GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glycos_trans_3N - Glycosyl transferase family helical bundle domain
Pfam: PF02885 (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: 66
Sequences: 2824
Seq/Len: 42.79
HH_delta: -0.067 (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
17_R59_K1.533892.764
8_K19_E1.461142.633
17_R56_G1.296632.336
14_D50_T1.267782.284
25_D64_H1.222232.202
14_D47_K1.176662.120
8_K13_E1.169742.108
21_K63_E1.108951.998
27_I37_I1.094531.972
39_A42_M1.043361.880
16_S19_E1.021941.841
23_A40_F1.016391.831
40_F44_L0.966341.741
21_K59_K0.859451.549
29_D64_H0.856341.543
52_E56_G0.853511.538
20_A57_F0.819591.477
51_P55_A0.811981.463
14_D52_E0.81091.461
24_F57_F0.802871.447
26_A31_E0.801641.444
45_R49_E0.760421.370
12_G47_K0.726731.310
15_L53_E0.671671.210
21_K25_D0.668831.205
5_I23_A0.667221.202
25_D29_D0.664731.198
33_S36_Q0.653341.177
23_A32_V0.631981.139
23_A37_I0.59951.080
25_D63_E0.58241.049
10_R42_M0.577311.040
32_V37_I0.575321.037
5_I22_A0.573271.033
55_A59_K0.570881.029
42_M46_M0.550360.992
17_R52_E0.541440.976
7_K11_D0.536660.967
21_K60_A0.507530.915
26_A32_V0.499950.901
58_A65_A0.496650.895
40_F57_F0.496330.894
58_A62_R0.482760.870
20_A56_G0.479270.864
21_K56_G0.477040.860
44_L49_E0.462490.833
56_G60_A0.460920.831
18_E21_K0.457250.824
25_D60_A0.454660.819
10_R45_R0.452880.816
24_F28_L0.443160.799
28_L61_M0.442840.798
58_A61_M0.440980.795
9_L43_A0.439310.792
35_A38_A0.422790.762
59_K63_E0.419670.756
23_A27_I0.405920.731
10_R46_M0.403230.727
60_A64_H0.395420.713
17_R21_K0.371580.670
22_A26_A0.368420.664
20_A24_F0.366830.661
48_G54_I0.36110.651
5_I26_A0.360240.649
12_G46_M0.349590.630
39_A43_A0.335190.604
11_D45_R0.3270.589
7_K10_R0.325450.586
22_A25_D0.321830.580
9_L46_M0.319970.577
38_A42_M0.319410.576
59_K62_R0.310350.559
15_L40_F0.308690.556
3_K7_K0.30430.548
49_E54_I0.30350.547
41_L44_L0.302780.546
51_P54_I0.301460.543
47_K53_E0.299430.540
54_I57_F0.29380.529
18_E22_A0.292350.527
61_M65_A0.290130.523
4_E8_K0.285890.515
57_F65_A0.280750.506
60_A63_E0.280590.506
32_V36_Q0.279670.504
16_S52_E0.274190.494
23_A26_A0.273410.493
17_R55_A0.27250.491
44_L48_G0.272230.491
5_I19_E0.269690.486
9_L44_L0.267680.482
41_L54_I0.267150.481
32_V40_F0.260470.469
7_K46_M0.25750.464
20_A49_E0.256710.463
44_L54_I0.256070.461
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
4hkmA199.6-0.067
3r88A199.6-0.063
1vquA199.6-0.049
1khdA199.6-0.046
1o17A199.6-0.046
2tptA199.6-0.038
1brwA199.6-0.036
3h5qA199.6-0.029
4eadA199.6-0.029
2dsjA199.6-0.028

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