GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CCG - Cysteine-rich domain
Pfam: PF02754 (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. )
Length: 85
Sequences: 6635
Seq/Len: 78.06
HH_delta: 0.104 (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
40_C80_C1.002512.321
50_D53_L0.956552.215
75_T81_Y0.950822.201
3_Y76_P0.884332.047
41_C80_C0.820971.901
7_C40_C0.797921.847
59_K63_K0.737281.707
5_P18_E0.720161.667
58_A83_Q0.718251.663
21_L25_L0.717221.661
6_G77_C0.672481.557
39_Q60_R0.672011.556
46_Y83_Q0.670261.552
63_K67_E0.62421.445
7_C80_C0.621841.440
21_L76_P0.611071.415
2_A70_A0.597761.384
19_K23_K0.595741.379
1_V74_V0.592721.372
22_R34_I0.590551.367
18_E22_R0.575771.333
43_A79_S0.574921.331
10_A18_E0.567821.315
19_K22_R0.564351.307
58_A62_L0.551891.278
7_C41_C0.532111.232
2_A68_A0.52491.215
22_R26_N0.519591.203
10_A14_Y0.51041.182
60_R64_E0.509651.180
54_A83_Q0.50771.175
55_E59_K0.50421.167
64_E67_E0.487731.129
25_L30_I0.485181.123
1_V30_I0.481351.114
63_K66_K0.479181.109
2_A65_I0.465431.078
65_I73_I0.464141.075
17_V21_L0.456761.057
72_T75_T0.45581.055
36_E39_Q0.45091.044
1_V72_T0.450441.043
20_A23_K0.450121.042
6_G75_T0.449241.040
57_V60_R0.447031.035
26_N32_V0.4471.035
62_L66_K0.437381.013
22_R32_V0.434561.006
3_Y18_E0.432671.002
65_I70_A0.426070.986
45_G53_L0.424290.982
7_C77_C0.419520.971
61_N64_E0.419180.970
47_F79_S0.415790.963
16_E19_K0.41410.959
17_V20_A0.41130.952
75_T84_L0.410240.950
46_Y54_A0.40150.930
10_A17_V0.399780.926
43_A83_Q0.397730.921
38_Q61_N0.392740.909
78_P82_M0.389570.902
43_A47_F0.389430.902
2_A73_I0.389080.901
2_A33_V0.385230.892
64_E68_A0.380610.881
56_K60_R0.374270.867
4_H61_N0.371060.859
53_L57_V0.362270.839
9_L13_N0.362110.838
45_G57_V0.361080.836
44_P77_C0.360570.835
61_N84_L0.354070.820
36_E64_E0.353520.818
59_K62_L0.351810.815
3_Y32_V0.351150.813
23_K26_N0.350750.812
35_P65_I0.35060.812
5_P34_I0.342290.792
23_K27_K0.339990.787
66_K69_G0.334150.774
73_I84_L0.332350.769
62_L65_I0.332240.769
44_P47_F0.330760.766
38_Q65_I0.330470.765
33_V70_A0.32860.761
56_K59_K0.328570.761
15_P19_K0.326750.756
2_A32_V0.326550.756
6_G81_Y0.323710.749
5_P38_Q0.315460.730
26_N29_G0.314920.729
46_Y51_E0.314190.727
47_F77_C0.314120.727
39_Q64_E0.313820.727
24_L28_L0.313270.725
37_N64_E0.31320.725
33_V68_A0.309380.716
2_A71_D0.305090.706
6_G9_L0.30380.703
14_Y17_V0.300520.696
43_A77_C0.299970.694
43_A46_Y0.294070.681
20_A24_L0.287950.667
47_F83_Q0.286590.664
5_P11_R0.286580.663
48_A83_Q0.286290.663
55_E58_A0.28540.661
15_P20_A0.285250.660
21_L24_L0.284680.659
3_Y21_L0.282850.655
25_L74_V0.282830.655
1_V32_V0.278350.644
24_L27_K0.276430.640
49_G73_I0.273260.633
2_A5_P0.272970.632
4_H44_P0.27210.630
6_G12_Y0.2710.627
45_G48_A0.269210.623
29_G32_V0.265670.615
60_R63_K0.265250.614
47_F57_V0.264940.613
46_Y50_D0.263280.610
43_A48_A0.26020.602
9_L43_A0.259610.601
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
3kwlA0.941299.50.104
3kwlA0.905998.80.358
3cf4A0.929498.60.398
3gkjA0.811844.20.817
3qntA0.823543.60.817
3c8yA0.882428.40.834
4h1hA0.9294220.842
3tlaA0.929420.50.844
4e5sA0.929416.60.85
2b3yA0.917616.40.85

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