GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L22 - Ribosomal protein L22pL17e
Pfam: PF00237 (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: 105
Sequences: 1818
Seq/Len: 17.31
HH_delta: -0.048 (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
5_N76_P0.820092.971
3_L46_L0.77542.809
17_A72_V0.771062.793
68_S104_K0.699172.533
25_V51_I0.623282.258
44_L48_K0.611742.216
3_L6_I0.610922.213
74_K77_Y0.55322.004
33_K44_L0.536531.944
23_M31_Q0.532181.928
23_M27_E0.525231.903
18_R21_R0.493611.788
81_I89_A0.493351.787
20_I47_L0.492161.783
29_I44_L0.483891.753
84_R90_G0.464361.682
24_S27_E0.460461.668
38_K42_F0.459261.664
74_K95_R0.452451.639
6_I42_F0.447821.622
8_I13_L0.447791.622
64_N105_E0.443491.607
82_R90_G0.441821.601
50_A103_L0.435071.576
17_A70_I0.435021.576
17_A43_I0.425751.542
81_I91_P0.423691.535
55_E62_P0.413491.498
73_N100_T0.407341.476
47_L51_I0.39831.443
47_L67_I0.385121.395
83_P89_A0.377711.368
77_Y95_R0.371891.347
81_I90_G0.370441.342
47_L101_V0.360391.306
29_I51_I0.354621.285
83_P90_G0.354261.283
49_S53_N0.351741.274
8_I39_A0.349561.266
71_W100_T0.34631.254
75_G96_T0.336591.219
43_I70_I0.336111.218
13_L43_I0.333561.208
77_Y93_R0.333241.207
68_S102_V0.326281.182
61_D64_N0.323411.172
13_L99_I0.322261.167
46_L99_I0.310841.126
15_E37_K0.308291.117
13_L97_S0.308081.116
69_E102_V0.307431.114
54_A65_L0.304631.104
19_L31_Q0.302731.097
14_R73_N0.299221.084
21_R69_E0.296951.076
70_I101_V0.293871.065
57_N60_L0.285711.035
19_L35_V0.281831.021
85_A90_G0.2730.989
16_V43_I0.267090.968
26_D62_P0.260970.945
11_K15_E0.260680.944
29_I48_K0.257160.932
46_L103_L0.254720.923
14_R74_K0.254120.921
29_I33_K0.252620.915
75_G98_H0.248370.900
7_R80_R0.242710.879
9_S38_K0.234630.850
39_A42_F0.234050.848
66_Y104_K0.233160.845
56_N60_L0.232440.842
67_I70_I0.231380.838
2_K100_T0.226730.821
24_S64_N0.225660.817
19_L23_M0.224020.812
15_E90_G0.21740.788
46_L101_V0.216520.784
20_I70_I0.216490.784
41_K44_L0.215730.781
10_P14_R0.214960.779
16_V39_A0.212610.770
4_R73_N0.211530.766
60_L105_E0.211090.765
26_D63_D0.211030.764
86_R90_G0.209920.760
78_L94_K0.207170.750
51_I62_P0.20690.750
3_L99_I0.204560.741
59_G104_K0.203070.736
65_L103_L0.20140.730
12_K16_V0.200730.727
3_L8_I0.200390.726
86_R89_A0.199990.724
49_S52_A0.199160.721
8_I97_S0.198810.720
82_R86_R0.19810.718
44_L51_I0.1950.706
44_L47_L0.19380.702
85_A91_P0.193480.701
14_R18_R0.192430.697
12_K40_A0.189780.687
60_L64_N0.188070.681
82_R92_I0.187540.679
80_R94_K0.18710.678
1_A50_A0.186350.675
5_N74_K0.185770.673
55_E60_L0.185320.671
26_D30_A0.184290.668
79_K92_I0.182570.661
12_K86_R0.180340.653
27_E31_Q0.17980.651
58_K105_E0.179250.649
50_A67_I0.178350.646
2_K73_N0.177550.643
9_S95_R0.176760.640
16_V32_L0.175980.637
52_A57_N0.169840.615
60_L70_I0.169780.615
90_G105_E0.169730.615
61_D88_R0.167510.607
21_R71_W0.167490.607
53_N80_R0.166180.602
10_P75_G0.165410.599
24_S68_S0.16470.597
29_I47_L0.164110.594
68_S103_L0.161910.587
38_K41_K0.159570.578
69_E105_E0.15940.577
31_Q35_V0.158970.576
20_I67_I0.158780.575
56_N86_R0.157880.572
4_R98_H0.157640.571
66_Y105_E0.156620.567
15_E35_V0.155660.564
53_N79_K0.153810.557
54_A85_A0.153590.556
9_S12_K0.153290.555
79_K88_R0.151960.550
23_M102_V0.151250.548
43_I99_I0.150970.547
32_L43_I0.150.543
45_K49_S0.149330.541
66_Y77_Y0.148930.540
52_A56_N0.148760.539
84_R92_I0.148140.537
92_I95_R0.147480.534
2_K59_G0.147160.533
73_N98_H0.146930.532
25_V35_V0.145880.528
76_P98_H0.145810.528
82_R85_A0.145590.527
7_R76_P0.145550.527
73_N76_P0.144560.524
80_R92_I0.144350.523
79_K95_R0.143440.520
77_Y96_T0.143420.520
69_E100_T0.142730.517
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
3bboU1100-0.048
2zjrP1100-0.047
3r8sS1100-0.039
3j3wS1100-0.037
2ftcM1100-0.016
1i4jA0.97141000.001
1vq8R0.99051000.006
3j39P0.99051000.013
3j21S0.99051000.015
3j3bP0.99051000.017

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