GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF4096 - Putative transposase of IS45 family (DUF4096)
Pfam: PF13340 (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: 75
Sequences: 1228
Seq/Len: 16.37
HH_delta: 0.874 (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
36_Y42_C1.088724.326
40_T43_P0.644212.560
45_R54_W0.626552.489
43_P46_D0.534072.122
27_L60_R0.52672.093
3_D28_R0.514632.045
47_L57_V0.479241.904
3_D6_W0.46231.837
58_Y62_R0.453871.803
2_S5_E0.443661.763
7_A10_E0.43141.714
39_R43_P0.43041.710
54_W58_Y0.409351.626
33_A57_V0.392581.560
29_E32_N0.38831.543
58_Y61_F0.387211.539
16_R19_R0.386451.535
62_R66_R0.381551.516
6_W28_R0.360341.432
1_L5_E0.351461.396
32_N50_D0.329611.310
21_G24_R0.32881.306
62_R65_S0.327291.300
24_R27_L0.320441.273
60_R64_W0.318951.267
32_N51_F0.31031.233
69_V72_R0.292041.160
55_S59_R0.291081.157
31_L70_W0.289781.151
37_V47_L0.286641.139
55_S58_Y0.280871.116
40_T46_D0.275161.093
24_R63_R0.264251.050
52_G60_R0.258881.029
35_L65_S0.251871.001
69_V73_L0.248020.985
33_A47_L0.247880.985
1_L35_L0.242970.965
30_V34_I0.235270.935
37_V42_C0.234160.930
47_L51_F0.231340.919
49_E52_G0.229910.914
52_G57_V0.227040.902
72_R75_Q0.226370.899
29_E51_F0.225720.897
13_L19_R0.225350.895
29_E52_G0.221340.879
17_K75_Q0.216170.859
25_I30_V0.214140.851
32_N35_L0.212330.844
29_E53_P0.207970.826
10_E75_Q0.205840.818
1_L9_I0.203270.808
34_I62_R0.200050.795
12_L38_L0.198050.787
61_F65_S0.196610.781
25_I29_E0.195990.779
56_T59_R0.192120.763
39_R46_D0.189470.753
53_P56_T0.189390.753
8_L12_L0.187840.746
27_L52_G0.187840.746
25_I53_P0.187760.746
44_W48_P0.187630.746
13_L27_L0.187120.743
56_T60_R0.185090.735
68_G71_E0.184450.733
14_P21_G0.184030.731
38_L42_C0.183870.731
59_R66_R0.182550.725
71_E75_Q0.182120.724
23_P27_L0.182050.723
24_R30_V0.180030.715
35_L38_L0.179850.715
45_R55_S0.179090.712
37_V40_T0.178630.710
39_R70_W0.178340.709
65_S70_W0.178080.708
53_P59_R0.177860.707
3_D7_A0.177010.703
40_T61_F0.174920.695
26_D29_E0.173470.689
7_A15_P0.173250.688
9_I31_L0.170560.678
64_W68_G0.170430.677
17_K71_E0.167650.666
30_V60_R0.166410.661
61_F70_W0.165340.657
46_D49_E0.163250.649
49_E72_R0.16310.648
35_L47_L0.163060.648
37_V51_F0.163050.648
57_V61_F0.162960.647
30_V53_P0.162820.647
31_L35_L0.162170.644
1_L19_R0.161470.642
14_P20_G0.159740.635
54_W57_V0.157230.625
27_L30_V0.156840.623
5_E12_L0.15590.619
33_A46_D0.155520.618
54_W62_R0.153450.610
31_L59_R0.153340.609
59_R63_R0.152950.608
14_P60_R0.150870.599
29_E71_E0.15050.598
11_P26_D0.150460.598
43_P70_W0.150360.597
6_W10_E0.148980.592
2_S40_T0.148910.592
33_A51_F0.148820.591
67_S72_R0.148480.590
4_E38_L0.14640.582
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
4bqqA0.533347.90.874
2qibA0.813333.40.885
4dyqA0.831.70.886
1tc3C0.666726.10.89
1jkoC0.6826.10.89
2y2zA0.906722.60.893
2optA0.7217.50.898
2hxoA0.8414.60.902
1ji8A0.6933140.902
2g7gA0.7867140.902
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