GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ig_3 - Immunoglobulin domain
Pfam: PF13927 (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: 75
Sequences: 21858
Seq/Len: 291.44
HH_delta: -0.015 (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
36_Y72_I2.094353.200
19_T55_T1.62782.487
19_T57_T1.576282.408
36_Y70_T1.550682.369
34_S74_S1.28191.958
34_S72_I1.205611.842
38_S41_S1.181441.805
24_A73_A1.173981.794
22_C71_C1.10761.692
38_S42_F1.037751.585
14_S17_S1.036021.583
21_T55_T1.001011.529
39_N42_F0.996761.523
13_T16_G0.980721.498
37_D41_S0.971161.484
12_V15_G0.968161.479
28_P31_P0.958121.464
37_D40_P0.942091.439
18_V58_I0.917091.401
5_S23_S0.911371.392
24_A33_I0.851921.302
13_T61_V0.846811.294
26_G31_P0.818511.251
35_W56_L0.814781.245
32_S74_S0.812441.241
58_I61_V0.779681.191
44_S47_R0.745851.140
33_I54_S0.74331.136
43_N46_S0.740041.131
49_S54_S0.720061.100
47_R51_S0.698241.067
40_P43_N0.697821.066
42_F45_N0.687891.051
8_P11_V0.685671.048
46_S50_S0.672381.027
23_S53_N0.670331.024
18_V61_V0.656291.003
47_R50_S0.654261.000
63_R66_N0.649660.993
48_G52_S0.639860.978
61_V66_N0.631170.964
62_T65_D0.625530.956
11_V16_G0.622930.952
41_S44_S0.618250.945
13_T17_S0.612360.936
45_N48_G0.587370.897
31_P73_A0.581460.888
58_I65_D0.562930.860
49_S53_N0.560190.856
48_G51_S0.558850.854
51_S54_S0.555560.849
10_P15_G0.554340.847
20_L69_Y0.546030.834
6_V9_P0.53770.822
58_I69_Y0.536960.820
31_P35_W0.531970.813
49_S52_S0.517020.790
32_S35_W0.515180.787
5_S11_V0.512790.783
66_N69_Y0.509230.778
9_P12_V0.503850.770
38_S45_N0.502940.768
31_P34_S0.489870.748
10_P13_T0.484390.740
21_T53_N0.482960.738
50_S53_N0.480850.735
37_D42_F0.476710.728
27_G31_P0.474310.725
24_A54_S0.472050.721
10_P14_S0.467050.714
39_N43_N0.463660.708
9_P13_T0.46090.704
15_G63_R0.455880.696
12_V17_S0.453070.692
61_V65_D0.446820.683
42_F46_S0.43770.669
11_V14_S0.430760.658
6_V21_T0.427940.654
32_S36_Y0.426070.651
50_S54_S0.425150.650
6_V11_V0.423460.647
41_S47_R0.42170.644
7_P11_V0.417640.638
40_P44_S0.417240.637
51_S57_T0.413490.632
24_A31_P0.41290.631
33_I73_A0.412190.630
23_S55_T0.404740.618
24_A27_G0.398780.609
37_D44_S0.397490.607
5_S25_E0.395530.604
43_N47_R0.394680.603
46_S49_S0.391680.598
48_G53_N0.388780.594
22_C35_W0.38830.593
38_S43_N0.384870.588
6_V10_P0.38390.587
5_S8_P0.37610.575
10_P17_S0.374860.573
54_S57_T0.372950.570
24_A71_C0.37290.570
28_P33_I0.364970.558
6_V23_S0.364680.557
26_G73_A0.351260.537
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
3v2aR0.986798-0.015
3rbsA198-0.012
2jllA0.986797.9-0.004
2yr3A0.986797.90.004
2id5A0.986797.90.006
3p2tA0.973397.90.015
3kldA0.986797.90.019
2gi7A0.8897.90.02
2y23A197.90.023
3rbsA197.80.027

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