GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Dimerisation - Dimerisation domain
Pfam: PF08100 (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: CL0123
Length: 51
Sequences: 1572
Seq/Len: 30.82
HH_delta: 0.065 (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_A50_L1.030752.803
10_G13_D0.924832.515
39_A42_M0.8572.331
23_L31_R0.68211.855
4_K8_E0.68031.850
24_S27_E0.638681.737
6_A12_P0.624951.700
26_S40_P0.611851.664
45_R48_R0.605191.646
2_A50_L0.559191.521
9_L38_S0.541261.472
38_S43_L0.505351.374
2_A49_L0.498171.355
15_I23_L0.487651.326
28_I43_L0.485281.320
32_L38_S0.454731.237
7_V12_P0.452061.229
10_G14_I0.442241.203
25_L44_D0.395141.075
41_P45_R0.394411.073
14_I31_R0.377281.026
44_D49_L0.376561.024
26_S30_A0.373451.016
6_A46_I0.365350.994
44_D48_R0.350320.953
27_E30_A0.337980.919
15_I22_P0.332480.904
6_A11_I0.329570.896
43_L47_M0.311520.847
11_I43_L0.309220.841
4_K7_V0.308630.839
5_C42_M0.301440.820
5_C46_I0.300960.818
23_L27_E0.300570.817
3_L7_V0.282760.769
48_R51_V0.279410.760
14_I32_L0.276030.751
25_L43_L0.274910.748
29_A33_P0.268360.730
15_I47_M0.257790.701
17_N31_R0.254980.693
4_K45_R0.25340.689
40_P44_D0.253150.688
24_S30_A0.252080.686
29_A40_P0.250010.680
2_A7_V0.247670.674
14_I28_I0.246620.671
3_L49_L0.246280.670
3_L50_L0.241280.656
2_A46_I0.238460.648
30_A41_P0.237350.645
11_I47_M0.235950.642
13_D41_P0.226770.617
16_H23_L0.223070.607
4_K38_S0.222530.605
12_P38_S0.221480.602
33_P40_P0.215330.586
8_E12_P0.214510.583
4_K48_R0.209360.569
6_A14_I0.206040.560
17_N21_G0.205030.558
12_P46_I0.204840.557
22_P28_I0.204660.557
27_E45_R0.203540.554
8_E49_L0.201320.547
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
3p9cA0.921698.50.065
4e70A0.90298.50.085
4a6dA0.90298.40.102
3dp7A0.90298.40.106
3lstA0.862798.30.122
3gwzA0.862798.30.128
3i53A0.862798.30.132
3reoA198.30.133
1zg3A0.90298.30.134
1x19A0.862798.20.151

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