GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S17 - Ribosomal protein S17
Pfam: PF00366 (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: CL0021
Length: 69
Sequences: 1582
Seq/Len: 22.93
HH_delta: -0.079 (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
36_M61_T1.884824.882
51_R68_E1.57254.073
15_R32_T1.365133.536
12_V66_V1.173723.040
9_D42_N1.029322.666
53_R65_V0.799962.072
53_R67_V0.7792.018
2_V49_K0.764111.979
6_D45_K0.737291.910
19_L30_K0.735991.907
13_V36_M0.702731.820
37_A52_I0.698571.810
21_Y26_K0.695381.801
6_D46_V0.683051.769
16_V35_Y0.656031.699
20_V31_R0.651921.689
44_C66_V0.629551.631
55_C65_V0.579941.502
11_T62_K0.571371.480
35_Y52_I0.570951.479
19_L28_Y0.546231.415
4_V15_R0.530621.375
44_C69_V0.526881.365
21_Y28_Y0.509411.320
13_V34_K0.486971.261
43_I69_V0.467241.210
12_V37_A0.45711.184
2_V15_R0.448491.162
8_M36_M0.443971.150
51_R67_V0.441581.144
39_D44_C0.434171.125
6_D12_V0.42551.102
14_V52_I0.417881.082
58_I65_V0.384640.996
17_E30_K0.375830.974
24_K28_Y0.352630.913
39_D42_N0.349480.905
38_H62_K0.3430.889
40_E65_V0.334070.865
18_R28_Y0.334060.865
59_S62_K0.332370.861
66_V69_V0.328840.852
37_A66_V0.317540.823
15_R34_K0.301020.780
17_E32_T0.298010.772
12_V44_C0.295640.766
2_V17_E0.287360.744
20_V29_I0.277410.719
43_I68_E0.273220.708
58_I63_R0.272070.705
24_K30_K0.268790.696
7_K13_V0.266540.690
28_Y31_R0.260260.674
9_D46_V0.258030.668
43_I65_V0.255240.661
18_R33_K0.254830.660
57_P63_R0.254360.659
11_T38_H0.250350.649
53_R63_R0.243560.631
55_C58_I0.236590.613
4_V13_V0.23350.605
46_V52_I0.229540.595
4_V34_K0.229140.594
4_V10_K0.228210.591
26_K29_I0.227910.590
55_C64_F0.22250.576
21_Y64_F0.220560.571
30_K33_K0.215810.559
33_K52_I0.215050.557
1_G4_V0.213910.554
12_V39_D0.212240.550
6_D44_C0.211880.549
10_K40_E0.209780.543
6_D37_A0.209230.542
29_I43_I0.207810.538
1_G47_G0.207760.538
2_V16_V0.206130.534
7_K46_V0.204890.531
13_V32_T0.203580.527
2_V60_K0.202070.523
19_L29_I0.201640.522
8_M25_Y0.200320.519
14_V50_V0.200260.519
53_R58_I0.197370.511
5_S54_E0.191690.497
11_T36_M0.190740.494
22_H29_I0.190410.493
25_Y55_C0.189530.491
37_A50_V0.188650.489
22_H27_K0.188190.487
14_V37_A0.186280.483
13_V61_T0.185860.481
55_C68_E0.184070.477
2_V35_Y0.181280.470
18_R60_K0.178190.462
49_K53_R0.1780.461
13_V54_E0.176920.458
28_Y55_C0.176130.456
30_K53_R0.175730.455
3_V50_V0.174790.453
49_K67_V0.173320.449
21_Y24_K0.173040.448
24_K31_R0.165660.429
8_M13_V0.16560.429
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
3bbnQ199.9-0.079
1qd7I199.9-0.07
2vqeQ199.9-0.063
2xzmQ199.9-0.055
3r8nQ199.9-0.047
2zkqq199.9-0.047
3iz6P199.9-0.045
3j20R199.9-0.044
3u5cL199.9-0.043
3j3aL199.9-0.04

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