GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EFP_N - Elongation factor P (EF-P) KOW-like domain
Pfam: PF08207 (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: CL0107
Length: 58
Sequences: 1308
Seq/Len: 22.55
HH_delta: -0.041 (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
16_E41_N1.142873.689
26_V34_F0.852072.750
5_L20_V0.660342.131
13_I50_K0.656722.120
41_N44_T0.551921.782
10_V17_P0.542051.750
14_D50_K0.533611.722
11_I58_V0.507721.639
2_A55_G0.507381.638
38_K49_E0.498691.610
53_R56_D0.493371.593
22_D38_K0.491041.585
18_Y48_V0.462771.494
16_E43_R0.438071.414
17_P43_R0.435881.407
37_V52_F0.415581.341
36_R51_T0.413581.335
35_V54_S0.402051.298
11_I39_L0.398081.285
23_F35_V0.375871.213
17_P42_L0.359191.159
26_V36_R0.358241.156
29_G33_A0.35421.143
27_K30_K0.343781.110
5_L58_V0.341991.104
5_L9_M0.33331.076
21_L40_K0.318781.029
5_L11_I0.31791.026
7_K22_D0.314851.016
28_P36_R0.309060.998
10_V19_V0.308770.997
2_A54_S0.306890.991
28_P34_F0.304870.984
18_Y39_L0.304340.982
40_K47_K0.298270.963
12_E17_P0.295530.954
38_K47_K0.2870.926
12_E15_G0.283860.916
25_H35_V0.274720.887
3_S20_V0.274070.885
5_L37_V0.270960.875
18_Y41_N0.267920.865
26_V30_K0.267360.863
28_P31_G0.266330.860
30_K34_F0.262540.847
7_K23_F0.259560.838
4_D22_D0.24940.805
2_A56_D0.249030.804
26_V31_G0.248250.801
30_K33_A0.244710.790
26_V29_G0.239880.774
9_M56_D0.229670.741
27_K31_G0.22920.740
36_R49_E0.228150.736
16_E44_T0.226050.730
18_Y42_L0.225070.726
32_G49_E0.221670.716
9_M20_V0.220110.710
19_V25_H0.220030.710
32_G53_R0.219670.709
39_L48_V0.215470.696
19_V24_Q0.208830.674
2_A20_V0.208810.674
33_A54_S0.208310.672
49_E52_F0.206190.666
5_L10_V0.203660.657
1_S57_K0.20050.647
9_M12_E0.199890.645
10_V46_S0.197370.637
8_G29_G0.197190.637
27_K33_A0.194880.629
29_G54_S0.18650.602
10_V32_G0.185320.598
1_S4_D0.182490.589
13_I52_F0.181450.586
29_G34_F0.180340.582
29_G45_G0.180340.582
2_A5_L0.178010.575
23_F37_V0.177440.573
17_P51_T0.174830.564
4_D35_V0.172170.556
54_S58_V0.170180.549
19_V43_R0.16980.548
32_G54_S0.166250.537
11_I18_Y0.164850.532
19_V53_R0.164270.530
43_R57_K0.162690.525
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
1uebA199.7-0.041
3a5zB199.7-0.038
1ybyA199.7-0.035
3treA199.7-0.026
3oyyA199.7-0.023
1iz6A199.70.001
3er0A199.70.001
1bkbA199.60.004
3cpfA199.60.004
3hksA199.60.005

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