GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1416 - Protein of unknown function (DUF1416)
Pfam: PF07210 (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: CL0287
Length: 85
Sequences: 9472
Seq/Len: 111.44
HH_delta: 0.277 (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_S46_D2.838624.190
13_R46_D2.154933.181
12_G47_F2.095383.093
29_L57_T2.019442.981
16_R73_A1.385552.045
11_T48_R1.36752.019
9_V48_R1.344211.984
28_L37_A1.305541.927
21_V24_A1.275681.883
25_Y38_E1.204091.777
47_F68_D1.178461.740
15_T68_D1.176151.736
15_T70_M1.171891.730
47_F58_V1.032291.524
22_G43_A1.009521.490
29_L59_R0.982051.450
9_V50_F0.96931.431
28_L51_A0.966931.427
39_V49_F0.908811.342
62_S65_G0.861411.272
11_T46_D0.84971.254
24_A41_T0.840911.241
24_A60_A0.819751.210
51_A54_G0.798511.179
15_T18_G0.795061.174
27_R38_E0.783761.157
18_G70_M0.7811.153
58_V69_A0.764071.128
13_R68_D0.743121.097
52_A55_S0.742571.096
28_L55_S0.711341.050
47_F82_D0.708591.046
19_E43_A0.700441.034
28_L49_F0.696591.028
79_H82_D0.693481.024
74_E77_G0.69221.022
27_R57_T0.689341.018
23_G40_V0.678141.001
17_D73_A0.674930.996
19_E22_G0.668540.987
24_A58_V0.668440.987
16_R72_T0.663180.979
27_R59_R0.650870.961
56_W61_L0.646620.955
58_V61_L0.642240.948
51_A56_W0.635660.938
22_G40_V0.622570.919
13_R20_P0.612350.904
14_V41_T0.595920.880
61_L65_G0.595240.879
51_A55_S0.585470.864
26_V41_T0.579150.855
59_R67_G0.57160.844
60_A83_V0.567220.837
8_T53_P0.562320.830
25_Y61_L0.538870.795
63_R66_N0.529780.782
21_V62_S0.524940.775
22_G60_A0.517280.764
28_L52_A0.511230.755
63_R67_G0.510070.753
56_W59_R0.510020.753
76_G80_E0.509180.752
77_G80_E0.508930.751
56_W60_A0.490520.724
64_G67_G0.479690.708
21_V41_T0.467810.691
25_Y40_V0.463510.684
78_V81_V0.456980.675
73_A76_G0.453850.670
30_D37_A0.445410.658
69_A73_A0.441520.652
62_S66_N0.440660.651
41_T45_G0.440240.650
76_G83_V0.436030.644
14_V24_A0.434010.641
54_G62_S0.400480.591
56_W62_S0.397730.587
43_A46_D0.384890.568
8_T67_G0.37950.560
8_T50_F0.378510.559
12_G39_V0.377570.557
37_A52_A0.367990.543
70_M73_A0.367850.543
38_E49_F0.359620.531
72_T75_G0.357170.527
28_L56_W0.349560.516
61_L67_G0.348430.514
27_R37_A0.348260.514
78_V83_V0.345920.511
23_G26_V0.332530.491
60_A65_G0.317670.469
69_A78_V0.316070.467
79_H83_V0.315160.465
24_A62_S0.309620.457
28_L50_F0.305470.451
37_A50_F0.303370.448
42_S45_G0.303150.448
22_G41_T0.303110.447
37_A49_F0.302020.446
21_V60_A0.299710.442
8_T64_G0.294110.434
8_T52_A0.292590.432
38_E63_R0.291650.431
16_R70_M0.289230.427
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
3mn8A0.964798.40.277
2nsmA0.952998.20.305
1uwyA0.9529980.35
1h8lA0.952997.90.37
1nkgA0.858896.60.526
3kcpA0.952992.80.627
3irpX192.50.63
4jdzB0.988287.40.668
3e8vA0.905983.20.686
3txaA0.879.10.698

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