GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PH_3 - PH domain
Pfam: PF14593 (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: 104
Sequences: 5777
Seq/Len: 55.55
HH_delta: 0.146 (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
15_K90_Q1.730714.475
19_V32_L1.267543.277
70_F92_V0.944832.443
15_K94_A0.925472.393
19_V83_D0.874912.262
83_D88_A0.844542.184
18_Y31_Q0.819762.120
32_L42_Y0.784372.028
40_L43_V0.749181.937
32_L81_L0.741811.918
18_Y29_K0.708361.832
21_K42_Y0.654171.691
71_F80_Y0.648261.676
16_Q33_I0.641091.658
20_K29_K0.636181.645
85_E89_Q0.630841.631
20_K82_E0.608541.574
84_P87_N0.577271.493
91_W95_I0.573171.482
90_Q94_A0.55691.440
35_T41_F0.556461.439
86_G90_Q0.552151.428
68_K82_E0.550721.424
69_T82_E0.548731.419
42_Y52_G0.542351.402
21_K30_R0.53871.393
34_L94_A0.533111.378
88_A92_V0.527851.365
22_R27_A0.525811.360
89_Q93_E0.525231.358
70_F83_D0.496621.284
33_I43_V0.471981.220
59_E74_T0.456691.181
27_A82_E0.446891.156
93_E97_E0.437051.130
14_L35_T0.430511.113
14_L36_D0.426081.102
39_R43_V0.419071.084
50_L53_E0.417081.078
16_Q46_K0.414671.072
15_K87_N0.409481.059
16_Q31_Q0.398881.031
30_R42_Y0.395571.023
43_V50_L0.39411.019
70_F88_A0.389731.008
17_G87_N0.386320.999
68_K88_A0.385920.998
45_P48_M0.383560.992
68_K85_E0.378750.979
73_H78_T0.370870.959
40_L44_D0.370620.958
18_Y45_P0.358980.928
94_A98_V0.355890.920
27_A31_Q0.338080.874
92_V96_E0.330630.855
59_E72_I0.325110.841
71_F78_T0.323950.838
58_K61_S0.322180.833
63_E71_F0.313540.811
56_W59_E0.307190.794
60_L63_E0.302780.783
23_K26_F0.300720.778
18_Y46_K0.291920.755
31_Q46_K0.291650.754
70_F95_I0.288590.746
54_I74_T0.286240.740
23_K77_R0.28390.734
39_R44_D0.277440.717
37_G55_P0.276960.716
44_D51_K0.274590.710
34_L98_V0.274370.709
54_I79_Y0.273160.706
39_R53_E0.27020.699
23_K28_K0.267120.691
59_E62_V0.263750.682
17_G31_Q0.258430.668
85_E88_A0.256440.663
72_I81_L0.253550.656
22_R25_L0.252620.653
39_R55_P0.252460.653
27_A69_T0.251810.651
22_R80_Y0.251210.650
43_V48_M0.250990.649
17_G21_K0.250610.648
74_T79_Y0.247690.640
66_S69_T0.244070.631
30_R52_G0.239680.620
92_V95_I0.239680.620
52_G79_Y0.236870.612
41_F53_E0.236850.612
69_T88_A0.235930.610
64_V85_E0.23550.609
64_V88_A0.235130.608
87_N91_W0.234970.608
37_G98_V0.233870.605
61_S96_E0.233760.604
70_F81_L0.228930.592
62_V65_K0.228230.590
19_V89_Q0.226140.585
69_T80_Y0.226140.585
73_H77_R0.224030.579
41_F52_G0.223910.579
94_A97_E0.223110.577
41_F50_L0.223040.577
32_L40_L0.221510.573
60_L96_E0.221090.572
31_Q84_P0.220920.571
60_L64_V0.220390.570
51_K54_I0.213850.553
24_G27_A0.21340.552
45_P50_L0.211660.547
25_L36_D0.210770.545
55_P59_E0.210370.544
89_Q97_E0.209870.543
31_Q45_P0.207150.536
61_S65_K0.206810.535
22_R26_F0.206710.534
61_S64_V0.206560.534
21_K95_I0.205270.531
66_S82_E0.204170.528
66_S71_F0.203970.527
53_E57_S0.20320.525
68_K71_F0.200850.519
36_D39_R0.200020.517
65_K69_T0.199020.515
30_R44_D0.197890.512
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
1w1gA0.990499.50.146
1btkA0.894299.50.183
2codA0.942399.40.203
1qqgA0.951999.40.213
1x1fA0.990499.40.216
1eazA0.990499.40.217
1wi1A0.942399.40.219
4h8sA0.990499.40.222
3ljuX0.990499.40.227
1u5eA0.980899.40.229

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