GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PH_9 - Pleckstrin homology domain
Pfam: PF15410 (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: 119
Sequences: 4013
Seq/Len: 33.72
HH_delta: 0.074 (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
6_L31_A0.985433.432
6_L101_A0.828812.887
31_A40_F0.821942.863
87_F111_I0.765112.665
40_F65_S0.641192.233
103_D106_E0.632792.204
28_Q102_S0.550981.919
101_A107_M0.542521.889
104_E108_N0.534031.860
5_I28_Q0.516331.798
87_F101_A0.502571.750
29_V40_F0.502181.749
88_R98_L0.502181.749
34_Q39_Y0.491331.711
31_A99_F0.485431.691
8_R40_F0.483621.684
32_V41_Y0.479821.671
33_L113_A0.462161.610
86_V100_Q0.445861.553
7_M100_Q0.432831.507
108_N112_D0.425721.483
110_W114_I0.422191.470
105_E109_E0.414751.444
87_F99_F0.411931.435
109_E113_A0.407021.418
5_I30_Y0.377751.316
8_R29_V0.377071.313
43_D46_S0.360551.256
85_N100_Q0.358611.249
9_K26_W0.35631.241
102_S106_E0.354551.235
107_M111_I0.344511.200
83_R100_Q0.337191.174
41_Y63_P0.335691.169
85_N107_M0.330011.149
71_H74_A0.325871.135
31_A38_L0.303461.057
111_I114_I0.300831.048
69_L72_A0.296631.033
23_K46_S0.295691.030
85_N104_E0.29051.012
7_M28_Q0.288691.005
87_F107_M0.288371.004
112_D116_Y0.286230.997
3_E30_Y0.276430.963
113_A116_Y0.275830.961
5_I44_E0.265230.924
76_I107_M0.264920.923
3_E44_E0.263470.918
106_E109_E0.259260.903
101_A111_I0.259210.903
88_R96_E0.258410.900
10_H23_K0.257480.897
104_E107_M0.256260.893
39_Y66_S0.255660.890
8_R99_F0.254960.888
26_W100_Q0.249340.868
33_L36_G0.249220.868
3_E32_V0.244480.851
32_V39_Y0.244230.851
102_S109_E0.24420.851
26_W86_V0.24350.848
63_P66_S0.238080.829
34_Q37_Q0.235930.822
90_R96_E0.233730.814
72_A91_T0.232430.810
106_E110_W0.231340.806
10_H27_K0.231140.805
37_Q68_S0.226220.788
4_G106_E0.225280.785
86_V98_L0.225020.784
111_I115_N0.22440.782
6_L99_F0.223030.777
29_V106_E0.222210.774
33_L38_L0.221430.771
112_D115_N0.218070.759
65_S68_S0.215930.752
83_R86_V0.214410.747
68_S90_R0.213790.745
75_E90_R0.211830.738
66_S69_L0.210680.734
86_V107_M0.20920.729
27_K31_A0.207070.721
8_R11_E0.206990.721
72_A75_E0.20620.718
26_W32_V0.204790.713
68_S71_H0.204570.712
70_H75_E0.20440.712
28_Q33_L0.204090.711
63_P80_Y0.202190.704
67_I91_T0.201350.701
71_H94_G0.200360.698
30_Y44_E0.198330.691
42_K64_D0.194930.679
30_Y41_Y0.19350.674
4_G8_R0.192460.670
29_V64_D0.192340.670
7_M102_S0.19190.668
36_G68_S0.190010.662
82_K113_A0.189420.660
87_F114_I0.188520.657
88_R91_T0.18810.655
105_E108_N0.187050.651
44_E47_P0.185840.647
28_Q44_E0.185810.647
4_G30_Y0.185650.647
5_I64_D0.185440.646
24_R27_K0.184870.644
28_Q81_T0.184280.642
83_R116_Y0.184160.641
77_A80_Y0.183820.640
8_R114_I0.183640.640
109_E116_Y0.182080.634
26_W98_L0.181520.632
73_L94_G0.180650.629
70_H73_L0.179540.625
26_W83_R0.178440.621
81_T84_K0.178170.621
75_E88_R0.178120.620
72_A89_L0.17780.619
64_D75_E0.175480.611
82_K90_R0.174830.609
33_L114_I0.1740.606
73_L78_S0.17130.597
62_K68_S0.170170.593
36_G72_A0.169860.592
80_Y100_Q0.16950.590
81_T100_Q0.168230.586
78_S87_F0.168120.586
95_S108_N0.167280.583
23_K106_E0.165280.576
72_A100_Q0.164860.574
66_S70_H0.164160.572
32_V63_P0.164030.571
92_A95_S0.162760.567
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
1wjmA0.91699.70.074
1droA0.932899.70.076
3pp2A0.95899.70.089
2p0dA0.941299.70.094
2j59M0.890899.60.099
3a8pA0.932899.60.107
3cxbB0.831999.60.109
3a8nA0.932899.60.113
1btnA0.890899.60.115
4h8sA0.806799.60.119

Page generated in 0.0161 seconds.