GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1255 - Protein of unknown function (DUF1255)
Pfam: PF06865 (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: CL0029
Length: 94
Sequences: 2171
Seq/Len: 23.1
HH_delta: 0.283 (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
51_E66_S0.956143.236
53_E62_W0.893383.024
51_E64_T0.873022.955
53_E82_K0.725282.455
51_E85_E0.724262.451
53_E84_K0.699392.367
53_E64_T0.653592.212
66_S69_E0.65252.208
57_P78_S0.643112.177
49_S67_A0.620692.101
55_K80_D0.576831.952
55_K62_W0.57091.932
42_P75_A0.487611.650
32_P85_E0.487061.648
36_T78_S0.480581.627
57_P77_S0.476261.612
46_E70_S0.47271.600
51_E84_K0.445111.507
42_P72_E0.443191.500
54_V73_V0.422971.432
45_M71_F0.417041.411
45_M81_V0.371081.256
36_T80_D0.360111.219
47_V52_L0.351021.188
54_V71_F0.33871.146
52_L65_Y0.337871.144
56_L77_S0.323321.094
44_R70_S0.320631.085
28_G43_E0.316521.071
16_T19_F0.304781.032
39_T79_F0.298691.011
52_L81_V0.295010.998
74_P77_S0.294830.998
56_L63_Q0.29480.998
45_M73_V0.293630.994
10_G34_E0.284750.964
73_V77_S0.281230.952
41_A72_E0.276610.936
17_F22_G0.262770.889
37_F79_F0.260590.882
32_P83_V0.256840.869
47_V65_Y0.25440.861
12_V35_Y0.251370.851
40_S76_N0.248130.840
30_M81_V0.247430.837
39_T43_E0.247420.837
62_W82_K0.242850.822
38_G78_S0.235560.797
14_S28_G0.234570.794
64_T84_K0.228140.772
79_F83_V0.223760.757
42_P74_P0.223510.756
19_F24_K0.216970.734
54_V65_Y0.216030.731
63_Q69_E0.215410.729
56_L62_W0.215410.729
39_T73_V0.214260.725
18_E48_V0.213770.724
37_F43_E0.211920.717
25_K44_R0.211410.716
33_G83_V0.211180.715
18_E21_D0.210280.712
43_E81_V0.209470.709
20_A70_S0.208750.707
37_F73_V0.208220.705
18_E46_E0.206080.697
55_K78_S0.205970.697
31_L83_V0.198320.671
30_M43_E0.197220.668
33_G52_L0.196160.664
45_M54_V0.19540.661
21_D25_K0.193890.656
47_V67_A0.193250.654
52_L84_K0.192350.651
55_K58_G0.191170.647
32_P63_Q0.191170.647
43_E83_V0.190810.646
45_M52_L0.190280.644
26_T73_V0.188990.640
25_K28_G0.188710.639
29_V44_R0.188480.638
30_M35_Y0.188090.637
37_F75_A0.187210.634
18_E72_E0.186950.633
65_Y71_F0.182880.619
55_K82_K0.18280.619
52_L83_V0.179860.609
15_I29_V0.175930.595
55_K63_Q0.175060.593
24_K41_A0.174690.591
28_G54_V0.171090.579
65_Y69_E0.170270.576
18_E29_V0.169810.575
34_E43_E0.167850.568
31_L40_S0.16640.563
21_D72_E0.166060.562
11_K16_T0.165890.561
31_L46_E0.161480.547
17_F48_V0.160630.544
48_V63_Q0.160040.542
15_I30_M0.159840.541
58_G62_W0.159320.539
14_S35_Y0.159240.539
54_V79_F0.158250.536
63_Q66_S0.15780.534
49_S78_S0.15690.531
67_A76_N0.155740.527
15_I35_Y0.155690.527
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
2oyzA0.989499.50.283
3hqxA199.40.335
3rnsA0.978799.40.336
3eo6A0.989499.40.338
3rnsA0.978799.20.375
4axoA0.978799.20.384
2ozjA0.978799.10.423
2pytA0.978799.10.428
1yhfA0.9787990.435
3fjsA0.9681990.443

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