GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ADH_zinc_N - Zinc-binding dehydrogenase
Pfam: PF00107 (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: 130
Sequences: 21186
Seq/Len: 162.97
HH_delta: 0.083 (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
27_L31_K2.35462.779
84_R109_T2.178632.571
11_K36_D2.144012.530
84_R111_R2.084082.459
7_I35_A2.046962.416
49_Q52_E2.025152.390
27_L38_V2.013582.376
28_E32_E2.008872.371
16_K37_H1.999062.359
24_E28_E1.822512.151
60_D80_R1.75112.066
28_E31_K1.71962.029
21_D27_L1.70722.015
29_L32_E1.653741.952
18_I59_V1.650751.948
79_L85_I1.634311.929
79_L108_I1.627521.921
62_V79_L1.593011.880
79_L83_G1.53891.816
62_V75_A1.53721.814
24_E40_D1.537081.814
22_R41_Y1.49181.760
37_H53_L1.466981.731
7_I19_A1.452041.714
16_K36_D1.351291.595
49_Q53_L1.343281.585
44_D49_Q1.304221.539
64_D67_G1.288971.521
40_D43_D1.275571.505
6_A63_I1.224581.445
24_E27_L1.188771.403
45_D48_E1.155931.364
24_E43_D1.154521.362
82_G107_E1.144481.351
77_K102_N1.128811.332
19_A30_A1.111071.311
103_L112_G1.097251.295
22_R42_S1.075681.269
31_K37_H1.060531.252
47_V51_R1.050331.239
47_V77_K1.047081.236
48_E52_E1.040791.228
47_V74_E1.040281.228
23_S26_K1.017451.201
4_L29_L1.002371.183
25_E28_E0.999341.179
31_K38_V0.995981.175
66_V71_T0.988421.166
18_I37_H0.95591.128
30_A35_A0.948921.120
19_A35_A0.942021.112
103_L110_I0.928151.095
65_C88_V0.92621.093
27_L40_D0.912371.077
61_V86_V0.903931.067
62_V85_I0.902921.066
119_E122_Q0.890461.051
59_V62_V0.890061.050
64_D85_I0.871031.028
6_A88_V0.868411.025
9_L124_A0.863611.019
73_Q77_K0.851561.005
121_F125_L0.845320.998
10_A15_A0.838360.989
74_E77_K0.826740.976
45_D49_Q0.826490.975
87_V110_I0.825940.975
20_T41_Y0.821310.969
70_D74_E0.815110.962
99_N102_N0.814870.962
61_V84_R0.7990.943
10_A17_V0.79570.939
86_V113_S0.792790.936
8_Q33_L0.782160.923
75_A85_I0.769170.908
6_A65_C0.765150.903
90_V104_M0.76490.903
121_F124_A0.761770.899
48_E51_R0.759260.896
7_I17_V0.75150.887
5_M9_L0.725210.856
21_D38_V0.72170.852
51_R54_T0.717310.846
86_V111_R0.710670.839
54_T58_G0.708940.837
46_F74_E0.708680.836
18_I53_L0.704040.831
66_V89_G0.70040.827
103_L108_I0.697930.824
102_N106_K0.688380.812
50_I59_V0.677930.800
71_T75_A0.668790.789
69_G97_S0.666850.787
122_Q125_L0.665940.786
73_Q102_N0.66580.786
107_E117_S0.664840.785
18_I39_I0.660440.779
101_M105_F0.653920.772
120_D123_E0.653470.771
15_A61_V0.652940.771
9_L13_M0.648270.765
5_M8_Q0.644970.761
7_I33_L0.644950.761
94_D97_S0.639790.755
21_D26_K0.634690.749
2_V88_V0.634040.748
47_V78_L0.633820.748
72_L87_V0.627730.741
73_Q95_P0.626780.740
43_D49_Q0.624030.736
8_Q12_A0.61920.731
102_N105_F0.599270.707
64_D87_V0.598510.706
18_I50_I0.597680.705
73_Q97_S0.593960.701
50_I54_T0.590550.697
96_I100_L0.588840.695
119_E123_E0.588030.694
7_I30_A0.58740.693
81_P106_K0.583970.689
113_S116_G0.58280.688
29_L33_L0.581240.686
117_S120_D0.580160.685
62_V78_L0.578060.682
22_R27_L0.570440.673
72_L85_I0.56990.673
64_D89_G0.567990.670
37_H49_Q0.560810.662
73_Q99_N0.557650.658
7_I11_K0.556750.657
71_T74_E0.555140.655
11_K17_V0.550460.650
114_W117_S0.546940.645
105_F114_W0.54610.644
113_S117_S0.533760.630
95_P99_N0.533040.629
107_E116_G0.52780.623
23_S40_D0.525490.620
1_G4_L0.524820.619
80_R83_G0.524550.619
46_F49_Q0.523510.618
30_A38_V0.521920.616
45_D74_E0.517050.610
21_D41_Y0.510870.603
51_R58_G0.50580.597
85_I110_I0.497330.587
63_I86_V0.495470.585
35_A38_V0.493740.583
8_Q11_K0.493390.582
18_I54_T0.490930.579
4_L33_L0.488190.576
104_M112_G0.487960.576
100_L103_L0.487940.576
24_E31_K0.486430.574
74_E78_L0.483570.571
15_A60_D0.483220.570
69_G73_Q0.481730.568
102_N108_I0.479210.566
101_M104_M0.477980.564
17_V36_D0.477740.564
46_F50_I0.476750.563
4_L8_Q0.475730.561
39_I49_Q0.473860.559
76_I108_I0.471110.556
50_I78_L0.47060.555
50_I55_G0.468850.553
72_L100_L0.46690.551
116_G121_F0.466440.550
69_G94_D0.464470.548
90_V105_F0.464170.548
11_K14_G0.463020.546
51_R55_G0.459440.542
70_D73_Q0.457810.540
76_I110_I0.456590.539
96_I99_N0.455180.537
20_T78_L0.449990.531
3_G21_D0.448730.530
107_E113_S0.448120.529
21_D40_D0.445250.525
58_G80_R0.443410.523
95_P98_F0.44340.523
109_T112_G0.439050.518
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
3uogA0.992399.70.083
1vj0A199.70.083
3pi7A0.992399.70.103
3krtA0.992399.70.103
3jv7A0.984699.70.105
3ip1A0.992399.70.109
3s2eA0.976999.70.114
4a2cA199.60.119
4ej6A0.984699.60.12
2d8aA0.992399.60.12

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