GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acylphosphatase - Acylphosphatase
Pfam: PF00708 (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: 91
Sequences: 2216
Seq/Len: 24.35
HH_delta: -0.001 (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
24_K28_R0.914942.334
11_S73_E0.902462.302
48_A58_F0.898652.292
26_I29_K0.89522.283
5_R49_E0.879092.242
18_G21_P0.830542.119
39_L45_E0.830382.118
49_E83_G0.810672.068
8_I59_I0.791082.018
22_F61_W0.780771.992
5_R47_E0.778621.986
37_R45_E0.726981.854
66_P69_A0.67811.730
9_I39_L0.648271.654
23_V62_L0.633841.617
7_R45_E0.631921.612
61_W65_G0.614071.566
30_L61_W0.613031.564
35_W91_R0.597331.524
6_Y78_E0.59071.507
32_L48_A0.58741.498
35_W47_E0.572931.461
52_E56_E0.561491.432
59_I76_V0.554571.415
8_I46_I0.545681.392
33_T87_D0.517131.319
6_Y76_V0.492831.257
10_V74_I0.484541.236
11_S75_E0.484131.235
17_V20_R0.473891.209
10_V46_I0.457041.166
48_A55_L0.450821.150
48_A62_L0.448091.143
29_K61_W0.445191.136
32_L50_G0.443161.130
24_K90_I0.434271.108
51_E54_Q0.410481.047
57_E60_K0.408191.041
8_I62_L0.396651.012
33_T49_E0.396321.011
10_V19_F0.394241.006
7_R47_E0.389640.994
57_E61_W0.3890.992
20_R44_V0.388390.991
26_I61_W0.386440.986
15_Q38_N0.386240.985
15_Q20_R0.381640.973
6_Y59_I0.37780.964
22_F69_A0.374310.955
30_L54_Q0.374010.954
30_L57_E0.370950.946
7_R77_E0.367120.936
49_E85_Y0.363480.927
21_P67_P0.363440.927
56_E60_K0.362970.926
46_I58_F0.360270.919
65_G69_A0.357520.912
50_G55_L0.35630.909
5_R85_Y0.35370.902
47_E79_L0.352450.899
37_R91_R0.35170.897
20_R38_N0.346160.883
7_R79_L0.341270.871
23_V36_V0.334770.854
10_V71_V0.33220.847
21_P24_K0.331910.847
14_V17_V0.326590.833
35_W46_I0.323370.825
50_G54_Q0.322370.822
6_Y55_L0.320090.816
30_L58_F0.317170.809
5_R81_P0.315320.804
17_V44_V0.312420.797
14_V44_V0.310580.792
26_I30_L0.307990.786
35_W45_E0.301790.770
47_E85_Y0.299190.763
38_N44_V0.293420.748
26_I58_F0.293140.748
5_R79_L0.293070.748
23_V58_F0.290750.742
17_V38_N0.290220.740
63_K74_I0.289040.737
8_I48_A0.288310.735
33_T85_Y0.285340.728
21_P25_R0.283970.724
7_R35_W0.280880.716
18_G62_L0.27980.714
9_I45_E0.27910.712
15_Q44_V0.277740.708
23_V46_I0.276050.704
21_P90_I0.271910.694
71_V74_I0.271730.693
21_P68_P0.270660.690
59_I63_K0.270310.690
52_E78_E0.269410.687
8_I76_V0.268750.686
14_V20_R0.267620.683
60_K64_K0.266390.680
36_V90_I0.262280.669
31_G54_Q0.251030.640
56_E78_E0.250680.639
82_E89_E0.249370.636
29_K65_G0.247480.631
39_L42_G0.240880.614
12_G15_Q0.240790.614
28_R87_D0.235170.600
10_V62_L0.232220.592
36_V46_I0.231080.589
60_K75_E0.2290.584
22_F66_P0.228270.582
14_V38_N0.225320.575
11_S39_L0.225230.575
18_G25_R0.224960.574
23_V61_W0.214910.548
16_G20_R0.21350.545
26_I36_V0.212160.541
21_P40_P0.21210.541
8_I74_I0.211830.540
53_E57_E0.209690.535
23_V48_A0.208330.531
86_S89_E0.20720.529
63_K66_P0.206720.527
56_E63_K0.205860.525
9_I75_E0.203910.520
9_I41_D0.201920.515
47_E82_E0.193160.493
82_E87_D0.191370.488
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
1w2iA0.98999.9-0.001
2gv1A199.90.007
3trgA0.98999.90.009
2lxfA0.98999.90.012
3vthA0.97899.90.018
2bjdA199.90.021
2fhmA0.97899.90.022
1urrA199.90.025
1ulrA0.96799.90.032
1apsA199.90.037

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