GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_IS1595 - ISXO2-like transposase domain
Pfam: PF12762 (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: CL0219
Length: 151
Sequences: 1619
Seq/Len: 10.72
HH_delta: 0.418 (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
39_G120_W0.583023.823
11_T124_K0.510893.350
114_N117_E0.408152.677
60_S63_T0.393512.581
39_G116_I0.370052.427
8_I78_I0.349242.290
121_S125_R0.344872.262
40_A67_I0.32242.114
58_D63_T0.308122.021
7_E43_R0.302311.982
117_E120_W0.265761.743
13_F37_V0.264671.736
10_E86_Y0.260081.706
116_I120_W0.259711.703
65_K69_Q0.24941.636
61_A88_G0.24851.630
61_A65_K0.219541.440
80_T103_K0.212291.392
11_T123_L0.211261.385
54_F70_E0.210971.384
64_L80_T0.208741.369
13_F127_L0.206141.352
79_I106_V0.204391.340
112_H115_W0.200031.312
13_F123_L0.198291.300
118_S122_R0.197621.296
11_T120_W0.193941.272
12_Y36_P0.191341.255
122_R126_W0.188751.238
66_P70_E0.188621.237
65_K91_K0.186711.224
84_R87_N0.179021.174
12_Y34_K0.178151.168
107_V112_H0.17591.154
118_S121_S0.17521.149
51_V119_F0.1741.141
54_F67_I0.171831.127
77_T104_G0.169141.109
56_V63_T0.165751.087
26_K30_G0.165131.083
107_V113_T0.164711.080
108_D111_V0.162981.069
80_T96_H0.158971.042
5_I79_I0.156961.029
66_P73_E0.156371.025
62_E70_E0.15471.014
64_L85_A0.153391.006
65_K88_G0.152631.001
40_A52_F0.152330.999
82_G100_N0.15150.994
41_V115_W0.146730.962
87_N105_F0.145560.955
57_P63_T0.144580.948
40_A118_S0.144570.948
66_P69_Q0.143440.941
98_T101_H0.141410.927
100_N103_K0.140170.919
107_V110_G0.139940.918
80_T86_Y0.139020.912
86_Y111_V0.138360.907
61_A87_N0.137860.904
59_R84_R0.137440.901
14_G33_N0.136980.898
75_G97_E0.13690.898
43_R112_H0.135770.890
107_V111_V0.135720.890
86_Y113_T0.135290.887
31_S56_V0.134860.884
38_F64_L0.13390.878
106_V113_T0.133670.877
74_P99_V0.133050.873
42_E68_I0.132330.868
115_W120_W0.131730.864
59_R83_W0.131430.862
94_Y98_T0.130850.858
106_V114_N0.129860.852
59_R85_A0.129750.851
12_Y59_R0.12720.834
39_G117_E0.12720.834
88_G92_D0.126390.829
56_V96_H0.125950.826
8_I80_T0.125780.825
83_W86_Y0.125020.820
79_I111_V0.124910.819
121_S128_K0.124820.819
18_N28_G0.124780.818
26_K63_T0.12450.816
7_E115_W0.12440.816
9_D81_D0.124310.815
68_I94_Y0.123990.813
122_R128_K0.123580.810
43_R113_T0.123320.809
111_V117_E0.123290.809
82_G109_G0.122860.806
91_K107_V0.122550.804
16_R30_G0.122080.801
74_P92_D0.122050.800
35_V82_G0.121590.797
122_R125_R0.12110.794
77_T125_R0.120590.791
44_N63_T0.120570.791
41_V119_F0.120510.790
11_T14_G0.120370.789
62_E90_A0.12030.789
70_E90_A0.120280.789
83_W108_D0.120110.788
115_W118_S0.12010.788
12_Y121_S0.119970.787
11_T37_V0.119360.783
54_F63_T0.119030.781
69_Q74_P0.1190.780
29_R33_N0.11880.779
80_T91_K0.117810.773
121_S127_L0.117530.771
66_P71_H0.117450.770
60_S71_H0.116840.766
95_D99_V0.116820.766
110_G115_W0.116470.764
123_L127_L0.116360.763
61_A91_K0.116250.762
78_I101_H0.116240.762
120_W124_K0.116120.761
7_E10_E0.116070.761
101_H117_E0.115090.755
8_I40_A0.115060.755
88_G91_K0.115040.754
79_I109_G0.114810.753
57_P69_Q0.114410.750
12_Y84_R0.114250.749
12_Y85_A0.113580.745
104_G107_V0.113390.744
32_K55_V0.112880.740
42_E76_S0.112770.740
84_R108_D0.11250.738
114_N120_W0.112130.735
78_I89_L0.111870.734
11_T59_R0.111380.730
37_V119_F0.111180.729
62_E66_P0.111010.728
53_M123_L0.110910.727
69_Q73_E0.110750.726
91_K97_E0.110540.725
82_G111_V0.110440.724
94_Y100_N0.109790.720
56_V124_K0.109760.720
76_S101_H0.109530.718
78_I94_Y0.108740.713
82_G117_E0.108580.712
95_D98_T0.108290.710
82_G108_D0.108090.709
6_V57_P0.107970.708
38_F56_V0.107760.707
54_F102_S0.107470.705
87_N108_D0.10690.701
96_H100_N0.106740.700
79_I97_E0.106710.700
64_L86_Y0.106480.698
76_S96_H0.106030.695
14_G34_K0.105720.693
5_I92_D0.105280.690
61_A69_Q0.10520.690
18_N102_S0.104960.688
73_E77_T0.104720.687
8_I12_Y0.10380.681
82_G98_T0.103550.679
97_E100_N0.103520.679
112_H118_S0.103150.676
118_S125_R0.103080.676
113_T117_E0.102780.674
26_K29_R0.102380.671
105_F108_D0.101010.662
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
2f7tA0.980199.80.418
3f2kA0.980199.70.424
3hotA0.980199.70.434
1c6vA0.834498.50.703
1c0mA0.867598.50.708
3av9A0.834498.40.711
1bcoA0.927298.40.715
3f9kA0.834498.30.719
3kksA0.827898.30.721
1ex4A0.834498.30.724

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