GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acyl-CoA_dh_2 - Acyl-CoA dehydrogenase C-terminal domain
Pfam: PF08028 (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: CL0087
Length: 134
Sequences: 13806
Seq/Len: 103.03
HH_delta: 0.094 (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
50_R96_E2.697412.985
43_R100_R2.516632.785
39_Y42_A2.007222.221
20_E24_G1.972042.182
112_R117_E1.947042.155
12_R55_R1.857832.056
17_E115_P1.779771.970
33_P36_D1.708971.891
117_E121_R1.686021.866
22_L104_L1.6671.845
54_A90_A1.636521.811
108_S114_S1.60471.776
63_R71_A1.556531.723
26_V33_P1.514731.676
22_L40_I1.510831.672
15_L51_L1.506531.667
32_A36_D1.477791.635
13_G17_E1.461521.617
95_R127_A1.401131.551
53_A89_H1.390941.539
27_R37_D1.388641.537
60_R64_R1.378211.525
11_A97_A1.34831.492
50_R93_L1.329611.471
60_R63_R1.311891.452
96_E100_R1.30991.450
32_A37_D1.300011.439
64_R82_R1.295211.433
11_A51_L1.278511.415
40_I104_L1.262981.398
95_R99_D1.247521.381
18_F101_L1.235611.367
17_E105_A1.224181.355
47_A97_A1.218251.348
48_A52_D1.210991.340
14_A98_V1.18261.309
17_E20_E1.172931.298
52_D60_R1.119921.239
12_R16_D1.109071.227
54_A93_L1.100261.218
8_L51_L1.095431.212
95_R120_W1.089151.205
5_A58_L1.076041.191
118_R122_D1.073091.188
13_G119_I1.072971.187
19_V23_R1.071661.186
64_R73_E1.06661.180
99_D124_R1.060681.174
22_L35_A1.046231.158
99_D127_A1.026591.136
15_L19_V1.02471.134
56_A60_R1.019221.128
47_A100_R1.017711.126
7_Y126_G1.007861.115
94_A123_V0.997371.104
23_R35_A0.947891.049
49_A88_A0.937671.038
99_D120_W0.922931.021
93_L96_E0.908251.005
46_E50_R0.904861.001
92_R96_E0.903731.000
102_F120_W0.89630.992
101_L116_L0.896170.992
22_L44_L0.891630.987
98_V123_V0.874430.968
10_I94_A0.871160.964
10_I119_I0.860160.952
61_A86_A0.853020.944
120_W124_R0.849270.940
15_L48_A0.832680.921
50_R100_R0.826690.915
48_A85_A0.819350.907
51_L97_A0.811090.898
7_Y91_A0.809770.896
46_E100_R0.801860.887
8_L54_A0.799170.884
124_R127_A0.792420.877
14_A101_L0.791150.876
42_A46_E0.781310.865
55_R59_Y0.766880.849
3_F6_V0.762640.844
17_E119_I0.758080.839
46_E96_E0.754070.834
52_D56_A0.749160.829
43_R104_L0.748510.828
57_L85_A0.740350.819
14_A119_I0.737660.816
12_R48_A0.735240.814
89_H93_L0.734720.813
19_V44_L0.730030.808
8_L58_L0.726310.804
50_R89_H0.722290.799
50_R53_A0.712060.788
57_L86_A0.710070.786
16_D20_E0.709840.786
18_F105_A0.708770.784
105_A116_L0.705650.781
102_F116_L0.701690.777
96_E99_D0.696450.771
115_P118_R0.693490.767
52_D55_R0.68850.762
58_L90_A0.683760.757
11_A93_L0.680760.753
20_E23_R0.679370.752
4_A90_A0.678160.750
10_I123_V0.676930.749
38_P42_A0.67510.747
95_R124_R0.674110.746
27_R30_G0.673040.745
22_L34_L0.666180.737
49_A85_A0.663280.734
98_V120_W0.656660.727
18_F22_L0.655750.726
49_A89_H0.654850.725
60_R82_R0.652790.722
13_G16_D0.651410.721
4_A58_L0.650770.720
18_F104_L0.648090.717
53_A57_L0.64760.717
112_R121_R0.644120.713
18_F47_A0.643470.712
43_R46_E0.643090.712
21_Y108_S0.63950.708
11_A54_A0.636630.705
13_G115_P0.635380.703
87_K91_A0.632770.700
39_Y43_R0.630690.698
12_R51_L0.624390.691
4_A86_A0.613390.679
34_L40_I0.603330.668
92_R127_A0.598760.663
108_S111_Y0.590420.653
98_V119_I0.590350.653
84_R87_K0.589080.652
102_F109_A0.583160.645
54_A89_H0.578150.640
103_R124_R0.576250.638
46_E49_A0.571570.633
6_V126_G0.559680.619
57_L89_H0.556540.616
47_A101_L0.555880.615
57_L61_A0.554410.614
40_I44_L0.548770.607
27_R34_L0.543920.602
52_D57_L0.538870.596
8_L12_R0.533160.590
81_A85_A0.533010.590
34_L37_D0.531040.588
52_D85_A0.530270.587
98_V116_L0.528080.584
50_R54_A0.521060.577
54_A97_A0.51990.575
93_L97_A0.51650.572
105_A114_S0.514830.570
5_A9_G0.513240.568
95_R123_V0.510810.565
40_I43_R0.504330.558
11_A94_A0.502070.556
10_I126_G0.499510.553
49_A53_A0.498540.552
37_D41_Q0.496710.550
25_R30_G0.496030.549
37_D40_I0.494020.547
50_R92_R0.492690.545
18_F44_L0.492630.545
15_L47_A0.49080.543
50_R97_A0.48810.540
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
3owaA0.985199.80.094
2rfqA199.80.096
2jbrA199.80.096
2or0A0.985199.80.099
3mkhA0.955299.80.101
4hr3A0.940399.80.109
4ktoA0.925499.70.11
3r7kA0.925499.70.11
2ix5A0.925499.70.112
3swoA0.925499.70.112

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