GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ADH_zinc_N_2 - Zinc-binding dehydrogenase
Pfam: PF13602 (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: CL0063
Length: 127
Sequences: 22542
Seq/Len: 177.5
HH_delta: 0.146 (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
108_E111_E2.837793.678
104_F115_R2.532653.283
102_R115_R2.229632.890
104_F112_A2.011792.608
105_P108_E1.980112.567
89_E93_E1.906362.471
114_E118_S1.876572.432
115_R120_H1.845632.392
111_E114_E1.65832.149
23_V38_S1.654212.144
111_E115_R1.645312.133
101_D115_R1.637432.122
42_L45_G1.609632.086
42_L47_V1.583452.052
23_V42_L1.545232.003
90_L95_K1.51391.962
46_R67_R1.397971.812
65_S68_Y1.392081.804
110_P114_E1.371411.778
8_D11_D1.35461.756
89_E92_A1.312121.701
25_D28_G1.25391.625
104_F108_E1.217971.579
26_T50_I1.135971.472
81_A85_E1.103841.431
109_A127_L1.100591.427
80_R83_A1.098731.424
86_E89_E1.088761.411
86_E90_L1.085311.407
27_V34_L1.070511.388
63_G68_Y1.064831.380
114_E117_E1.047541.358
64_R68_Y1.043671.353
20_V23_V0.994751.289
113_H117_E0.948311.229
85_E89_E0.92281.196
54_L57_F0.91371.184
22_V48_V0.895861.161
25_D47_V0.895341.161
115_R125_V0.892731.157
63_G66_I0.892061.156
37_A40_K0.888041.151
82_E85_E0.879791.140
23_V47_V0.848551.100
14_F37_A0.844821.095
88_A92_A0.843961.094
38_S47_V0.842561.092
60_R68_Y0.840461.089
36_D40_K0.815171.057
100_I103_V0.811171.051
46_R65_S0.793911.029
55_P58_A0.79281.028
44_G63_G0.792691.027
15_A19_G0.787691.021
90_L93_E0.787371.021
102_R111_E0.771151.000
104_F127_L0.757960.982
63_G70_F0.756880.981
62_K68_Y0.755760.980
22_V46_R0.741870.962
67_R70_F0.740160.959
15_A18_G0.736450.955
60_R63_G0.723710.938
68_Y72_F0.72130.935
65_S70_F0.721230.935
55_P59_R0.717080.929
124_K127_L0.71190.923
90_L94_G0.711250.922
121_A125_V0.706110.915
104_F125_V0.705450.914
42_L64_R0.705020.914
110_P113_H0.70460.913
31_G34_L0.704560.913
3_A6_V0.698950.906
65_S71_L0.696270.902
68_Y71_L0.695760.902
61_L64_R0.689280.893
84_L88_A0.663560.860
62_K70_F0.660550.856
115_R121_A0.649080.841
20_V41_L0.642110.832
27_V51_G0.635490.824
62_K65_S0.634340.822
56_S59_R0.631660.819
23_V41_L0.628440.815
63_G69_S0.626910.813
27_V31_G0.626840.813
116_L121_A0.613250.795
115_R118_S0.60920.790
53_D56_S0.607540.787
64_R69_S0.602160.781
63_G67_R0.596060.773
13_D37_A0.595950.772
69_S72_F0.589040.764
106_L109_A0.58790.762
102_R125_V0.587490.761
59_R63_G0.579860.752
85_E88_A0.579430.751
33_S37_A0.578990.750
82_E86_E0.577820.749
25_D51_G0.576550.747
63_G72_F0.572360.742
64_R70_F0.565960.734
104_F111_E0.56520.733
57_F60_R0.565040.732
60_R69_S0.563550.730
66_I70_F0.560050.726
5_E8_D0.558480.724
62_K67_R0.550380.713
5_E15_A0.55010.713
37_A41_L0.549160.712
112_A115_R0.545170.707
59_R64_R0.542190.703
24_I48_V0.535780.694
9_Y14_F0.534910.693
91_V96_L0.532150.690
61_L70_F0.528650.685
65_S72_F0.528040.684
26_T51_G0.525620.681
87_L90_L0.524240.680
91_V98_P0.523590.679
65_S69_S0.521730.676
99_P122_R0.520960.675
55_P60_R0.514360.667
113_H116_L0.510.661
25_D38_S0.505350.655
62_K66_I0.505250.655
67_R72_F0.50520.655
34_L37_A0.502710.652
83_A86_E0.502030.651
90_L96_L0.497470.645
18_G21_D0.492510.638
7_I12_T0.492220.638
1_L99_P0.490620.636
84_L87_L0.489140.634
6_V9_Y0.486280.630
24_I50_I0.483050.626
46_R49_S0.479860.622
116_L125_V0.478110.620
102_R108_E0.476030.617
60_R72_F0.473210.613
32_E36_D0.471820.612
34_L38_S0.470610.610
32_E37_A0.465420.603
66_I72_F0.463650.601
54_L58_A0.461590.598
39_R47_V0.456860.592
81_A84_L0.455930.591
25_D49_S0.455120.590
38_S41_L0.454090.589
101_D125_V0.452250.586
59_R68_Y0.447890.581
109_A113_H0.447820.580
101_D121_A0.446210.578
100_I126_V0.441780.573
63_G71_L0.441460.572
80_R84_L0.441370.572
101_D122_R0.440670.571
62_K69_S0.43440.563
112_A127_L0.433380.562
59_R66_I0.433190.561
34_L47_V0.43140.559
38_S42_L0.43130.559
64_R67_R0.42950.557
118_S121_A0.42540.551
116_L119_G0.423350.549
66_I69_S0.423260.549
67_R71_L0.420830.545
60_R65_S0.416650.540
4_D7_I0.415890.539
11_D14_F0.415350.538
61_L68_Y0.409680.531
39_R42_L0.404210.524
92_A95_K0.397690.515
61_L66_I0.395490.513
7_I15_A0.395310.512
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
4j6fA0.960699.30.146
1h2bA0.944999.30.148
3slkA0.968599.30.161
4a2cA0.968599.20.175
2h6eA0.960699.20.184
4eezA0.960699.20.19
4ilkA0.960699.10.208
3krtA0.960699.10.209
4hfmA0.960699.10.21
1vj0A0.960699.10.219

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