GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Disintegrin - Disintegrin
Pfam: PF00200 (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: 76
Sequences: 992
Seq/Len: 13.05
HH_delta: -0.11 (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_K30_A0.909864.160
8_C14_C0.572932.619
58_D61_E0.505942.313
31_Q42_Q0.46472.125
58_D73_D0.463712.120
20_D23_T0.462222.113
44_K48_T0.461842.111
5_E25_K0.438412.004
4_E7_D0.420851.924
43_F64_N0.412531.886
5_E26_L0.409671.873
61_E73_D0.389461.781
59_L62_Y0.347741.590
6_C9_G0.347241.588
51_R73_D0.318681.457
18_C41_C0.306131.400
4_E9_G0.295291.350
39_N44_K0.295221.350
20_D25_K0.290171.327
1_E7_D0.28471.302
31_Q43_F0.282071.290
20_D27_K0.281051.285
51_R61_E0.280691.283
43_F68_A0.279911.280
26_L30_A0.277281.268
1_E4_E0.269531.232
51_R58_D0.264651.210
35_G56_E0.264541.209
1_E6_C0.260141.189
32_C38_C0.251131.148
56_E67_S0.250821.147
8_C35_G0.246321.126
59_L75_Y0.240021.097
32_C37_C0.219391.003
16_D71_P0.217980.997
20_D68_A0.210410.962
64_N71_P0.196050.896
45_P55_N0.19340.884
39_N53_A0.192850.882
49_V52_P0.19280.881
49_V62_Y0.192240.879
15_N74_V0.191050.873
19_C37_C0.187660.858
61_E65_G0.184610.844
3_G7_D0.183880.841
59_L74_V0.181210.828
62_Y74_V0.178910.818
55_N71_P0.178330.815
15_N28_P0.17760.812
47_G63_C0.176870.809
19_C38_C0.176490.807
45_P62_Y0.175050.800
38_C41_C0.174530.798
26_L31_Q0.172670.789
64_N67_S0.170580.780
15_N49_V0.167230.765
17_P33_S0.167060.764
59_L71_P0.166150.760
14_C35_G0.16610.759
10_S13_E0.165920.759
49_V60_P0.165110.755
2_E74_V0.16450.752
19_C41_C0.16360.748
33_S71_P0.163510.748
3_G6_C0.16250.743
39_N42_Q0.162010.741
30_A34_N0.161620.739
46_S66_S0.161260.737
2_E12_E0.161040.736
11_P44_K0.160220.733
4_E8_C0.158360.724
65_G70_C0.157620.721
49_V53_A0.15550.711
58_D65_G0.154520.706
23_T53_A0.153020.700
43_F72_P0.151990.695
69_E72_P0.151360.692
40_N68_A0.149970.686
25_K29_G0.149240.682
37_C41_C0.148760.680
46_S71_P0.148130.677
13_E40_N0.147570.675
35_G59_L0.146640.670
36_P44_K0.146380.669
66_S74_V0.146150.668
53_A56_E0.145870.667
57_C63_C0.145720.666
16_D33_S0.145460.665
13_E53_A0.144890.662
31_Q54_T0.144550.661
42_Q69_E0.144320.660
48_T72_P0.143070.654
13_E54_T0.142410.651
64_N69_E0.141430.647
11_P39_N0.14090.644
10_S56_E0.140430.642
17_P64_N0.140320.642
40_N53_A0.139990.640
45_P49_V0.13950.638
52_P62_Y0.138030.631
40_N66_S0.137760.630
13_E39_N0.134830.616
21_A44_K0.134360.614
15_N40_N0.134040.613
13_E62_Y0.133540.611
25_K34_N0.132120.604
2_E54_T0.129060.590
47_G62_Y0.128860.589
8_C55_N0.128650.588
51_R59_L0.128650.588
18_C38_C0.127070.581
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
3k7lA199.9-0.11
2dw0A199.9-0.051
3g5cA0.973799.9-0.049
2e3xA199.9-0.047
2eroA0.986899.90
2ao7A0.986899.90.056
3uciA0.921199.80.087
1j2lA0.907999.80.112
3k7nA0.776399.80.171
2m75A0.921199.70.214

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