GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DDE_Tnp_1_6 - Transposase DDE domain
Pfam: PF13751 (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: 125
Sequences: 810
Seq/Len: 6.48
HH_delta: 0.906 (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
6_Q32_D0.406393.466
4_A38_L0.23672.019
104_G107_K0.236312.015
33_C36_C0.222421.897
2_C36_C0.21861.864
100_F111_E0.20041.709
102_Y107_K0.193351.649
88_F92_K0.18971.618
2_C33_C0.185351.581
87_V119_Y0.182051.553
10_F13_E0.180741.541
90_T119_Y0.180091.536
2_C42_C0.174131.485
70_T73_G0.174031.484
10_F26_Y0.173911.483
120_N123_R0.171361.461
27_R52_T0.16941.445
2_C8_L0.169151.443
1_I7_I0.168931.441
74_K77_Y0.168851.440
45_S48_G0.166671.421
89_G94_N0.166341.419
37_P40_E0.165771.414
88_F108_V0.160961.373
101_R111_E0.160841.372
11_K29_S0.159761.362
112_F116_A0.159671.362
91_I115_A0.15671.336
36_C42_C0.1551.322
83_K86_G0.151281.290
29_S32_D0.150411.283
33_C42_C0.1461.245
89_G119_Y0.143851.227
86_G90_T0.142461.215
76_L79_Q0.141871.210
97_L115_A0.141621.208
8_L42_C0.138451.181
93_R98_R0.137351.171
100_F112_F0.136091.161
101_R119_Y0.136031.160
73_G80_R0.133461.138
115_A118_A0.133351.137
108_V111_E0.132331.129
90_T95_H0.130191.110
68_L83_K0.129481.104
43_T49_R0.129341.103
53_I56_H0.128841.099
79_Q83_K0.128661.097
64_M67_R0.128251.094
95_H119_Y0.127311.086
118_A121_L0.126871.082
95_H122_K0.126231.077
46_K52_T0.126141.076
46_K66_E0.125961.074
81_S86_G0.122811.047
13_E26_Y0.120691.029
19_N71_E0.120371.027
61_R81_S0.11941.018
3_P42_C0.119061.015
8_L28_Y0.116780.996
89_G111_E0.116080.990
110_I119_Y0.115940.989
30_K39_R0.115080.981
53_I62_E0.114830.979
75_E79_Q0.114060.973
33_C39_R0.113660.969
29_S50_R0.111730.953
107_K110_I0.111730.953
58_E90_T0.111270.949
65_R116_A0.110360.941
67_R73_G0.110030.938
91_I119_Y0.109890.937
19_N23_R0.109480.934
112_F115_A0.108470.925
94_N119_Y0.108170.923
46_K91_I0.108020.921
14_Y23_R0.107580.917
107_K121_L0.106870.911
4_A37_P0.106850.911
45_S49_R0.106180.906
113_L116_A0.106010.904
87_V90_T0.105640.901
100_F116_A0.103660.884
101_R106_E0.103660.884
102_Y111_E0.103450.882
97_L111_E0.103390.882
61_R70_T0.103310.881
30_K34_K0.103150.880
101_R116_A0.1030.878
21_Y79_Q0.102910.878
22_Q25_F0.10270.876
63_K106_E0.102690.876
68_L73_G0.102090.871
90_T94_N0.101580.866
92_K111_E0.101280.864
102_Y113_L0.100960.861
5_G63_K0.100220.855
54_R61_R0.099520.849
58_E61_R0.099280.847
14_Y27_R0.098720.842
89_G108_V0.09860.841
76_L104_G0.098580.841
8_L87_V0.098170.837
39_R43_T0.098110.837
109_R113_L0.097670.833
58_E62_E0.097280.830
1_I5_G0.097130.828
116_A119_Y0.0970.827
89_G101_R0.096740.825
31_E40_E0.096730.825
90_T102_Y0.096410.822
91_I112_F0.096370.822
13_E55_P0.096120.820
87_V91_I0.096090.819
28_Y92_K0.096080.819
25_F48_G0.096020.819
77_Y80_R0.095790.817
74_K81_S0.09560.815
64_M110_I0.094920.810
84_V115_A0.094660.807
37_P79_Q0.094410.805
3_P49_R0.093810.800
11_K14_Y0.093720.799
37_P71_E0.092820.792
100_F119_Y0.092780.791
102_Y114_L0.092780.791
81_S88_F0.092480.789
70_T102_Y0.092350.788
100_F107_K0.092340.788
105_L109_R0.092140.786
36_C39_R0.091860.783
24_Y28_Y0.091830.783
103_R109_R0.091780.783
99_R103_R0.091460.780
77_Y86_G0.091370.779
97_L101_R0.091370.779
58_E94_N0.091240.778
9_R44_K0.091030.776
30_K38_L0.09090.775
45_S91_I0.090710.774
6_Q30_K0.090140.769
83_K89_G0.089740.765
12_G50_R0.089680.765
92_K108_V0.089630.764
4_A41_Q0.089530.764
8_L36_C0.089480.763
92_K99_R0.089360.762
54_R59_D0.089340.762
97_L113_L0.089320.762
87_V112_F0.088960.759
13_E22_Q0.088950.759
88_F111_E0.088930.758
9_R31_E0.088910.758
68_L86_G0.088840.758
83_K88_F0.088830.758
53_I88_F0.088320.753
22_Q78_K0.087750.748
40_E62_E0.087530.746
7_I25_F0.087490.746
114_L120_N0.087470.746
108_V120_N0.087460.746
44_K63_K0.087180.743
66_E72_E0.086720.740
87_V100_F0.086610.739
9_R22_Q0.086520.738
28_Y84_V0.086490.738
9_R32_D0.086410.737
41_Q62_E0.085860.732
73_G123_R0.08570.731
39_R42_C0.085110.726
73_G87_V0.084940.724
52_T55_P0.08490.724
103_R111_E0.084850.724
67_R70_T0.084630.722
68_L87_V0.084570.721
61_R68_L0.084550.721
95_H100_F0.08450.721
53_I58_E0.084360.719
33_C38_L0.084120.717
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
1keaA0.36836.20.906
2abkA0.36814.90.921
1kg2A0.4412.90.923
1ornA0.4488.80.928
2h7gX0.884.70.936
2k5dA0.3763.90.938
3vp7A0.4163.10.941
1g5tA0.46430.941
2qkdA0.962.90.942
4ddpA0.6242.70.943
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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