GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L11 - Ribosomal protein L11 RNA binding domain
Pfam: PF00298 (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. )
Length: 69
Sequences: 1761
Seq/Len: 25.52
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
21_K25_E1.494043.381
29_T68_K1.360883.080
9_L67_I1.250312.830
36_Y40_K1.103592.498
32_L59_I1.097072.483
12_A37_E0.957952.168
36_Y55_V0.928582.102
9_L30_I0.922032.087
31_T34_Q0.887232.008
5_T58_V0.855461.936
21_K24_K0.80791.828
33_K36_Y0.753331.705
32_L55_V0.645841.462
32_L36_Y0.636751.441
20_S25_E0.627041.419
14_G34_Q0.584411.323
49_K53_S0.57021.290
8_L41_I0.569721.289
34_Q37_E0.569381.289
7_W10_K0.568871.287
37_E41_I0.538091.218
35_I55_V0.537141.216
15_I67_I0.530031.200
35_I58_V0.525331.189
6_S61_T0.524631.187
13_A30_I0.520371.178
51_L55_V0.517061.170
23_G26_K0.515381.166
10_K17_K0.493971.118
2_T44_K0.491021.111
46_L54_A0.486161.100
35_I59_I0.482091.091
56_K59_I0.479571.085
37_E40_K0.474151.073
48_A54_A0.459741.040
40_K43_Q0.457721.036
50_S53_S0.455361.031
3_P41_I0.454621.029
13_A28_G0.446071.010
26_K68_K0.439880.996
33_K37_E0.431810.977
43_Q54_A0.430860.975
40_K51_L0.430520.974
28_G67_I0.42520.962
17_K20_S0.423990.960
10_K15_I0.420490.952
22_P26_K0.395380.895
53_S56_K0.394770.893
12_A38_I0.392880.889
12_A34_Q0.385990.874
36_Y51_L0.380810.862
43_Q48_A0.379670.859
39_A51_L0.370590.839
55_V59_I0.363910.824
3_P8_L0.355840.805
19_S23_G0.351150.795
47_N57_S0.350570.793
6_S20_S0.327180.740
30_I69_V0.324670.735
11_K14_G0.315240.713
5_T8_L0.311240.704
2_T5_T0.311010.704
22_P25_E0.302460.685
62_A66_G0.294030.665
52_E55_V0.293720.665
19_S25_E0.290970.659
32_L35_I0.290260.657
2_T39_A0.289330.655
17_K25_E0.287930.652
48_A53_S0.282940.640
52_E56_K0.281660.637
49_K57_S0.277990.629
15_I27_V0.276540.626
9_L13_A0.275150.623
8_L11_K0.271980.616
49_K56_K0.268830.608
30_I38_I0.268380.607
3_P64_S0.264310.598
12_A41_I0.263220.596
42_K45_D0.262140.593
19_S26_K0.26150.592
11_K16_K0.25550.578
43_Q47_N0.252770.572
4_P42_K0.251460.569
37_E63_R0.245850.556
48_A57_S0.243170.550
60_G64_S0.242530.549
41_I44_K0.240830.545
4_P45_D0.23930.542
28_G68_K0.237190.537
20_S23_G0.235910.534
4_P65_M0.234640.531
7_W61_T0.231280.523
5_T30_I0.229220.519
11_K68_K0.228730.518
11_K41_I0.228280.517
18_G27_V0.226550.513
9_L62_A0.223470.506
30_I67_I0.223050.505
13_A27_V0.22210.503
15_I18_G0.217430.492
18_G67_I0.216990.491
39_A43_Q0.216530.490
6_S18_G0.21330.483
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
1hc8A199.9-0.006
3bboK199.90.012
3r8sI199.90.016
1mmsA199.90.019
1vq8I199.90.025
3j21H199.90.027
3egvB199.90.029
1qa6A0.97199.90.031
2ftcG199.90.032
3j3bK199.90.066

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