/Len: 74.52
HH_delta: -0.041 (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
24_E28_E2.185294.154
2_E53_V1.254222.384
29_T59_M0.998641.898
2_E57_K0.968591.841
5_E43_I0.939521.786
30_G52_Q0.934061.776
55_K58_K0.920961.751
3_R43_I0.868791.651
28_E59_M0.863621.642
17_K20_S0.859551.634
50_P54_E0.854061.623
35_I44_V0.812291.544
29_T55_K0.785141.492
54_E57_K0.740621.408
49_S52_Q0.725991.380
24_E59_M0.708031.346
11_V42_D0.705081.340
10_L13_R0.678331.289
23_K27_E0.669311.272
48_G53_V0.652941.241
46_I57_K0.644491.225
23_K26_E0.642071.221
21_N24_E0.633651.205
13_R21_N0.629081.196
26_E32_K0.618351.175
36_P45_T0.615091.169
31_V52_Q0.60631.153
46_I60_I0.601491.143
22_I26_E0.549761.045
51_E55_K0.53391.015
31_V46_I0.521520.991
4_I57_K0.521260.991
15_I19_G0.515130.979
16_G19_G0.503170.956
11_V35_I0.489330.930
38_D43_I0.487060.926
25_I56_A0.476290.905
52_Q55_K0.470780.895
55_K59_M0.464420.883
3_R45_T0.455150.865
51_E54_E0.441270.839
25_I33_I0.439820.836
11_V36_P0.43740.831
54_E58_K0.436250.829
6_V14_I0.430.817
9_S12_G0.428760.815
7_P10_L0.42590.810
6_V44_V0.424610.807
36_P43_I0.420760.800
48_G56_A0.419010.797
28_E55_K0.413070.785
31_V48_G0.412390.784
8_S42_D0.40270.765
6_V42_D0.393920.749
34_Q45_T0.385010.732
25_I29_T0.364790.693
22_I33_I0.360970.686
37_D47_S0.348020.662
4_I7_P0.338740.644
15_I23_K0.331740.631
14_I22_I0.329030.625
37_D45_T0.326390.620
29_T56_A0.323920.616
26_E31_V0.322160.612
51_E58_K0.315160.599
20_S24_E0.313630.596
38_D42_D0.308770.587
12_G16_G0.301230.573
5_E38_D0.296030.563
15_I35_I0.29580.562
12_G20_S0.295090.561
11_V44_V0.289670.551
14_I17_K0.288810.549
44_V60_I0.288460.548
2_E54_E0.284730.541
3_R48_G0.283090.538
29_T52_Q0.282660.537
37_D43_I0.282610.537
24_E45_T0.277620.528
20_S27_E0.272320.518
2_E50_P0.27120.516
25_I59_M0.2660.506
46_I56_A0.258230.491
36_P42_D0.258210.491
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
3n89A199.1-0.041
2dgrA199.1-0.035
2ctlA199-0.019
2ctmA199-0.007
2cteA199-0.002
1vigA1990.001
2hh3A1990.005
1x4mA1990.006
2ctkA1990.006
2hh2A1990.006

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