GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EF-hand_9 - EF-hand domain
Pfam: PF14658 (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: CL0220
Length: 66
Sequences: 16730
Seq/Len: 253.48
HH_delta: -0.197 (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
14_R52_S2.703663.934
17_V38_Q1.756082.555
7_F23_Y1.473512.144
12_T19_D1.391192.024
17_V41_I1.244391.811
54_N57_T1.112781.619
9_T22_T1.110611.616
44_L61_I1.085171.579
45_D48_G1.072621.561
8_D11_K1.05591.536
6_A26_A1.014631.476
44_L53_V1.007741.466
55_F59_L0.974191.417
5_D11_K0.967451.408
16_P19_D0.963411.402
8_D13_G0.936861.363
10_Q19_D0.923691.344
33_E36_E0.923381.344
21_I34_E0.916571.334
7_F15_V0.891621.297
49_R57_T0.876091.275
49_R54_N0.874531.272
45_D49_R0.870731.267
49_R52_S0.84941.236
8_D19_D0.848931.235
4_F58_F0.843171.227
8_D12_T0.834861.215
55_F58_F0.787171.145
45_D51_G0.774141.126
4_F55_F0.737151.073
32_P36_E0.728751.060
9_T19_D0.7221.051
47_E54_N0.682180.993
42_N48_G0.668620.973
17_V21_I0.661920.963
38_Q42_N0.655830.954
10_Q16_P0.655150.953
12_T16_P0.63410.923
20_L40_L0.625570.910
5_D55_F0.580910.845
47_E57_T0.567530.826
14_R54_N0.563330.820
16_P52_S0.56280.819
46_P60_A0.555390.808
39_D43_E0.554960.807
56_D60_A0.551430.802
20_L41_I0.54760.797
21_I32_P0.547090.796
46_P49_R0.530530.772
3_A6_A0.524040.762
58_F62_M0.522260.760
46_P57_T0.522160.760
6_A62_M0.516340.751
36_E39_D0.510080.742
34_E38_Q0.504390.734
6_A23_Y0.502380.731
3_A7_F0.495980.722
22_T25_R0.493690.718
9_T12_T0.489410.712
39_D42_N0.476720.694
21_I25_R0.470580.685
22_T26_A0.465560.677
15_V19_D0.457340.665
7_F26_A0.452550.658
54_N59_L0.450040.655
21_I37_L0.446210.649
2_T6_A0.44120.642
43_E46_P0.439960.640
42_N46_P0.433720.631
34_E37_L0.427040.621
28_T33_E0.426760.621
23_Y29_G0.426610.621
24_L40_L0.425520.619
20_L61_I0.420410.612
24_L55_F0.418420.609
25_R32_P0.410190.597
25_R28_T0.408370.594
21_I38_Q0.407750.593
26_A29_G0.406280.591
23_Y58_F0.405760.590
25_R31_S0.401630.584
17_V42_N0.399570.581
23_Y27_V0.399530.581
7_F24_L0.399020.581
37_L41_I0.395190.575
42_N51_G0.394830.574
45_D57_T0.394110.573
5_D8_D0.385490.561
56_D59_L0.38390.559
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
2lv7A0.939498.6-0.197
2lmtA0.954598.5-0.17
4gjfA0.969798.5-0.162
3mwuA0.969798.5-0.158
3tz1A0.969798.4-0.143
3i5gB0.954598.4-0.143
1djxA0.969798.4-0.137
3i5gC0.969798.4-0.135
2lhiA0.954598.4-0.126
1sjjA0.969798.4-0.124

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