GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S16 - Ribosomal protein S16
Pfam: PF00886 (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: 62
Sequences: 1477
Seq/Len: 23.82
HH_delta: -0.016 (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
53_Y57_K1.644254.124
50_R53_Y1.534083.848
29_L51_I1.158672.906
33_D36_P0.98382.468
27_E50_R0.868152.178
48_F52_K0.80382.016
4_R7_R0.742621.863
14_V29_L0.724821.818
31_F45_K0.695991.746
15_A19_S0.693211.739
36_P43_Q0.676541.697
52_K56_S0.660011.656
9_F31_F0.642571.612
11_R28_E0.641411.609
15_A25_F0.600451.506
55_L61_P0.597441.499
2_M11_R0.568561.426
46_L51_I0.562661.411
20_P25_F0.549691.379
25_F28_E0.541921.359
38_P42_K0.537391.348
53_Y56_S0.510631.281
12_I46_L0.510461.280
7_R35_I0.49211.234
2_M28_E0.485871.219
52_K55_L0.485211.217
17_S62_T0.475291.192
47_N50_R0.451211.132
14_V26_I0.444671.115
50_R57_K0.408671.025
19_S24_K0.407521.022
33_D43_Q0.401121.006
1_R8_P0.398250.999
20_P23_G0.387780.973
16_D26_I0.387330.972
42_K45_K0.383090.961
35_I43_Q0.358260.899
28_E31_F0.354650.890
27_E54_W0.350060.878
9_F35_I0.332450.834
51_I61_P0.326740.820
15_A20_P0.311880.782
35_I42_K0.306880.770
9_F33_D0.300970.755
8_P35_I0.299990.752
31_F44_I0.286380.718
38_P43_Q0.284530.714
3_G30_G0.277550.696
42_K52_K0.276540.694
54_W57_K0.275940.692
48_F51_I0.254890.639
37_N42_K0.252750.634
55_L60_Q0.252310.633
37_N43_Q0.251720.631
2_M9_F0.240280.603
18_R23_G0.237560.596
13_V25_F0.237240.595
2_M48_F0.233770.586
6_K48_F0.233010.584
32_Y38_P0.230050.577
51_I55_L0.225690.566
11_R32_Y0.224960.564
2_M22_D0.219040.549
14_V51_I0.215150.540
15_A24_K0.214660.538
45_K48_F0.213430.535
10_Y34_P0.211610.531
27_E53_Y0.207140.520
38_P52_K0.204250.512
4_R50_R0.20350.510
36_P42_K0.202990.509
33_D42_K0.202770.509
48_F57_K0.202040.507
19_S25_F0.197950.497
6_K9_F0.194150.487
20_P31_F0.190460.478
6_K36_P0.189560.475
14_V56_S0.187840.471
31_F43_Q0.187240.470
8_P34_P0.182460.458
44_I49_E0.181190.454
16_D23_G0.178050.447
20_P55_L0.177870.446
30_G58_G0.177130.444
21_R62_T0.175680.441
49_E52_K0.175590.440
15_A18_R0.172860.434
47_N51_I0.17210.432
5_K33_D0.17050.428
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
3r8nP0.983999.9-0.016
3bn0A0.935599.9-0.011
3pysP0.967799.9-0.01
4khpP0.967799.9-0.01
4juwP0.967799.9-0.01
3bbnP0.919499.90.003
4h3sA0.935522.40.888
3dxoA0.580620.60.889
1vq8L0.790318.10.892
4f11A0.774215.70.895

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