GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ald_Xan_dh_C - Aldehyde oxidase and xanthine dehydrogenase ab hammerhead domain
Pfam: PF01315 (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: 111
Sequences: 2945
Seq/Len: 26.53
HH_delta: -0.003 (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
41_M102_L1.482833.351
16_L45_V1.385683.131
92_T95_A1.375783.109
25_I109_E1.373643.104
25_I28_A1.250582.826
41_M95_A1.163662.630
29_R108_E1.139812.576
27_H110_L1.086622.456
37_E104_K1.083872.449
21_V103_V1.071382.421
45_V91_E1.032432.333
31_K106_E1.023762.314
91_E95_A0.976552.207
28_A107_Y0.968232.188
31_K108_E0.89772.029
18_A87_L0.88411.998
32_S106_E0.882771.995
90_A96_A0.882171.994
79_R83_Q0.775821.753
35_T39_L0.757931.713
11_P15_M0.737821.667
21_V100_A0.718991.625
38_A103_V0.714911.616
29_R77_K0.71491.616
29_R76_D0.685971.550
12_P15_M0.685161.548
19_A97_R0.670321.515
27_H77_K0.663941.500
34_D104_K0.646231.460
19_A100_A0.611081.381
39_L46_A0.604631.366
44_V90_A0.595761.346
19_A93_R0.587331.327
37_E40_A0.579571.310
35_T47_V0.518891.173
20_F84_P0.512991.159
93_R97_R0.504411.140
41_M99_A0.490261.108
25_I107_Y0.488361.104
24_P85_V0.484761.096
37_E102_L0.478371.081
30_I33_I0.475071.074
19_A96_A0.472791.068
98_D102_L0.46661.054
20_F87_L0.465751.053
50_A75_D0.461721.043
27_H111_P0.451771.021
35_T103_V0.4441.003
36_S39_L0.441580.998
94_E98_D0.437080.988
49_T52_D0.434060.981
22_R84_P0.429650.971
30_I107_Y0.425660.962
21_V86_A0.421550.953
71_P75_D0.418960.947
44_V96_A0.417760.944
60_G67_D0.406250.918
60_G66_H0.403470.912
21_V105_V0.396380.896
43_G99_A0.388480.878
74_A83_Q0.386670.874
95_A99_A0.38010.859
48_I89_V0.374330.846
32_S104_K0.372330.841
18_A89_V0.368450.833
49_T73_L0.368270.832
57_N60_G0.36660.828
47_V86_A0.363350.821
59_N67_D0.363160.821
30_I105_V0.361480.817
85_V107_Y0.36090.816
6_Y9_D0.359480.812
45_V89_V0.359080.811
77_K110_L0.353650.799
96_A100_A0.344160.778
29_R110_L0.342560.774
17_Y93_R0.340940.770
88_V100_A0.338630.765
23_S81_V0.337710.763
51_E75_D0.336530.761
43_G91_E0.333240.753
28_A110_L0.327870.741
4_A7_V0.327710.741
85_V105_V0.323550.731
51_E76_D0.314860.712
24_P107_Y0.314850.712
47_V88_V0.313710.709
44_V99_A0.307910.696
68_E83_Q0.307410.695
30_I74_A0.30240.683
35_T49_T0.30210.683
26_A81_V0.297740.673
86_A103_V0.297250.672
17_Y92_T0.296380.670
99_A102_L0.294880.666
60_G71_P0.29140.659
86_A105_V0.290280.656
1_T4_A0.287190.649
16_L89_V0.284580.643
100_A103_V0.284310.643
50_A76_D0.283390.640
58_P67_D0.278850.630
41_M98_D0.276540.625
46_A89_V0.27540.622
78_V107_Y0.275090.622
53_I74_A0.273510.618
90_A99_A0.27350.618
5_R10_I0.272650.616
59_N66_H0.269950.610
60_G68_E0.264240.597
55_G59_N0.260640.589
59_N72_V0.260.588
24_P81_V0.259080.585
98_D101_E0.257470.582
33_I85_V0.257080.581
67_D71_P0.256970.581
38_A47_V0.254550.575
78_V81_V0.244420.552
23_S78_V0.244180.552
30_I85_V0.243980.551
28_A105_V0.242990.549
39_L51_E0.242770.549
71_P74_A0.242190.547
43_G95_A0.23920.541
33_I105_V0.238280.538
40_A104_K0.236510.534
35_T38_A0.235640.533
34_D37_E0.234680.530
44_V47_V0.234460.530
80_Y84_P0.234450.530
23_S26_A0.233030.527
4_A18_A0.231390.523
58_P66_H0.229010.518
34_D38_A0.228420.516
74_A78_V0.226510.512
58_P71_P0.225880.510
53_I72_V0.225030.509
68_E72_V0.224070.506
25_I78_V0.223530.505
38_A99_A0.222290.502
80_Y83_Q0.221450.500
89_V99_A0.219220.495
59_N71_P0.217640.492
39_L44_V0.215610.487
53_I73_L0.21490.486
33_I47_V0.213030.481
66_H71_P0.212840.481
23_S28_A0.212770.481
18_A73_L0.208480.471
72_V75_D0.207890.470
58_P68_E0.207660.469
41_M44_V0.207490.469
7_V83_Q0.204830.463
97_R100_A0.203980.461
15_M18_A0.203830.461
5_R11_P0.200160.452
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
3uncA0.955100-0.003
1n62B0.9911000.004
1t3qB0.9821000.006
3nvzC0.9551000.01
1ffvB0.9911000.015
3hrdA0.9641000.016
3zyvA0.92791000.018
1rm6A0.9641000.02
2w3sB0.9641000.026
1vlbA11000.046

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