GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Kringle - Kringle domain
Pfam: PF00051 (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: 79
Sequences: 1078
Seq/Len: 13.65
HH_delta: -0.072 (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
18_S72_E0.642143.193
23_L30_P0.532522.648
28_Q33_H0.470522.340
17_E59_R0.389991.939
10_R45_G0.386721.923
23_L31_H0.360461.792
6_G60_P0.352571.753
6_G53_N0.333071.656
57_D71_W0.310881.546
57_D73_Y0.303781.511
14_N21_P0.300711.495
24_P48_H0.286211.423
22_C25_W0.285191.418
74_C79_C0.284151.413
20_K72_E0.282021.402
15_V19_G0.278951.387
31_H64_T0.278771.386
13_V60_P0.272491.355
49_N52_R0.269761.341
2_Y60_P0.264391.315
20_K66_D0.257641.281
62_C74_C0.25541.270
20_K69_I0.252721.257
60_P76_I0.247651.232
2_Y78_K0.246861.228
2_Y15_V0.236791.178
37_T40_S0.235521.171
23_L33_H0.233631.162
13_V76_I0.231591.152
1_C9_Y0.230631.147
54_P61_W0.22521.120
10_R46_L0.222671.107
4_G8_D0.22051.096
60_P78_K0.220461.096
23_L64_T0.214821.068
8_D45_G0.210691.048
1_C4_G0.204841.019
38_P41_Y0.203771.013
55_D59_R0.203671.013
43_E75_D0.202061.005
34_S40_S0.199990.995
64_T67_P0.198860.989
64_T72_E0.193380.962
30_P33_H0.191530.952
31_H67_P0.191270.951
75_D78_K0.189260.941
30_P64_T0.187660.933
55_D61_W0.187370.932
9_Y22_C0.181890.904
21_P24_P0.181090.901
39_S44_A0.178490.888
21_P65_K0.178190.886
31_H66_D0.176580.878
6_G9_Y0.175840.874
28_Q76_I0.175710.874
62_C79_C0.175040.870
5_N8_D0.173970.865
44_A48_H0.171260.852
23_L65_K0.170390.847
76_I79_C0.170080.846
21_P49_N0.168110.836
11_G22_C0.167590.833
23_L28_Q0.167430.833
38_P42_P0.167420.833
1_C10_R0.166030.826
53_N62_C0.161890.805
65_K69_I0.161760.804
28_Q31_H0.160240.797
9_Y25_W0.159850.795
19_G22_C0.15980.795
52_R74_C0.158840.790
15_V32_K0.158280.787
10_R47_G0.157430.783
12_T50_Y0.156820.780
1_C22_C0.156640.779
13_V77_P0.154930.770
44_A47_G0.154160.767
13_V24_P0.153860.765
37_T42_P0.153710.764
66_D71_W0.152670.759
30_P66_D0.152360.758
5_N56_G0.150880.750
32_K75_D0.150750.750
23_L27_S0.148980.741
21_P48_H0.148860.740
17_E72_E0.147530.734
17_E73_Y0.146770.730
7_Q27_S0.145610.724
48_H68_G0.145560.724
34_S39_S0.144210.717
33_H64_T0.143380.713
41_Y47_G0.143370.713
17_E21_P0.143040.711
25_W62_C0.142650.709
3_T18_S0.14230.708
31_H65_K0.140150.697
12_T60_P0.138620.689
23_L29_S0.138240.687
26_N29_S0.138010.686
25_W51_C0.136870.681
7_Q12_T0.136530.679
24_P34_S0.136420.678
54_P74_C0.136270.678
61_W71_W0.135950.676
50_Y60_P0.135580.674
42_P46_L0.13530.673
7_Q56_G0.134760.670
52_R62_C0.134560.669
61_W73_Y0.134540.669
57_D61_W0.134330.668
4_G37_T0.133710.665
30_P65_K0.13350.664
43_E55_D0.132890.661
8_D76_I0.132730.660
2_Y47_G0.132540.659
46_L54_P0.131530.654
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
1jfnA0.987399.9-0.072
4durA0.987399.9-0.069
2qj2A0.987399.9-0.065
1i71A0.987399.9-0.062
4hzhA0.987399.9-0.05
3nxpA0.987399.9-0.048
4hzhA0.987399.9-0.045
1ki0A0.987399.9-0.042
3sp8A0.987399.9-0.039
3e6pL0.987399.9-0.038

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