GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SH3_4 - Bacterial SH3 domain
Pfam: PF06347 (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: 4387
Seq/Len: 79.76
HH_delta: 0.062 (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_G15_S2.68863.974
37_C50_K2.122063.136
32_C37_C1.696722.508
38_K45_T1.563222.310
5_V52_L1.53012.261
27_V39_V1.394822.062
12_S15_S1.345591.989
6_N17_V1.340561.981
28_R40_R1.135071.678
22_E25_V1.118771.654
40_R45_T1.117711.652
31_E38_K1.105441.634
9_S16_P1.075321.589
4_E20_R1.022621.511
5_V48_V0.974381.440
37_C53_L0.943221.394
30_I40_R0.942691.393
30_I38_K0.91131.347
49_H52_L0.907421.341
30_I45_T0.904121.336
29_V37_C0.773661.143
8_R17_V0.762271.127
4_E22_E0.721131.066
27_V53_L0.686481.015
6_N20_R0.685891.014
38_K47_W0.67410.996
13_S49_H0.663790.981
7_L19_A0.654210.967
9_S15_S0.652220.964
35_G50_K0.637450.942
48_V53_L0.635690.940
7_L46_G0.620190.917
32_C50_K0.604130.893
9_S18_V0.593980.878
19_A44_R0.580910.859
41_A44_R0.571790.845
7_L21_L0.541330.800
6_N49_H0.529160.782
21_L27_V0.528150.781
7_L39_V0.527370.779
21_L25_V0.517210.764
25_V41_A0.497760.736
4_E23_P0.494380.731
11_P36_W0.489150.723
6_N52_L0.482530.713
11_P47_W0.439420.649
19_A25_V0.431410.638
7_L48_V0.426550.630
5_V49_H0.412130.609
6_N13_S0.397390.587
19_A42_D0.382350.565
35_G49_H0.368990.545
40_R43_G0.365790.541
8_R12_S0.353230.522
13_S52_L0.346040.511
17_V20_R0.332430.491
8_R36_W0.330840.489
6_N36_W0.317690.470
22_E41_A0.314660.465
26_P29_V0.311180.460
41_A46_G0.309180.457
39_V48_V0.305910.452
8_R49_H0.292930.433
18_V46_G0.28890.427
16_P23_P0.288490.426
21_L41_A0.287750.425
28_R34_G0.286840.424
50_K53_L0.284120.420
19_A41_A0.284090.420
13_S18_V0.281250.416
7_L18_V0.279290.413
38_K46_G0.27240.403
8_R15_S0.268030.396
19_A22_E0.266820.394
29_V32_C0.253910.375
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
2kq8A198.70.062
2kt8A198.70.078
2krsA198.70.083
3npfA0.981898.50.127
3h41A198.20.213
3npfA1980.264
2hbwA0.963697.80.309
3h41A0.981897.30.387
1xovA197.10.419
3m1uA196.70.448

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