GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF3116 - Protein of unknown function (DUF3116)
Pfam: PF11313 (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: CL0123
Length: 85
Sequences: 33215
Seq/Len: 390.76
HH_delta: 0.182 (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
52_E59_R2.652522.428
58_F69_S2.422532.217
22_T25_H2.219282.031
15_F29_E2.218162.030
60_D69_S2.071331.896
58_F71_T2.057221.883
27_T41_K1.978761.811
9_I47_T1.95741.792
9_I50_W1.796071.644
20_N69_S1.685461.543
21_A29_E1.584451.450
42_N46_Y1.546691.416
17_K78_L1.513291.385
23_I45_L1.472131.347
48_V68_Y1.435971.314
40_T43_E1.434211.313
9_I54_N1.395661.277
71_T74_G1.369661.254
24_N28_F1.360291.245
12_I47_T1.319071.207
43_E47_T1.292641.183
45_L49_Y1.288071.179
20_N60_D1.277811.170
21_A25_H1.267291.160
39_F44_L1.260051.153
12_I44_L1.239541.135
39_F43_E1.22661.123
43_E46_Y1.217351.114
25_H29_E1.18431.084
16_V57_I1.17921.079
59_R66_K1.176471.077
49_Y52_E1.142711.046
40_T46_Y1.136071.040
27_T44_L1.13031.035
50_W54_N1.102551.009
49_Y53_E1.097931.005
56_Y77_L1.087630.995
15_F21_A1.081890.990
25_H28_F1.072290.981
42_N45_L1.070940.980
59_R68_Y1.070890.980
76_E80_E1.051110.962
77_L80_E1.042970.955
41_K45_L1.039620.952
73_K76_E1.022450.936
11_Q15_F1.002040.917
23_I41_K0.997140.913
46_Y50_W0.989310.905
23_I48_V0.986380.903
47_T50_W0.967320.885
55_G73_K0.963360.882
61_N67_R0.959670.878
23_I44_L0.955760.875
24_N41_K0.943670.864
17_K70_L0.931410.852
48_V57_I0.920730.843
15_F26_L0.914070.837
12_I26_L0.909720.833
76_E79_A0.90240.826
15_F30_F0.878670.804
50_W53_E0.859040.786
10_Y14_N0.852440.780
73_K77_L0.84720.775
13_L56_Y0.84280.771
23_I68_Y0.839440.768
63_N66_K0.837770.767
72_E75_K0.836390.766
62_N65_E0.833780.763
70_L75_K0.817660.748
46_Y49_Y0.807380.739
11_Q14_N0.802190.734
75_K79_A0.802020.734
74_G77_L0.789380.722
62_N66_K0.784690.718
52_E57_I0.770460.705
18_D29_E0.767620.703
70_L74_G0.767450.702
61_N66_K0.765670.701
16_V21_A0.764780.700
14_N17_K0.764270.700
30_F44_L0.750430.687
27_T31_I0.740240.678
22_T66_K0.72150.660
56_Y73_K0.717520.657
13_L70_L0.710870.651
72_E76_E0.708250.648
15_F18_D0.703230.644
17_K75_K0.702490.643
44_L48_V0.701080.642
30_F39_F0.685260.627
12_I16_V0.682610.625
10_Y78_L0.676050.619
18_D21_A0.673460.616
71_T75_K0.671170.614
14_N78_L0.661870.606
39_F50_W0.653630.598
16_V20_N0.64820.593
59_R67_R0.642260.588
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
3f6vA0.917698.80.182
3f6oA0.917698.80.202
3df8A0.905998.70.233
4esbA0.988298.70.233
1xmaA198.70.234
3hhhA0.988298.70.236
4esfA0.988298.70.238
2oqgA0.917698.70.238
2hztA0.917698.60.243
3l7wA0.964798.60.245

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