GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_1_2 - Transposase DDE domain
Pfam: PF13586 (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: 88
Sequences: 2976
Seq/Len: 33.82
HH_delta: 0.701 (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
48_W52_R0.93763.526
16_L21_I0.674942.538
62_R77_F0.57672.169
47_R51_E0.55462.085
70_L73_S0.552492.077
49_V52_R0.485131.824
3_A25_I0.466881.756
9_S12_L0.451851.699
12_L15_Y0.443031.666
6_G9_S0.442031.662
14_E18_E0.420891.583
75_L79_H0.404481.521
46_R49_V0.379411.427
1_V21_I0.364961.372
30_R33_K0.351611.322
77_F81_A0.346331.302
55_A59_R0.344461.295
79_H83_I0.333811.255
51_E54_F0.329291.238
17_R23_P0.326581.228
80_L83_I0.318491.198
53_T57_L0.313491.179
11_A14_E0.308581.160
52_R56_W0.301081.132
71_A75_L0.298441.122
15_Y18_E0.297711.119
26_P44_Y0.296731.116
67_Y74_F0.295831.112
27_K32_K0.294021.106
52_R55_A0.290351.092
57_L81_A0.289291.088
57_L82_C0.282061.061
16_L19_R0.281771.060
38_K41_F0.281171.057
2_L24_V0.2771.042
48_W56_W0.274731.033
78_V82_C0.269661.014
41_F45_K0.2681.008
79_H82_C0.265420.998
1_V16_L0.264590.995
23_P26_P0.263350.990
61_R68_E0.261130.982
19_R22_R0.258860.973
5_K44_Y0.258710.973
75_L83_I0.257240.967
26_P29_G0.256760.965
54_F82_C0.25580.962
2_L43_L0.254810.958
10_R14_E0.2520.948
40_D43_L0.250950.944
4_D7_Y0.250180.941
13_R37_R0.249240.937
40_D44_Y0.24820.933
67_Y70_L0.247190.929
8_D28_R0.245730.924
15_Y19_R0.244690.920
27_K37_R0.244010.918
72_S76_A0.243030.914
17_R20_G0.241260.907
72_S80_L0.240590.905
58_K64_A0.239370.900
62_R68_E0.238770.898
68_E73_S0.237020.891
27_K38_K0.235840.887
55_A60_F0.23560.886
8_D13_R0.23430.881
48_W55_A0.234120.880
56_W59_R0.232610.875
69_K74_F0.229840.864
12_L16_L0.225930.850
2_L44_Y0.22240.836
2_L26_P0.221150.832
4_D47_R0.220650.830
14_E20_G0.219180.824
11_A22_R0.218970.823
56_W61_R0.217220.817
7_Y47_R0.216920.816
2_L46_R0.216750.815
27_K30_R0.215070.809
50_V53_T0.212660.800
42_R46_R0.212260.798
67_Y71_A0.210630.792
8_D23_P0.208340.783
75_L82_C0.208140.783
8_D25_I0.20740.780
5_K28_R0.206360.776
68_E77_F0.206270.776
6_G51_E0.204140.768
54_F62_R0.203750.766
10_R31_R0.202840.763
49_V53_T0.198910.748
4_D51_E0.196770.740
29_G32_K0.195340.735
11_A18_E0.193640.728
5_K26_P0.191970.722
28_R31_R0.191920.722
73_S76_A0.191190.719
19_R27_K0.190960.718
16_L23_P0.190710.717
11_A15_Y0.186820.702
18_E38_K0.186450.701
63_L77_F0.186230.700
66_R74_F0.185730.698
17_R59_R0.185720.698
45_K48_W0.185160.696
27_K39_F0.184620.694
43_L46_R0.183380.690
8_D30_R0.182870.688
64_A68_E0.179950.677
29_G42_R0.179930.677
17_R22_R0.179330.674
24_V39_F0.179320.674
50_V54_F0.179240.674
36_P39_F0.17720.666
27_K31_R0.176240.663
12_L33_K0.176060.662
33_K38_K0.175180.659
22_R27_K0.173790.653
66_R69_K0.172560.649
76_A79_H0.172220.648
37_R40_D0.17110.643
2_L41_F0.17090.643
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
1musA194.40.701
4fw1A0.852386.20.755
1ex4A0.818283.90.762
1c6vA0.818283.10.764
3av9A0.818282.80.765
1cxqA0.852381.70.768
1k6yA0.818281.30.769
1c0mA0.840979.30.773
3kksA0.806878.20.775
4fw2A0.8523770.777
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