GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_60s - 60s Acidic ribosomal protein
Pfam: PF00428 (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: 88
Sequences: 1195
Seq/Len: 13.58
HH_delta: 0.04 (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
72_E75_E0.685533.002
8_K20_A0.531932.329
7_I27_A0.421731.847
10_V13_A0.410361.797
68_E72_E0.39781.742
82_D86_G0.377651.654
70_K74_E0.369711.619
71_K74_E0.36941.617
53_A56_A0.367081.607
80_D83_M0.359241.573
23_L27_A0.359191.573
81_D87_L0.357961.567
67_E71_K0.354251.551
34_D37_E0.351671.540
84_G88_F0.344131.507
65_A69_E0.333331.460
42_G45_G0.310251.358
41_N44_A0.308741.352
82_D85_F0.307341.346
8_K23_L0.302831.326
25_L29_A0.302441.324
69_E73_E0.29691.300
4_A24_E0.29671.299
8_K11_L0.292151.279
5_E8_K0.287961.261
83_M87_L0.287731.260
20_A24_E0.287531.259
67_E70_K0.283211.240
66_A69_E0.274981.204
3_T6_N0.270731.185
75_E79_E0.262291.148
8_K12_K0.259591.137
77_E80_D0.258971.134
65_A68_E0.25571.120
64_A67_E0.254831.116
7_I40_A0.253231.109
66_A70_K0.252611.106
77_E83_M0.251271.100
29_A32_G0.249911.094
81_D85_F0.24881.089
28_K33_K0.246751.080
19_E22_W0.244481.070
7_I23_L0.240211.052
11_L23_L0.238241.043
70_K73_E0.236411.035
6_N10_V0.233741.023
43_S46_M0.23221.017
81_D84_G0.228621.001
71_K75_E0.226760.993
27_A30_L0.22620.990
50_A53_A0.22520.986
61_A65_A0.223660.979
16_V19_E0.219780.962
38_L43_S0.219190.960
23_L26_F0.216930.950
4_A8_K0.21260.931
29_A34_D0.211440.926
16_V41_N0.211210.925
38_L45_G0.208290.912
6_N9_K0.201340.882
2_P45_G0.198860.871
25_L43_S0.19840.869
25_L28_K0.197860.866
40_A44_A0.196070.859
9_K44_A0.195830.857
1_E6_N0.19540.856
10_V26_F0.195120.854
2_P42_G0.194270.851
63_A66_A0.192940.845
15_G18_V0.191860.840
69_E74_E0.191140.837
9_K12_K0.189730.831
2_P6_N0.189590.830
80_D87_L0.18820.824
54_A65_A0.187970.823
11_L16_V0.187280.820
5_E38_L0.187250.820
21_I25_L0.187120.819
78_E82_D0.182470.799
12_K17_E0.180830.792
30_L35_I0.18070.791
79_E83_M0.180680.791
8_K18_V0.177810.779
22_W30_L0.17770.778
9_K41_N0.176660.774
18_V22_W0.172450.755
70_K84_G0.171330.750
17_E36_K0.169280.741
12_K26_F0.169140.741
7_I25_L0.168930.740
34_D39_I0.168530.738
52_A57_A0.168240.737
40_A43_S0.168090.736
22_W27_A0.167860.735
24_E28_K0.166690.730
61_A64_A0.164620.721
26_F85_F0.164050.718
80_D84_G0.163810.717
64_A70_K0.162780.713
80_D86_G0.162450.711
33_K37_E0.161920.709
57_A61_A0.161540.707
4_A18_V0.160540.703
57_A60_A0.159990.701
11_L17_E0.159750.699
9_K79_E0.159660.699
15_G27_A0.159370.698
12_K15_G0.159220.697
51_A54_A0.158320.693
7_I31_E0.157690.690
30_L33_K0.154740.678
22_W28_K0.15460.677
36_K44_A0.154330.676
54_A58_A0.152590.668
67_E75_E0.152160.666
3_T9_K0.150870.661
32_G35_I0.150.657
3_T61_A0.149240.653
63_A67_E0.14910.653
20_A23_L0.148670.651
7_I11_L0.147780.647
27_A46_M0.147720.647
15_G30_L0.146830.643
36_K43_S0.146820.643
4_A27_A0.146160.640
85_F88_F0.146030.639
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
3iz5t0.988699.80.04
3izct0.977399.80.047
3izcv0.988699.80.061
3iz5v0.988699.80.069
3j3bu199.80.093
3j3bs0.988699.80.095
3iz5s0.965999.60.183
2zkrg0.965999.60.19
3u5iq0.943299.60.203
3j3bq0.965999.60.211

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