GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Str_synth - Strictosidine synthase
Pfam: PF03088 (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: CL0186
Length: 89
Sequences: 14665
Seq/Len: 164.78
HH_delta: 0.166 (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
8_D11_T1.574162.318
4_D63_A1.510662.225
12_V71_V1.376962.028
7_Q68_E1.363092.008
43_D46_T1.30951.929
41_R50_T1.207561.778
61_G75_E1.202261.771
2_D61_G1.19131.755
43_D47_K1.102221.623
65_S69_S1.066021.570
6_D64_L1.065331.569
72_L83_R1.058951.560
6_D11_T1.050341.547
40_L49_T1.039581.531
38_R51_V1.017711.499
75_E80_R0.991011.460
4_D62_V0.966921.424
6_D13_Y0.940621.385
40_L51_V0.940581.385
7_Q66_P0.926911.365
45_S87_K0.923391.360
60_N77_G0.91861.353
11_T41_R0.915681.349
60_N76_T0.914781.347
56_L59_P0.901741.328
75_E82_L0.868291.279
42_Y49_T0.83541.230
2_D16_D0.817961.205
73_V84_Y0.787571.160
55_G59_P0.776881.144
4_D64_L0.763931.125
39_L74_A0.763821.125
58_F77_G0.760831.121
5_V64_L0.719681.060
11_T69_S0.719551.060
64_L86_L0.710591.047
75_E78_R0.701581.033
11_T43_D0.697811.028
5_V44_P0.689441.015
14_F41_R0.685921.010
65_S72_L0.679141.000
53_L56_L0.67430.993
56_L75_E0.667810.984
7_Q64_L0.66160.974
65_S68_E0.657820.969
43_D48_E0.652390.961
14_F42_Y0.648210.955
43_D85_W0.645630.951
11_T45_S0.632990.932
15_T42_Y0.629620.927
13_Y72_L0.623550.918
14_F64_L0.622180.916
78_R82_L0.606670.893
13_Y86_L0.590930.870
13_Y41_R0.58440.861
16_D59_P0.574170.846
46_T49_T0.543910.801
18_S60_N0.533680.786
57_Y77_G0.533140.785
41_R52_L0.523260.771
55_G74_A0.521920.769
65_S71_V0.50610.745
17_S58_F0.499660.736
44_P86_L0.498860.735
44_P47_K0.497470.733
74_A81_I0.493780.727
14_F62_V0.491950.725
51_V54_D0.49160.724
16_D62_V0.482020.710
16_D38_R0.480750.708
42_Y84_Y0.474970.700
73_V83_R0.454030.669
18_S77_G0.453630.668
48_E51_V0.441610.650
69_S87_K0.433030.638
37_G41_R0.420960.620
16_D40_L0.419080.617
5_V12_V0.415530.612
81_I84_Y0.411280.606
3_L15_T0.410510.605
19_S76_T0.408940.602
69_S86_L0.405260.597
6_D12_V0.403110.594
44_P48_E0.402560.593
3_L62_V0.400360.590
12_V41_R0.399870.589
50_T53_L0.398320.587
58_F76_T0.397830.586
57_Y78_R0.397060.585
14_F40_L0.395740.583
76_T79_Y0.395490.582
6_D65_S0.390810.576
65_S83_R0.390690.575
16_D19_S0.386620.569
14_F73_V0.384230.566
38_R52_L0.383090.564
76_T80_R0.383080.564
64_L68_E0.377190.556
14_F72_L0.373490.550
65_S73_V0.372170.548
69_S85_W0.372060.548
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
3sreA0.966398.80.166
2fp8A0.988898.60.226
4a0pA0.820298.50.245
3hrpA0.76498.50.259
3m0cC0.820298.50.261
1n7dA0.820298.50.261
2ymuA0.786598.40.263
3v65B0.820298.40.266
4h5iA0.786598.40.271
3v64C0.820298.40.272

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