GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Hydrolase_6 - Haloacid dehalogenase-like hydrolase
Pfam: PF13344 (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: 101
Sequences: 26776
Seq/Len: 265.11
HH_delta: 0.172 (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
87_G91_L2.512343.048
20_V24_D1.874452.274
41_S48_A1.801632.186
73_Y76_E1.665112.020
72_E76_E1.650252.002
25_A29_R1.571381.906
52_K57_P1.395871.693
27_R33_V1.371841.664
74_L80_G1.303861.582
34_V62_E1.265731.535
93_E97_E1.259241.528
74_L83_V1.255771.523
70_A73_Y1.25481.522
26_L31_K1.245791.511
47_Y50_K1.24021.504
24_D59_D1.195471.450
85_V95_L1.187571.441
48_A52_K1.183241.435
24_D28_E1.165281.414
25_A28_E1.154981.401
72_E75_K1.109161.346
85_V94_E1.069251.297
79_G82_K1.067541.295
49_K53_K1.065631.293
37_T47_Y1.059461.285
18_G21_E1.033921.254
21_E24_D1.031291.251
60_E73_Y1.00171.215
32_P61_D0.991841.203
94_E98_A0.991151.202
73_Y77_H0.979651.188
21_E25_A0.963371.169
38_N89_D0.959341.164
22_A25_A0.95851.163
39_N47_Y0.952411.155
60_E63_I0.931511.130
71_A75_K0.929451.128
34_V77_H0.922351.119
49_K52_K0.905331.098
91_L94_E0.903851.096
75_K97_E0.903471.096
32_P58_V0.894721.085
41_S45_E0.894571.085
48_A57_P0.871241.057
78_K82_K0.866611.051
27_R61_D0.853391.035
27_R57_P0.850541.032
19_A22_A0.843511.023
62_E76_E0.835441.013
71_A97_E0.825951.002
20_V55_G0.820120.995
80_G83_V0.813730.987
93_E96_R0.806410.978
90_G93_E0.804560.976
27_R59_D0.801580.972
19_A23_L0.800230.971
45_E48_A0.788950.957
16_I19_A0.788610.957
38_N90_G0.785560.953
85_V91_L0.784660.952
68_M72_E0.777750.943
46_E50_K0.770040.934
71_A74_L0.763390.926
34_V73_Y0.760720.923
16_I39_N0.750040.910
45_E49_K0.734920.892
46_E49_K0.72670.882
47_Y65_T0.72590.881
92_R96_R0.723350.877
39_N65_T0.722640.877
36_L85_V0.714530.867
36_L69_A0.714340.867
18_G22_A0.70660.857
38_N94_E0.683810.830
67_G71_A0.681190.826
70_A74_L0.672580.816
35_F51_L0.665150.807
31_K84_Y0.642350.779
47_Y51_L0.630820.765
41_S65_T0.630310.765
39_N85_V0.629910.764
24_D27_R0.626890.760
23_L33_V0.615570.747
51_L59_D0.609370.739
78_K83_V0.6080.738
36_L73_Y0.606810.736
22_A26_L0.605630.735
27_R30_G0.595960.723
37_T88_S0.593310.720
39_N89_D0.58280.707
71_A98_A0.57690.700
15_P56_I0.571660.693
69_A72_E0.570260.692
26_L33_V0.569930.691
75_K78_K0.5620.682
17_P21_E0.560280.680
51_L56_I0.559870.679
33_V60_E0.55950.679
15_P20_V0.548710.666
94_E97_E0.546010.662
26_L86_L0.541480.657
92_R95_L0.539320.654
67_G70_A0.538230.653
48_A51_L0.537360.652
15_P18_G0.531340.645
81_K99_G0.529930.643
22_A86_L0.528760.641
82_K99_G0.528240.641
34_V58_V0.525650.638
91_L98_A0.517680.628
20_V53_K0.512640.622
55_G58_V0.503720.611
13_N39_N0.501820.609
36_L91_L0.497820.604
41_S62_E0.495420.601
40_S45_E0.483410.586
71_A80_G0.482490.585
23_L27_R0.482170.585
68_M71_A0.471990.573
85_V90_G0.466040.565
74_L98_A0.463960.563
23_L60_E0.459190.557
24_D55_G0.456520.554
65_T68_M0.455510.553
15_P54_L0.453330.550
38_N50_K0.450230.546
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
4jdpA199.40.172
3kc2A0.970399.30.187
3ib6A199.30.195
3zvlA0.980299.30.197
2gmwA0.980299.30.219
2wm8A0.970399.20.227
3n07A0.970399.20.246
1zjjA199.20.246
1k1eA0.970399.20.249
3eprA199.20.252

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