GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PH_10 - Pleckstrin homology domain
Pfam: PF15411 (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: 116
Sequences: 1347
Seq/Len: 11.61
HH_delta: 0.194 (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
9_L115_A0.467433.143
27_Y36_C0.321832.164
77_S109_L0.282621.900
26_V35_C0.279551.879
80_K83_S0.278741.874
13_L103_F0.267961.802
110_E114_S0.239981.613
86_L113_R0.224081.507
105_N108_Q0.223621.503
13_L26_V0.212951.432
68_Y72_I0.210991.419
81_P84_Y0.209681.410
86_L101_L0.206641.389
26_V33_L0.206431.388
31_K36_C0.201231.353
15_V35_C0.198481.334
112_W116_L0.194171.305
63_L66_R0.192851.297
74_E78_S0.189721.276
24_Y37_K0.189471.274
40_K60_K0.188891.270
77_S80_K0.184461.240
9_L111_Q0.184331.239
74_E77_S0.183641.235
27_Y61_L0.182731.229
59_T63_L0.181991.224
25_E36_C0.178291.199
96_L101_L0.173291.165
109_L112_W0.172881.162
28_L33_L0.172751.161
26_V101_L0.169621.140
32_I39_V0.168441.132
86_L109_L0.168291.131
6_E104_R0.167711.128
19_D24_Y0.162131.090
31_K104_R0.159691.074
105_N109_L0.159031.069
83_S96_L0.155391.045
100_T106_E0.154961.042
89_S100_T0.153151.030
11_G115_A0.153021.029
99_F106_E0.152491.025
79_S82_G0.151141.016
30_E33_L0.151091.016
65_G68_Y0.149961.008
6_E10_H0.148280.997
72_I96_L0.146420.984
8_L16_G0.146120.982
71_N90_W0.145340.977
111_Q115_A0.14530.977
77_S81_P0.145190.976
10_H104_R0.144830.974
24_Y35_C0.144080.969
39_V62_Q0.143120.962
106_E114_S0.142380.957
107_E111_Q0.140470.944
75_V96_L0.139190.936
103_F113_R0.138140.929
40_K114_S0.137960.928
26_V39_V0.137750.926
6_E66_R0.13750.924
99_F102_R0.136680.919
10_H25_E0.136110.915
81_P86_L0.135690.912
75_V78_S0.135160.909
12_T86_L0.134710.906
15_V97_E0.133850.900
60_K72_I0.133230.896
110_E113_R0.131450.884
109_L113_R0.130530.878
11_G108_Q0.130420.877
106_E110_E0.129810.873
84_Y106_E0.129560.871
22_R26_V0.126850.853
25_E108_Q0.126550.851
80_K95_E0.124890.840
113_R116_L0.124620.838
38_E101_L0.124350.836
37_K64_K0.124140.835
8_L12_T0.123860.833
12_T38_E0.123560.831
88_I96_L0.123170.828
11_G16_G0.122440.823
35_C99_F0.121630.818
74_E89_S0.121590.817
111_Q116_L0.121550.817
20_S27_Y0.120890.813
9_L14_T0.120140.808
14_T23_E0.119890.806
38_E41_P0.119890.806
20_S64_K0.119850.806
104_R108_Q0.119540.804
85_S100_T0.118940.800
26_V111_Q0.118720.798
27_Y30_E0.118530.797
36_C95_E0.118480.797
8_L41_P0.118070.794
104_R107_E0.117740.792
24_Y27_Y0.117730.792
24_Y64_K0.117650.791
35_C40_K0.116820.785
23_E100_T0.116350.782
74_E79_S0.116170.781
75_V79_S0.115750.778
69_I76_S0.115680.778
26_V30_E0.115670.778
25_E106_E0.115410.776
108_Q111_Q0.115270.775
9_L17_K0.114350.769
68_Y71_N0.113840.765
22_R32_I0.11360.764
76_S79_S0.113310.762
24_Y66_R0.112780.758
111_Q114_S0.11270.758
11_G23_E0.112640.757
68_Y115_A0.112520.756
37_K59_T0.112410.756
85_S89_S0.112390.756
36_C66_R0.111810.752
78_S81_P0.110890.746
30_E37_K0.110870.745
13_L101_L0.110470.743
72_I88_I0.110270.741
14_T21_E0.110190.741
108_Q115_A0.109180.734
38_E61_L0.108580.730
34_L98_N0.108050.726
16_G61_L0.107860.725
100_T110_E0.107760.724
29_F34_L0.107650.724
78_S87_Q0.107460.722
6_E18_D0.106980.719
60_K63_L0.106570.716
110_E115_A0.106350.715
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
1fhoA0.853499.70.194
1ntyA0.879399.60.261
2rgnB0.905299.60.265
1kz7A0.896699.60.266
3ksyA0.879399.60.298
2dfkA0.844899.60.299
2pz1A0.844899.60.303
2vrwB0.81999.50.306
3ky9A0.81999.50.308
1dbhA0.879399.50.315

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