GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ig_2 - Immunoglobulin domain
Pfam: PF13895 (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: CL0011
Length: 80
Sequences: 20783
Seq/Len: 259.79
HH_delta: -0.106 (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
34_Y63_R1.982572.972
59_N75_S1.718382.576
34_Y61_T1.709142.562
59_N77_N1.690212.534
21_C62_C1.681452.521
18_T48_F1.434782.151
16_S48_F1.407932.111
16_S50_P1.352532.028
32_Q65_S1.323291.984
11_V52_V1.308391.962
61_T73_S1.263921.895
35_K58_G1.251361.876
32_Q63_R1.240231.859
25_G29_P1.18961.783
12_E15_D1.123551.684
13_E54_P1.110191.664
36_N40_I1.1061.658
17_V78_V1.065851.598
11_V17_V1.050371.575
23_V64_A1.028081.541
61_T75_S1.017831.526
33_W47_L0.951191.426
23_V31_V0.91661.374
36_N61_T0.809871.214
63_R71_N0.798021.196
19_L76_V0.771731.157
32_Q39_P0.769521.154
34_Y39_P0.760911.141
11_V15_D0.760621.140
38_S41_N0.75931.138
11_V78_V0.75231.128
54_P57_S0.749511.124
43_S46_G0.736831.105
29_P64_A0.721021.081
53_S56_D0.706141.059
16_S51_N0.704561.056
31_V64_A0.700571.050
65_S71_N0.678411.017
30_Q65_S0.672361.008
25_G66_N0.663280.994
66_N70_S0.65390.980
17_V49_I0.64470.967
49_I52_V0.64020.960
65_S70_S0.623310.934
35_K60_Y0.623020.934
19_L78_V0.620420.930
17_V52_V0.615450.923
63_R73_S0.579320.869
52_V56_D0.54080.811
42_S46_G0.533630.800
25_G28_P0.533270.799
42_S45_N0.53250.798
13_E53_S0.50920.763
52_V57_S0.506860.760
19_L60_Y0.502710.754
49_I56_D0.496470.744
19_L33_W0.482590.723
63_R72_T0.458810.688
40_I43_S0.45810.687
36_N58_G0.454810.682
40_I44_Q0.444130.666
41_N46_G0.439550.659
66_N69_G0.435060.652
72_T76_V0.426580.640
72_T75_S0.410340.615
36_N59_N0.409520.614
14_G51_N0.408470.612
23_V27_P0.407110.610
47_L51_N0.402260.603
29_P66_N0.401740.602
16_S49_I0.400090.600
39_P42_S0.397760.596
70_S73_S0.396750.595
74_T77_N0.389570.584
50_P53_S0.388710.583
68_S74_T0.38760.581
61_T72_T0.384770.577
37_G42_S0.38140.572
39_P43_S0.38080.571
71_N74_T0.377980.567
41_N45_N0.375130.562
69_G72_T0.37120.557
23_V62_C0.357830.536
31_V47_L0.355090.532
70_S75_S0.352210.528
57_S77_N0.351780.527
26_N29_P0.346860.520
57_S60_Y0.345610.518
49_I58_G0.340440.510
19_L49_I0.34020.510
37_G40_I0.322340.483
16_S52_V0.321560.482
36_N45_N0.318490.477
35_K56_D0.317180.476
37_G61_T0.315750.473
36_N75_S0.315710.473
71_N75_S0.31080.466
22_S28_P0.303330.455
13_E52_V0.302020.453
42_S75_S0.299950.450
70_S74_T0.299870.450
40_I45_N0.29690.445
52_V58_G0.296310.444
38_S44_Q0.29520.443
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
2v5mA0.987598.4-0.106
3v2aR0.987598.3-0.082
1e07A0.97598.2-0.07
3knbB0.987598.2-0.056
3knbA0.987598.2-0.055
3qs9E0.987598.2-0.048
2id5A0.987598.2-0.048
3dmkA0.987598.1-0.039
2jllA0.987598.1-0.036
3qs7E0.987598.1-0.034

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