GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_1_3 - Transposase DDE domain
Pfam: PF13612 (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: 155
Sequences: 2353
Seq/Len: 15.18
HH_delta: 0.759 (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
49_H91_Y0.965275.107
52_V134_I0.701413.711
50_L138_F0.69163.659
13_F142_K0.553132.927
131_R135_E0.482462.553
16_P43_F0.404272.139
49_H64_T0.397052.101
50_L58_I0.392722.078
53_N57_E0.367321.944
66_A70_D0.362791.920
69_H72_K0.351461.860
39_A45_G0.351041.857
88_D135_E0.335821.777
56_G140_Q0.323441.711
132_R136_T0.320431.695
14_P45_G0.306931.624
133_I136_T0.306541.622
71_R90_G0.304671.612
9_I133_I0.288421.526
13_F48_L0.2861.513
10_I87_G0.279991.481
58_I137_V0.274721.454
49_H60_A0.268271.419
11_D135_E0.261551.384
52_V137_V0.259891.375
87_G109_T0.259051.371
17_V20_N0.24911.318
53_N59_V0.247181.308
45_G66_A0.242521.283
124_D128_L0.236881.253
51_L85_L0.236381.251
8_Y59_V0.231751.226
48_L63_L0.230941.222
11_D131_R0.227021.201
8_Y85_L0.224281.187
136_T140_Q0.222361.177
11_D70_D0.220341.166
117_N120_M0.220271.165
71_R92_I0.216681.146
64_T73_V0.213631.130
139_S143_N0.211581.119
50_L137_V0.211051.117
135_E138_F0.210151.112
124_D127_L0.206531.093
11_D88_D0.203271.076
87_G107_L0.196131.038
131_R134_I0.195671.035
136_T139_S0.19511.032
71_R93_S0.193261.023
58_I61_F0.190671.009
8_Y51_L0.186210.985
134_I138_F0.184470.976
56_G136_T0.184020.974
51_L59_V0.183080.969
92_I109_T0.182880.968
86_F108_I0.180050.953
12_S47_K0.179190.948
114_N117_N0.17870.946
140_Q143_N0.178310.943
35_R57_E0.177520.939
135_E139_S0.177340.938
95_E106_K0.176120.932
47_K70_D0.174450.923
86_F130_K0.173440.918
37_Y41_G0.172030.910
89_K125_K0.171710.909
76_E79_E0.171560.908
89_K109_T0.170750.903
108_I111_R0.170430.902
127_L141_L0.169550.897
122_L125_K0.168770.893
92_I112_R0.168140.890
88_D131_R0.166890.883
52_V133_I0.166680.882
35_R38_C0.166020.878
55_S123_F0.160430.849
90_G135_E0.160130.847
15_I48_L0.159660.845
92_I107_L0.159580.844
69_H89_K0.158350.838
46_F65_P0.158020.836
111_R124_D0.157460.833
12_S73_V0.156460.828
74_L94_K0.156380.827
17_V44_Y0.156290.827
137_V141_L0.155550.823
18_C21_I0.155310.822
68_V72_K0.15530.822
14_P132_R0.154870.819
64_T91_Y0.15470.819
60_A77_L0.153730.813
74_L78_S0.153340.811
69_H90_G0.15330.811
19_H44_Y0.153150.810
122_L126_L0.150610.797
140_Q145_F0.15020.795
7_I54_D0.150070.794
38_C66_A0.149880.793
49_H77_L0.149560.791
7_I86_F0.148880.788
65_P68_V0.148090.784
12_S70_D0.14750.780
84_K92_I0.147180.779
118_K121_P0.147050.778
134_I139_S0.146630.776
49_H87_G0.144560.765
84_K106_K0.144210.763
21_I118_K0.1440.762
12_S139_S0.143550.760
34_Y67_N0.141540.749
12_S135_E0.140270.742
33_A36_G0.139930.740
88_D134_I0.139880.740
61_F65_P0.139340.737
136_T144_Q0.13820.731
14_P38_C0.13680.724
116_K119_L0.135560.717
79_E95_E0.134760.713
130_K133_I0.134570.712
33_A38_C0.134110.710
110_P124_D0.133590.707
8_Y84_K0.133260.705
125_K129_R0.132970.704
34_Y113_K0.132540.701
138_F142_K0.132210.700
111_R123_F0.132040.699
137_V140_Q0.131620.696
12_S49_H0.131230.694
60_A91_Y0.130410.690
87_G90_G0.130330.690
56_G87_G0.130270.689
70_D90_G0.130070.688
84_K108_I0.129640.686
107_L128_L0.12930.684
86_F128_L0.128730.681
128_L131_R0.127710.676
76_E122_L0.127560.675
72_K75_E0.126950.672
55_S62_T0.12660.670
13_F138_F0.126570.670
51_L77_L0.126030.667
35_R44_Y0.124890.661
85_L119_L0.12470.660
111_R120_M0.124520.659
49_H73_V0.124160.657
123_F145_F0.12390.656
114_N118_K0.123510.653
79_E85_L0.123440.653
140_Q144_Q0.123440.653
84_K129_R0.123310.652
70_D88_D0.122340.647
94_K106_K0.122220.647
37_Y40_M0.121690.644
8_Y145_F0.121450.643
54_D133_I0.120810.639
64_T68_V0.120390.637
57_E63_L0.119810.634
126_L129_R0.11970.633
48_L58_I0.119420.632
128_L132_R0.11940.632
50_L134_I0.119350.631
112_R115_M0.119140.630
89_K112_R0.118920.629
94_K107_L0.117930.624
139_S144_Q0.117830.623
20_N33_A0.117810.623
80_N118_K0.117790.623
18_C45_G0.117540.622
118_K123_F0.117290.621
48_L116_K0.117110.620
42_W48_L0.116650.617
123_F127_L0.11650.616
111_R114_N0.116490.616
68_V120_M0.116040.614
36_G39_A0.1160.614
76_E116_K0.115960.614
51_L65_P0.115460.611
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
1musA0.935597.60.759
3hotA0.858185.80.866
1c0mA0.748469.70.884
1bcoA0.812966.30.887
3kksA0.709757.70.892
4fw1A0.748457.10.892
1cxqA0.748449.40.897
1ex4A0.72944.50.9
3av9A0.72939.40.903
4fcyA0.819434.70.906
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0244 seconds.