GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acyl-CoA_ox_N - Acyl-coenzyme A oxidase N-terminal
Pfam: PF14749 (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: 125
Sequences: 11109
Seq/Len: 88.87
HH_delta: 0.32 (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
29_D56_R2.462743.535
118_K124_I2.40213.448
118_K123_E2.269213.257
23_E82_M2.114643.035
109_E113_A2.067142.967
42_S46_R1.851212.657
108_T111_Q1.8142.604
67_D104_M1.639582.353
24_S28_S1.574152.259
15_K75_A1.511792.170
17_E21_E1.440782.068
82_M85_L1.439012.066
56_R59_K1.357211.948
113_A117_P1.348421.935
39_Y43_R1.281171.839
16_L19_R1.186871.704
51_L55_R1.173521.684
109_E112_Q1.165381.673
15_K78_I1.161111.667
114_K118_K1.103791.584
20_R24_S1.095821.573
110_E114_K1.091721.567
117_P121_N1.08971.564
19_R82_M1.087371.561
21_E60_L1.082641.554
26_I86_I1.078451.548
17_E20_R1.076251.545
22_I62_K1.052551.511
23_E27_E1.032581.482
56_R60_L1.01041.450
55_R59_K0.997281.431
118_K121_N0.956911.374
69_N112_Q0.951761.366
55_R123_E0.88691.273
107_G111_Q0.877381.259
25_L56_R0.870611.250
68_D73_D0.86041.235
110_E113_A0.857881.231
16_L20_R0.852421.224
19_R78_I0.832911.196
55_R58_I0.830321.192
66_W120_E0.829261.190
21_E62_K0.819431.176
112_Q116_L0.803551.153
22_I26_I0.794461.140
25_L60_L0.786461.129
66_W100_I0.765051.098
64_L79_G0.761311.093
111_Q115_W0.745611.070
58_I63_Q0.742571.066
69_N109_E0.725981.042
19_R23_E0.725181.041
26_I83_Y0.72091.035
51_L54_A0.704861.012
102_T106_Q0.695250.998
18_R75_A0.688650.988
66_W104_M0.686990.986
14_E17_E0.679070.975
99_F102_T0.67620.971
21_E24_S0.665180.955
26_I30_P0.640760.920
25_L29_D0.638430.916
39_Y42_S0.635160.912
25_L57_L0.635110.912
53_K56_R0.629580.904
100_I119_A0.623590.895
19_R81_L0.61990.890
27_E85_L0.617360.886
65_G76_F0.601110.863
22_I79_G0.595780.855
101_P105_G0.594580.853
25_L53_K0.588720.845
67_D71_D0.578460.830
18_R22_I0.545690.783
40_F43_R0.54420.781
49_R52_R0.54280.779
108_T112_Q0.53870.773
99_F119_A0.532090.764
41_L45_E0.531330.763
24_S27_E0.528990.759
76_F97_G0.528120.758
40_F44_E0.523090.751
94_L98_M0.510460.733
42_S45_E0.509860.732
103_I107_G0.499490.717
43_R48_E0.495680.711
30_P53_K0.481820.692
47_Y50_A0.48090.690
23_E85_L0.48080.690
62_K79_G0.478380.687
76_F80_L0.476840.684
58_I122_Y0.474410.681
101_P104_M0.464150.666
68_D71_D0.463620.665
27_E86_I0.460150.660
48_E52_R0.459710.660
52_R56_R0.459630.660
29_D60_L0.455920.654
91_P94_L0.448560.644
54_A91_P0.445160.639
92_L96_F0.442290.635
18_R79_G0.44030.632
115_W124_I0.439040.630
52_R55_R0.437740.628
14_E75_A0.436810.627
14_E21_E0.436480.627
115_W118_K0.434680.624
42_S48_E0.434360.623
95_H119_A0.433270.622
93_G96_F0.433010.622
43_R47_Y0.431690.620
99_F103_I0.431240.619
92_L95_H0.427050.613
21_E72_P0.424720.610
27_E33_S0.422920.607
100_I116_L0.41510.596
48_E51_L0.401460.576
100_I104_M0.393520.565
80_L84_V0.393520.565
93_G97_G0.392170.563
107_G112_Q0.391670.562
106_Q111_Q0.390950.561
65_G101_P0.390390.560
104_M112_Q0.388730.558
98_M101_P0.387390.556
98_M102_T0.386430.555
41_L44_E0.383880.551
69_N120_E0.383290.550
64_L74_D0.382050.548
50_A54_A0.381310.547
83_Y92_L0.378410.543
57_L62_K0.371790.534
28_S60_L0.366930.527
99_F105_G0.366010.525
30_P90_L0.364640.523
81_L85_L0.360630.518
69_N107_G0.359280.516
39_Y52_R0.35260.506
66_W69_N0.351970.505
69_N116_L0.349490.502
84_V88_E0.345380.496
69_N117_P0.342140.491
84_V87_D0.340940.489
25_L30_P0.338040.485
78_I82_M0.332940.478
91_P96_F0.328710.472
43_R87_D0.32790.471
17_E24_S0.327850.471
30_P34_K0.324560.466
49_R91_P0.322960.464
92_L97_G0.322540.463
23_E86_I0.322450.463
80_L83_Y0.320740.460
43_R50_A0.317670.456
97_G101_P0.317660.456
111_Q114_K0.315290.453
94_L99_F0.314930.452
20_R23_E0.313620.450
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
4ktoA0.94499.30.32
2ix5A0.93699.30.323
1bucA0.90499.20.332
2ddhA0.95299.20.337
1w07A0.9299.20.337
2pg0A0.94499.20.344
2vigA0.91299.20.345
3swoA0.93699.20.348
2d29A0.91299.20.35
3p4tA0.93699.20.353

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