GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L16 - Ribosomal protein L16pL10e
Pfam: PF00252 (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: 133
Sequences: 1436
Seq/Len: 10.8
HH_delta: 0 (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
111_E115_K0.685323.242
26_L32_G0.661373.129
116_E119_K0.596112.820
118_L131_F0.589572.789
35_A127_I0.552122.612
30_D106_G0.545392.580
57_L105_I0.506492.396
110_N113_E0.503922.384
122_A129_T0.502322.376
53_I63_L0.469382.220
111_E133_S0.46082.180
73_V91_H0.451052.134
40_R95_R0.430042.034
41_L127_I0.416271.969
49_A125_L0.41441.960
31_Y131_F0.39661.876
71_H95_R0.376721.782
53_I121_A0.372481.762
41_L67_V0.363841.721
13_P71_H0.355681.683
37_E128_K0.350021.656
47_E50_R0.33681.593
56_Y113_E0.328981.556
34_K130_K0.319761.513
28_F66_R0.316761.498
115_K131_F0.316231.496
21_K24_N0.312861.480
42_T45_Q0.310191.467
53_I105_I0.306741.451
33_L122_A0.306171.448
74_T89_I0.295451.398
49_A103_F0.289041.367
34_K132_V0.287971.362
6_Y9_Y0.286121.354
75_K90_D0.281691.333
14_R17_Y0.279871.324
4_T9_Y0.278511.318
119_K123_K0.278041.315
32_G132_V0.276951.310
56_Y116_E0.272541.289
41_L102_I0.269851.277
11_K40_R0.267411.265
76_K80_T0.265671.257
57_L113_E0.26451.251
67_V100_Q0.259291.227
32_G101_I0.257921.220
105_I118_L0.254731.205
23_G27_K0.248211.174
73_V95_R0.24751.171
9_Y72_P0.243411.151
81_R92_W0.242381.147
27_K66_R0.240371.137
101_I132_V0.239941.135
54_N63_L0.233371.104
57_L60_N0.233251.103
67_V102_I0.230561.091
63_L105_I0.227171.075
56_Y119_K0.223251.056
56_Y120_R0.220471.043
20_S100_Q0.219451.038
77_P80_T0.219381.038
43_S91_H0.217851.031
4_T92_W0.21261.006
75_K84_K0.212331.004
70_H100_Q0.211691.001
105_I114_A0.210540.996
15_I38_P0.208570.987
40_R130_K0.203160.961
28_F44_N0.203060.961
17_Y95_R0.200060.946
15_I71_H0.199980.946
9_Y71_H0.197180.933
75_K91_H0.1970.932
15_I95_R0.196670.930
30_D133_S0.195380.924
26_L101_I0.194840.922
84_K89_I0.194430.920
37_E127_I0.193980.918
29_G64_W0.189390.896
39_G127_I0.188240.890
45_Q126_P0.185130.876
26_L132_V0.184020.871
43_S92_W0.18230.862
39_G103_F0.181610.859
9_Y89_I0.181170.857
11_K73_V0.180320.853
35_A100_Q0.180060.852
4_T89_I0.179070.847
11_K76_K0.179040.847
36_L130_K0.178620.845
51_I54_N0.17420.824
2_K92_W0.173780.822
17_Y38_P0.17370.822
55_R59_K0.173010.818
63_L118_L0.17240.816
3_R7_R0.171190.810
46_L67_V0.170970.809
34_K101_I0.170950.809
103_F125_L0.170630.807
15_I73_V0.169470.802
117_A121_A0.168510.797
6_Y19_K0.167670.793
107_G110_N0.166070.786
111_E131_F0.16580.784
67_V127_I0.163560.774
80_T123_K0.161440.764
115_K133_S0.161430.764
81_R104_E0.16110.762
32_G104_E0.159570.755
10_Q89_I0.159510.755
84_K92_W0.158010.747
38_P97_K0.157180.744
55_R117_A0.156510.740
11_K79_E0.155380.735
107_G114_A0.152390.721
40_R73_V0.152380.721
77_P88_K0.151630.717
49_A121_A0.150820.713
38_P98_P0.150640.713
57_L114_A0.149710.708
112_E132_V0.148930.705
109_V131_F0.147610.698
113_E119_K0.147560.698
56_Y82_M0.147480.698
2_K62_K0.14620.692
75_K88_K0.146160.691
103_F106_G0.145650.689
83_G86_K0.145180.687
53_I133_S0.144530.684
62_K106_G0.144460.683
6_Y43_S0.143850.680
20_S24_N0.141960.672
33_L102_I0.141280.668
71_H93_V0.140850.666
27_K105_I0.140140.663
112_E119_K0.139490.660
65_I128_K0.138950.657
9_Y70_H0.138570.656
50_R55_R0.138360.655
6_Y21_K0.137980.653
42_T91_H0.137670.651
60_N84_K0.137210.649
43_S51_I0.13670.647
109_V114_A0.136680.647
72_P89_I0.135880.643
30_D60_N0.134670.637
17_Y133_S0.134430.636
75_K133_S0.13430.635
19_K24_N0.133790.633
82_M86_K0.13370.632
19_K131_F0.133490.631
84_K94_A0.133120.630
40_R71_H0.132970.629
78_L84_K0.132470.627
29_G104_E0.132240.626
11_K95_R0.132070.625
78_L89_I0.131610.623
24_N34_K0.13120.621
19_K25_K0.131180.621
113_E132_V0.129660.613
115_K119_K0.129430.612
40_R126_P0.129390.612
120_R129_T0.129010.610
116_E120_R0.128930.610
17_Y98_P0.128870.610
70_H92_W0.128820.609
56_Y63_L0.128620.608
37_E48_A0.128530.608
52_A120_R0.128310.607
49_A120_R0.127930.605
110_N133_S0.127750.604
18_G122_A0.12580.595
51_I75_K0.125510.594
101_I104_E0.125460.594
33_L117_A0.125130.592
10_Q14_R0.125090.592
13_P38_P0.124740.590
25_K30_D0.124360.588
102_I127_I0.12360.585
57_L63_L0.123520.584
105_I112_E0.123110.582
35_A96_V0.122980.582
23_G100_Q0.122890.581
3_R91_H0.12250.579
17_Y78_L0.122470.579
116_E123_K0.122090.578
25_K53_I0.12170.576
52_A121_A0.121570.575
96_V112_E0.121560.575
60_N123_K0.12140.574
62_K74_T0.12080.571
41_L49_A0.120710.571
36_L128_K0.120580.570
46_L102_I0.120550.570
56_Y112_E0.120520.570
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
2zjrJ0.97741000
3bboO0.97741000.003
3r8sM0.96991000.006
2ftcI0.87221000.123
1ffkF0.97741000.137
2zkrh0.99251000.172
1vq8H0.99251000.174
3j3bI0.99251000.179
3j0lJ0.99251000.18
3iz5I0.99251000.183

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