GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L18e - Ribosomal protein L18eL15
Pfam: PF00828 (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: 129
Sequences: 2131
Seq/Len: 16.52
HH_delta: 0.056 (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
116_K120_E1.122853.899
111_F126_V1.071473.720
108_A111_F0.841422.922
107_K127_V0.815562.832
78_D81_I0.754242.619
96_G114_S0.695932.416
113_K116_K0.65272.266
105_T125_E0.641522.228
61_S97_K0.627992.181
64_Q101_T0.592242.056
3_K8_G0.580072.014
111_F116_K0.568931.975
113_K117_E0.568181.973
20_G23_H0.559061.941
76_E107_K0.54221.883
62_K65_E0.516211.792
80_K84_D0.500421.738
94_V108_A0.491461.706
79_G109_H0.481261.671
100_L104_L0.46991.632
5_K11_H0.465991.618
60_L118_K0.451.563
12_K16_G0.435491.512
119_I124_G0.434561.509
63_L106_I0.428111.487
57_P112_S0.427361.484
117_E121_A0.422171.466
64_Q102_K0.416771.447
81_I85_A0.40351.401
11_H16_G0.391651.360
59_N96_G0.386381.342
77_I82_L0.383781.333
93_K110_R0.371421.290
76_E105_T0.367341.276
17_R28_E0.36471.266
34_L38_L0.346981.205
117_E120_E0.346921.205
27_F31_Q0.34681.204
59_N95_L0.344491.196
77_I104_L0.336751.169
11_H15_R0.334541.162
99_E118_K0.330161.146
45_N53_R0.326221.133
28_E37_R0.323431.123
15_R22_K0.32041.113
32_M35_Y0.317091.101
6_T11_H0.313591.089
7_R16_G0.309841.076
94_V106_I0.308521.071
116_K128_T0.299361.039
81_I84_D0.292721.016
47_H53_R0.291051.011
3_K7_R0.288491.002
78_D107_K0.288011.000
94_V119_I0.287740.999
6_T12_K0.280220.973
24_R35_Y0.277390.963
114_S117_E0.274420.953
10_G13_G0.270110.938
59_N97_K0.265660.922
62_K97_K0.264760.919
41_R44_N0.264730.919
108_A119_I0.264560.919
63_L104_L0.262830.913
14_G18_S0.260660.905
55_Y91_Y0.260010.903
106_I119_I0.255920.889
62_K87_L0.254760.885
56_P90_G0.252460.877
111_F128_T0.250960.871
95_L112_S0.250670.870
120_E125_E0.25030.869
105_T127_V0.247310.859
66_L87_L0.246470.856
9_R16_G0.245760.853
111_F119_I0.239780.833
106_I109_H0.238930.830
110_R128_T0.237080.823
25_P35_Y0.236230.820
55_Y110_R0.231950.805
108_A126_V0.230480.800
60_L96_G0.224340.779
56_P89_K0.224260.779
95_L98_G0.220260.765
56_P91_Y0.218990.760
32_M36_R0.218680.759
95_L118_K0.218440.758
98_G118_K0.216560.752
15_R23_H0.215190.747
9_R15_R0.214610.745
102_K105_T0.213440.741
3_K9_R0.212910.739
116_K126_V0.212830.739
119_I126_V0.211870.736
103_P125_E0.210830.732
59_N112_S0.207340.720
94_V111_F0.207250.720
11_H19_G0.205860.715
47_H118_K0.205370.713
77_I81_I0.204860.711
45_N55_Y0.204190.709
20_G24_R0.203780.708
18_S23_H0.202440.703
28_E31_Q0.201290.699
82_L88_I0.199520.693
5_K8_G0.196450.682
9_R12_K0.194240.674
57_P110_R0.194190.674
79_G83_V0.194180.674
32_M120_E0.192310.668
116_K125_E0.190970.663
14_G19_G0.190510.662
54_E89_K0.190460.661
53_R91_Y0.189850.659
83_V87_L0.18970.659
80_K103_P0.188870.656
27_F30_G0.188790.656
64_Q103_P0.188780.655
79_G88_I0.186440.647
61_S64_Q0.184370.640
78_D84_D0.182510.634
20_G25_P0.181960.632
84_D88_I0.181410.630
35_Y38_L0.181230.629
14_G23_H0.180580.627
78_D82_L0.179980.625
54_E109_H0.178780.621
7_R56_P0.178780.621
12_K92_V0.178630.620
82_L86_G0.17860.620
10_G42_G0.177760.617
27_F34_L0.176720.614
64_Q100_L0.176580.613
7_R11_H0.174960.608
7_R14_G0.174780.607
28_E33_P0.174280.605
77_I106_I0.173210.601
63_L105_T0.172890.600
91_Y110_R0.172120.598
27_F32_M0.171890.597
59_N93_K0.170680.593
119_I123_G0.170110.591
44_N47_H0.169820.590
42_G46_P0.168710.586
106_I111_F0.168140.584
103_P122_A0.168130.584
99_E114_S0.168030.583
16_G19_G0.167190.581
20_G41_R0.167120.580
13_G29_G0.165590.575
77_I85_A0.165360.574
5_K15_R0.165290.574
39_P42_G0.164420.571
42_G45_N0.163420.567
5_K41_R0.162560.564
16_G20_G0.160820.558
15_R20_G0.160180.556
106_I126_V0.159010.552
62_K66_L0.15830.550
88_I92_V0.158160.549
53_R57_P0.157720.548
6_T9_R0.157690.548
14_G20_G0.157650.547
28_E32_M0.157470.547
57_P94_V0.156910.545
109_H128_T0.156880.545
40_K124_G0.156790.544
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
3j3wL0.92251000.056
3r8sL0.9071000.072
2zjrI0.9071000.084
3bboN0.95351000.085
3v2dP0.89921000.09
1vq8L0.93021000.179
4a17K0.97671000.231
3j3ba0.9381000.24
3j21L0.953599.90.247
3j39a0.93899.90.266

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