GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SH3_2 - Variant SH3 domain
Pfam: PF07653 (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: CL0010
Length: 55
Sequences: 8087
Seq/Len: 147.04
HH_delta: -0.254 (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
10_A17_S2.419333.170
38_G47_F2.104112.757
22_D40_N1.932042.531
7_D19_K1.885422.470
36_W49_S1.843762.416
4_A18_F1.707582.237
25_E39_E1.665322.182
37_L44_R1.574942.064
47_F52_V1.572732.061
39_E44_R1.446451.895
3_R23_V1.319481.729
29_E37_L1.27191.666
19_K22_D1.205271.579
37_L46_W1.16811.530
18_F24_I1.165341.527
5_I53_E1.125541.475
2_Y52_V1.122191.470
7_D20_K1.111211.456
6_F51_Y1.102891.445
3_R53_E1.043811.368
24_I38_G1.007671.320
40_N43_R0.98221.287
27_L39_E0.882011.156
18_F47_F0.854941.120
16_L38_G0.846451.109
6_F50_S0.794831.041
27_L44_R0.788161.033
9_V17_S0.740910.971
18_F38_G0.673630.883
10_A15_E0.664590.871
30_K36_W0.656070.860
16_L45_G0.65370.857
12_D15_E0.628390.823
19_K40_N0.585570.767
8_Y15_E0.575140.754
15_E46_W0.568650.745
30_K33_D0.563950.739
4_A24_I0.533210.699
24_I47_F0.528030.692
35_W48_P0.52280.685
11_E15_E0.516220.676
35_W51_Y0.508430.666
48_P51_Y0.507720.665
8_Y11_E0.505160.662
2_Y26_V0.495250.649
45_G48_P0.491720.644
24_I40_N0.472460.619
27_L37_L0.465830.610
8_Y35_W0.458050.600
30_K49_S0.451790.592
4_A22_D0.445260.583
39_E42_G0.444160.582
31_D46_W0.438560.575
16_L40_N0.434380.569
3_R21_G0.426280.559
26_V39_E0.407680.534
26_V36_W0.405440.531
9_V19_K0.404530.530
36_W47_F0.403210.528
31_D34_G0.403060.528
30_K46_W0.39660.520
31_D49_S0.396210.519
34_G49_S0.373750.490
26_V38_G0.372390.488
36_W52_V0.359080.470
6_F9_V0.356540.467
31_D36_W0.353070.463
11_E46_W0.352580.462
4_A7_D0.347570.455
34_G46_W0.342020.448
25_E29_E0.329220.431
49_S52_V0.327960.430
11_E17_S0.312190.409
17_S43_R0.31110.408
21_G24_I0.307020.402
21_G25_E0.303820.398
20_K34_G0.303060.397
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
2pz1A0.981898.5-0.254
2de0X0.981898.4-0.25
1mv3A0.981898.4-0.249
3jv3A0.981898.4-0.248
2h8hA0.981898.4-0.246
2lx7A0.981898.4-0.245
2lj0A0.981898.4-0.245
2dybA0.981898.4-0.241
2eyzA0.981898.4-0.24
1fmkA0.981898.4-0.236

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