GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
3HCDH - 3-hydroxyacyl-CoA dehydrogenase C-terminal domain
Pfam: PF00725 (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: CL0106
Length: 97
Sequences: 4527
Seq/Len: 46.67
HH_delta: 0.045 (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
60_E78_K1.577723.299
34_R45_E1.487853.111
25_S28_D1.36512.854
80_M85_R1.142292.389
56_Y78_K1.134412.372
79_E83_E1.105332.311
56_Y60_E1.045362.186
47_A55_V0.992352.075
33_M43_P0.906511.896
24_A29_I0.8931.867
56_Y81_V0.834231.744
75_P79_E0.828991.733
5_N58_I0.79911.671
19_V29_I0.767841.606
33_M37_L0.742091.552
17_R20_E0.678081.418
53_D86_L0.673711.409
78_K82_E0.665871.392
41_M49_L0.66051.381
20_E74_S0.65211.364
17_R21_E0.61771.292
19_V26_P0.607081.269
20_E76_L0.605561.266
12_L47_A0.603671.262
15_A44_F0.582381.218
11_L39_F0.579431.212
76_L80_M0.569831.192
14_E21_E0.564111.180
31_R34_R0.556821.164
13_N74_S0.553561.158
47_A52_L0.552781.156
24_A28_D0.537431.124
17_R74_S0.515651.078
60_E64_A0.513451.074
41_M45_E0.512411.071
18_L23_V0.496561.038
45_E49_L0.496021.037
54_V57_H0.493691.032
54_V58_I0.491521.028
32_A36_G0.485591.015
26_P44_F0.484181.012
31_R35_Y0.482461.009
9_A58_I0.481551.007
53_D57_H0.469190.981
63_A72_R0.46670.976
79_E82_E0.462650.967
64_A67_G0.462160.966
40_P46_L0.452530.946
60_E63_A0.440190.920
29_I44_F0.436140.912
32_A37_L0.433060.906
60_E73_P0.43160.902
12_L50_V0.429160.897
34_R42_G0.42710.893
52_L80_M0.426980.893
15_A29_I0.421260.881
4_V32_A0.415890.870
9_A55_V0.414060.866
18_L24_A0.409220.856
75_P78_K0.408970.855
57_H60_E0.406530.850
52_L81_V0.40580.849
53_D81_V0.401380.839
28_D31_R0.393740.823
11_L43_P0.393050.822
6_R14_E0.388690.813
8_L46_L0.387940.811
48_D84_G0.387350.810
63_A67_G0.384980.805
5_N54_V0.371560.777
32_A35_Y0.367480.768
58_I61_Y0.366140.766
13_N59_L0.366080.765
61_Y64_A0.365620.765
12_L16_A0.363420.760
63_A73_P0.363410.760
4_V10_A0.360450.754
46_L50_V0.357580.748
8_L12_L0.354450.741
50_V54_V0.351210.734
20_E75_P0.349440.731
7_L11_L0.348830.729
44_F47_A0.345430.722
27_E31_R0.342370.716
76_L79_E0.337460.706
19_V44_F0.335720.702
16_A47_A0.335050.701
56_Y82_E0.333190.697
77_L81_V0.332770.696
63_A68_D0.32940.689
5_N9_A0.327110.684
5_N50_V0.321680.673
66_L69_R0.319810.669
4_V8_L0.3170.663
62_L66_L0.313450.655
55_V59_L0.310260.649
26_P48_D0.309660.648
20_E79_E0.309230.647
63_A66_L0.30460.637
16_A76_L0.304130.636
16_A77_L0.300410.628
10_A13_N0.298220.624
57_H61_Y0.296660.620
59_L73_P0.28990.606
12_L46_L0.287640.601
50_V55_V0.284710.595
4_V37_L0.28470.595
12_L55_V0.281980.590
14_E18_L0.280940.587
41_M46_L0.280320.586
30_D33_M0.280260.586
56_Y59_L0.279230.584
39_F46_L0.278420.582
4_V46_L0.278410.582
5_N10_A0.277630.581
9_A12_L0.277210.580
19_V76_L0.276870.579
81_V86_L0.276460.578
72_R75_P0.276220.578
30_D48_D0.272990.571
8_L40_P0.267950.560
28_D36_G0.262740.549
30_D42_G0.261490.547
68_D72_R0.261190.546
28_D32_A0.260570.545
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
3mogA199.90.045
4b3hA0.958899.90.077
1f0yA199.90.077
4e12A0.969199.90.081
1wdkA0.969199.90.085
2wtbA0.969199.90.088
3zwcA0.979499.90.102
3ctvA0.969199.90.111
3k6jA0.907299.90.112
1zejA0.989799.90.114

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