GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1902 - Domain of unknown function (DUF1902)
Pfam: PF08972 (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: CL0438
Length: 54
Sequences: 2176
Seq/Len: 40.3
HH_delta: 0.13 (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
18_S42_I1.151572.488
26_T37_K1.063912.299
16_A34_L1.030892.227
30_T33_E0.90171.948
44_E48_L0.86991.879
15_V27_E0.770571.665
37_K40_V0.769131.662
21_V45_L0.716151.547
18_S38_L0.712961.540
13_V27_E0.690051.491
28_A34_L0.684251.478
8_D11_A0.678771.467
26_T40_V0.677591.464
28_A33_E0.660521.427
16_A38_L0.654861.415
17_T25_V0.621061.342
40_V44_E0.557411.204
45_L48_L0.51791.119
24_L45_L0.51671.116
21_V42_I0.504721.090
41_M44_E0.497311.074
16_A26_T0.486041.050
36_E39_R0.481461.040
14_W31_L0.479121.035
35_I39_R0.477841.032
3_I38_L0.477771.032
6_F17_T0.476591.030
32_E39_R0.460230.994
13_V29_D0.448970.970
24_L41_M0.448220.968
8_D12_G0.446220.964
23_G45_L0.438760.948
9_E12_G0.437390.945
44_E47_E0.43550.941
21_V46_L0.424010.916
31_L35_I0.41780.903
28_A37_K0.4140.894
26_T41_M0.390810.844
5_A34_L0.385430.833
4_R19_D0.382980.827
42_I45_L0.362440.783
15_V25_V0.353240.763
32_E36_E0.351430.759
3_I16_A0.338660.732
41_M45_L0.333670.721
7_W12_G0.330660.714
5_A31_L0.316460.684
19_D23_G0.310110.670
21_V24_L0.306170.661
16_A28_A0.305890.661
43_P47_E0.301260.651
17_T24_L0.28740.621
8_D13_V0.286020.618
32_E35_I0.277550.600
18_S45_L0.270640.585
39_R43_P0.266410.576
36_E40_V0.265060.573
29_D33_E0.264330.571
5_A14_W0.262360.567
32_E47_E0.262270.567
22_P43_P0.26080.563
12_G29_D0.257720.557
19_D24_L0.25670.555
6_F15_V0.254220.549
25_V45_L0.249840.540
40_V43_P0.241670.522
38_L42_I0.240730.520
3_I18_S0.23480.507
4_R17_T0.230980.499
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
3kwrA0.96398.90.13
2yztA0.944498.80.172
1wv8A198.70.182
2dsyA0.925998.70.191
3k6qA0.981596.20.553
4fflA0.944428.90.783
1iu8A123.90.791
1jw3A0.8333230.793
2j58A0.851919.80.799
4d86A0.981517.40.803

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