GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_TL5_C - Ribosomal protein TL5 C-terminal domain
Pfam: PF14693 (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: 1391
Seq/Len: 15.81
HH_delta: 0.013 (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
12_V45_E1.172164.103
10_H43_S0.915473.204
11_F26_Q0.721592.526
6_E30_E0.695712.435
13_G49_S0.691292.420
4_K34_E0.668932.341
36_L39_D0.621232.174
20_K52_E0.593822.079
35_C68_V0.555831.946
52_E55_D0.551351.930
59_V70_I0.536781.879
4_K32_E0.503311.762
34_E69_E0.494761.732
6_E32_E0.48231.688
65_P68_V0.458631.605
2_K34_E0.457431.601
51_L57_I0.432511.514
28_L76_T0.420621.472
11_F79_A0.420531.472
60_S75_E0.41311.446
5_V40_I0.410341.436
17_G22_G0.408581.430
13_G48_V0.396331.387
31_V62_L0.388381.359
22_G81_V0.387531.356
60_S74_P0.381191.334
33_V68_V0.379611.329
2_K69_E0.375971.316
10_H45_E0.375761.315
22_G53_I0.371451.300
56_S77_V0.366051.281
11_F48_V0.351741.231
77_V80_S0.33681.179
13_G47_D0.336321.177
7_V41_P0.334691.172
51_L55_D0.33161.161
64_L70_I0.319711.119
24_L79_A0.316911.109
14_E19_K0.31511.103
16_P50_G0.314991.103
25_Q82_V0.308061.078
32_E72_D0.304211.065
39_D67_G0.301651.056
56_S80_S0.300771.053
39_D66_E0.294441.031
2_K36_L0.288541.010
34_E71_L0.287161.005
46_V57_I0.280750.983
15_S18_V0.276930.969
16_P52_E0.26370.923
58_H61_D0.262380.918
53_I83_A0.262240.918
51_L56_S0.261260.914
28_L59_V0.260420.912
18_V24_L0.259640.909
16_P49_S0.258280.904
28_L78_V0.255020.893
24_L81_V0.248120.868
11_F57_I0.245420.859
17_G21_G0.244210.855
50_G63_K0.24380.853
54_G83_A0.23240.813
7_V33_V0.230390.806
34_E59_V0.229310.803
27_V80_S0.2290.802
44_I64_L0.225610.790
51_L81_V0.221830.776
15_S48_V0.217470.761
72_D76_T0.216430.758
48_V51_L0.211860.742
47_D50_G0.208170.729
20_K50_G0.203020.711
23_I82_V0.202880.710
28_L72_D0.200230.701
27_V77_V0.199890.700
1_E37_P0.197140.690
26_Q29_R0.19530.684
25_Q80_S0.195130.683
62_L70_I0.193870.679
64_L68_V0.193620.678
35_C40_I0.191670.671
12_V47_D0.190540.667
18_V22_G0.190450.667
44_I65_P0.188360.659
78_V85_R0.187590.657
3_V35_C0.18530.649
39_D68_V0.184260.645
31_V72_D0.183060.641
46_V51_L0.181070.634
16_P20_K0.179920.630
38_A46_V0.17950.628
33_V44_I0.179220.627
41_P68_V0.179040.627
43_S46_V0.174560.611
15_S22_G0.173950.609
9_V26_Q0.17230.603
31_V59_V0.171680.601
24_L48_V0.169610.594
58_H77_V0.169250.592
5_V41_P0.169170.592
71_L76_T0.16830.589
8_P43_S0.166040.581
73_D76_T0.164810.577
59_V72_D0.163920.574
28_L31_V0.163560.573
59_V78_V0.16280.570
56_S82_V0.160070.560
22_G83_A0.159850.560
51_L62_L0.159730.559
23_I84_P0.15480.542
40_I83_A0.153750.538
59_V64_L0.153180.536
9_V64_L0.152660.534
5_V25_Q0.152430.534
9_V42_E0.150240.526
2_K37_P0.150050.525
42_E82_V0.146160.512
17_G48_V0.145040.508
9_V35_C0.144910.507
17_G81_V0.144410.505
20_K35_C0.143950.504
21_G24_L0.142860.500
35_C39_D0.142630.499
33_V83_A0.142090.497
4_K71_L0.141860.497
21_G85_R0.140530.492
16_P19_K0.140520.492
44_I70_I0.139740.489
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
2zjrS199.90.013
1feuA199.90.023
2kpsA0.943289.70.818
2l3uA0.954586.90.826
2kq1A0.977382.40.836
3lu0A0.931858.50.862
4kn7A0.931858.50.862
3lywA0.954557.90.862
1bdfA0.943256.10.864
2a6hA0.954535.40.879

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