GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acyl-CoA_dh_C - Acetyl-CoA dehydrogenase C-terminal like
Pfam: PF12806 (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. )
Length: 130
Sequences: 1132
Seq/Len: 8.71
HH_delta: 0.828 (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
39_T60_Y0.885895.238
35_L64_F0.483082.856
98_A128_L0.46332.739
2_L68_V0.397562.350
35_L67_V0.387222.289
70_A104_F0.344442.036
73_W76_Q0.309791.832
62_M110_R0.302291.787
59_D106_R0.302181.787
9_F71_W0.30171.784
7_Q36_R0.284181.680
2_L6_I0.283471.676
92_F96_K0.282661.671
38_A63_L0.273491.617
80_A93_Y0.262861.554
22_A26_A0.260211.538
10_I32_L0.24671.459
123_D127_A0.242621.434
66_Y110_R0.237491.404
115_A119_E0.234921.389
77_A97_I0.233471.380
37_E119_E0.233131.378
24_L27_A0.220151.302
49_D123_D0.218441.291
113_A117_A0.215641.275
75_R79_A0.215561.274
63_L115_A0.210681.246
112_D116_A0.20961.239
21_L77_A0.206721.222
102_F117_A0.205371.214
69_G73_W0.203211.201
102_F107_I0.202471.197
34_A115_A0.201781.193
73_W106_R0.200841.187
66_Y103_Y0.199471.179
66_Y114_L0.199431.179
70_A108_L0.197991.171
24_L104_F0.197821.170
79_A83_A0.196181.160
77_A100_A0.196131.160
3_L32_L0.194511.150
41_W119_E0.194071.147
124_S127_A0.19131.131
45_Q52_L0.189751.122
36_R40_A0.18871.116
105_Q124_S0.188381.114
7_Q32_L0.18781.110
24_L101_R0.184611.091
9_F78_L0.183411.084
11_A26_A0.181861.075
4_A8_A0.179951.064
23_A27_A0.179131.059
62_M114_L0.178881.058
29_Q33_E0.177081.047
31_A67_V0.175481.037
7_Q33_E0.175071.035
23_A101_R0.172971.023
9_F74_L0.172611.021
6_I71_W0.172341.019
35_L63_L0.171961.017
42_L118_I0.171851.016
21_L81_Q0.171351.013
59_D114_L0.170921.011
33_E37_E0.169451.002
112_D115_A0.168630.997
6_I32_L0.165190.977
82_K85_A0.165060.976
28_L104_F0.162870.963
63_L118_I0.161960.958
4_A36_R0.161170.953
3_L36_R0.159110.941
54_G57_A0.158920.940
42_L56_A0.15560.920
34_A38_A0.155590.920
72_L76_Q0.155220.918
21_L78_L0.153450.907
14_A25_A0.153350.907
21_L25_A0.151910.898
92_F99_T0.150340.889
24_L100_A0.14970.885
55_A122_D0.14970.885
30_Q36_R0.14880.880
96_K99_T0.147540.872
20_E101_R0.146990.869
92_F95_G0.146970.869
9_F12_E0.146210.864
65_G92_F0.14620.864
34_A111_A0.146190.864
13_A29_Q0.145970.863
8_A11_A0.145920.863
24_L74_L0.14570.861
61_L126_M0.145450.860
62_M66_Y0.145370.859
106_R124_S0.145140.858
3_L7_Q0.144970.857
40_A44_A0.144840.856
40_A43_L0.142630.843
28_L74_L0.14170.838
10_I29_Q0.141650.837
68_V72_L0.14150.837
110_R114_L0.141120.834
119_E123_D0.141120.834
82_K94_Q0.140730.832
106_R121_G0.140660.832
58_V61_L0.140060.828
31_A70_A0.139710.826
34_A70_A0.139220.823
62_M65_G0.138850.821
86_E94_Q0.138730.820
27_A101_R0.137620.814
2_L5_E0.136970.810
31_A38_A0.135550.801
34_A37_E0.135350.800
59_D73_W0.135330.800
102_F106_R0.134580.796
54_G126_M0.134220.794
83_A93_Y0.133780.791
67_V108_L0.13350.789
7_Q11_A0.131330.776
67_V111_A0.131290.776
83_A107_I0.131250.776
27_A109_P0.130390.771
78_L82_K0.130350.771
50_P57_A0.129540.766
43_L46_A0.129520.766
57_A62_M0.129490.766
9_F13_A0.12890.762
10_I25_A0.128760.761
66_Y73_W0.128730.761
34_A112_D0.128290.758
72_L75_R0.126990.751
30_Q33_E0.126860.750
76_Q96_K0.125170.740
103_Y107_I0.124810.738
94_Q97_I0.124580.737
69_G103_Y0.124440.736
10_I28_L0.123840.732
73_W96_K0.123080.728
11_A14_A0.122870.726
60_Y77_A0.121470.718
106_R126_M0.121350.717
64_F68_V0.121030.716
41_W45_Q0.120580.713
25_A45_Q0.120340.711
8_A14_A0.120170.710
4_A7_Q0.120070.710
104_F108_L0.119680.708
12_E71_W0.119320.705
4_A40_A0.119280.705
51_E127_A0.119190.705
73_W104_F0.119110.704
38_A118_I0.118770.702
25_A31_A0.118550.701
105_Q109_P0.118170.699
120_A124_S0.118070.698
57_A93_Y0.117880.697
102_F121_G0.117620.695
26_A123_D0.117220.693
5_E8_A0.116960.691
20_E116_A0.116840.691
59_D66_Y0.116450.688
38_A70_A0.11620.687
48_A129_P0.116050.686
33_E82_K0.115440.683
56_A125_L0.114670.678
69_G76_Q0.114620.678
12_E74_L0.113620.672
6_I92_F0.112930.668
124_S128_L0.112240.664
2_L71_W0.112110.663
51_E126_M0.111920.662
79_A123_D0.111880.661
25_A74_L0.111770.661
56_A118_I0.11170.660
5_E71_W0.111630.660
14_A78_L0.111160.657
79_A93_Y0.110830.655
5_E41_W0.110560.654
7_Q10_I0.10970.649
12_E78_L0.109680.648
109_P112_D0.109480.647
28_L99_T0.109060.645
10_I70_A0.109010.644
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
2z1qA0.861594.10.828
2okuA0.846292.60.837
2uxwA0.961590.90.845
2pmrA0.60778.60.923
1z5hA0.33854.70.931
2choA0.92314.60.932
2v5dA0.86924.40.933
2v5cA0.884640.933
2l10A0.88463.60.935
1s0pA0.85383.50.935
If you are interested in a protein containing this domain,
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