GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
EFP - Elongation factor P (EF-P) OB domain
Pfam: PF01132 (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: CL0021
Length: 55
Sequences: 1673
Seq/Len: 30.42
HH_delta: 0.006 (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
2_R18_D1.102742.661
3_E44_E1.075452.596
7_L24_Q1.018332.458
5_Q19_T0.911262.199
3_E46_Q0.900442.173
19_T44_E0.849172.049
5_Q44_E0.819021.977
15_V26_E0.817711.973
4_M25_I0.781031.885
13_N26_E0.755471.823
40_K43_M0.719671.737
9_K29_K0.669141.615
10_D13_N0.634151.530
13_N28_P0.600021.448
47_V54_P0.590741.426
17_M24_Q0.587541.418
28_P31_Q0.586191.415
4_M47_V0.576911.392
8_Y15_V0.557511.346
6_Y9_K0.557081.344
16_F32_L0.552541.334
1_R48_L0.529951.279
16_F45_V0.524341.265
9_K12_D0.518641.252
12_D29_K0.514191.241
49_F54_P0.514051.241
2_R49_F0.483351.167
27_V31_Q0.472991.142
9_K14_Y0.449911.086
50_Y55_I0.44491.074
29_K36_L0.438331.058
9_K15_V0.421231.017
39_L43_M0.413870.999
10_D26_E0.401580.969
4_M18_D0.399380.964
2_R20_E0.393140.949
14_Y36_L0.386930.934
14_Y29_K0.35720.862
19_T22_Y0.341810.825
18_D25_I0.337880.815
1_R46_Q0.329790.796
34_D37_K0.319220.770
17_M22_Y0.316420.764
1_R41_E0.3120.753
9_K36_L0.293590.709
4_M45_V0.290560.701
10_D15_V0.290310.701
49_F52_G0.285620.689
20_E43_M0.27180.656
1_R42_G0.27010.652
10_D51_E0.262480.633
6_Y42_G0.261060.630
14_Y32_L0.25890.625
50_Y53_K0.256280.619
11_G15_V0.253070.611
15_V24_Q0.250040.603
25_I49_F0.245050.591
18_D21_T0.244510.590
51_E55_I0.243870.589
1_R54_P0.240050.579
33_G36_L0.23930.578
35_A45_V0.237530.573
32_L48_L0.236220.570
32_L35_A0.234880.567
14_Y42_G0.232930.562
6_Y40_K0.229910.555
7_L22_Y0.226270.546
12_D27_V0.222130.536
9_K26_E0.220730.533
3_E48_L0.214610.518
27_V54_P0.212220.512
32_L39_L0.210990.509
6_Y24_Q0.20860.503
2_R53_K0.206910.499
14_Y38_F0.205550.496
32_L53_K0.196710.475
39_L55_I0.196130.473
32_L45_V0.194610.470
12_D26_E0.194520.469
4_M50_Y0.193260.466
36_L39_L0.192810.465
13_N55_I0.192730.465
34_D38_F0.19110.461
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
3a5zB199.70.006
1ybyA199.70.019
3treA199.70.019
3oyyA0.981899.60.047
1uebA0.981899.60.049
1bkbA199.50.136
1iz6A199.40.174
2eifA0.945599.30.221
3cpfA199.30.227
3er0A199.20.269

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