GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EFG_IV - Elongation factor G domain IV
Pfam: PF03764 (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: CL0329
Length: 120
Sequences: 3024
Seq/Len: 25.2
HH_delta: 0.089 (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
11_K120_G1.370983.618
65_E69_Q1.340463.537
17_E32_K1.264953.338
14_E36_R1.210913.195
50_E88_T1.188023.135
45_N65_E1.029812.717
38_E86_K0.977252.579
37_V87_V0.977132.578
82_V116_L0.931322.457
114_E118_K0.930362.455
44_G84_D0.930032.454
38_E88_T0.900672.377
12_E38_E0.787462.078
46_I86_K0.78222.064
32_K93_E0.780782.060
101_P105_R0.768052.027
36_R90_T0.764792.018
48_V86_K0.730581.928
34_I90_T0.708841.870
70_S105_R0.689321.819
12_E36_R0.675581.783
42_G84_D0.67081.770
35_L111_A0.670681.770
14_E90_T0.65661.733
100_S103_A0.649491.714
36_R88_T0.641021.691
45_N69_Q0.611441.613
63_A101_P0.598931.580
40_L43_G0.597541.577
68_F87_V0.58271.538
10_T120_G0.580221.531
36_R50_E0.568851.501
72_L85_V0.554541.463
45_N72_L0.534351.410
68_F108_A0.516631.363
40_L46_I0.491241.296
114_E117_K0.488531.289
13_V16_V0.483491.276
17_E34_I0.479651.266
18_E110_R0.47631.257
18_E21_K0.471.240
35_L68_F0.469341.238
76_P116_L0.455451.202
51_T55_Q0.450181.188
14_E34_I0.448451.183
112_F116_L0.440561.162
47_F89_L0.432221.140
64_I89_L0.429081.132
48_V88_T0.42631.125
56_L89_L0.417091.101
43_G46_I0.416181.098
57_P94_Y0.405891.071
16_V114_E0.405351.070
27_K100_S0.40111.058
13_V119_A0.400211.056
50_E90_T0.394791.042
40_L86_K0.393981.040
82_V112_F0.391571.033
9_I116_L0.368080.971
49_D52_E0.364410.962
71_A109_R0.362490.956
69_Q73_S0.359640.949
33_V89_L0.353460.933
106_A109_R0.346940.915
33_V108_A0.336020.887
95_H98_D0.335820.886
2_Q59_E0.331890.876
109_R113_R0.331260.874
49_D61_Q0.325150.858
82_V85_V0.322970.852
19_T32_K0.322110.850
72_L112_F0.31680.836
19_T30_F0.316540.835
18_E22_R0.313120.826
21_K28_R0.306290.808
10_T119_A0.3060.807
16_V115_A0.305650.807
9_I115_A0.303250.800
45_N85_V0.299990.792
49_D58_K0.297390.785
29_Q100_S0.296840.783
37_V115_A0.295620.780
9_I119_A0.291560.769
111_A115_A0.288560.761
71_A112_F0.285510.753
19_T23_Q0.281440.743
20_F110_R0.281030.742
51_T61_Q0.279760.738
16_V119_A0.274940.725
76_P117_K0.274270.724
29_Q103_A0.272650.719
4_A81_P0.264280.697
55_Q91_D0.263190.694
110_R113_R0.263040.694
68_F112_F0.26280.693
108_A112_F0.262760.693
43_G84_D0.259940.686
107_A111_A0.257610.680
33_V56_L0.25430.671
70_S109_R0.25350.669
64_I108_A0.248510.656
52_E55_Q0.246110.649
53_G95_H0.241790.638
67_G108_A0.241620.638
40_L44_G0.241320.637
2_Q80_Y0.239280.631
37_V68_F0.239080.631
18_E31_A0.238190.628
87_V112_F0.238160.628
71_A116_L0.2380.628
102_G105_R0.237060.626
37_V116_L0.236690.625
102_G106_A0.236180.623
18_E114_E0.234710.619
58_K61_Q0.233680.617
16_V37_V0.233480.616
17_E31_A0.230350.608
34_I91_D0.228550.603
23_Q26_G0.228250.602
21_K32_K0.227880.601
64_I67_G0.227680.601
43_G48_V0.226720.598
92_G95_H0.225010.594
106_A110_R0.221020.583
18_E32_K0.220920.583
67_G71_A0.220650.582
72_L82_V0.219690.580
66_E69_Q0.219090.578
51_T54_G0.216760.572
99_S104_F0.215860.570
4_A59_E0.215540.569
28_R53_G0.215410.568
40_L84_D0.215040.567
47_F65_E0.21460.566
85_V112_F0.214430.566
3_V59_E0.21390.564
56_L61_Q0.213770.564
51_T89_L0.212790.561
45_N68_F0.212530.561
28_R98_D0.210710.556
16_V111_A0.208350.550
70_S73_S0.208260.550
56_L64_I0.207330.547
37_V119_A0.207020.546
27_K109_R0.206790.546
82_V87_V0.206590.545
13_V118_K0.205710.543
17_E21_K0.205650.543
59_E96_E0.202790.535
6_R20_F0.199280.526
60_F104_F0.197710.522
61_Q89_L0.196810.519
23_Q28_R0.196750.519
12_E119_A0.193990.512
52_E58_K0.190910.504
28_R92_G0.190380.502
66_E105_R0.189560.500
12_E90_T0.187740.495
22_R102_G0.187290.494
18_E34_I0.186590.492
5_Y80_Y0.186410.492
83_T87_V0.185160.489
63_A67_G0.183370.484
70_S101_P0.182760.482
56_L92_G0.182750.482
73_S109_R0.182560.482
55_Q61_Q0.181990.480
92_G99_S0.181990.480
16_V34_I0.181920.480
49_D65_E0.18190.480
43_G76_P0.180980.478
62_D65_E0.180590.477
22_R26_G0.180550.476
11_K39_P0.18010.475
54_G57_P0.177790.469
19_T31_A0.176880.467
8_T85_V0.176470.466
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
2xexA0.991799.90.089
1darA0.991799.90.092
2rdo70.991799.90.092
2dy1A0.97599.90.109
4fn5A199.80.204
3j25A0.966799.80.207
1n0uA0.991799.80.245
3j3az0.9599.80.262
3vqtA0.483397.20.752
2h5eA0.491756.30.878

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