GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3880 - DUF based on E rectale Gene description (DUF3880)
Pfam: PF12996 (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: 79
Sequences: 13058
Seq/Len: 165.29
HH_delta: 0.312 (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
21_Y42_F3.02944.383
25_F46_L1.845172.669
30_V34_R1.755352.540
30_V43_Y1.625062.351
30_V41_V1.618162.341
23_F44_L1.483282.146
24_T41_V1.417562.051
27_R43_Y1.330131.924
25_F29_F1.297521.877
27_R30_V1.2491.807
24_T30_V1.219651.764
24_T29_F1.148311.661
27_R31_E1.135231.642
66_Y69_D1.04411.511
24_T33_Y1.008851.460
14_S18_S0.968811.402
49_N53_F0.932351.349
25_F45_P0.905381.310
19_Y22_I0.897071.298
68_C71_S0.867371.255
31_E34_R0.855931.238
49_N52_R0.84281.219
29_F32_E0.831611.203
31_E35_N0.786251.137
28_S32_E0.784051.134
42_F45_P0.771221.116
54_R57_P0.765931.108
34_R41_V0.757541.096
32_E36_L0.728851.054
72_F76_L0.716151.036
14_S17_N0.708521.025
34_R38_A0.677190.980
16_A22_I0.668660.967
51_E54_R0.656550.950
32_E35_N0.625490.905
28_S31_E0.622190.900
26_D29_F0.620010.897
15_I19_Y0.613670.888
55_P59_D0.5950.861
13_Y17_N0.594810.861
34_R37_G0.592220.857
29_F47_A0.582290.842
54_R58_V0.563530.815
33_Y41_V0.535890.775
25_F77_Y0.53570.775
25_F47_A0.535620.775
29_F77_Y0.526180.761
52_R55_P0.523740.758
64_K67_E0.516090.747
34_R40_N0.492730.713
29_F75_S0.488220.706
25_F73_V0.484660.701
46_L77_Y0.484340.701
72_F77_Y0.478820.693
26_D75_S0.463870.671
24_T43_Y0.459790.665
47_A75_S0.455880.660
65_K68_C0.452790.655
47_A74_G0.44410.642
48_A53_F0.443380.641
29_F33_Y0.436850.632
22_I41_V0.433440.627
52_R56_I0.426310.617
27_R45_P0.424020.613
46_L73_V0.422550.611
29_F46_L0.422480.611
55_P58_V0.421990.611
50_P54_R0.420030.608
53_F57_P0.413660.598
29_F76_L0.41170.596
25_F28_S0.410970.595
16_A38_A0.410310.594
29_F72_F0.407750.590
56_I59_D0.401080.580
43_Y46_L0.399660.578
19_Y25_F0.398390.576
23_F45_P0.397150.575
69_D72_F0.39620.573
72_F75_S0.395480.572
16_A77_Y0.394610.571
23_F42_F0.383830.555
50_P55_P0.375260.543
57_P64_K0.37430.542
50_P53_F0.371450.537
36_L44_L0.361960.524
30_V33_Y0.36050.522
54_R59_D0.35070.507
34_R39_E0.348340.504
48_A75_S0.343790.497
59_D66_Y0.34210.495
13_Y16_A0.337730.489
25_F72_F0.337240.488
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
2hy7A0.9367980.312
2jjmA0.987397.70.381
3s28A197.60.389
3okpA197.60.392
2r60A197.60.393
2qzsA197.60.394
3oy2A197.60.397
1rzuA197.50.403
3vueA197.50.407
4hlnA197.50.413

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