GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Transposase_20 - Transposase IS116IS110IS902 family
Pfam: PF02371 (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: CL0198
Length: 87
Sequences: 2449
Seq/Len: 28.15
HH_delta: 0.787 (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
3_L6_S0.839882.917
22_I34_L0.774012.688
38_A64_L0.748652.600
29_K33_Q0.692752.406
70_Q73_W0.663092.303
30_S33_Q0.639832.222
28_F37_Y0.62772.180
5_T12_P0.624792.170
46_Q51_V0.591642.055
35_A41_A0.534551.857
17_T67_A0.499771.736
14_T67_A0.474161.647
4_L15_A0.466621.621
69_Y73_W0.46321.609
14_T71_A0.440591.530
66_R70_Q0.439641.527
73_W76_I0.43081.496
10_I15_A0.425531.478
21_E61_N0.415141.442
58_K65_R0.411721.430
37_Y61_N0.396081.376
21_E63_R0.380411.321
22_I25_I0.37941.318
10_I14_T0.378831.316
47_S51_V0.368141.279
60_G65_R0.3471.205
5_T15_A0.327391.137
56_I60_G0.314041.091
56_I65_R0.303851.055
44_P51_V0.303471.054
65_R69_Y0.303371.054
41_A59_R0.300431.043
35_A42_P0.299161.039
18_L64_L0.295251.026
17_T63_R0.294681.024
35_A40_L0.292491.016
33_Q36_S0.289271.005
3_L7_I0.288131.001
10_I18_L0.284020.986
41_A57_S0.283020.983
72_A75_A0.277420.964
22_I38_A0.27680.961
74_S78_H0.275550.957
41_A44_P0.273150.949
16_A20_A0.269430.936
66_R69_Y0.26790.931
71_A75_A0.264230.918
39_G48_G0.259760.902
10_I71_A0.259190.900
4_L10_I0.258930.899
40_L69_Y0.253150.879
46_Q49_K0.251230.873
60_G69_Y0.249090.865
67_A71_A0.242880.844
13_I17_T0.242860.844
45_Y54_G0.240930.837
36_S42_P0.238950.830
56_I69_Y0.23220.807
44_P53_S0.227740.791
36_S41_A0.223840.777
73_W77_R0.223530.776
45_Y50_K0.220260.765
43_R69_Y0.220240.765
39_G65_R0.220020.764
18_L34_L0.219670.763
14_T70_Q0.21820.758
52_R55_R0.217370.755
43_R57_S0.216840.753
23_G27_R0.215960.750
13_I16_A0.215320.748
30_S47_S0.214010.743
70_Q74_S0.213480.741
2_E12_P0.211410.734
71_A74_S0.209530.728
6_S19_L0.209110.726
33_Q53_S0.208910.726
17_T21_E0.206320.717
23_G26_S0.206020.716
23_G59_R0.2060.716
14_T64_L0.204790.711
36_S48_G0.202360.703
31_A35_A0.198860.691
40_L68_L0.19880.690
65_R68_L0.197780.687
32_K53_S0.196720.683
40_L65_R0.196530.683
22_I37_Y0.196510.683
7_I71_A0.194060.674
27_R30_S0.189660.659
20_A63_R0.18750.651
18_L24_D0.186680.648
35_A44_P0.185590.645
16_A63_R0.183240.636
35_A59_R0.182580.634
33_Q47_S0.181670.631
7_I10_I0.181320.630
27_R47_S0.180610.627
62_R76_I0.179430.623
60_G68_L0.178060.618
9_G74_S0.174890.607
63_R66_R0.172990.601
58_K62_R0.172140.598
12_P16_A0.171080.594
17_T31_A0.170430.592
46_Q50_K0.169590.589
14_T18_L0.169440.589
54_G57_S0.165630.575
2_E26_S0.163420.568
19_L29_K0.162960.566
5_T11_G0.162730.565
29_K78_H0.159070.553
61_N64_L0.1590.552
2_E6_S0.158760.551
48_G52_R0.157770.548
22_I33_Q0.157490.547
21_E38_A0.157210.546
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
3arcU0.758694.40.787
1keaA194.40.787
3c65A0.609293.60.794
2bgwA0.6552930.798
2i5hA0.8391920.805
2duyA0.574791.80.806
2eduA0.678291.70.806
1s5lU0.747191.50.807
2abkA0.97791.50.807
2lyhA0.620791.50.807
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