GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S21 - Ribosomal protein S21
Pfam: PF01165 (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: 57
Sequences: 806
Seq/Len: 14.14
HH_delta: -0.025 (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
38_E46_R1.128284.886
30_E34_R0.679722.944
37_Y40_P0.486782.108
5_V14_A0.449151.945
22_V27_I0.436951.892
9_E17_R0.414991.797
28_L31_L0.367291.591
21_K24_R0.344011.490
44_R48_R0.339221.469
11_V14_A0.325421.409
18_F22_V0.284771.233
49_S52_W0.284161.231
2_T25_N0.272361.179
10_D13_R0.270641.172
25_N31_L0.258691.120
48_R52_W0.247381.071
2_T55_R0.24721.071
33_K36_F0.239641.038
5_V13_R0.23941.037
20_R41_S0.238621.033
37_Y41_S0.236261.023
13_R16_R0.23571.021
26_G39_K0.232011.005
19_K28_L0.229360.993
34_R51_R0.229320.993
25_N29_K0.228360.989
8_G28_L0.227490.985
30_E33_K0.225220.975
6_R25_N0.225110.975
23_R35_R0.223970.970
3_V27_I0.218280.945
30_E42_E0.215850.935
19_K24_R0.215280.932
12_E51_R0.210810.913
7_D19_K0.209620.908
32_R44_R0.207390.898
27_I43_K0.204330.885
4_K29_K0.202910.879
43_K46_R0.199750.865
19_K32_R0.19470.843
2_T21_K0.19070.826
29_K50_E0.19020.824
7_D17_R0.189860.822
16_R23_R0.18950.821
34_R37_Y0.18740.812
29_K45_K0.184840.800
20_R42_E0.184180.798
16_R19_K0.181830.787
35_R39_K0.178540.773
9_E18_F0.177550.769
22_V35_R0.177240.768
4_K8_G0.17510.758
46_R52_W0.17360.752
32_R35_R0.173470.751
13_R23_R0.171250.742
22_V25_N0.170970.740
42_E48_R0.170550.739
42_E45_K0.169480.734
38_E43_K0.168530.730
31_L34_R0.167220.724
13_R25_N0.164060.710
33_K47_K0.162640.704
52_W55_R0.162080.702
25_N52_W0.16130.699
46_R50_E0.160270.694
38_E50_E0.159510.691
12_E15_L0.15830.686
36_F43_K0.157780.683
6_R13_R0.157730.683
51_R54_R0.156060.676
13_R55_R0.153940.667
47_K55_R0.150190.650
12_E17_R0.148290.642
33_K50_E0.147290.638
24_R30_E0.147110.637
49_S54_R0.146010.632
6_R9_E0.143250.620
16_R54_R0.143210.620
6_R32_R0.142870.619
8_G13_R0.141910.615
8_G21_K0.141790.614
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
3bbnU199.5-0.025
3i1mU199.50.027
3r8nU0.894799.30.107
1pchA0.508822.20.827
4dciA0.561418.80.833
2eenA0.842114.10.842
2rc8A0.754413.70.842
1ka5A0.491212.50.845
1kklH0.491210.30.85
2vhjA0.35099.10.853

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