GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ADH_N - Alcohol dehydrogenase GroES-like domain
Pfam: PF08240 (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: CL0296
Length: 109
Sequences: 15313
Seq/Len: 140.49
HH_delta: 0.006 (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
7_K44_V3.017693.678
9_R42_V2.91843.557
5_L44_V2.457782.995
57_D108_P2.314622.821
39_G94_G2.237462.727
1_P48_P2.22382.710
7_K98_Y2.109812.571
54_K57_D2.092612.550
2_G49_G2.006012.445
1_P49_G2.003882.442
7_K42_V1.925992.347
4_V106_L1.893882.308
39_G61_V1.86272.270
5_L100_V1.737422.117
67_C81_C1.700262.072
52_D103_A1.665262.029
14_C37_H1.658192.021
42_V58_R1.633511.991
45_A55_V1.591571.940
5_L45_A1.570811.914
58_R109_V1.565651.908
53_F57_D1.554641.895
47_G50_V1.531141.866
46_V55_V1.514331.845
44_V98_Y1.436891.751
5_L98_Y1.385381.688
53_F108_P1.314611.602
43_V53_F1.312331.599
8_V39_G1.251391.525
3_E100_V1.224641.492
2_G102_P1.195221.457
14_C38_E1.129681.377
9_R58_R1.121851.367
9_R40_V1.104941.347
4_V53_F1.073341.308
11_A94_G1.071651.306
6_V59_V1.059661.291
16_S37_H1.037971.265
2_G103_A1.015831.238
69_E74_L1.011871.233
46_V54_K0.984331.200
53_F106_L0.975611.189
3_E102_P0.949371.157
15_G19_H0.927341.130
6_V41_G0.924241.126
8_V99_V0.92141.123
62_S107_V0.869511.060
11_A95_F0.859731.048
16_S19_H0.852631.039
40_V58_R0.843071.027
33_L92_D0.822121.002
7_K97_E0.80410.980
12_G38_E0.799130.974
44_V55_V0.788790.961
10_A40_V0.775310.945
51_T103_A0.774450.944
69_E83_N0.77130.940
46_V50_V0.770670.939
50_V103_A0.759480.926
39_G99_V0.748150.912
8_V11_A0.738290.900
101_V106_L0.717530.874
18_L22_E0.713360.869
59_V106_L0.675050.823
20_I33_L0.669850.816
19_H22_E0.660660.805
30_K33_L0.652050.795
13_I95_F0.647390.789
28_P31_F0.639230.779
77_R80_L0.636650.776
65_I105_N0.628890.766
15_G18_L0.628680.766
60_V109_V0.625230.762
54_K108_P0.621510.757
4_V103_A0.617570.753
36_G95_F0.610630.744
14_C17_D0.608290.741
2_G48_P0.605190.738
18_L21_R0.594910.725
23_G28_P0.591910.721
61_V101_V0.583640.711
68_G104_R0.581550.709
86_V89_L0.579910.707
29_P33_L0.570960.696
2_G47_G0.567280.691
82_P85_E0.562930.686
46_V57_D0.543250.662
35_L95_F0.536160.653
15_G21_R0.517570.631
26_P29_P0.515760.629
88_G93_G0.508580.620
20_I27_P0.507860.619
96_A99_V0.498330.607
16_S20_I0.494030.602
65_I84_P0.48330.589
20_I23_G0.472330.576
51_T54_K0.471150.574
93_G99_V0.469630.572
64_N105_N0.468520.571
16_S38_E0.448720.547
34_I92_D0.446340.544
12_G95_F0.445980.544
8_V41_G0.441480.538
86_V90_G0.438890.535
41_G59_V0.438730.535
74_L77_R0.438270.534
30_K92_D0.437720.533
4_V43_V0.435470.531
43_V57_D0.432310.527
62_S78_P0.431910.526
4_V46_V0.430.524
42_V45_A0.428290.522
23_G31_F0.424570.517
94_G99_V0.4240.517
34_I96_A0.420840.513
15_G37_H0.416630.508
52_D55_V0.415940.507
78_P105_N0.413950.504
20_I89_L0.40950.499
3_E47_G0.408580.498
15_G62_S0.403480.492
103_A106_L0.400170.488
64_N86_V0.398570.486
2_G104_R0.396170.483
85_E91_L0.394450.481
102_P105_N0.394230.480
93_G96_A0.394220.480
14_C19_H0.385160.469
19_H37_H0.381380.465
92_D96_A0.380540.464
74_L81_C0.378120.461
6_V61_V0.378010.461
28_P33_L0.377350.460
20_I29_P0.376910.459
68_G78_P0.37080.452
87_L99_V0.370520.452
68_G102_P0.370360.451
40_V109_V0.369850.451
11_A36_G0.366820.447
46_V52_D0.365910.446
84_P90_G0.361130.440
68_G74_L0.360020.439
10_A58_R0.357940.436
61_V94_G0.355520.433
62_S105_N0.35330.431
21_R31_F0.349530.426
69_E104_R0.348410.425
55_V58_R0.346730.423
4_V80_L0.346320.422
62_S65_I0.344670.420
64_N84_P0.344310.420
100_V103_A0.342750.418
52_D108_P0.341640.416
33_L90_G0.341360.416
20_I28_P0.340410.415
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
2dq4A199.90.006
1h2bA199.90.009
4ej6A0.981799.90.01
3s2eA199.90.011
2d8aA199.90.011
2eihA199.90.015
1jvbA199.90.016
4a2cA0.972599.90.02
3ip1A199.90.022
1rjwA199.90.023

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