GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TrkA_C - TrkA-C domain
Pfam: PF02080 (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. )
Length: 71
Sequences: 8328
Seq/Len: 117.3
HH_delta: -0.019 (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
35_R52_D1.80843.275
6_V48_L1.422392.576
35_R49_Q1.367662.477
13_V50_A1.236852.240
33_I46_T1.08631.967
16_T47_V1.051051.903
16_T19_E1.048111.898
15_K19_E1.001791.814
3_E55_I0.997261.806
17_L30_I0.975541.766
3_E53_I0.956531.732
18_K45_D0.92131.668
59_D62_D0.914031.655
31_V57_V0.912391.652
8_E50_A0.892491.616
23_P29_R0.858161.554
35_R46_T0.846471.533
58_G63_I0.83531.513
27_G62_D0.809671.466
5_R53_I0.795371.440
14_G49_Q0.777221.407
12_L20_L0.733861.329
28_V58_G0.717131.299
4_V56_V0.709951.286
62_D65_R0.698671.265
18_K44_G0.687491.245
21_D24_E0.674251.221
33_I52_D0.660571.196
49_Q52_D0.654471.185
38_E41_I0.612151.108
32_A55_I0.574371.040
34_K39_I0.572171.036
34_K53_I0.562081.018
43_D46_T0.540550.979
34_K55_I0.535120.969
58_G62_D0.527540.955
48_L54_L0.524380.950
2_V63_I0.521290.944
13_V49_Q0.519680.941
30_I56_V0.512010.927
42_P46_T0.506580.917
22_L28_V0.487230.882
6_V10_S0.469190.850
14_G50_A0.466980.846
14_G47_V0.464340.841
28_V63_I0.463140.839
29_R57_V0.450560.816
29_R44_G0.448080.811
6_V13_V0.447770.811
29_R41_I0.44610.808
32_A39_I0.444280.804
2_V60_P0.443090.802
2_V58_G0.439320.796
15_K20_L0.438520.794
9_N12_L0.437320.792
64_E68_E0.434150.786
56_V66_F0.425290.770
37_G40_I0.401570.727
3_E31_V0.399790.724
4_V67_R0.398270.721
5_R51_G0.396620.718
10_S50_A0.393960.713
22_L30_I0.381560.691
17_L48_L0.380670.689
23_P28_V0.373180.676
34_K37_G0.372190.674
30_I44_G0.371290.672
32_A57_V0.370630.671
64_E67_R0.366050.663
31_V34_K0.359960.652
15_K47_V0.354050.641
7_P50_A0.353950.641
60_P64_E0.344720.624
9_N13_V0.342530.620
38_E58_G0.337220.611
13_V16_T0.335030.607
24_E28_V0.334690.606
16_T45_D0.334580.606
28_V62_D0.333280.603
35_R40_I0.332250.602
12_L66_F0.331560.600
41_I57_V0.320610.581
47_V51_G0.311390.564
13_V48_L0.307540.557
47_V50_A0.301710.546
2_V67_R0.299880.543
42_P57_V0.299840.543
58_G66_F0.292950.530
2_V41_I0.290170.525
4_V66_F0.289780.525
27_G30_I0.287890.521
23_P44_G0.287490.521
23_P32_A0.278470.504
39_I46_T0.277120.502
10_S13_V0.275640.499
34_K38_E0.27540.499
29_R32_A0.272640.494
11_P15_K0.271370.491
17_L42_P0.269070.487
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
1vctA199-0.019
3l4bC0.971898.90.035
3jxoA0.971898.90.036
4gx0A198.90.04
4gx0A0.985998.80.054
2aefA198.80.072
1lnqA198.70.088
4g65A198.60.125
4j91A198.60.125
4g65A0.971898.60.126

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