GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GTP_EFTU_D2 - Elongation factor Tu domain 2
Pfam: PF03144 (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: CL0023
Length: 74
Sequences: 11836
Seq/Len: 159.95
HH_delta: -0.007 (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
52_A58_V2.243583.552
14_K17_D1.757712.783
18_K34_K1.567572.482
4_A67_I1.497632.371
12_T51_G1.422022.251
14_K51_G1.420882.249
12_T49_V1.298972.056
34_K59_A1.251241.981
19_V35_I1.245451.972
12_T47_E1.159711.836
6_G60_I1.080071.710
37_S48_A1.073891.700
49_V52_A1.05141.665
14_K47_E1.007711.595
48_A54_A0.894221.416
21_V67_I0.887011.404
56_D73_L0.878791.391
15_K50_A0.822591.302
13_L35_I0.822491.302
21_V73_L0.802591.271
12_T53_N0.791231.253
7_R53_N0.784841.243
37_S44_D0.779531.234
68_R71_D0.746831.182
5_T41_F0.726961.151
40_M43_G0.714821.132
15_K48_A0.701911.111
6_G58_V0.658841.043
37_S57_I0.655671.038
15_K44_D0.649121.028
8_V54_A0.638771.011
21_V33_V0.614480.973
8_V48_A0.611290.968
36_K59_A0.61120.968
6_G56_D0.592740.938
6_G54_A0.585460.927
13_L48_A0.584330.925
36_K57_I0.57010.903
13_L38_I0.564660.894
15_K37_S0.530340.840
40_M45_V0.521520.826
15_K38_I0.513860.814
33_V64_N0.5080.804
67_I71_D0.502630.796
33_V67_I0.498980.790
3_V59_A0.495660.785
63_L67_I0.491290.778
33_V63_L0.486380.770
40_M49_V0.481460.762
39_F44_D0.474790.752
42_N45_V0.473830.750
8_V52_A0.470.744
7_R52_A0.439950.697
40_M52_A0.433910.687
65_D68_R0.426160.675
45_V54_A0.426050.675
19_V33_V0.425380.673
8_V58_V0.418010.662
36_K61_I0.411760.652
15_K46_Q0.407080.644
62_G65_D0.403870.639
39_F42_N0.402630.637
9_Y72_T0.40010.633
5_T55_G0.399480.632
4_A63_L0.396920.628
13_L56_D0.39360.623
41_F59_A0.393070.622
64_N67_I0.391470.620
10_S43_G0.387750.614
21_V71_D0.385060.610
39_F43_G0.383270.607
44_D55_G0.377280.597
4_A73_L0.37510.594
1_G16_G0.368040.583
3_V41_F0.368040.583
7_R55_G0.355280.562
43_G62_G0.351570.557
7_R50_A0.348580.552
52_A55_G0.346910.549
38_I48_A0.341080.540
67_I73_L0.340080.538
48_A61_I0.338080.535
39_F48_A0.337010.534
2_R36_K0.331570.525
2_R68_R0.331180.524
13_L58_V0.329950.522
3_V46_Q0.329540.522
10_S20_R0.323450.512
8_V11_G0.319390.506
33_V59_A0.319150.505
19_V73_L0.318970.505
16_G34_K0.318910.505
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
3vqtA0.918999-0.007
2h5eA0.918998.90.007
3tr5A0.918998.90.018
4fn5A0.918998.90.021
2xexA0.918998.90.023
2rdo70.918998.90.027
1darA0.918998.90.03
2dy1A0.891998.70.086
1n0uA0.986598.60.129
3j2k70.918998.60.138

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