GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LpxD - UDP-3-O-3-hydroxymyristoyl glucosamine N-acyltransferase LpxD
Pfam: PF04613 (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: 72
Sequences: 1201
Seq/Len: 16.68
HH_delta: 0.139 (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_G37_G1.222344.481
58_V64_A0.917773.364
7_G18_D0.868523.184
11_L20_S0.55812.046
43_E59_D0.55642.040
14_A36_A0.530141.943
6_S17_G0.526331.929
9_A18_D0.517391.897
5_I38_A0.483581.773
42_P61_P0.422451.549
23_D62_R0.392861.440
40_L58_V0.392531.439
56_I64_A0.37981.392
14_A18_D0.374431.373
16_P35_K0.360461.321
19_I38_A0.360431.321
40_L68_L0.35931.317
31_L39_V0.356251.306
21_F62_R0.353181.295
3_I37_G0.352531.292
24_N27_Y0.34471.264
63_L66_A0.343951.261
12_E30_E0.326231.196
67_K70_Q0.295561.084
42_P57_I0.293881.077
8_V69_L0.293261.075
61_P65_F0.287991.056
41_V57_I0.286681.051
28_L45_F0.269270.987
3_I54_A0.269080.986
8_V72_F0.267780.982
65_F69_L0.266220.976
34_S53_K0.264430.969
44_E61_P0.263420.966
40_L65_F0.262430.962
15_G35_K0.261160.957
9_A13_E0.257850.945
42_P45_F0.257130.943
20_S34_S0.254290.932
15_G18_D0.250760.919
27_Y62_R0.245990.902
8_V68_L0.244340.896
44_E57_I0.242880.890
67_K71_L0.241540.885
2_D35_K0.239120.877
11_L34_S0.237290.870
10_P13_E0.235730.864
21_F24_N0.233450.856
46_A57_I0.232190.851
22_L45_F0.229780.842
31_L65_F0.227310.833
22_L31_L0.226580.831
9_A14_A0.21680.795
62_R66_A0.215330.789
8_V19_I0.213670.783
20_S39_V0.210750.773
11_L22_L0.208370.764
43_E57_I0.208130.763
8_V70_Q0.206240.756
10_P23_D0.20370.747
29_K33_N0.202280.742
39_V53_K0.201390.738
29_K32_K0.201180.738
24_N62_R0.199430.731
28_L50_P0.198420.727
63_L67_K0.198030.726
7_G72_F0.197760.725
20_S36_A0.196020.719
9_A19_I0.195210.716
14_A34_S0.194650.714
24_N30_E0.193610.710
8_V65_F0.191010.700
22_L39_V0.190050.697
13_E26_K0.189970.696
19_I68_L0.189340.694
11_L37_G0.188150.690
4_E35_K0.184130.675
51_E54_A0.182510.669
6_S16_P0.18190.667
2_D51_E0.180440.661
5_I37_G0.179440.658
35_K59_D0.178480.654
50_P54_A0.178120.653
44_E51_E0.176870.648
35_K52_G0.176740.648
42_P62_R0.176480.647
32_K50_P0.17640.647
23_D27_Y0.176170.646
14_A61_P0.17540.643
68_L72_F0.174690.640
31_L72_F0.17270.633
2_D63_L0.172230.631
15_G33_N0.17090.627
2_D59_D0.170470.625
6_S18_D0.169280.621
16_P43_E0.167760.615
10_P27_Y0.164610.603
62_R65_F0.16440.603
11_L30_E0.163460.599
44_E47_E0.162750.597
68_L71_L0.162670.596
25_P60_N0.161760.593
27_Y30_E0.161460.592
26_K71_L0.16050.588
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
4e79A199.40.139
3eh0A0.972299.10.246
3pmoA0.972299.10.258
2iu8A198.50.412
2wtzA190.50.726
1e8cA185.50.748
3r5dA0.888981.30.76
1gg4A0.944466.30.786
2am1A0.930665.20.788
1igrA18.70.863

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