GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EFG_C - Elongation factor G C-terminus
Pfam: PF00679 (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: CL0437
Length: 89
Sequences: 6160
Seq/Len: 69.21
HH_delta: 0.053 (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_E76_S1.528852.752
8_S46_E1.471692.649
8_S76_S1.356782.442
24_D57_F1.322122.380
37_P43_V1.277722.300
33_L48_E1.230972.216
8_S74_E1.141282.054
48_E77_G1.09351.968
48_E79_R1.081361.946
34_S46_E1.049241.889
25_L30_G1.042961.877
61_L69_A0.980541.765
12_S44_V0.964031.735
24_D64_L0.960631.729
6_I79_R0.951831.713
36_D46_E0.943581.698
83_G87_D0.920251.656
23_S27_K0.901791.623
65_T69_A0.901461.623
15_E43_V0.88221.588
13_V21_V0.87781.580
31_E48_E0.834771.503
31_E79_R0.827071.489
10_E46_E0.824321.484
75_F78_Y0.81911.474
24_D60_E0.790541.423
13_V69_A0.787281.417
10_E44_V0.784431.412
7_M51_V0.758781.366
8_S33_L0.714161.285
8_S48_E0.702581.265
35_M43_V0.660761.189
25_L49_I0.65841.185
60_E64_L0.62271.121
3_L80_P0.621761.119
18_L43_V0.61281.103
9_V71_F0.610111.098
38_I44_V0.591741.065
29_R53_E0.590181.062
81_V85_I0.587741.058
14_P68_R0.584261.052
15_E41_D0.582781.049
18_L35_M0.58051.045
22_I32_I0.578471.041
7_M54_L0.572221.030
27_K60_E0.566081.019
2_L81_V0.559541.007
7_M73_M0.550290.991
9_V54_L0.542520.977
18_L37_P0.525280.946
4_E29_R0.512870.923
9_V47_A0.510010.918
23_S26_S0.509270.917
32_I35_M0.505460.910
56_G59_S0.496590.894
15_E40_G0.483540.870
22_I26_S0.477540.860
58_R71_F0.477020.859
2_L86_L0.471910.849
28_R60_E0.464520.836
56_G60_E0.457930.824
38_I42_R0.457380.823
22_I35_M0.455320.820
36_D44_V0.448950.808
10_E72_S0.447520.806
28_R56_G0.446280.803
18_L45_I0.443560.798
28_R53_E0.442780.797
16_E66_S0.442520.797
20_K64_L0.442170.796
58_R62_R0.440660.793
84_D87_D0.436030.785
38_I41_D0.423770.763
12_S38_I0.420280.757
30_G49_I0.417280.751
9_V49_I0.40760.734
53_E56_G0.3960.713
14_P42_R0.394880.711
17_Y68_R0.392760.707
24_D27_K0.388820.700
14_P17_Y0.385120.693
26_S47_A0.378440.681
25_L47_A0.377530.680
5_P50_P0.362950.653
82_P85_I0.361280.650
9_V73_M0.360280.649
15_E18_L0.357860.644
18_L22_I0.353820.637
19_G22_I0.353420.636
15_E37_P0.353140.636
54_L73_M0.351810.633
17_Y66_S0.350230.630
11_I69_A0.349660.629
12_S70_S0.346710.624
12_S42_R0.346520.624
51_V73_M0.345480.622
51_V54_L0.345330.622
58_R73_M0.345170.621
9_V25_L0.341370.614
19_G23_S0.339030.610
5_P30_G0.338650.610
6_I81_V0.338020.608
33_L46_E0.329110.592
4_E50_P0.327040.589
21_V65_T0.325170.585
49_I54_L0.324470.584
16_E68_R0.324340.584
74_E86_L0.322470.580
59_S63_S0.316030.569
27_K64_L0.313990.565
80_P83_G0.312040.562
57_F61_L0.307570.554
50_P53_E0.307030.553
32_I47_A0.305810.550
76_S79_R0.303920.547
80_P86_L0.299170.539
6_I77_G0.298450.537
27_K86_L0.298220.537
6_I82_P0.296190.533
11_I25_L0.292650.527
10_E74_E0.292310.526
31_E82_P0.29140.525
5_P78_Y0.289960.522
23_S64_L0.28640.516
82_P86_L0.285110.513
29_R82_P0.28370.511
28_R54_L0.282970.509
30_G50_P0.280760.505
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
4fn5A0.988899.40.053
1darA0.988899.30.073
2xexA0.988899.30.074
2rdo70.988899.30.075
3j25A0.988899.30.075
3j3az199.30.081
2dy1A0.988899.30.081
1n0uA199.30.095
3e3xA199.20.144
2yweA199.10.182

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