GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acyl-CoA_dh_N - Acyl-CoA dehydrogenase N-terminal domain
Pfam: PF02771 (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: CL0544
Length: 113
Sequences: 15217
Seq/Len: 134.66
HH_delta: 0.021 (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
18_E39_A2.786873.449
108_R113_E2.562713.172
99_E103_E2.47053.057
12_R70_E2.371652.935
60_S63_E2.220492.748
25_E29_D2.091922.589
98_S101_Q1.800672.229
4_Q63_E1.790952.216
51_P94_A1.75652.174
70_E73_R1.63252.020
13_E17_E1.584641.961
99_E102_K1.563731.935
22_H26_W1.554371.924
39_A42_E1.504631.862
6_A10_E1.501721.859
38_R42_E1.452631.798
103_E107_P1.409521.744
104_K108_R1.356451.679
34_R38_R1.30571.616
107_P111_S1.275131.578
6_A9_E1.273151.576
8_R70_E1.253031.551
2_E6_A1.246981.543
5_Q8_R1.238021.532
4_Q60_S1.234171.527
11_A45_L1.223621.514
9_E13_E1.206081.493
10_E43_A1.194051.478
59_L63_E1.192911.476
15_A74_A1.192111.475
4_Q66_I1.190651.474
108_R111_S1.185261.467
52_E58_G1.181231.462
12_R16_E1.177411.457
14_F39_A1.131631.401
41_G46_L1.126581.394
14_F43_A1.114391.379
22_H25_E1.091581.351
100_E104_K1.087351.346
38_R41_G1.082811.340
48_L67_V1.033631.279
8_R66_I1.02451.268
39_A43_A1.012881.254
54_Y102_K1.004631.243
50_V110_A0.996441.233
100_E103_E0.99221.228
97_G101_Q0.974731.206
5_Q9_E0.971081.202
75_D78_L0.966111.196
53_E103_E0.963731.193
10_E45_L0.943411.168
15_A71_L0.931271.153
38_R113_E0.928781.149
24_A28_E0.888951.100
11_A15_A0.887031.098
22_H35_E0.852991.056
101_Q105_W0.843961.044
49_A64_L0.825211.021
10_E13_E0.819671.014
62_L66_I0.816881.011
50_V90_A0.80650.998
102_K106_L0.792230.980
7_L63_E0.771020.954
16_E20_A0.769690.953
15_A19_I0.767280.950
14_F18_E0.75040.929
82_L85_H0.726560.899
2_E5_Q0.712140.881
72_A79_A0.706250.874
8_R12_R0.700110.866
4_Q62_L0.689170.853
51_P54_Y0.687020.850
89_G92_P0.676990.838
53_E56_G0.675290.836
35_E39_A0.669170.828
3_E6_A0.667260.826
92_P96_F0.66450.822
14_F40_L0.663710.821
19_I36_V0.6410.793
34_R37_W0.639750.792
64_L87_S0.639750.792
98_S102_K0.639420.791
89_G109_L0.632740.783
11_A67_V0.63220.782
47_G110_A0.632070.782
50_V94_A0.624010.772
53_E102_K0.621180.769
36_V78_L0.618550.766
13_E16_E0.603220.747
8_R69_E0.600030.743
36_V39_A0.595290.737
54_Y99_E0.593570.735
12_R73_R0.591290.732
20_A23_A0.590450.731
66_I69_E0.588750.729
35_E38_R0.585790.725
16_E73_R0.578220.716
82_L86_Q0.577780.715
91_P95_K0.569490.705
14_F36_V0.566820.701
84_V88_L0.565830.700
48_L59_L0.557430.690
53_E99_E0.554730.687
64_L68_L0.553830.685
31_R34_R0.551940.683
97_G102_K0.544120.673
105_W108_R0.538950.667
26_W75_D0.536910.664
90_A109_L0.536370.664
62_L65_A0.532550.659
10_E57_L0.528660.654
80_F83_G0.524320.649
7_L11_A0.519320.643
26_W31_R0.513240.635
61_P64_L0.509780.631
81_A84_V0.509440.630
53_E58_G0.509410.630
89_G93_I0.508710.630
3_E63_E0.504660.625
20_A74_A0.492250.609
14_F19_I0.490070.607
22_H36_V0.48980.606
18_E42_E0.488550.605
7_L67_V0.488540.605
101_Q104_K0.481030.595
25_E28_E0.472150.584
16_E74_A0.469630.581
37_W40_L0.467350.578
93_I97_G0.466870.578
88_L91_P0.461270.571
25_E31_R0.45960.569
54_Y106_L0.45910.568
91_P94_A0.458970.568
13_E43_A0.456410.565
50_V54_Y0.456040.564
40_L45_L0.455510.564
68_L72_A0.448860.556
37_W81_A0.448270.555
104_K107_P0.446850.553
8_R63_E0.437440.541
41_G112_G0.435510.539
26_W33_P0.435240.539
19_I78_L0.434350.538
49_A91_P0.43290.536
68_L79_A0.429760.532
87_S92_P0.425710.527
66_I70_E0.42280.523
92_P95_K0.412370.510
65_A69_E0.409480.507
90_A94_A0.40650.503
79_A83_G0.405980.502
94_A102_K0.405660.502
12_R74_A0.403850.500
96_F101_Q0.402170.498
26_W36_V0.401220.497
80_F84_V0.398830.494
51_P58_G0.398150.493
40_L71_L0.398080.493
40_L78_L0.39010.483
23_A74_A0.389520.482
76_A79_A0.386650.479
26_W77_S0.386430.478
23_A75_D0.386080.478
9_E12_R0.382210.473
97_G100_E0.380860.471
49_A86_Q0.380660.471
72_A83_G0.380240.471
54_Y103_E0.379490.470
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
4ktoA199.80.021
4iv6A0.991299.70.033
3ii9A199.70.035
3p4tA199.70.041
3r7kA199.70.043
3pfdA0.991299.70.046
2jifA199.70.047
2ebaA199.70.047
2d29A199.70.051
3nf4A0.991299.70.051

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