GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4415 - Domain of unknown function (DUF4415)
Pfam: PF14384 (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: 62
Sequences: 534
Seq/Len: 8.61
HH_delta: 0.777 (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
36_D55_N0.81213.320
38_D59_R0.803763.286
43_F57_A0.719182.940
6_T9_E0.560952.293
57_A61_Y0.470351.923
5_L9_E0.445111.820
5_L10_F0.436721.786
43_F54_I0.386971.582
35_L54_I0.385921.578
29_K37_P0.36631.498
36_D59_R0.364681.491
42_W62_V0.359761.471
10_F14_A0.331651.356
43_F61_Y0.325521.331
29_K44_K0.297381.216
55_N59_R0.294911.206
42_W50_Y0.290191.186
33_I41_E0.286281.170
46_Q53_R0.256031.047
14_A17_A0.253891.038
6_T10_F0.248431.016
43_F62_V0.239760.980
15_K18_K0.236550.967
39_V55_N0.229170.937
39_V62_V0.226970.928
38_D55_N0.217240.888
9_E14_A0.212910.870
7_D47_G0.21280.870
57_A62_V0.212640.869
38_D43_F0.211640.865
5_L17_A0.210950.862
5_L14_A0.208270.851
18_K26_K0.206760.845
34_R52_T0.206480.844
56_E60_K0.203640.833
41_E45_A0.194670.796
34_R40_L0.193770.792
7_D13_R0.192730.788
39_V59_R0.190850.780
42_W46_Q0.189710.776
35_L40_L0.188230.770
33_I60_K0.188090.769
47_G53_R0.186410.762
53_R56_E0.185520.758
28_K52_T0.182860.748
48_K53_R0.180780.739
45_A49_G0.180680.739
31_V40_L0.175020.716
28_K34_R0.173910.711
42_W61_Y0.171020.699
6_T41_E0.170940.699
44_K50_Y0.169040.691
32_T50_Y0.167490.685
34_R49_G0.16580.678
27_P37_P0.160250.655
57_A60_K0.158830.649
34_R47_G0.15840.648
48_K54_I0.156440.640
7_D12_A0.156150.638
56_E61_Y0.155840.637
12_A17_A0.154910.633
51_Q55_N0.154770.633
34_R51_Q0.154760.633
7_D44_K0.152620.624
30_Q33_I0.152390.623
32_T51_Q0.151630.620
34_R44_K0.149140.610
37_P41_E0.148390.607
9_E15_K0.147490.603
29_K41_E0.146030.597
48_K57_A0.145370.594
13_R37_P0.144570.591
37_P44_K0.141440.578
39_V49_G0.137940.564
51_Q58_L0.137670.563
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
2k9iA0.6613910.777
2cpgA0.5806800.809
2adlA0.5806780.813
2gpeA0.596874.80.818
2ay0A0.596871.20.823
2hzaA0.564569.20.825
1bazA0.661367.70.827
2kelA0.758165.40.829
2bj7A0.596863.20.832
1mntA0.612953.90.841
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