GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
I-set - Immunoglobulin I-set domain
Pfam: PF07679 (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: 90
Sequences: 23480
Seq/Len: 260.89
HH_delta: -0.242 (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
22_C73_C2.095513.196
35_Y74_V2.041153.113
36_K69_G1.628612.484
12_V63_V1.599852.440
19_T59_T1.574872.402
19_T57_S1.516472.313
35_Y72_T1.451492.214
17_S59_T1.39152.122
17_S61_K1.358512.072
33_T76_S1.336952.039
13_K16_E1.261541.924
37_N72_T1.190191.815
76_S81_E1.132071.727
12_V18_V1.112571.697
33_T74_V1.111651.696
14_E65_R1.110671.694
34_W58_L1.07811.644
37_N41_L1.067331.628
21_E57_S1.051231.603
12_V16_E1.000991.527
74_V81_E0.988821.508
24_V75_A0.969211.478
26_G30_P0.942861.438
24_V32_V0.903141.377
35_Y40_P0.896731.368
77_N80_G0.8891.356
39_R42_T0.888011.354
46_R49_I0.827971.263
44_S47_Y0.811171.237
23_E55_S0.79881.218
33_T40_P0.793151.210
65_R68_A0.755471.152
18_V60_I0.735441.122
36_K71_Y0.71311.088
17_S62_N0.705431.076
46_R67_D0.698031.065
60_I63_V0.693761.058
60_I67_D0.670041.022
18_V63_V0.648060.988
50_E53_G0.647950.988
48_Q61_K0.64680.987
32_V56_S0.64310.981
31_T76_S0.628350.958
48_Q51_S0.61810.943
21_E55_S0.615830.939
37_N40_P0.602240.919
7_P10_V0.581330.887
64_T67_D0.567990.866
9_D13_K0.557920.851
79_S82_A0.556880.849
32_V75_A0.550860.840
51_S56_S0.548240.836
60_I71_Y0.519160.792
47_Y51_S0.514660.785
15_G62_N0.503380.768
27_N30_P0.49090.749
45_Q49_I0.486350.742
32_V73_C0.482910.737
63_V67_D0.479940.732
47_Y50_E0.47760.728
20_L71_Y0.475220.725
48_Q59_T0.465440.710
38_G41_L0.456280.696
26_G77_N0.454930.694
7_P11_T0.452350.690
15_G64_T0.448420.684
48_Q52_D0.442170.674
30_P75_A0.435280.664
37_N69_G0.432980.660
20_L34_W0.432930.660
37_N70_T0.42790.653
10_V18_V0.421140.642
63_V68_A0.417750.637
56_S59_T0.416380.635
38_G70_T0.413660.631
36_K67_D0.410330.626
39_R43_S0.410070.625
8_K11_T0.40960.625
23_E56_S0.401840.613
52_D55_S0.398880.608
50_E59_T0.394570.602
10_V16_E0.389520.594
10_V21_E0.38930.594
11_T68_A0.384990.587
30_P77_N0.377130.575
63_V69_G0.371780.567
67_D71_Y0.363490.554
68_A71_Y0.36290.554
37_N43_S0.358840.547
9_D12_V0.358710.547
49_I53_G0.357670.546
15_G63_V0.355780.543
50_E55_S0.355740.543
35_Y81_E0.355570.542
9_D20_L0.349690.533
46_R64_T0.348240.531
28_P77_N0.347170.530
35_Y38_G0.345950.528
30_P33_T0.34580.527
7_P20_L0.345330.527
44_S48_Q0.34420.525
51_S54_G0.343950.525
38_G72_T0.342370.522
26_G29_P0.340190.519
23_E57_S0.339620.518
17_S63_V0.338420.516
15_G65_R0.337980.515
17_S60_I0.337160.514
48_Q53_G0.331880.506
28_P31_T0.331020.505
27_N77_N0.330520.504
14_E68_A0.32960.503
24_V56_S0.328260.501
76_S80_G0.326660.498
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
3knbB199-0.242
3knbA198.9-0.208
3b43A198.9-0.185
2cqvA198.9-0.18
1nctA198.9-0.176
3utoA198.8-0.175
2lqrA198.8-0.173
3v2aR0.977898.8-0.17
3qp3A198.8-0.167
3b43A198.8-0.164

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