GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S13 - Ribosomal protein S13S18
Pfam: PF00416 (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: CL0303
Length: 107
Sequences: 1532
Seq/Len: 14.32
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
41_K50_Q1.092334.045
79_L86_R0.888093.289
100_R103_T0.863213.197
88_I92_K0.75192.784
27_K62_H0.739352.738
27_K30_Q0.725132.685
57_I61_N0.70382.606
14_Y39_P0.698532.587
34_K57_I0.652932.418
13_I43_V0.631982.340
50_Q53_K0.622422.305
30_Q34_K0.600822.225
25_R29_K0.569292.108
71_Q75_N0.56392.088
67_D70_R0.551192.041
33_K39_P0.525781.947
14_Y29_K0.521791.932
7_L16_A0.51631.912
34_K61_N0.515571.909
35_L57_I0.513021.900
36_G53_K0.478931.774
10_N44_G0.478631.772
56_K60_K0.46991.740
18_T25_R0.457721.695
6_N9_G0.435861.614
13_I46_L0.432681.602
57_I62_H0.387891.436
29_K39_P0.38561.428
16_A43_V0.37921.404
26_R30_Q0.373981.385
63_L71_Q0.358011.326
80_K91_R0.356481.320
83_K91_R0.344241.275
29_K33_K0.332571.232
41_K45_D0.331851.229
49_E53_K0.32221.193
30_Q62_H0.321381.190
15_I18_T0.318071.178
21_Y72_V0.315371.168
38_N41_K0.314771.166
16_A19_K0.314351.164
53_K56_K0.305521.131
13_I37_I0.301791.118
47_S50_Q0.268580.995
14_Y25_R0.267170.989
56_K59_E0.267120.989
87_G90_H0.266390.986
88_I96_V0.259950.963
25_R28_A0.258210.956
57_I60_K0.25460.943
23_I58_I0.251820.933
58_I64_I0.246260.912
14_Y28_A0.242470.898
2_I51_I0.23560.872
12_P42_K0.235350.872
35_L54_L0.234740.869
21_Y69_K0.233690.865
28_A32_C0.231620.858
9_G44_G0.230890.855
74_E77_K0.229840.851
95_P105_A0.228320.845
52_D56_K0.227730.843
9_G16_A0.226590.839
84_S88_I0.224210.830
13_I32_C0.223710.828
11_K19_K0.222840.825
26_R29_K0.215880.799
7_L43_V0.212510.787
1_R106_R0.212320.786
95_P104_N0.212230.786
3_L59_E0.212180.786
48_D52_D0.211460.783
78_R86_R0.20780.770
48_D51_I0.206350.764
46_L51_I0.20450.757
72_V92_K0.203090.752
73_R77_K0.20010.741
12_P38_N0.199550.739
7_L14_Y0.198680.736
73_R80_K0.197390.731
16_A100_R0.195380.724
80_K88_I0.193880.718
15_I25_R0.193350.716
55_R59_E0.191910.711
13_I42_K0.19170.710
6_N52_D0.19070.706
74_E81_K0.187850.696
3_L55_R0.187160.693
83_K88_I0.186460.690
14_Y40_N0.185150.686
74_E82_I0.184720.684
73_R81_K0.183970.681
4_G66_N0.182430.676
13_I41_K0.182320.675
11_K16_A0.182010.674
9_G51_I0.18150.672
21_Y63_L0.181040.670
9_G13_I0.180950.670
70_R78_R0.179940.666
39_P51_I0.179480.665
85_Y92_K0.178050.659
77_K81_K0.177520.657
5_T9_G0.176580.654
4_G103_T0.176250.653
7_L58_I0.176180.652
46_L70_R0.174770.647
8_P69_K0.173440.642
31_I62_H0.173360.642
10_N42_K0.172880.640
68_L71_Q0.171850.636
72_V76_I0.171540.635
5_T8_P0.170810.633
35_L61_N0.170310.631
98_G101_T0.168610.624
33_K36_G0.16670.617
12_P43_V0.16590.614
38_N82_I0.165370.612
32_C54_L0.164540.609
39_P54_L0.164390.609
31_I54_L0.163670.606
2_I60_K0.162760.603
44_G60_K0.162730.603
7_L48_D0.162720.603
75_N90_H0.161640.599
65_E95_P0.161390.598
4_G65_E0.158240.586
65_E69_K0.158010.585
2_I7_L0.156820.581
3_L64_I0.15680.581
80_K83_K0.156010.578
69_K81_K0.155590.576
16_A41_K0.154720.573
7_L51_I0.152270.564
23_I105_A0.151090.560
9_G59_E0.151080.559
32_C37_I0.150310.557
47_S53_K0.149830.555
89_R99_Q0.148770.551
8_P19_K0.147340.546
31_I57_I0.146570.543
12_P40_N0.146110.541
1_R6_N0.145930.540
52_D102_K0.145730.540
46_L67_D0.145450.539
77_K86_R0.145250.538
34_K60_K0.145050.537
6_N82_I0.144190.534
44_G63_L0.143880.533
10_N19_K0.143190.530
102_K107_T0.143170.530
5_T65_E0.142970.529
30_Q57_I0.142930.529
21_Y61_N0.142460.528
30_Q33_K0.142050.526
69_K91_R0.141420.524
1_R7_L0.140690.521
80_K96_V0.140520.520
85_Y95_P0.140490.520
33_K60_K0.140410.520
27_K57_I0.139980.518
86_R97_R0.13950.517
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
2vqeM1100-0.022
2xzmM1100-0.01
3r8nM0.9907100-0.003
3zeyM11000.001
3j20O11000.002
3iz6M11000.003
3u5cS11000.008
3j38S11000.015
3bbnM0.88791000.089
4itqA0.588896.70.832

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