GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acyl-CoA_dh_1 - Acyl-CoA dehydrogenase C-terminal domain
Pfam: PF00441 (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: 150
Sequences: 14024
Seq/Len: 93.49
HH_delta: 0.053 (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
63_R101_D2.460323.316
56_R105_E2.212632.982
35_E39_R1.759252.371
76_R80_A1.708152.302
117_E122_E1.649582.223
27_R68_R1.633592.202
52_A55_R1.600142.157
37_A109_L1.541262.077
46_P49_E1.502262.025
32_E120_P1.428211.925
122_E126_R1.411241.902
113_R119_N1.388131.871
41_R46_P1.353781.825
67_M95_A1.348731.818
37_A53_V1.340471.807
30_L64_L1.31191.768
97_E138_N1.284341.731
45_K49_E1.249241.684
66_A94_F1.236081.666
28_R32_E1.19941.617
77_R87_E1.187551.601
100_Q132_T1.180141.591
73_R77_R1.176561.586
42_Q50_H1.173151.581
101_D105_E1.144741.543
60_M102_I1.141551.539
53_V109_L1.140941.538
45_K50_H1.114151.502
26_A102_I1.113661.501
73_R76_R1.105971.491
14_E135_G1.0881.467
33_A106_A1.067281.439
63_R98_L1.06491.435
32_E35_E1.060111.429
32_E110_L1.052491.419
29_A103_A1.050011.415
27_R31_D1.034951.395
4_W8_L1.022431.378
26_A64_L0.999931.348
67_M98_L0.990211.335
100_Q104_E0.985351.328
65_E73_R0.968131.305
60_M105_E0.967971.305
34_I38_R0.964811.300
23_L64_L0.964381.300
61_A65_E0.961171.296
56_R139_E0.948191.278
20_A71_V0.938261.265
28_R124_L0.937511.264
30_L34_I0.926621.249
77_R82_Q0.913631.231
59_D142_R0.910141.227
104_E132_T0.909411.226
69_A73_R0.902191.216
99_A128_A0.889981.200
37_A48_A0.889191.199
93_Y142_R0.887791.197
104_E129_R0.873841.178
12_N85_P0.871211.174
100_Q125_Y0.870871.174
89_A141_Q0.851451.148
106_A121_L0.84991.146
93_Y138_N0.848521.144
130_A134_Y0.843731.137
129_R132_T0.835121.126
107_M125_Y0.834161.124
97_E101_D0.831291.120
38_R48_A0.822291.108
37_A57_L0.815371.099
98_L101_D0.806511.087
131_F134_Y0.790241.065
59_D63_R0.775391.045
132_T138_N0.774391.044
74_A91_A0.773391.042
103_A128_A0.754981.018
55_R59_D0.75481.017
63_R105_E0.754741.017
104_E125_Y0.754121.016
22_A131_F0.753351.015
64_L102_I0.730210.984
125_Y129_R0.726450.979
59_D105_E0.717610.967
61_A90_I0.716540.966
62_A93_Y0.709330.956
123_R127_D0.700810.945
23_L71_V0.694670.936
63_R94_F0.69450.936
65_E69_A0.692630.934
29_A124_L0.688990.929
29_A106_A0.68720.926
25_I124_L0.686940.926
23_L67_M0.683570.921
34_I57_L0.681930.919
59_D101_D0.68120.918
30_L61_A0.678870.915
19_A91_A0.670360.904
31_D35_E0.669830.903
32_E124_L0.667610.900
54_R143_N0.667330.899
96_T138_N0.662680.893
70_L91_A0.662120.892
13_H78_L0.658830.888
143_N147_R0.656890.885
25_I99_A0.656620.885
65_E68_R0.64720.872
19_A71_V0.64630.871
5_A9_D0.640950.864
70_L90_I0.640590.863
37_A47_L0.637850.860
56_R109_L0.636760.858
62_A90_I0.635890.857
18_I135_G0.63470.856
35_E38_R0.629170.848
55_R143_N0.628020.847
94_F98_L0.625750.843
101_D104_E0.619910.836
73_R87_E0.618260.833
141_Q144_Q0.617150.832
68_R72_Y0.613150.826
27_R61_A0.606640.818
100_Q129_R0.602460.812
33_A110_L0.601930.811
63_R66_A0.601230.810
33_A109_L0.600090.809
138_N142_R0.598350.807
110_L121_L0.594010.801
97_E142_R0.588920.794
137_T140_V0.586990.791
16_L75_A0.584820.788
26_A98_L0.581280.784
56_R59_D0.579290.781
25_I128_A0.579160.781
103_A125_Y0.577860.779
51_P55_R0.573470.773
40_R43_F0.572930.772
47_L53_V0.572290.771
33_A37_A0.571240.770
120_P123_R0.568880.767
66_A70_L0.565790.763
75_A79_D0.562210.758
107_M121_L0.561510.757
36_Y113_R0.560360.755
11_L15_R0.558170.752
54_R146_A0.556830.751
97_E132_T0.556440.750
33_A60_M0.550.741
22_A96_T0.548410.739
107_M114_G0.548190.739
71_V95_A0.543940.733
67_M94_F0.538480.726
26_A67_M0.537150.724
28_R31_D0.531670.717
19_A95_A0.531220.716
62_A94_F0.520380.701
84_D87_E0.519290.700
11_L14_E0.517360.697
103_A124_L0.515720.695
52_A56_R0.515460.695
60_M106_A0.513940.693
47_L50_H0.513740.692
12_N88_A0.513460.692
77_R80_A0.511860.690
113_R116_T0.510730.688
100_Q128_A0.508580.686
140_V143_N0.504090.679
53_V57_L0.5040.679
28_R120_P0.502440.677
27_R64_L0.500160.674
50_H53_V0.500040.674
16_L88_A0.496410.669
90_I145_I0.494310.666
6_V9_D0.49250.664
23_L27_R0.490930.662
50_H54_R0.489150.659
136_G141_Q0.487980.658
129_R133_I0.487620.657
65_E90_I0.482890.651
56_R108_Q0.482080.650
59_D62_A0.479310.646
9_D12_N0.470530.634
140_V144_Q0.469090.632
98_L102_I0.461830.622
93_Y145_I0.455610.614
62_A66_A0.451770.609
103_A121_L0.446230.601
7_A11_L0.446220.601
8_L12_N0.442530.596
43_F50_H0.44170.595
65_E70_L0.440330.594
63_R67_M0.435650.587
18_I134_Y0.43550.587
5_A8_L0.431490.582
99_A103_A0.427230.576
42_Q47_L0.42720.576
20_A24_G0.425030.573
6_V10_T0.424250.572
33_A57_L0.42420.572
26_A99_A0.421040.568
63_R102_I0.420030.566
26_A29_A0.419580.566
53_V56_R0.417770.563
70_L94_F0.417710.563
41_R44_G0.415180.560
92_K96_T0.411960.555
67_M102_I0.411150.554
110_L119_N0.408540.551
104_E108_Q0.408440.551
63_R97_E0.404910.546
32_E121_L0.40250.543
144_Q147_R0.40040.540
41_R49_E0.394110.531
117_E126_R0.392770.529
93_Y141_Q0.392590.529
38_R41_R0.391010.527
51_P54_R0.389480.525
108_Q139_E0.388580.524
113_R118_D0.388330.523
36_Y119_N0.387220.522
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
3owaA199.90.053
2z1qA199.90.059
3pfdA199.90.06
4ktoA199.90.064
4hr3A199.90.065
2jifA199.90.068
1ukwA199.90.07
1egdA199.90.071
2dvlA199.90.073
3nf4A199.90.073

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