GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF349 - Domain of Unknown Function (DUF349)
Pfam: PF03993 (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: 77
Sequences: 854
Seq/Len: 11.09
HH_delta: 0.863 (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
42_E65_E0.904144.124
35_K69_I0.543712.480
35_K38_A0.439112.003
37_E41_E0.375951.715
51_D54_E0.360921.646
38_A42_E0.351571.604
24_E27_A0.346551.581
40_I44_E0.343121.565
6_R10_A0.327341.493
33_L72_V0.319651.458
29_R71_P0.315831.441
30_E34_E0.314571.435
58_E61_E0.313481.430
31_E34_E0.303371.384
61_E65_E0.299851.368
32_N72_V0.296681.353
14_F18_R0.290811.327
7_F15_F0.28711.310
35_K65_E0.274891.254
34_E38_A0.273791.249
42_E58_E0.273471.247
43_A59_I0.271721.239
42_E45_A0.270321.233
12_D16_D0.269641.230
34_E37_E0.26861.225
61_E64_Q0.267891.222
29_R33_L0.267541.220
54_E58_E0.266381.215
13_A17_R0.261951.195
41_E44_E0.25761.175
32_N69_I0.257131.173
49_S52_W0.255251.164
8_R12_D0.249521.138
38_A41_E0.247071.127
57_E61_E0.243041.109
52_W55_A0.241841.103
41_E45_A0.240471.097
2_E6_R0.239531.093
50_E55_A0.235751.075
45_A58_E0.234241.069
21_F25_Q0.233941.067
53_K57_E0.232571.061
4_W10_A0.230551.052
33_L40_I0.224731.025
12_D15_F0.208880.953
4_W36_K0.207670.947
43_A62_L0.20690.944
31_E35_K0.206750.943
19_K23_E0.204490.933
63_Q66_W0.19970.911
43_A51_D0.197330.900
27_A31_E0.196410.896
51_D55_A0.195640.892
39_L62_L0.194860.889
26_D29_R0.194140.886
8_R15_F0.190790.870
14_F17_R0.189630.865
1_D5_K0.187310.854
9_A47_A0.185920.848
4_W11_C0.184360.841
39_L69_I0.183650.838
22_F25_Q0.183110.835
46_L58_E0.183030.835
7_F31_E0.183020.835
28_E31_E0.18250.833
49_S55_A0.178770.815
69_I72_V0.177480.810
8_R19_K0.174180.795
70_G73_P0.17360.792
40_I43_A0.17310.790
6_R66_W0.171670.783
36_K70_G0.171440.782
35_K53_K0.169020.771
43_A46_L0.168990.771
11_C15_F0.168570.769
39_L43_A0.166060.758
6_R44_E0.162450.741
39_L58_E0.16240.741
26_D30_E0.161840.738
15_F19_K0.158640.724
13_A31_E0.157860.720
42_E46_L0.155520.709
59_I63_Q0.15520.708
19_K22_F0.155190.708
3_L11_C0.154620.705
7_F19_K0.154370.704
2_E5_K0.153360.700
11_C14_F0.153350.700
36_K72_V0.152580.696
56_A59_I0.149360.681
7_F27_A0.149040.680
1_D8_R0.14870.678
22_F26_D0.146840.670
37_E40_I0.146090.666
24_E71_P0.145960.666
65_E68_E0.145850.665
64_Q68_E0.145490.664
22_F67_K0.145360.663
11_C72_V0.144950.661
36_K69_I0.144610.660
52_W56_A0.144590.660
1_D13_A0.144580.660
3_L74_R0.144080.657
61_E71_P0.143770.656
23_E75_K0.143080.653
46_L62_L0.142510.650
47_A55_A0.141170.644
12_D75_K0.140770.642
19_K71_P0.140530.641
20_E24_E0.140520.641
57_E68_E0.140060.639
57_E60_K0.137450.627
40_I67_K0.136720.624
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
1sesA0.935122.30.863
3u5iq0.636415.40.872
2wl8A1150.873
1jocA0.584414.50.874
3qneA0.96112.70.876
2dq0A0.96110.10.882
2dq3A0.9618.60.885
2wvxA0.571480.886
2y9yB17.40.888
2higA0.59747.40.888
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