GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_1_2 - Transposase DDE domain
Pfam: PF13586 (v26) Consensus Sequence
Clan: CL0219
Length: 88
Sequences: 2130
Seq/Len: 24.2
HH_delta: 0.649 (11Mar13)
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
48_W52_R0.812543.465
16_L21_I0.62472.664
70_L73_S0.536942.289
9_S12_L0.52872.254
62_R77_F0.443321.890
4_D7_Y0.394681.683
49_V52_R0.377121.608
3_A25_I0.365511.558
75_L79_Y0.358311.528
6_G9_S0.357341.524
52_R55_A0.356951.522
46_R49_V0.349141.489
14_Q18_E0.342021.458
11_A14_Q0.322561.375
12_L15_W0.313821.338
55_A59_R0.313341.336
13_R37_R0.311091.326
73_S76_A0.291361.242
26_P44_Y0.285911.219
62_R68_E0.281311.199
72_E76_A0.279171.190
48_W56_W0.278121.186
27_P37_R0.269531.149
24_V44_Y0.269371.149
69_K80_L0.265711.133
69_K74_F0.265531.132
67_Y71_A0.261741.116
54_F62_R0.258211.101
43_L46_R0.257741.099
48_W55_A0.257331.097
68_E77_F0.257131.096
27_P32_K0.252631.077
15_W19_R0.249091.062
8_D28_R0.243611.039
2_L24_V0.240791.027
8_D23_P0.239731.022
2_L44_Y0.239511.021
41_F45_P0.239191.020
71_A75_L0.237061.011
15_W18_E0.235821.006
16_L19_R0.235161.003
66_R74_F0.234040.998
52_R56_W0.230570.983
5_K28_R0.23040.982
67_Y74_F0.229140.977
17_R23_P0.228480.974
23_P26_P0.225930.963
50_V53_T0.225410.961
61_R68_E0.223970.955
64_A67_Y0.222510.949
26_P29_G0.221750.946
2_L46_R0.219470.936
56_W61_R0.219190.935
2_L26_P0.214480.915
27_P30_R0.213150.909
14_Q19_R0.21270.907
44_Y66_R0.208880.891
11_A20_G0.206870.882
46_R52_R0.205340.876
14_Q38_R0.205320.875
53_T57_L0.20490.874
24_V40_D0.203470.868
1_V16_L0.201390.859
12_L16_L0.200830.856
57_L63_L0.198530.847
76_A80_L0.198030.844
58_K64_A0.196460.838
8_D13_R0.196140.836
69_K73_S0.19550.834
70_L80_L0.191110.815
27_P31_R0.190230.811
76_A79_Y0.18920.807
61_R66_R0.187270.798
22_R37_R0.185340.790
40_D43_L0.1820.776
59_R64_A0.181940.776
10_D14_Q0.18180.775
60_F65_T0.180090.768
64_A71_A0.179170.764
49_V56_W0.179050.763
72_E79_Y0.178920.763
11_A15_W0.177640.757
17_R59_R0.177470.757
28_R31_R0.175950.750
24_V39_F0.174870.746
27_P39_F0.174760.745
10_D31_R0.174650.745
1_V21_I0.174180.743
2_L43_L0.17070.728
8_D31_R0.170290.726
7_Y47_R0.170120.725
14_Q17_R0.169350.722
5_K44_Y0.168990.721
22_R33_K0.168790.720
63_L77_F0.167640.715
64_A78_V0.166660.711
57_L61_R0.166460.710
3_A8_D0.16560.706
14_Q20_G0.165470.706
56_W59_R0.165420.705
21_I31_R0.165120.704
11_A18_E0.163790.698
22_R45_P0.163050.695
15_W42_E0.163040.695
5_K29_G0.161720.690
68_E73_S0.160940.686
40_D48_W0.160730.685
49_V53_T0.160330.684
47_R51_E0.159990.682
33_K41_F0.159520.680
22_R27_P0.159180.679
70_L77_F0.158770.677
60_F73_S0.157170.670
29_G32_K0.156330.667
69_K72_E0.156070.665
27_P38_R0.155810.664
33_K46_R0.155490.663
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
1musA196.50.649
1cxqA0.852374.50.783
1k6yA0.818273.80.784
1ex4A0.818273.50.784
3av9A0.818272.90.786
1c6vA0.818272.10.787
1c0mA0.8409720.787
3kksA0.806869.40.79
3hphA0.818267.40.793
2x78A0.8295640.798
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