GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L20 - Ribosomal protein L20
Pfam: PF00453 (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: 108
Sequences: 1263
Seq/Len: 11.69
HH_delta: -0.022 (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
20_A38_V0.947823.778
95_A99_I0.795323.170
71_H106_K0.761823.037
5_R9_A0.733472.924
68_A78_F0.720222.871
80_N84_K0.69052.752
52_K55_D0.610812.435
37_Q41_A0.605422.413
65_N69_R0.586732.339
48_D51_L0.549412.190
27_R37_Q0.547612.183
101_D104_S0.536772.140
47_R51_L0.526832.100
51_L54_R0.525562.095
96_D100_N0.505612.015
30_C33_I0.483351.927
33_I36_Q0.467131.862
26_R30_C0.466331.859
93_I96_D0.464281.851
74_S77_R0.454741.813
103_E106_K0.447991.786
51_L55_D0.436961.742
26_R29_N0.435921.738
36_Q40_K0.422391.684
19_L42_L0.391361.560
102_P106_K0.389931.554
55_D58_R0.361641.442
82_L108_L0.361511.441
73_L77_R0.361481.441
40_K44_Y0.339961.355
31_Y35_K0.337541.346
7_V11_K0.334341.333
39_M42_L0.330491.317
35_K39_M0.321981.283
89_L93_I0.31121.241
77_R80_N0.305981.220
25_G28_S0.305821.219
68_A71_H0.302761.207
84_K88_E0.300231.197
81_G85_A0.296031.180
8_V11_K0.287621.147
57_R79_I0.283171.129
59_L63_R0.28241.126
17_L34_A0.281241.121
68_A73_L0.266391.062
7_V13_R0.264981.056
58_R62_T0.263251.049
41_A44_Y0.262451.046
26_R33_I0.261751.043
90_N93_I0.258651.031
97_L101_D0.249840.996
8_V12_R0.246150.981
8_V13_R0.245690.979
97_L104_S0.244650.975
24_R30_C0.237420.946
104_S107_S0.237310.946
19_L38_V0.236270.942
23_F37_Q0.235580.939
81_G84_K0.232830.928
16_I34_A0.225080.897
89_L108_L0.221490.883
16_I38_V0.209550.835
57_R61_I0.20880.832
3_V6_G0.207910.829
70_E102_P0.207480.827
57_R91_R0.206920.825
97_L108_L0.206390.823
22_G50_K0.201730.804
67_A102_P0.201130.802
36_Q39_M0.197110.786
15_K19_L0.196820.785
71_H102_P0.194730.776
6_G11_K0.190320.759
47_R54_R0.188460.751
42_L50_K0.186550.744
67_A72_G0.183440.731
103_E107_S0.183390.731
1_M8_V0.182440.727
67_A71_H0.182350.727
52_K56_F0.182130.726
24_R41_A0.180240.718
70_E106_K0.179030.714
31_Y34_A0.178480.711
76_S80_N0.178470.711
39_M62_T0.1780.710
26_R37_Q0.177850.709
70_E86_N0.17750.708
39_M43_Q0.176350.703
26_R36_Q0.175710.700
43_Q46_Y0.173390.691
64_I79_I0.173220.690
78_F108_L0.171010.682
28_S58_R0.170470.680
17_L31_Y0.170180.678
42_L45_A0.169890.677
10_R13_R0.169420.675
79_I83_K0.16940.675
61_I75_Y0.168750.673
41_A62_T0.168380.671
73_L103_E0.168080.670
13_R17_L0.168070.670
6_G15_K0.16680.665
64_I95_A0.16390.653
52_K99_I0.161970.646
97_L100_N0.161280.643
16_I35_K0.160720.641
23_F36_Q0.160540.640
88_E97_L0.158560.632
100_N103_E0.158040.630
78_F89_L0.15780.629
62_T90_N0.157610.628
4_K13_R0.157570.628
23_F41_A0.157320.627
6_G9_A0.155680.621
5_R8_V0.154460.616
40_K43_Q0.151960.606
90_N99_I0.151580.604
71_H97_L0.151380.603
32_R43_Q0.150580.600
10_R15_K0.150060.598
17_L72_G0.148410.592
24_R27_R0.147740.589
33_I39_M0.146930.586
77_R81_G0.146550.584
58_R72_G0.14630.583
9_A31_Y0.146260.583
30_C35_K0.145970.582
60_W64_I0.14590.582
27_R41_A0.145720.581
4_K108_L0.144820.577
17_L23_F0.144770.577
51_L58_R0.144650.577
74_S83_K0.143060.570
97_L106_K0.14280.569
32_R36_Q0.142760.569
37_Q40_K0.142620.569
39_M99_I0.142220.567
14_K87_I0.141660.565
3_V22_G0.141630.565
10_R21_K0.141560.564
96_D99_I0.140990.562
81_G101_D0.140920.562
5_R33_I0.140850.561
61_I80_N0.139930.558
73_L81_G0.139880.558
13_R31_Y0.139670.557
40_K89_L0.138520.552
16_I39_M0.137110.547
16_I19_L0.136730.545
13_R25_G0.136330.543
27_R100_N0.136310.543
42_L90_N0.135860.542
21_K74_S0.135860.542
19_L107_S0.135280.539
77_R85_A0.135140.539
42_L46_Y0.135020.538
53_K92_K0.134630.537
5_R32_R0.133440.532
61_I79_I0.133170.531
22_G46_Y0.131910.526
41_A58_R0.13190.526
28_S31_Y0.131580.525
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
2zjrN1100-0.022
3j3wQ1100-0.021
3v2dU1100-0.021
3r8sQ1100-0.019
2ghjA0.9907100-0.014
3bboS1100-0.007
2ftcL0.99071000.028
3izcH0.990722.50.938
1i1nA0.3889150.942
2lvsA0.805614.30.943

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