GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hydrolase_like - HAD-hyrolase-like
Pfam: PF13242 (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: CL0137
Length: 75
Sequences: 14531
Seq/Len: 193.75
HH_delta: -0.02 (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
28_G34_D3.875664.058
38_A45_T2.292.398
12_Q16_R2.214582.319
35_I45_T1.972992.066
44_D66_D1.97052.063
39_K66_D1.921162.012
36_E40_A1.819771.906
14_L21_P1.701221.781
10_L37_A1.698291.778
26_M38_A1.682241.762
70_D74_E1.654221.732
25_V46_I1.654131.732
7_P11_E1.628621.705
14_L24_C1.58821.663
49_L70_D1.574781.649
14_L43_I1.549521.623
46_I69_V1.393581.459
12_Q15_K1.3811.446
49_L68_V1.375461.440
13_A17_L1.360341.424
26_M34_D1.331411.394
20_D23_R1.330291.393
46_I67_Y1.327711.390
10_L26_M1.289491.350
30_S33_T1.263871.323
32_E36_E1.201281.258
50_T72_L1.173451.229
8_G12_Q1.160311.215
25_V44_D1.150881.205
44_D67_Y1.146531.201
10_L43_I1.088261.140
71_D74_E1.078281.129
19_V24_C1.07091.121
24_C43_I1.042941.092
27_V46_I0.986181.033
26_M43_I0.955451.000
11_E41_A0.910320.953
39_K45_T0.909240.952
35_I65_P0.888870.931
10_L28_G0.872280.913
11_E21_P0.856850.897
47_L68_V0.851170.891
11_E15_K0.806670.845
27_V72_L0.805560.844
48_V72_L0.803060.841
7_P40_A0.791480.829
19_V23_R0.779830.817
33_T36_E0.777580.814
37_A41_A0.777570.814
26_M37_A0.766450.803
14_L41_A0.741120.776
13_A37_A0.736960.772
8_G11_E0.731820.766
54_S57_D0.727240.762
47_L58_L0.716680.750
9_M12_Q0.715280.749
38_A43_I0.71410.748
39_K64_K0.713940.748
50_T53_Y0.71330.747
9_M37_A0.713170.747
21_P24_C0.69970.733
3_G30_S0.692230.725
33_T37_A0.684070.716
69_V72_L0.67820.710
35_I47_L0.67330.705
6_S9_M0.6610.692
27_V48_V0.659210.690
68_V71_D0.63590.666
32_E52_V0.620540.650
49_L53_Y0.613010.642
27_V34_D0.597370.626
21_P43_I0.592850.621
3_G6_S0.571790.599
45_T66_D0.568210.595
69_V74_E0.567650.594
34_D41_A0.556040.582
32_E53_Y0.555920.582
54_S58_L0.555110.581
55_P58_L0.553660.580
11_E14_L0.549730.576
9_M13_A0.548050.574
13_A16_R0.547850.574
53_Y57_D0.544630.570
36_E39_K0.537780.563
3_G52_V0.532220.557
14_L17_L0.530170.555
10_L38_A0.525380.550
5_P34_D0.524930.550
36_E63_H0.514430.539
64_K68_V0.498640.522
47_L65_P0.498380.522
14_L19_V0.495720.519
29_D33_T0.488940.512
26_M33_T0.486020.509
67_Y70_D0.46490.487
36_E64_K0.460760.482
7_P41_A0.458920.481
10_L41_A0.451820.473
26_M35_I0.447550.469
65_P68_V0.444650.466
24_C41_A0.442620.463
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
4jdpA199.4-0.02
2hx1A199.30.05
1yv9A199.20.067
3eprA199.20.085
3l8hA0.986799.20.087
4gibA0.8899.20.088
1ynsA0.946799.10.097
3kbbA0.986799.10.102
3qgmA199.10.113
2oycA199.10.115

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