GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HMG_box_2 - HMG-box domain
Pfam: PF09011 (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: CL0114
Length: 73
Sequences: 3049
Seq/Len: 41.77
HH_delta: -0.066 (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
64_R68_E1.47552.854
52_E56_E1.316142.546
18_M42_R1.293012.501
18_M21_E1.22312.366
61_D64_R1.175222.273
47_S50_E1.030541.993
46_L50_E0.90091.743
15_M39_I0.861871.667
63_E67_R0.854181.652
41_E45_S0.820491.587
53_P57_R0.817681.582
17_E54_Y0.778871.507
38_E41_E0.769041.488
8_P61_D0.761871.474
12_N15_M0.739631.431
38_E42_R0.732991.418
13_L57_R0.727351.407
31_S34_E0.723741.400
57_R61_D0.715851.385
8_P16_K0.715451.384
14_F46_L0.692791.340
13_L61_D0.687981.331
18_M39_I0.682471.320
8_P12_N0.67791.311
62_K66_E0.638641.235
55_E59_K0.638331.235
57_R60_E0.633291.225
48_E55_E0.614931.189
64_R67_R0.602351.165
15_M19_R0.597091.155
36_M40_S0.593951.149
56_E59_K0.581711.125
32_F36_M0.579441.121
59_K63_E0.575291.113
48_E52_E0.570721.104
65_Y69_M0.564121.091
11_Y43_W0.54761.059
56_E60_E0.540551.046
34_E37_K0.531261.028
15_M36_M0.526671.019
21_E25_E0.504990.977
63_E66_E0.500790.969
60_E63_E0.499850.967
10_A55_E0.491720.951
20_K23_K0.486210.940
20_K24_E0.485570.939
17_E57_R0.478110.925
65_Y70_K0.477140.923
14_F42_R0.476470.922
43_W51_K0.434330.840
9_S12_N0.426170.824
4_P65_Y0.418850.810
46_L53_P0.412220.797
52_E55_E0.411950.797
42_R45_S0.405360.784
22_V39_I0.39360.761
11_Y40_S0.391080.756
10_A58_A0.389130.753
8_P13_L0.386210.747
58_A62_K0.385110.745
51_K55_E0.380880.737
67_R71_E0.380860.737
14_F54_Y0.380150.735
30_Q34_E0.362230.701
67_R70_K0.361930.700
42_R46_L0.35990.696
32_F39_I0.358380.693
18_M22_V0.346290.670
40_S44_K0.342550.663
16_K20_K0.341290.660
41_E44_K0.340270.658
14_F39_I0.337610.653
50_E53_P0.336650.651
48_E51_K0.333970.646
11_Y15_M0.33240.643
7_P65_Y0.330310.639
19_R35_V0.32980.638
66_E70_K0.326160.631
12_N16_K0.325540.630
12_N32_F0.317170.614
25_E28_Q0.316220.612
12_N36_M0.306830.594
12_N40_S0.305480.591
33_R37_K0.301590.583
6_R11_Y0.296680.574
16_K19_R0.291570.564
22_V27_G0.281670.545
22_V35_V0.28090.543
19_R23_K0.279290.540
9_S32_F0.27920.540
14_F18_M0.276420.535
33_R36_M0.276020.534
24_E27_G0.274480.531
47_S53_P0.274140.530
22_V25_E0.273930.530
9_S36_M0.271480.525
60_E64_R0.270180.523
6_R12_N0.269760.522
52_E59_K0.268310.519
12_N19_R0.267380.517
8_P33_R0.262940.509
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
1k99A0.986399.6-0.066
2co9A0.986399.6-0.064
2crjA0.986399.6-0.063
2cs1A0.986399.6-0.062
2e6oA0.986399.6-0.053
1j46A0.986399.6-0.052
2gzkA0.986399.6-0.05
2yrqA0.986399.6-0.05
1hryA0.986399.6-0.05
4euwA0.986399.6-0.05

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