GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acetyltransf_11 - Udp N-acetylglucosamine O-acyltransferase Domain 2
Pfam: PF13720 (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: 83
Sequences: 1076
Seq/Len: 12.96
HH_delta: 0.249 (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
58_E75_R0.974643.933
32_E66_E0.82383.324
4_P73_F0.820253.310
68_R72_D0.552522.230
23_L36_L0.483281.950
49_T52_E0.463991.872
5_F69_E0.457831.847
3_P6_M0.447011.804
10_G13_A0.419111.691
3_P44_F0.406811.642
43_L74_I0.402421.624
22_G25_R0.388351.567
54_L74_I0.384711.552
8_V13_A0.379881.533
48_L53_A0.367951.485
34_S38_R0.362891.464
55_E59_E0.358851.448
15_I82_C0.356311.438
5_F66_E0.354671.431
43_L70_I0.343121.385
15_I44_F0.339241.369
2_V8_V0.336611.358
18_L36_L0.333961.348
29_S32_E0.32651.318
54_L75_R0.319831.291
39_A67_V0.305341.232
30_K34_S0.301681.217
20_L37_R0.300551.213
72_D76_N0.287921.162
50_L54_L0.287141.159
42_I57_L0.277391.119
77_S80_G0.27351.104
71_V75_R0.271931.097
74_I81_I0.271221.094
17_G40_Y0.26811.082
43_L57_L0.267211.078
3_P81_I0.265061.070
3_P70_I0.262841.061
36_L40_Y0.262071.058
48_L56_E0.256271.034
35_A67_V0.255261.030
39_A57_L0.252641.019
8_V12_P0.251221.014
42_I60_E0.244480.987
34_S37_R0.237660.959
38_R42_I0.233190.941
72_D75_R0.232150.937
21_V24_R0.229720.927
22_G26_R0.22890.924
58_E71_V0.227020.916
42_I56_E0.226450.914
32_E64_S0.221490.894
56_E60_E0.220230.889
29_S66_E0.216480.874
5_F58_E0.216240.873
9_A12_P0.212610.858
23_L26_R0.212530.858
52_E55_E0.210010.847
46_S56_E0.208980.843
9_A16_R0.208550.842
65_P69_E0.208480.841
19_N22_G0.207390.837
21_V25_R0.20730.837
39_A70_I0.206930.835
1_D79_R0.206710.834
77_S81_I0.206030.831
24_R30_K0.20480.826
40_Y44_F0.198970.803
80_G83_R0.198680.802
59_E62_P0.196810.794
69_E72_D0.194550.785
54_L71_V0.189880.766
12_P44_F0.188260.760
55_E58_E0.188060.759
4_P43_L0.188010.759
65_P68_R0.187270.756
20_L24_R0.186840.754
8_V82_C0.186140.751
30_K33_I0.185920.750
24_R33_I0.18430.744
7_L21_V0.182180.735
1_D77_S0.181380.732
32_E35_A0.180910.730
42_I61_Y0.178760.721
9_A41_R0.177820.718
20_L50_L0.176950.714
3_P80_G0.175610.709
6_M15_I0.174060.702
56_E59_E0.17310.699
36_L73_F0.172030.694
9_A15_I0.170050.686
45_R49_T0.169970.686
31_E55_E0.16710.674
45_R80_G0.164820.665
45_R53_A0.162660.656
63_D76_N0.162360.655
36_L70_I0.160040.646
57_L61_Y0.157540.636
74_I77_S0.157250.635
3_P15_I0.156960.633
61_Y68_R0.15670.632
23_L41_R0.156270.631
11_N14_R0.155430.627
52_E63_D0.155260.627
20_L30_K0.15510.626
3_P23_L0.155050.626
43_L73_F0.154350.623
64_S68_R0.154190.622
50_L71_V0.153830.621
63_D68_R0.151290.610
18_L33_I0.151090.610
6_M70_I0.149120.602
15_I41_R0.14850.599
42_I46_S0.147830.597
40_Y81_I0.146990.593
62_P78_K0.146790.592
55_E75_R0.146730.592
77_S83_R0.146570.591
50_L53_A0.145840.589
42_I45_R0.14560.588
40_Y52_E0.145260.586
10_G16_R0.14490.585
7_L14_R0.144530.583
17_G20_L0.144350.582
35_A38_R0.143720.580
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
4e6uA199.80.249
3hsqA199.80.255
3r0sA0.963999.80.256
4eqyA199.80.258
3t57A199.80.263
1j2zA0.98899.80.272
2qiaA199.70.31
1xatA0.807297.60.734
3fs8A0.807297.50.737
3eevA0.795297.50.738

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