GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Poly_export - Polysaccharide biosynthesisexport protein
Pfam: PF02563 (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: 82
Sequences: 2069
Seq/Len: 25.23
HH_delta: 0.064 (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
51_V59_A1.544284.447
54_L62_E1.354083.899
13_L35_V1.042653.002
13_L59_A0.978352.817
36_D40_T0.861942.482
62_E66_R0.824022.373
40_T50_K0.785972.263
59_A78_V0.707422.037
18_V32_E0.585891.687
20_R32_E0.577761.664
35_V51_V0.559571.611
23_V67_L0.547761.577
43_L67_L0.539951.555
54_L59_A0.470111.354
55_T58_E0.463941.336
15_P52_A0.452981.304
66_R69_K0.441731.272
40_T48_P0.44081.269
20_R81_A0.438841.264
46_I66_R0.433041.247
56_L60_E0.429471.237
34_T79_T0.423191.219
61_E65_Q0.416141.198
62_E65_Q0.412021.186
18_V34_T0.401291.156
18_V81_A0.389811.122
21_I43_L0.384251.106
12_R58_E0.38011.095
51_V62_E0.377051.086
56_L80_V0.363991.048
63_I76_V0.36121.040
22_S30_S0.357851.030
61_E64_K0.357131.028
33_Y41_I0.357071.028
36_D48_P0.351321.012
32_E81_A0.349291.006
54_L58_E0.344350.992
11_Y14_G0.340870.982
41_I51_V0.33660.969
19_L35_V0.333580.961
71_Y74_P0.331880.956
64_K68_Q0.331770.955
21_I78_V0.331590.955
65_Q68_Q0.331290.954
11_Y80_V0.325880.938
45_L70_Y0.321310.925
12_R55_T0.313120.902
14_G52_A0.311390.897
63_I67_L0.304670.877
60_E64_K0.302440.871
20_R79_T0.297490.857
60_E78_V0.296480.854
14_G25_G0.295150.850
41_I49_V0.295150.850
20_R31_G0.295060.850
19_L51_V0.294360.848
41_I59_A0.287010.826
42_S77_S0.284230.818
23_V76_V0.283620.817
46_I70_Y0.275610.794
10_E57_E0.274480.790
59_A62_E0.273570.788
18_V79_T0.271330.781
42_S48_P0.270590.779
57_E60_E0.268040.772
33_Y79_T0.266270.767
48_P57_E0.260.749
49_V62_E0.256810.740
60_E77_S0.248530.716
50_K54_L0.24760.713
42_S64_K0.236940.682
26_W71_Y0.235330.678
17_D21_I0.233870.673
20_R77_S0.23340.672
10_E37_P0.228830.659
26_W75_Q0.22840.658
71_Y76_V0.226640.653
57_E61_E0.226590.652
63_I68_Q0.224940.648
50_K53_G0.220040.634
63_I66_R0.218770.630
61_E72_R0.215250.620
59_A63_I0.212110.611
19_L56_L0.204190.588
8_P48_P0.201960.582
67_L71_Y0.201360.580
65_Q69_K0.20040.577
23_V43_L0.200220.577
25_G45_L0.198710.572
24_F60_E0.198090.570
56_L59_A0.197950.570
11_Y56_L0.197240.568
48_P69_K0.196990.567
17_D35_V0.19690.567
22_S31_G0.194630.560
29_L45_L0.193390.557
28_E71_Y0.193170.556
19_L78_V0.191630.552
64_K73_D0.189340.545
19_L41_I0.189070.544
42_S60_E0.18720.539
14_G24_F0.18540.534
43_L46_I0.184380.531
20_R30_S0.182240.525
16_G34_T0.180880.521
28_E70_Y0.180760.521
21_I33_Y0.18060.520
28_E37_P0.180560.520
65_Q72_R0.179550.517
10_E50_K0.179280.516
18_V27_P0.175570.506
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
2j58A199.80.064
3pa8A0.93961.40.836
3glkA155.70.841
2l25A0.365947.40.849
1lnsA0.609844.90.851
3lzkA0.463444.70.851
3jrxA142.70.853
4bejA0.890235.90.858
1mpxA0.56134.30.86
3fauA0.43929.50.864

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