GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S4 - Ribosomal protein S4S9 N-terminal domain
Pfam: PF00163 (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: 94
Sequences: 1717
Seq/Len: 18.27
HH_delta: 0.126 (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
81_L88_N0.638812.655
56_E59_K0.629182.615
88_N91_Q0.595062.473
14_L62_F0.558372.320
73_R77_I0.541412.250
27_I30_Y0.523192.174
72_R76_K0.506872.106
77_I80_K0.458631.906
32_L39_W0.455361.892
3_Y6_P0.402741.674
77_I81_L0.402631.673
34_P37_H0.37061.540
8_C11_P0.366841.524
14_L55_R0.354861.475
81_L92_L0.351291.460
47_L51_G0.339741.412
4_R7_K0.337781.404
11_P17_K0.330711.374
10_L62_F0.321761.337
20_L23_K0.318551.324
72_R79_A0.316581.316
81_L91_Q0.31621.314
35_G38_G0.300641.249
51_G55_R0.298781.242
8_C17_K0.29551.228
73_R76_K0.292471.215
39_W47_L0.291751.212
69_K73_R0.285391.186
83_G86_G0.284771.183
66_I74_Y0.282751.175
54_L57_K0.279531.162
10_L14_L0.278281.156
84_V87_E0.270551.124
34_P38_G0.263081.093
62_F67_L0.260041.081
26_L30_Y0.25641.066
74_Y92_L0.255281.061
22_E39_W0.254321.057
11_P25_K0.251161.044
88_N92_L0.250561.041
74_Y89_L0.236370.982
79_A85_T0.235920.980
14_L18_L0.235830.980
83_G88_N0.228920.951
54_L58_Q0.228730.951
61_R67_L0.228130.948
32_L36_Q0.22780.947
25_K30_Y0.225910.939
47_L55_R0.225850.939
9_K54_L0.222630.925
60_L91_Q0.218860.910
15_G51_G0.217820.905
87_E91_Q0.214330.891
67_L87_E0.211440.879
8_C26_L0.210270.874
76_K80_K0.210220.874
49_R53_Q0.209950.872
7_K10_L0.208410.866
3_Y10_L0.207330.862
57_K68_E0.206950.860
50_Y56_E0.205420.854
22_E27_I0.204210.849
7_K16_E0.203420.845
22_E26_L0.201560.838
55_R62_F0.201090.836
32_L38_G0.201080.836
76_K81_L0.199440.829
78_A85_T0.199390.829
86_G90_L0.19850.825
75_G89_L0.197780.822
76_K87_E0.197320.820
9_K12_R0.196130.815
81_L87_E0.196070.815
76_K79_A0.195150.811
56_E61_R0.193070.802
3_Y9_K0.192070.798
50_Y58_Q0.191780.797
69_K79_A0.191310.795
23_K28_R0.18710.778
25_K29_R0.186410.775
71_L76_K0.185840.772
16_E25_K0.185540.771
56_E91_Q0.184230.766
64_Y69_K0.184180.765
8_C27_I0.183990.765
12_R35_G0.182720.759
49_R52_L0.181550.754
58_Q68_E0.181450.754
13_R74_Y0.179590.746
29_R36_Q0.179420.746
68_E86_G0.178970.744
64_Y78_A0.177570.738
61_R68_E0.176850.735
11_P14_L0.173720.722
65_G69_K0.171480.713
50_Y78_A0.170960.710
84_V90_L0.170250.708
68_E78_A0.169440.704
60_L90_L0.167840.697
48_S52_L0.167190.695
17_K23_K0.166450.692
33_R36_Q0.166270.691
16_E32_L0.165250.687
19_W23_K0.164670.684
32_L46_K0.164390.683
28_R82_K0.164150.682
55_R73_R0.164020.682
50_Y64_Y0.163910.681
30_Y33_R0.163840.681
17_K21_T0.163830.681
14_L19_W0.163270.678
63_Y71_L0.162350.675
57_K83_G0.162030.673
33_R38_G0.16190.673
54_L61_R0.161780.672
46_K50_Y0.161160.670
64_Y70_Q0.160130.665
77_I92_L0.159750.664
75_G79_A0.159740.664
71_L75_G0.159520.663
26_L29_R0.159120.661
33_R40_R0.158820.660
33_R77_I0.15670.651
69_K77_I0.156450.650
61_R84_V0.155730.647
54_L64_Y0.155340.646
72_R75_G0.155240.645
89_L94_E0.154220.641
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
3r8nD0.925599.80.126
2vqeD0.978799.70.216
3bbnD0.925599.70.225
3u5cJ1990.466
3iz6C198.90.491
1c05A0.531998.90.492
3zey6198.80.508
3j20D0.989498.80.516
2xzmD198.60.548
1t7sA0.7663.60.915

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