GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DEDD_Tnp_IS110 - Transposase
Pfam: PF01548 (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. )
Length: 144
Sequences: 2498
Seq/Len: 17.35
HH_delta: 0.809 (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
51_V106_L0.941634.273
81_V102_I0.561832.549
131_R135_V0.556792.526
137_E140_Q0.548922.491
137_E144_R0.532142.415
10_T27_K0.493742.240
4_I38_L0.485572.203
51_V102_I0.452342.052
139_T143_N0.451692.049
14_C99_A0.447272.029
82_K85_R0.445842.023
50_V71_I0.441192.002
52_M73_V0.425751.932
135_V138_R0.424841.928
13_V38_L0.415141.884
4_I11_H0.409331.857
16_I103_A0.399411.812
31_D34_G0.391231.775
65_F68_D0.381551.731
12_D27_K0.374921.701
138_R142_K0.365751.660
93_K98_D0.36521.657
49_L74_V0.36251.645
104_R108_R0.347931.579
7_S12_D0.346051.570
64_D122_R0.335441.522
35_L65_F0.333181.512
7_S10_T0.33041.499
137_E141_L0.3281.488
42_L50_V0.322781.465
35_L61_P0.319371.449
2_V15_V0.315341.431
3_G103_A0.309931.406
140_Q143_N0.309571.405
26_F41_W0.300571.364
6_V52_M0.296571.346
141_L144_R0.296461.345
39_L65_F0.296341.345
130_R134_L0.290811.320
28_F34_G0.287831.306
65_F69_A0.286731.301
4_I13_V0.28591.297
85_R101_A0.283761.288
12_D25_R0.273171.239
2_V13_V0.271491.232
63_A73_V0.270811.229
16_I107_R0.270691.228
118_S121_I0.270411.227
14_C100_R0.270191.226
130_R141_L0.268071.216
52_M63_A0.267711.215
4_I62_L0.262761.192
1_F107_R0.260731.183
2_V42_L0.26061.182
92_A97_I0.258361.172
12_D96_K0.257051.166
7_S11_H0.25571.160
79_L83_R0.253861.152
136_K140_Q0.252721.147
54_A78_P0.251511.141
40_D43_A0.248841.129
36_E40_D0.246791.120
76_V81_V0.239051.085
28_F41_W0.23861.083
11_H30_N0.238141.081
133_Q144_R0.236841.075
51_V76_V0.235531.069
50_V66_L0.234611.065
100_R104_R0.233131.058
63_A75_V0.227071.030
54_A75_V0.226441.027
55_T58_Y0.225491.023
37_K40_D0.223241.013
42_L66_L0.220210.999
59_W75_V0.220140.999
6_V11_H0.217690.988
15_V45_L0.216240.981
25_R100_R0.215020.976
118_S122_R0.213180.967
130_R144_R0.2130.966
119_E123_A0.211390.959
95_D98_D0.20910.949
29_E34_G0.209070.949
34_G38_L0.208910.948
14_C103_A0.207520.942
139_T142_K0.2060.935
58_Y77_N0.203460.923
11_H28_F0.201870.916
74_V106_L0.200690.911
132_E136_K0.198220.899
67_Q116_V0.195810.888
135_V139_T0.195720.888
33_A37_K0.193740.879
130_R133_Q0.1930.876
49_L72_E0.192330.873
13_V41_W0.191460.869
3_G99_A0.191320.868
120_E123_A0.189180.858
122_R126_E0.18620.845
39_L69_A0.185860.843
40_D44_S0.184960.839
5_D8_K0.184690.838
76_V105_L0.184490.837
52_M75_V0.184210.836
133_Q140_Q0.184050.835
43_A71_I0.183960.835
14_C25_R0.18330.832
17_D23_L0.183260.832
1_F106_L0.181470.823
47_P72_E0.179720.815
133_Q136_K0.177280.804
39_L71_I0.177130.804
39_L43_A0.1770.803
2_V50_V0.175640.797
68_D119_E0.174090.790
2_V5_D0.172830.784
34_G37_K0.170950.776
133_Q137_E0.169990.771
44_S68_D0.169820.771
35_L62_L0.168880.766
15_V24_R0.167810.761
22_K100_R0.16780.761
100_R110_Q0.167370.759
97_I102_I0.166790.757
77_N80_Q0.165570.751
6_V58_Y0.164950.748
91_R97_I0.164760.748
2_V48_V0.164290.745
25_R96_K0.163180.740
17_D20_G0.162980.740
126_E130_R0.161920.735
124_L128_V0.158360.719
52_M102_I0.158190.718
56_G82_K0.157620.715
102_I105_L0.157310.714
51_V111_L0.157040.713
52_M59_W0.157020.712
33_A36_E0.156380.710
27_K96_K0.155920.707
32_P36_E0.155660.706
28_F38_L0.15440.701
79_L91_R0.153230.695
7_S59_W0.152960.694
40_D69_A0.152330.691
52_M66_L0.152230.691
81_V105_L0.151160.686
40_D47_P0.150780.684
49_L106_L0.15070.684
97_I101_A0.150540.683
4_I66_L0.150460.683
117_P122_R0.150450.683
124_L144_R0.150120.681
36_E136_K0.149920.680
30_N35_L0.149610.679
84_F105_L0.149260.677
54_A94_T0.148760.675
125_R128_V0.148720.675
63_A67_Q0.148420.673
63_A116_V0.147310.668
122_R125_R0.146110.663
17_D21_E0.145040.658
104_R107_R0.143850.653
61_P65_F0.143790.652
121_I124_L0.143650.652
24_R41_W0.142570.647
84_F108_R0.142010.644
35_L69_A0.141770.643
77_N82_K0.137330.623
13_V28_F0.13690.621
14_C22_K0.13660.620
81_V101_A0.136190.618
99_A103_A0.135930.617
29_E43_A0.135790.616
66_L71_I0.135440.615
126_E129_R0.134750.611
53_E58_Y0.134260.609
54_A102_I0.133840.607
42_L49_L0.133830.607
52_M56_G0.133640.606
22_K25_R0.132430.601
27_K33_A0.132370.601
3_G66_L0.131590.597
117_P125_R0.131550.597
78_P81_V0.131260.596
13_V26_F0.130840.594
17_D107_R0.130670.593
63_A114_V0.129410.587
127_L131_R0.129390.587
50_V73_V0.12860.584
103_A125_R0.128330.582
25_R99_A0.127990.581
19_N47_P0.127620.579
18_P139_T0.127270.577
19_N27_K0.126930.576
94_T102_I0.12680.575
37_K43_A0.126480.574
62_L66_L0.126330.573
125_R129_R0.125990.572
36_E65_F0.125710.570
59_W63_A0.12540.569
105_L109_G0.125060.567
74_V113_P0.124830.566
3_G14_C0.124290.564
132_E142_K0.124070.563
39_L66_L0.123250.559
46_G67_Q0.122770.557
7_S76_V0.12260.556
24_R45_L0.122370.555
90_R100_R0.121740.552
7_S62_L0.121520.551
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
4ep4A0.930696.90.809
1hjrA0.916796.60.816
1vhxA0.840394.70.844
3psfA0.972294.60.845
3psiA0.972294.30.847
1nu0A0.770892.80.855
3bzcA0.993192.50.857
3c6aA0.937592.30.858
1iv0A0.576489.30.868
3cpeA0.951486.90.873
If you are interested in a protein containing this domain,
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