GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trp_repressor - Trp repressor protein
Pfam: PF01371 (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: 87
Sequences: 3437
Seq/Len: 39.51
HH_delta: 0.269 (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
62_S65_T0.918482.524
50_K58_E0.882032.424
65_T68_R0.85552.351
53_R63_I0.767162.108
39_W75_Y0.697781.918
46_L69_V0.665381.829
38_R68_R0.621571.708
52_Y63_I0.608641.673
61_V68_R0.599161.647
52_Y69_V0.565781.555
39_W72_C0.564441.551
39_W68_R0.531071.460
17_E21_D0.528541.453
53_R57_E0.506811.393
45_L58_E0.503471.384
50_K54_E0.496491.365
64_A67_T0.48481.332
61_V66_I0.477421.312
46_L55_I0.471851.297
55_I66_I0.459761.264
36_A39_W0.446151.226
21_D24_E0.442871.217
67_T71_R0.442211.215
64_A70_S0.439261.207
55_I69_V0.42981.181
19_C23_F0.426891.173
11_L18_E0.426231.171
52_Y55_I0.421951.160
45_L50_K0.418091.149
18_E22_F0.41011.127
33_E40_Q0.387161.064
69_V73_L0.382491.051
23_F27_C0.377171.037
65_T71_R0.37691.036
37_Q41_V0.374221.029
53_R56_A0.365531.005
24_E27_C0.364511.002
45_L59_T0.362930.997
11_L14_K0.354560.974
38_R62_S0.354230.974
20_Y23_F0.34560.950
25_D28_T0.344210.946
35_L39_W0.343960.945
52_Y64_A0.338990.932
51_S54_E0.337260.927
62_S67_T0.332860.915
13_L16_E0.323710.890
52_Y66_I0.320350.880
54_E57_E0.317220.872
42_A72_C0.315020.866
56_A66_I0.314530.864
17_E20_Y0.313730.862
42_A69_V0.313340.861
14_K22_F0.310160.852
19_C22_F0.309090.850
36_A75_Y0.301290.828
37_Q40_Q0.297050.816
67_T70_S0.295460.812
24_E28_T0.294450.809
42_A68_R0.291910.802
39_W67_T0.291730.802
64_A69_V0.290460.798
16_E20_Y0.289260.795
14_K18_E0.28860.793
45_L48_E0.284320.781
72_C76_G0.283490.779
11_L15_D0.281960.775
34_A75_Y0.280750.772
34_A38_R0.262450.721
26_L33_E0.260090.715
40_Q43_K0.259830.714
52_Y67_T0.258660.711
70_S74_K0.257990.709
48_E73_L0.256410.705
63_I70_S0.254050.698
42_A46_L0.253140.696
73_L77_D0.252740.695
60_G72_C0.251610.692
23_F26_L0.250260.688
27_C35_L0.247110.679
30_D33_E0.247050.679
41_V59_T0.243470.669
68_R71_R0.23990.659
27_C30_D0.237470.653
63_I69_V0.235560.647
39_W71_R0.234840.645
55_I59_T0.233550.642
35_L42_A0.233050.641
13_L18_E0.232720.640
42_A61_V0.229770.631
51_S73_L0.228940.629
12_S35_L0.227550.625
22_F25_D0.22640.622
18_E23_F0.22550.620
47_D74_K0.224530.617
56_A59_T0.223990.616
51_S56_A0.221770.610
41_V45_L0.22170.609
26_L57_E0.221010.607
69_V72_C0.21970.604
45_L55_I0.21580.593
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
1jhgA0.9885990.269
3korA0.988598.80.306
3frwA0.988598.80.313
1or7A0.988598.70.344
4kn7X0.988598.70.356
3hugA198.60.358
3vdoA0.95498.60.362
1rp3A0.965598.60.367
3iydF0.988598.60.369
2q1zA0.919598.50.391

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