GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SH3_3 - Bacterial SH3 domain
Pfam: PF08239 (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: 4765
Seq/Len: 86.64
HH_delta: -0.009 (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
8_G13_S2.825734.260
37_Y51_S2.261193.409
30_E37_Y1.814812.736
3_L53_Y1.647972.485
38_K46_T1.565922.361
4_N15_V1.38872.094
10_S13_S1.383422.086
25_V39_V1.34422.027
29_G38_K1.299181.959
20_P23_E1.241611.872
7_S14_P1.155941.743
28_L38_K1.018831.536
37_Y54_L0.916391.382
50_S53_Y0.889111.340
4_N18_Q0.884061.333
27_V37_Y0.865621.305
28_L46_T0.859241.295
6_R15_V0.775161.169
3_L49_V0.770511.162
49_V54_L0.747851.127
7_S13_S0.732821.105
25_V54_L0.699951.055
7_S16_I0.694931.048
5_V47_G0.673781.016
4_N50_S0.634640.957
30_E51_S0.634470.957
19_L23_E0.631920.953
17_G45_K0.607770.916
5_V17_G0.571760.862
5_V19_L0.564810.852
5_V39_V0.561040.846
41_T45_K0.548080.826
11_T50_S0.540720.815
23_E42_Y0.536460.809
3_L50_S0.52950.798
38_K48_W0.523640.789
4_N53_Y0.515540.777
9_P36_W0.505910.763
19_L25_V0.490780.740
4_N11_T0.485720.732
39_V49_V0.467020.704
42_Y45_K0.450550.679
24_K41_T0.424450.640
15_V18_Q0.410330.619
6_R50_S0.408660.616
19_L42_Y0.407690.615
26_T41_T0.403480.608
51_S54_L0.401360.605
17_G23_E0.398780.601
17_G43_D0.392020.591
5_V49_V0.391850.591
31_S48_W0.38260.577
33_D51_S0.37010.558
9_P48_W0.353840.533
4_N36_W0.35250.531
41_T44_G0.34140.515
16_I47_G0.341060.514
15_V20_P0.337990.510
26_T42_Y0.332940.502
17_G20_P0.332630.501
6_R53_Y0.330230.498
6_R36_W0.315450.476
6_R13_S0.31240.471
6_R10_S0.302640.456
17_G41_T0.292060.440
17_G21_K0.291770.440
12_N33_D0.286290.432
32_G38_K0.28280.426
11_T53_Y0.281060.424
29_G48_W0.278720.420
23_E41_T0.275610.416
30_E33_D0.26630.401
31_S51_S0.265890.401
8_G14_P0.262010.395
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
2kq8A0.945598.7-0.009
2kt8A0.945598.60.013
2krsA0.945598.60.019
3npfA0.945598.50.048
3h41A0.963698.10.161
3npfA0.963698.10.182
2hbwA0.945597.60.272
1xovA0.945597.60.288
3h41A0.945597.50.292
3m1uA0.981896.60.403

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