GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S18 - Ribosomal protein S18
Pfam: PF01084 (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: 54
Sequences: 1150
Seq/Len: 21.3
HH_delta: 0.009 (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
34_C37_Q1.40115.070
33_L41_L0.70982.569
19_I54_L0.659362.386
33_L37_Q0.629652.278
25_I45_I0.524751.899
12_V53_L0.483791.751
44_A47_R0.476381.724
11_N14_L0.468111.694
7_I44_A0.46221.673
35_A39_R0.451321.633
37_Q40_K0.428021.549
4_N40_K0.374141.354
13_E16_S0.341641.236
4_N14_L0.329541.192
17_Q26_L0.320111.158
28_R50_Q0.319951.158
28_R35_A0.319671.157
7_I41_L0.30931.119
26_L50_Q0.289611.048
38_Q42_A0.289161.046
18_F23_G0.274730.994
5_E14_L0.274010.992
18_F26_L0.273920.991
15_L54_L0.271270.982
22_T34_C0.267410.968
19_I23_G0.265550.961
42_A46_K0.262430.950
11_N32_G0.260920.944
5_E40_K0.248340.899
10_K47_R0.244750.886
46_K51_L0.234910.850
3_N6_Y0.232330.841
26_L30_I0.228060.825
9_Y24_K0.227560.823
24_K46_K0.224360.812
9_Y29_R0.224130.811
6_Y40_K0.22380.810
46_K49_R0.222970.807
5_E34_C0.22140.801
22_T28_R0.219020.793
20_S26_L0.217910.789
17_Q42_A0.216130.782
24_K29_R0.213260.772
33_L43_K0.212540.769
39_R42_A0.209270.757
25_I46_K0.206380.747
17_Q47_R0.203580.737
40_K43_K0.203490.736
23_G54_L0.203110.735
4_N43_K0.19860.719
38_Q52_G0.1960.709
14_L40_K0.195070.706
15_L18_F0.19470.705
41_L44_A0.190490.689
5_E12_V0.189920.687
20_S24_K0.18850.682
26_L42_A0.185120.670
12_V16_S0.184650.668
43_K47_R0.183210.663
4_N7_I0.180750.654
32_G37_Q0.178790.647
13_E50_Q0.178630.646
8_D11_N0.178440.646
3_N7_I0.177460.642
14_L17_Q0.177350.642
13_E35_A0.176240.638
19_I30_I0.174130.630
10_K29_R0.171640.621
20_S30_I0.170770.618
24_K49_R0.170410.617
46_K50_Q0.169150.612
25_I38_Q0.168620.610
24_K51_L0.168240.609
3_N43_K0.167580.606
12_V22_T0.167440.606
7_I25_I0.166660.603
6_Y33_L0.166250.602
17_Q40_K0.165040.597
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
3bbnR0.981599.80.009
2vqeR199.80.013
3i1mR199.70.017
3r8nR0.907499.70.026
4igcD152.60.832
1twfA149.80.835
3h0gA130.30.853
4aybC126.50.857
3mu7A0.888924.90.859
3e6uA0.981520.60.864

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