GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Transglycosylas - Transglycosylase-like domain
Pfam: PF06737 (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: CL0037
Length: 77
Sequences: 6166
Seq/Len: 80.08
HH_delta: 0.164 (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
31_L62_A1.615222.641
27_Y34_S1.41622.316
12_Q16_G1.317542.154
7_W63_E1.265222.069
28_Y53_A1.170181.913
23_T27_Y1.125191.840
51_D57_E1.066381.744
31_L59_I1.012471.655
28_Y52_Q0.974721.594
10_I66_Y0.96721.581
26_G34_S0.965441.579
37_T65_L0.88891.453
11_A30_G0.858821.404
33_F65_L0.858691.404
12_Q17_G0.854061.396
8_D17_G0.853561.396
11_A31_L0.849451.389
11_A59_I0.831111.359
35_Q39_R0.805051.316
33_F61_V0.748571.224
18_N21_I0.747311.222
41_Y68_R0.741931.213
33_F58_Q0.721921.180
25_N34_S0.721071.179
22_N53_A0.716631.172
57_E60_A0.713871.167
57_E61_V0.707961.158
11_A17_G0.666271.089
7_W31_L0.647411.059
28_Y35_Q0.642781.051
43_G61_V0.639941.046
18_N22_N0.61851.011
64_K67_A0.617911.010
54_S57_E0.61421.004
60_A64_K0.603560.987
40_A68_R0.601660.984
56_A60_A0.596150.975
6_D9_A0.589250.963
64_K68_R0.584290.955
52_Q57_E0.580510.949
52_Q58_Q0.577980.945
8_D12_Q0.556950.911
30_G59_I0.549120.898
58_Q62_A0.548130.896
59_I63_E0.547970.896
30_G55_R0.545360.892
23_T26_G0.544560.890
61_V64_K0.529360.866
22_N28_Y0.526280.860
10_I31_L0.509930.834
41_Y61_V0.50320.823
27_Y35_Q0.486750.796
62_A66_Y0.48620.795
11_A15_S0.483530.791
36_S40_A0.481290.787
34_S37_T0.477060.780
13_C16_G0.473840.775
41_Y64_K0.472920.773
29_G32_Q0.469510.768
17_G22_N0.467140.764
63_E66_Y0.461710.755
20_A53_A0.444070.726
19_W30_G0.440830.721
61_V65_L0.435360.712
7_W11_A0.430620.704
44_S50_P0.412480.674
27_Y32_Q0.40540.663
52_Q61_V0.397130.649
33_F37_T0.392540.642
26_G35_Q0.385020.630
6_D66_Y0.382530.625
54_S58_Q0.373930.611
15_S21_I0.373750.611
19_W55_R0.371020.607
63_E67_A0.368840.603
10_I13_C0.366010.598
37_T41_Y0.361340.591
37_T40_A0.360360.589
41_Y65_L0.355690.582
45_G54_S0.355570.581
50_P57_E0.355480.581
33_F38_W0.354320.579
41_Y44_S0.35130.574
10_I62_A0.347770.569
17_G20_A0.344770.564
14_E17_G0.340730.557
14_E30_G0.337890.552
15_S18_N0.331240.542
7_W59_I0.32790.536
49_R52_Q0.32430.530
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
1qsaA199.50.164
3t21A199.40.21
3w6bA199.30.234
3eo5A199.30.252
4emnA0.96199.20.275
3gxrA0.883199.20.288
1qusA199.10.31
1lmqA199.10.311
2z2fA199.10.323
2nwdX199.10.325

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