GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
adh_short - short chain dehydrogenase
Pfam: PF00106 (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: 167
Sequences: 88599
Seq/Len: 530.53
HH_delta: -0.105 (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
105_E113_F3.554482.645
63_D66_S3.45262.569
105_E109_R3.414662.541
3_V83_I3.356762.498
132_N159_T3.199322.381
109_R113_F3.082432.294
153_A157_G2.963312.205
68_R121_A2.956872.200
134_S156_R2.884642.147
86_N132_N2.738232.038
119_A162_L2.661391.981
37_S41_Q2.628961.956
19_A23_R2.605681.939
123_L166_L2.603951.938
14_R18_R2.545521.894
2_T27_V2.514591.871
31_T59_C2.410791.794
8_A30_L2.409661.793
59_C66_S2.358041.755
71_I122_L2.221681.653
64_P101_E2.108941.569
3_V20_L2.055361.530
111_N151_S2.037781.516
14_R43_L2.036951.516
115_P155_L2.025341.507
112_L154_A2.005881.493
18_R46_E1.985211.477
14_R46_E1.975481.470
64_P117_L1.95921.458
34_S39_G1.955691.455
2_T80_P1.953691.454
69_A73_E1.942321.445
9_S32_S1.928011.435
19_A22_R1.883761.402
64_P68_R1.858711.383
84_L118_L1.844781.373
66_S69_A1.836661.367
2_T29_I1.813081.349
27_V53_K1.812761.349
57_I73_E1.80261.341
84_L122_L1.784061.328
27_V31_T1.780431.325
41_Q45_Q1.76231.311
44_I48_K1.750441.303
68_R72_E1.74771.301
108_F112_L1.746671.300
100_S103_E1.73611.292
40_A56_F1.732341.289
87_N133_I1.723221.282
37_S58_E1.711121.273
29_I74_V1.677931.249
67_I118_L1.668991.242
15_A18_R1.656041.232
85_I133_I1.655531.232
68_R124_P1.654641.231
148_Y152_K1.651841.229
101_E117_L1.64441.224
31_T70_L1.642261.222
113_F117_L1.637161.218
64_P120_K1.626551.210
27_V55_T1.625021.209
6_T86_N1.581681.177
5_I17_A1.566991.166
59_C70_L1.563841.164
29_I57_I1.538551.145
65_E69_A1.530931.139
4_L81_L1.521871.133
92_S106_R1.512351.125
116_F158_L1.504941.120
1_K82_D1.503781.119
69_A72_E1.503621.119
111_N152_K1.494511.112
86_N119_A1.491791.110
34_S38_E1.450541.079
18_R22_R1.450231.079
90_I110_V1.445531.076
119_A130_I1.428091.063
41_Q44_I1.40991.049
10_S39_G1.397881.040
29_I55_T1.38841.033
62_S109_R1.373971.022
16_L85_I1.369141.019
45_Q48_K1.356681.010
10_S14_R1.353591.007
57_I70_L1.346931.002
15_A19_A1.335410.994
62_S106_R1.320270.983
99_L147_A1.309450.974
119_A158_L1.304420.971
61_L114_G1.292910.962
95_S98_D1.292550.962
90_I106_R1.287580.958
81_L122_L1.284580.956
138_G156_R1.265730.942
92_S103_E1.244970.926
44_I56_F1.243280.925
108_F113_F1.239410.922
39_G42_E1.234130.918
121_A124_P1.232620.917
80_P125_Q1.222370.910
65_E68_R1.221530.909
59_C67_I1.212650.902
157_G160_Q1.203950.896
102_E106_R1.203760.896
116_F120_K1.202870.895
94_G103_E1.197350.891
4_L31_T1.192490.887
42_E46_E1.189280.885
115_P132_N1.179110.877
103_E106_R1.177030.876
160_Q163_A1.167240.869
2_T82_D1.164560.867
42_E45_Q1.161950.865
17_A30_L1.153570.858
108_F150_A1.150130.856
48_K51_G1.144550.852
30_L54_I1.143270.851
86_N118_L1.141990.850
27_V52_A1.136870.846
38_E41_Q1.126170.838
4_L70_L1.125740.838
117_L121_A1.12010.834
16_L87_N1.11480.830
32_S40_A1.109580.826
71_I121_A1.109390.826
38_E42_E1.106410.823
67_I117_L1.095090.815
101_E120_K1.094240.814
101_E113_F1.083510.806
137_A149_S1.083130.806
110_V114_G1.077630.802
67_I121_A1.076150.801
6_T118_L1.073930.799
161_S165_E1.058520.788
104_L113_F1.055590.786
64_P121_A1.05350.784
21_A52_A1.051840.783
108_F154_A1.049780.781
156_R160_Q1.043640.777
43_L46_E1.041030.775
27_V30_L1.039090.773
61_L88_A1.038110.773
48_K53_K1.032580.768
14_R42_E1.031540.768
12_I16_L1.026020.764
84_L130_I1.020510.759
83_I129_K1.019910.759
75_I80_P1.018790.758
149_S157_G1.015530.756
37_S56_F1.014930.755
62_S110_V1.010770.752
89_G111_N1.001620.745
149_S153_A0.996010.741
106_R109_R0.995530.741
88_A114_G0.990110.737
139_V156_R0.985740.734
20_L83_I0.98490.733
21_A47_L0.981520.730
113_F116_F0.977730.728
101_E105_E0.976150.726
162_L166_L0.96720.720
153_A156_R0.966710.719
104_L147_A0.954990.711
34_S37_S0.952540.709
86_N115_P0.952440.709
21_A54_I0.950840.708
116_F154_A0.948520.706
21_A53_K0.947450.705
43_L47_L0.941380.701
58_E66_S0.938920.699
27_V32_S0.929750.692
146_S165_E0.927490.690
44_I54_I0.927270.690
97_D166_L0.926390.689
115_P119_A0.917010.682
108_F151_S0.916270.682
16_L20_L0.916070.682
75_I125_Q0.914060.680
119_A132_N0.910920.678
135_S148_Y0.89960.669
82_D128_G0.899470.669
107_V151_S0.895070.666
71_I74_V0.891850.664
153_A160_Q0.891570.663
6_T88_A0.890720.663
72_E75_I0.890330.663
83_I131_V0.884260.658
55_T73_E0.884190.658
63_D67_I0.884040.658
18_R47_L0.881450.656
47_L52_A0.877770.653
112_L150_A0.875260.651
107_V147_A0.870140.648
132_N155_L0.867780.646
150_A154_A0.865080.644
160_Q164_A0.859410.640
10_S34_S0.859330.640
135_S138_G0.852620.635
93_D145_M0.841160.626
157_G161_S0.84080.626
66_S70_L0.839550.625
71_I84_L0.836740.623
13_G87_N0.836050.622
18_R21_A0.833760.620
6_T87_N0.832150.619
2_T74_V0.832110.619
8_A17_A0.831290.619
90_I107_V0.827780.616
94_G98_D0.825570.614
16_L19_A0.825110.614
117_L120_K0.824410.614
142_S145_M0.823860.613
57_I74_V0.823440.613
144_G165_E0.818390.609
115_P118_L0.818110.609
161_S164_A0.816390.608
40_A44_I0.807780.601
47_L54_I0.802340.597
112_L155_L0.800560.596
147_A151_S0.792360.590
150_A161_S0.781090.581
70_L74_V0.773870.576
71_I75_I0.771860.574
32_S56_F0.771480.574
29_I81_L0.771420.574
9_S33_R0.769110.572
4_L84_L0.768720.572
155_L159_T0.768580.572
106_R110_V0.765510.570
74_V81_L0.764780.569
112_L151_S0.763250.568
141_G157_G0.761520.567
104_L116_F0.757520.564
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
4g81D0.98299.9-0.105
4ag3A0.98299.9-0.104
4iuyA0.98299.9-0.092
4fgsA0.964199.9-0.069
3gedA0.958199.9-0.066
4iqgC0.98299.9-0.06
3sjuA0.98299.9-0.045
4iboA0.98299.9-0.037
4fn4A0.98299.9-0.036
4gh5A0.98299.9-0.036

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