GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AAA_18 - AAA domain
Pfam: PF13238 (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: CL0023
Length: 129
Sequences: 15758
Seq/Len: 122.16
HH_delta: 0.328 (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
104_E107_K1.65793.298
100_C105_L1.330662.647
17_E20_E1.282362.551
106_R110_K1.213822.415
107_K111_K1.076052.141
6_I105_L0.997821.985
101_S104_E0.994241.978
3_I15_A0.973971.938
100_C104_E0.927071.844
17_E21_R0.909081.809
15_A19_A0.851161.693
14_I17_E0.828051.647
16_K19_A0.82171.635
8_G109_L0.817421.626
14_I98_L0.807941.607
16_K20_E0.785661.563
103_E107_K0.770951.534
62_S65_Q0.768791.529
38_S41_D0.753241.498
58_E62_S0.747041.486
28_D32_E0.718151.429
52_D55_F0.693621.380
100_C108_R0.683321.359
58_E61_D0.671141.335
34_D37_D0.669261.331
62_S66_A0.666041.325
102_P106_R0.665271.323
70_M73_G0.632081.257
9_S100_C0.621591.237
24_D27_R0.621551.236
27_R30_A0.608311.210
36_V39_I0.602751.199
3_I18_L0.59241.179
39_I42_N0.585661.165
25_I29_I0.581021.156
47_E50_R0.571911.138
105_L109_L0.563561.121
12_T79_D0.561551.117
33_E36_V0.56141.117
49_K52_D0.561051.116
6_I102_P0.558521.111
37_D42_N0.553791.102
4_S97_F0.550151.094
5_G11_K0.543441.081
10_G108_R0.537041.068
23_G27_R0.533771.062
57_D61_D0.529441.053
18_L22_L0.527061.049
63_I66_A0.527021.048
24_D28_D0.520511.035
107_K110_K0.519871.034
61_D65_Q0.508591.012
90_L93_I0.5071.009
90_L94_K0.506641.008
32_E35_I0.500430.996
34_D38_S0.499220.993
26_I30_A0.49910.993
37_D40_D0.48850.972
86_E89_R0.481710.958
47_E51_L0.481180.957
104_E108_R0.481070.957
37_D41_D0.480760.956
35_I38_S0.479960.955
50_R54_E0.479630.954
2_G83_S0.479570.954
13_T17_E0.478440.952
52_D56_Q0.475210.945
54_E57_D0.471680.938
87_L91_F0.471260.938
13_T108_R0.470170.935
106_R109_L0.467870.931
85_L88_E0.466130.927
29_I32_E0.464370.924
56_Q60_L0.462260.920
7_P105_L0.462070.919
55_F58_E0.449820.895
15_A26_I0.445190.886
38_S42_N0.443160.882
81_I87_L0.438240.872
30_A33_E0.427160.850
3_I98_L0.423780.843
80_G84_N0.422350.840
15_A77_I0.422110.840
6_I9_S0.421780.839
5_G10_G0.420290.836
1_I96_I0.419360.834
48_N51_L0.419140.834
60_L64_I0.418150.832
80_G83_S0.416410.828
31_P35_I0.414220.824
84_N87_L0.413330.822
9_S105_L0.412080.820
84_N88_E0.410260.816
53_M57_D0.409930.816
7_P109_L0.409290.814
51_L54_E0.405870.807
46_K50_R0.405050.806
91_F94_K0.403530.803
36_V40_D0.400720.797
58_E64_I0.394820.785
99_D102_P0.39070.777
5_G9_S0.390530.777
89_R92_D0.389960.776
8_G112_R0.387730.771
57_D64_I0.387380.771
81_I84_N0.386430.769
13_T16_K0.386050.768
14_I18_L0.37850.753
70_M75_N0.377830.752
51_L56_Q0.373210.742
6_I97_F0.373050.742
89_R93_I0.366820.730
30_A34_D0.364030.724
59_L63_I0.363570.723
57_D60_L0.36240.721
19_A22_L0.36050.717
80_G88_E0.359510.715
22_L77_I0.3580.712
28_D31_P0.357810.712
82_L86_E0.352160.701
14_I21_R0.351730.700
9_S98_L0.350510.697
33_E37_D0.349420.695
46_K49_K0.346860.690
26_I56_Q0.346080.688
102_P105_L0.344980.686
89_R94_K0.343730.684
19_A26_I0.343270.683
82_L87_L0.342110.681
35_I39_I0.339930.676
4_S7_P0.338190.673
73_G76_I0.336340.669
50_R53_M0.335320.667
29_I62_S0.33490.666
47_E52_D0.334770.666
103_E106_R0.333320.663
23_G26_I0.332260.661
83_S88_E0.332060.661
58_E63_I0.329490.655
77_I80_G0.327730.652
32_E37_D0.326490.650
54_E58_E0.326190.649
71_N74_R0.326080.649
86_E90_L0.32510.647
25_I28_D0.324620.646
109_L113_G0.324480.646
99_D105_L0.323450.643
79_D82_L0.321710.640
2_G7_P0.321250.639
12_T16_K0.317990.633
34_D42_N0.317010.631
9_S80_G0.312620.622
60_L63_I0.311120.619
59_L64_I0.308390.614
55_F59_L0.306480.610
9_S97_F0.300590.598
83_S87_L0.300370.598
9_S12_T0.299090.595
104_E111_K0.296220.589
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
3fb4A0.976799.10.328
3tlxA0.976799.10.333
3dl0A0.976799.10.333
3sr0A0.953599.10.334
3t61A0.9302990.34
2rhmA0.969990.342
3lw7A0.969990.354
3iijA0.9225990.355
3umfA0.9767990.356
1uj2A1990.357

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