GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
3HCDH_N - 3-hydroxyacyl-CoA dehydrogenase NAD binding domain
Pfam: PF02737 (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: 180
Sequences: 17420
Seq/Len: 96.78
HH_delta: -0.005 (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
164_R168_R2.041083.051
1_K24_E1.864382.787
3_A79_A1.81132.708
32_P36_E1.755442.624
157_P161_D1.744622.608
26_T70_T1.621322.424
7_A27_L1.55892.331
3_A76_A1.45282.172
95_E99_E1.435292.146
23_Y169_S1.411682.110
72_D75_E1.376692.058
36_E40_K1.351052.020
105_P108_T1.305541.952
31_S34_A1.25641.878
1_K26_T1.237841.851
156_S159_T1.232411.842
164_R176_V1.230831.840
39_R69_F1.207181.805
161_D164_R1.131311.691
86_I96_L1.078551.612
18_F166_L1.068461.597
2_V18_F1.06451.591
35_L69_F1.061161.586
33_E36_E1.058081.582
74_E103_I1.012761.514
26_T68_S1.010671.511
104_C108_T1.003051.500
84_E110_L0.99371.486
24_E68_S0.974891.457
26_T78_D0.974461.457
36_E39_R0.971531.452
12_R37_R0.962111.438
94_Q98_A0.958221.433
165_A168_R0.938611.403
165_A169_S0.928881.389
160_V176_V0.915641.369
28_Y73_L0.910321.361
17_L20_R0.904871.353
15_A27_L0.904311.352
71_T75_E0.90251.349
29_D34_A0.88211.319
35_L39_R0.875011.308
101_D127_S0.861281.288
18_F170_L0.846641.266
151_P160_V0.838771.254
1_K78_D0.836971.251
76_A79_A0.829911.241
95_E98_A0.828281.238
160_V164_R0.827281.237
32_P71_T0.820411.226
4_V83_I0.819351.225
109_I159_T0.818491.224
135_M167_L0.813071.216
78_D105_P0.812651.215
94_Q125_A0.803821.202
131_R159_T0.801931.199
34_A37_R0.79751.192
81_L109_I0.793951.187
4_V15_A0.791241.183
157_P176_V0.783051.171
37_R40_K0.779151.165
70_T75_E0.776661.161
80_D105_P0.773931.157
17_L170_L0.76651.146
81_L166_L0.765861.145
16_A20_R0.760291.137
136_H162_R0.757451.132
37_R41_R0.755291.129
121_E124_A0.742591.110
4_V11_G0.740991.108
161_D165_A0.740231.107
19_A67_I0.733141.096
146_L172_K0.725821.085
26_T79_A0.719751.076
136_H159_T0.717231.072
98_A102_E0.716871.072
131_R156_S0.712161.065
16_A41_R0.707771.058
1_K80_D0.690181.032
3_A82_V0.688421.029
111_A163_V0.686721.027
7_A29_D0.679051.015
99_E102_E0.674591.008
12_R41_R0.66891.000
168_R174_P0.659220.986
167_L174_P0.659040.985
158_E162_R0.658590.985
85_A113_N0.653170.976
33_E37_R0.651360.974
35_L71_T0.644880.964
101_D126_L0.641160.959
161_D176_V0.637740.953
14_I170_L0.637370.953
81_L163_V0.636780.952
151_P157_P0.63430.948
159_T162_R0.631820.945
2_V23_Y0.614920.919
113_N116_S0.613720.917
5_I28_Y0.613490.917
104_C110_L0.610470.913
109_I163_V0.607420.908
73_L103_I0.604770.904
162_R165_A0.598560.895
7_A38_A0.587180.878
158_E161_D0.586760.877
128_R131_R0.583040.872
114_T117_L0.58260.871
3_A28_Y0.582090.870
29_D35_L0.580350.868
147_V167_L0.579920.867
168_R173_T0.572840.856
10_M14_I0.572760.856
4_V14_I0.57040.853
32_P35_L0.568780.850
90_L114_T0.564890.844
11_G29_D0.563710.843
133_I163_V0.559640.837
98_A125_A0.550650.823
90_L121_E0.54590.816
112_S116_S0.544990.815
11_G15_A0.541090.809
74_E99_E0.540640.808
74_E77_V0.538870.806
135_M147_V0.533450.797
14_I18_F0.531260.794
7_A15_A0.51850.775
149_V164_R0.515370.770
82_V108_T0.513220.767
94_Q121_E0.512890.767
81_L162_R0.506050.757
112_S119_I0.505490.756
164_R174_P0.503690.753
81_L111_A0.501990.750
129_P132_F0.499380.747
2_V83_I0.496630.742
75_E78_D0.495890.741
98_A101_D0.494830.740
17_L21_A0.493790.738
2_V166_L0.493510.738
10_M113_N0.492820.737
21_A169_S0.492520.736
73_L99_E0.490470.733
2_V81_L0.489570.732
80_D107_D0.485950.726
118_S121_E0.483750.723
113_N137_F0.483630.723
112_S115_S0.478620.716
120_S153_P0.477430.714
14_I85_A0.470690.704
155_T159_T0.46880.701
3_A26_T0.465820.696
107_D131_R0.464580.695
15_A25_V0.46430.694
136_H156_S0.461020.689
90_L94_Q0.460520.688
152_G155_T0.456470.682
85_A141_P0.455440.681
159_T163_V0.453360.678
119_I134_G0.452670.677
10_M13_G0.450280.673
130_E156_S0.450110.673
100_L104_C0.444730.665
120_S124_A0.443560.663
23_Y166_L0.440860.659
82_V104_C0.43790.655
16_A142_H0.437390.654
9_T138_F0.437060.653
121_E125_A0.436050.652
12_R34_A0.43360.648
26_T76_A0.426650.638
156_S161_D0.426090.637
7_A11_G0.424210.634
164_R175_V0.421980.631
12_R16_A0.421670.630
147_V151_P0.419930.628
10_M85_A0.417990.625
90_L117_L0.416720.623
123_A152_G0.415520.621
148_E151_P0.414140.619
161_D168_R0.40970.612
31_S35_L0.408480.611
1_K79_A0.407810.610
28_Y99_E0.404150.604
82_V100_L0.401670.600
147_V150_V0.399350.597
9_T145_P0.398870.596
14_I83_I0.398370.596
68_S78_D0.397850.595
32_P39_R0.395760.592
73_L76_A0.394470.590
85_A114_T0.393660.589
27_L67_I0.389480.582
135_M163_V0.387270.579
27_L38_A0.38610.577
4_V85_A0.385140.576
97_F122_L0.384990.576
77_V103_I0.383930.574
68_S75_E0.383650.574
28_Y70_T0.383520.573
18_F83_I0.383350.573
116_S119_I0.381950.571
9_T12_R0.381290.570
109_I162_R0.380910.569
34_A38_A0.375340.561
79_A82_V0.373820.559
108_T111_A0.373130.558
12_R38_A0.37150.555
19_A25_V0.369580.553
114_T119_I0.369370.552
13_G16_A0.368690.551
123_A126_L0.368250.551
9_T87_P0.367060.549
122_L132_F0.367060.549
139_N144_M0.366660.548
38_A41_R0.36650.548
100_L103_I0.366440.548
127_S130_E0.365950.547
145_P148_E0.363940.544
30_R35_L0.363520.543
73_L77_V0.363050.543
146_L149_V0.362310.542
28_Y76_A0.362010.541
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
3adoA199.9-0.005
4b3hA199.90.003
3k6jA0.983399.90.024
3mogA199.90.032
1wdkA199.90.039
2wtbA199.90.04
3zwcA0.988999.90.049
2dpoA199.90.084
1zcjA0.988999.90.101
4e12A199.80.116

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