GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hydrolase_4 - Putative lysophospholipase
Pfam: PF12146 (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: CL0028
Length: 79
Sequences: 28700
Seq/Len: 363.29
HH_delta: 0.04 (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
52_R73_D3.300083.516
18_V45_A2.405852.563
27_E31_R2.187782.331
18_V47_F2.057652.192
22_V51_H2.042542.176
22_V74_L1.917692.043
29_S50_D1.674571.784
23_H51_H1.582861.686
19_V44_Y1.544231.645
23_H54_H1.513871.613
29_S56_R1.505291.604
29_S48_A1.479741.576
16_K45_A1.437421.531
47_F77_F1.43671.531
21_I46_V1.417021.510
17_A44_Y1.368781.458
38_F42_Q1.347191.435
49_Y74_L1.293051.378
22_V49_Y1.260731.343
38_F41_E1.255751.338
40_A46_V1.246791.328
36_A48_A1.224791.305
21_I32_Y1.207761.287
20_V78_I1.201321.280
51_H70_Y1.188161.266
66_S69_D1.121141.194
26_G54_H1.067371.137
25_F51_H1.022031.089
20_V49_Y0.995881.061
49_Y77_F0.99351.058
36_A46_V0.947511.009
36_A40_A0.941761.003
40_A43_G0.940311.002
32_Y36_A0.90760.967
35_L38_F0.899380.958
37_E40_A0.893250.952
19_V46_V0.87340.930
25_F54_H0.85980.916
71_V75_H0.852060.908
50_D55_G0.851750.907
69_D72_D0.850760.906
65_D69_D0.836330.891
34_H37_E0.826460.880
19_V39_L0.817130.871
72_D75_H0.816620.870
20_V74_L0.807950.861
32_Y35_L0.784240.836
21_I48_A0.781190.832
30_G56_R0.778310.829
18_V44_Y0.776580.827
33_A48_A0.765260.815
68_D72_D0.763510.813
67_F70_Y0.757690.807
30_G33_A0.756650.806
24_G27_E0.752720.802
54_H70_Y0.738250.787
72_D76_Q0.737950.786
51_H54_H0.719630.767
37_E41_E0.691240.736
53_G58_E0.688660.734
50_D57_S0.682450.727
53_G57_S0.672340.716
23_H49_Y0.662370.706
75_H78_I0.610860.651
74_L78_I0.60630.646
70_Y73_D0.596910.636
26_G31_R0.594230.633
31_R34_H0.591420.630
21_I39_L0.591020.630
35_L39_L0.588160.627
28_H54_H0.58780.626
24_G54_H0.587210.626
73_D76_Q0.579930.618
28_H31_R0.564880.602
65_D70_Y0.564580.601
31_R35_L0.559780.596
68_D71_V0.559140.596
64_I69_D0.5570.593
27_E30_G0.555640.592
43_G46_V0.544440.580
20_V47_F0.542140.578
61_R64_I0.537120.572
21_I36_A0.534810.570
73_D77_F0.531230.566
39_L46_V0.518570.552
63_H66_S0.514230.548
33_A37_E0.507360.541
40_A45_A0.503620.537
60_K63_H0.501790.535
23_H28_H0.500080.533
52_R70_Y0.48870.521
29_S36_A0.487570.519
25_F28_H0.486640.518
51_H74_L0.474850.506
22_V25_F0.473890.505
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
1b6gA0.987399.20.04
2xt0A0.987399.20.044
3hjuA199.10.062
3pe6A199.10.074
1zoiA0.96299.10.074
1thtA0.987399.10.075
1q0rA0.974799.10.08
2wflA0.924199.10.083
3v48A0.974799.10.085
1a88A0.96299.10.09

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