GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_Tnp_IS630 - Transposase
Pfam: PF01710 (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: CL0123
Length: 119
Sequences: 7977
Seq/Len: 67.03
HH_delta: 0.319 (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
21_I36_Y1.144562.294
22_R32_R1.060812.126
72_A80_R1.0052.014
25_A35_V0.946811.897
34_T38_W0.940441.885
62_L65_L0.936281.876
10_R14_Y0.936011.876
72_A76_E0.906751.817
21_I39_L0.905061.814
73_T76_E0.904731.813
20_S23_E0.900961.805
19_K23_E0.861931.727
32_R36_Y0.848941.701
84_S87_T0.82661.656
86_S89_W0.821551.646
11_V35_V0.818861.641
33_N36_Y0.814141.631
63_K67_E0.796441.596
14_Y27_R0.793281.590
89_W93_K0.742781.488
85_P89_W0.717161.437
74_L89_W0.691841.386
14_Y17_K0.683161.369
34_T37_R0.667061.337
22_R26_K0.666171.335
87_T91_A0.660731.324
31_S34_T0.647481.297
21_I32_R0.644321.291
19_K27_R0.643831.290
9_Q13_A0.630691.264
62_L66_V0.628181.259
61_E64_A0.610561.223
15_I24_A0.603421.209
83_V88_I0.594491.191
64_A68_E0.581771.166
61_E65_L0.579721.162
14_Y19_K0.579151.161
23_E27_R0.576661.156
24_A28_F0.574391.151
60_D63_K0.57011.142
30_V35_V0.559941.122
78_A88_I0.558771.120
86_S90_R0.55821.119
33_N37_R0.525821.054
75_R85_P0.523031.048
30_V34_T0.520181.042
30_V38_W0.514081.030
24_A35_V0.50651.015
91_A94_R0.503221.008
8_R38_W0.499871.002
74_L92_L0.494970.992
60_D64_A0.482720.967
78_A85_P0.473190.948
84_S90_R0.471460.945
88_I92_L0.469550.941
15_I39_L0.465490.933
47_L51_P0.460830.923
74_L88_I0.459940.922
63_K95_L0.459350.920
36_Y40_K0.457860.918
87_T90_R0.454630.911
23_E26_K0.448280.898
77_L92_L0.441790.885
31_S36_Y0.439070.880
91_A95_L0.438490.879
62_L91_A0.434510.871
10_R13_A0.432850.867
63_K66_V0.426830.855
60_D95_L0.425670.853
70_P77_L0.425370.852
8_R12_L0.415170.832
74_L85_P0.413670.829
65_L69_N0.407160.816
83_V91_A0.403480.809
49_P52_R0.397570.797
65_L68_E0.395020.792
39_L49_P0.39350.789
75_R79_E0.392340.786
38_W41_R0.389830.781
44_T52_R0.38740.776
73_T78_A0.387290.776
76_E79_E0.382670.767
14_Y24_A0.381860.765
7_L11_V0.379130.760
87_T94_R0.373980.749
48_E51_P0.372150.746
7_L28_F0.368190.738
25_A32_R0.363330.728
46_D50_K0.362470.726
10_R27_R0.361010.723
84_S89_W0.359810.721
21_I35_V0.358410.718
7_L10_R0.350640.703
88_I95_L0.343450.688
77_L81_L0.340360.682
50_K54_R0.338460.678
13_A16_E0.332320.666
37_R40_K0.329840.661
66_V69_N0.328480.658
11_V24_A0.326970.655
14_Y28_F0.323890.649
7_L24_A0.323650.649
42_K46_D0.322330.646
61_E67_E0.321470.644
47_L50_K0.319030.639
89_W98_T0.317320.636
7_L30_V0.314290.630
25_A31_S0.313170.628
70_P73_T0.313020.627
35_V39_L0.310770.623
64_A67_E0.310150.622
40_K43_E0.309130.619
85_P92_L0.308430.618
48_E52_R0.308150.617
73_T77_L0.308120.617
49_P53_G0.306830.615
33_N40_K0.306320.614
14_Y18_G0.305260.612
90_R94_R0.305240.612
50_K53_G0.30490.611
39_L43_E0.304290.610
74_L83_V0.29650.594
41_R44_T0.294080.589
76_E80_R0.294070.589
69_N72_A0.293230.588
65_L80_R0.289690.581
78_A82_G0.288910.579
64_A95_L0.284620.570
7_L35_V0.282870.567
25_A30_V0.282710.567
41_R45_G0.279110.559
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
3hotA199.40.319
1u78A0.991699.40.33
2lvsA0.840399.30.349
1pdnC0.806799.10.414
1k78A0.8571990.429
2k27A0.974898.80.478
2elhA0.563980.607
1hlvA0.798397.80.63
3gbgA0.899297.70.639
2jn6A0.764797.60.649

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