GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PEP-utilizers - PEP-utilising enzyme mobile domain
Pfam: PF00391 (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: 80
Sequences: 3854
Seq/Len: 48.17
HH_delta: -0.038 (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
11_G32_A1.411533.413
33_G75_L1.410783.411
68_K71_D1.381813.341
17_E37_E0.963492.330
37_E64_T0.942852.280
17_E38_E0.917662.219
49_A56_A0.915652.214
76_D79_S0.861512.083
13_I73_V0.811611.962
62_D66_A0.752131.819
37_E60_V0.747611.808
9_P12_V0.715491.730
10_E30_R0.644071.557
63_A67_I0.640621.549
34_I49_A0.636431.539
15_V35_V0.578371.398
43_S47_I0.535891.296
37_E62_D0.531511.285
35_V60_V0.52651.273
37_E65_E0.522221.263
24_L52_L0.515541.247
67_I73_V0.510851.235
57_I77_G0.506621.225
8_L12_V0.495851.199
9_P30_R0.49011.185
16_A36_T0.489091.183
43_S46_A0.457311.106
21_P44_H0.455991.103
57_I75_L0.449631.087
15_V73_V0.440351.065
13_I33_G0.435681.053
77_G80_G0.417871.010
39_G44_H0.415311.004
57_I80_G0.409580.990
28_L31_V0.406490.983
25_A55_P0.4050.979
37_E61_G0.402890.974
27_D31_V0.400980.970
62_D65_E0.396960.960
19_L28_L0.393010.950
12_V69_D0.392670.949
15_V63_A0.390910.945
15_V67_I0.379880.919
27_D30_R0.376550.910
8_L27_D0.369740.894
18_E38_E0.36420.881
28_L52_L0.35510.859
35_V75_L0.350910.848
34_I56_A0.348310.842
12_V32_A0.346750.838
24_L49_A0.337170.815
21_P36_T0.330990.800
24_L56_A0.327870.793
34_I45_A0.326930.791
21_P50_R0.319040.771
34_I54_I0.317670.768
8_L11_G0.314620.761
25_A29_Q0.313690.758
14_L30_R0.309290.748
67_I71_D0.306860.742
19_L48_L0.305070.738
23_D50_R0.303370.734
23_D51_E0.300640.727
19_L45_A0.297270.719
18_E43_S0.296440.717
8_L31_V0.294310.712
24_L28_L0.291960.706
66_A71_D0.290750.703
50_R77_G0.284110.687
55_P75_L0.283070.684
31_V54_I0.28250.683
34_I58_V0.281330.680
19_L44_H0.281310.680
47_I51_E0.279430.676
29_Q47_I0.278230.673
22_S48_L0.269810.652
22_S42_T0.265610.642
15_V37_E0.263480.637
12_V30_R0.261630.633
36_T39_G0.261140.631
51_E56_A0.260690.630
16_A45_A0.26010.629
10_E32_A0.259840.628
36_T40_G0.257730.623
11_G30_R0.256450.620
23_D36_T0.256060.619
29_Q52_L0.254670.616
42_T74_T0.254080.614
64_T69_D0.25340.613
13_I75_L0.252380.610
65_E68_K0.246930.597
40_G47_I0.241660.584
51_E55_P0.240210.581
22_S74_T0.23940.579
53_G56_A0.239320.579
14_L28_L0.23850.577
29_Q32_A0.238260.576
14_L31_V0.236790.573
19_L31_V0.236430.572
36_T56_A0.236160.571
28_L34_I0.233490.565
56_A59_G0.229810.556
23_D59_G0.228410.552
46_A80_G0.227970.551
68_K72_W0.225530.545
16_A21_P0.224080.542
23_D27_D0.222980.539
61_G66_A0.22110.535
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
2x0sA0.97599.8-0.038
2e28A0.987599.8-0.016
2olsA0.97599.8-0.014
3t05A0.987599.8-0.013
1h6zA0.987599.7-0.001
1vbgA0.987599.7-0
1kblA0.987599.70.001
1zymA0.987599.70.01
2hwgA0.97599.70.012
2wqdA0.97599.70.014

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