GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PH_8 - Pleckstrin homology domain
Pfam: PF15409 (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: CL0266
Length: 89
Sequences: 6088
Seq/Len: 68.4
HH_delta: -0.082 (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
19_F30_Y1.208523.287
72_A78_F0.942292.563
30_Y41_G0.898582.444
19_F70_L0.888522.416
74_S77_D0.823472.239
59_I82_V0.774232.105
58_R71_K0.713391.940
20_V31_Y0.700481.905
75_Q79_Q0.695071.890
17_R30_Y0.677931.844
80_R84_A0.675911.838
81_W85_L0.662911.803
16_K73_K0.637011.732
4_L71_K0.599171.629
73_K77_D0.588231.600
60_D69_H0.580661.579
79_Q83_S0.555551.511
76_E80_R0.537171.461
78_F82_V0.526761.433
33_N36_S0.521941.419
31_Y39_L0.507391.380
6_K14_W0.494421.345
57_R71_K0.4871.324
4_L16_K0.484461.317
5_K17_R0.470591.280
21_L84_A0.466051.267
29_S42_S0.465721.267
19_F28_L0.458161.246
59_I72_A0.454971.237
14_W71_K0.454261.235
82_V86_Q0.441991.202
75_Q78_F0.439491.195
45_V48_A0.430321.170
57_R75_Q0.429111.167
48_A63_S0.419911.142
59_I78_F0.418181.137
24_E29_S0.405461.103
60_D67_I0.404021.099
83_S87_K0.399491.086
51_S60_D0.398781.084
32_R40_R0.384141.045
57_R78_F0.384011.044
48_A61_I0.37861.030
27_T42_S0.377071.025
29_S39_L0.37351.016
50_I53_N0.366940.998
39_L42_S0.353950.963
27_T44_D0.341850.930
59_I70_L0.338190.920
5_K30_Y0.334260.909
62_D67_I0.332410.904
48_A70_L0.328610.894
43_I68_W0.328080.892
18_Y33_N0.328010.892
20_V29_S0.327890.892
55_K58_R0.322160.876
25_K44_D0.319520.869
46_S51_S0.313110.851
14_W69_H0.297220.808
44_D47_L0.296480.806
32_R36_S0.295520.804
9_K13_G0.294750.802
24_E27_T0.292350.795
84_A87_K0.289840.788
63_S68_W0.288190.784
21_L24_E0.286430.779
77_D81_W0.284170.773
20_V24_E0.283020.770
51_S54_K0.279640.760
18_Y34_Q0.278850.758
52_A78_F0.277880.756
55_K71_K0.276130.751
55_K60_D0.272690.742
57_R60_D0.267780.728
44_D48_A0.266510.725
14_W18_Y0.265670.722
28_L85_L0.26370.717
15_H71_K0.258570.703
14_W58_R0.254130.691
17_R32_R0.253190.689
17_R41_G0.25310.688
43_I85_L0.246690.671
5_K66_E0.244690.665
13_G18_Y0.243080.661
75_Q87_K0.238490.649
19_F48_A0.232570.632
63_S67_I0.232470.632
12_Q15_H0.231740.630
41_G68_W0.227470.619
27_T38_K0.226090.615
13_G41_G0.224410.610
72_A82_V0.224180.610
29_S48_A0.224010.609
28_L43_I0.222350.605
36_S39_L0.218730.595
26_G65_D0.21760.592
19_F72_A0.217120.590
10_P65_D0.215840.587
30_Y70_L0.215750.587
63_S66_E0.215550.586
62_D66_E0.21380.581
50_I82_V0.212950.579
18_Y36_S0.210960.574
42_S46_S0.209840.571
83_S86_Q0.208990.568
5_K45_V0.206890.563
26_G46_S0.206050.560
5_K85_L0.205150.558
36_S64_G0.203810.554
77_D80_R0.202680.551
79_Q87_K0.202640.551
58_R78_F0.201950.549
19_F44_D0.199450.542
58_R69_H0.199320.542
78_F83_S0.198810.541
73_K76_E0.197330.537
4_L10_P0.196760.535
73_K80_R0.195730.532
14_W61_I0.194520.529
21_L28_L0.194150.528
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
1wi1A0.977599.5-0.082
1x1fA0.966399.5-0.057
2q13A0.966399.4-0.031
3ljuX0.977599.4-0.03
1v88A0.955199.4-0.03
1v5pA0.977599.4-0.026
2dhkA0.977599.4-0.025
2r09A0.966399.4-0.024
3ljuX0.988899.4-0.02
4h8sA0.966399.4-0.018

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