GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S7 - Ribosomal protein S7pS5e
Pfam: PF00177 (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: 148
Sequences: 1530
Seq/Len: 10.34
HH_delta: -0.035 (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
19_D62_K0.679843.557
29_L42_V0.520472.723
105_E109_K0.491832.573
55_K63_Q0.488122.554
53_T124_I0.481472.519
124_I127_S0.428112.240
44_K116_S0.42392.218
47_E50_K0.418192.188
22_V46_L0.406642.127
135_K139_E0.40372.112
68_V103_I0.402862.108
21_L96_I0.397182.078
69_K95_R0.382252.000
42_V46_L0.370041.936
50_K56_N0.36321.900
48_I117_E0.360291.885
49_I60_I0.355641.861
27_N35_K0.353211.848
50_K57_P0.337491.766
125_D130_K0.33281.741
48_I116_S0.33131.733
106_A133_A0.329151.722
9_K93_K0.326571.708
46_L61_L0.325221.701
129_N134_I0.318031.664
69_K99_A0.313921.642
73_E94_R0.310011.622
68_V133_A0.30571.599
66_E69_K0.302841.584
48_I120_A0.295971.548
29_L38_A0.292411.530
41_I115_F0.285871.496
71_L95_R0.284741.490
28_R96_I0.273921.433
25_F61_L0.271941.423
25_F42_V0.268911.407
25_F100_I0.265041.387
112_E118_R0.258831.354
49_I124_I0.250871.312
121_N125_D0.247631.295
60_I127_S0.246831.291
114_S117_E0.245431.284
75_R88_V0.24031.257
68_V123_I0.234111.225
136_K140_L0.233131.220
25_F104_L0.231.203
106_A109_K0.228541.196
26_I39_E0.227831.192
55_K60_I0.223661.170
52_K121_N0.223481.169
21_L65_I0.214441.122
112_E121_N0.214131.120
55_K59_Q0.207841.087
48_I52_K0.207091.083
22_V42_V0.206131.078
24_K30_M0.205231.074
49_I53_T0.205071.073
46_L49_I0.2051.072
37_K40_K0.203451.064
67_N129_N0.200581.049
64_A67_N0.200121.047
76_S83_T0.197781.035
53_T127_S0.197381.033
25_F123_I0.197371.033
5_G8_K0.19551.023
56_N59_Q0.19421.016
35_K55_K0.190220.995
29_L104_L0.186650.976
65_I99_A0.186650.976
106_A132_S0.185840.972
49_I127_S0.185120.968
58_I113_K0.182380.954
85_Q147_N0.181370.949
80_G84_Y0.181040.947
30_M95_R0.180530.944
100_I104_L0.180510.944
75_R86_V0.179770.940
16_K47_E0.177680.930
62_K66_E0.177640.929
24_K96_I0.177180.927
102_W140_L0.176980.926
59_Q63_Q0.175720.919
64_A126_A0.175150.916
97_F101_K0.175130.916
98_L101_K0.174990.915
15_P141_H0.173620.908
68_V134_I0.173210.906
48_I51_K0.170830.894
107_A115_F0.170380.891
6_R96_I0.168430.881
47_E51_K0.167810.878
112_E130_K0.167360.876
74_V83_T0.167260.875
71_L120_A0.167160.875
21_L100_I0.166820.873
90_I98_L0.166240.870
31_K37_K0.163860.857
49_I123_I0.162690.851
67_N94_R0.161390.844
6_R9_K0.161240.844
6_R42_V0.159360.834
134_I137_K0.158480.829
76_S91_S0.157420.824
98_L102_W0.156710.820
84_Y98_L0.155380.813
71_L137_K0.154730.809
5_G76_S0.154580.809
16_K50_K0.15310.801
21_L31_K0.153070.801
67_N127_S0.151560.793
138_E142_K0.151270.791
25_F65_I0.150950.790
4_K111_K0.150760.789
30_M96_I0.150590.788
110_R121_N0.150530.788
8_K50_K0.149390.782
89_P92_P0.149160.780
67_N123_I0.148890.779
23_K27_N0.148480.777
14_D43_Y0.147170.770
14_D17_F0.14670.767
72_V76_S0.146520.767
116_S120_A0.146450.766
18_N22_V0.146030.764
107_A110_R0.145630.762
27_N30_M0.145610.762
6_R75_R0.144490.756
74_V85_Q0.143390.750
31_K104_L0.142090.743
69_K96_I0.141390.740
137_K141_H0.1410.738
82_K88_V0.140090.733
103_I112_E0.140090.733
115_F143_M0.139810.731
37_K41_I0.139560.730
65_I69_K0.139250.728
77_I84_Y0.138630.725
41_I119_L0.138490.725
78_K85_Q0.138410.724
63_Q127_S0.137720.720
20_P23_K0.137380.719
104_L130_K0.137370.719
28_R100_I0.137160.718
67_N126_A0.136940.716
31_K108_R0.136490.714
45_A119_L0.136320.713
50_K60_I0.136310.713
95_R99_A0.136230.713
78_K147_N0.135750.710
24_K28_R0.135290.708
30_M59_Q0.135210.707
73_E79_K0.135010.706
65_I100_I0.134360.703
143_M146_A0.134090.702
68_V99_A0.133990.701
72_V97_F0.133680.699
43_Y77_I0.133170.697
77_I91_S0.1330.696
44_K114_S0.132960.696
62_K76_S0.132910.695
65_I134_I0.132550.693
99_A121_N0.131420.688
93_K97_F0.131180.686
111_K148_R0.130970.685
4_K7_Y0.13090.685
55_K66_E0.130740.684
115_F135_K0.129670.678
62_K120_A0.128850.674
99_A123_I0.12880.674
26_I43_Y0.128780.674
23_K39_E0.128350.671
28_R105_E0.127990.670
29_L39_E0.127760.668
21_L95_R0.126970.664
57_P107_A0.12670.663
40_K44_K0.126550.662
15_P39_E0.126260.661
74_V101_K0.126160.660
50_K53_T0.125820.658
49_I120_A0.125530.657
48_I63_Q0.125310.656
41_I89_P0.125270.655
28_R65_I0.125030.654
145_E148_R0.124950.654
25_F119_L0.124290.650
75_R90_I0.122980.643
125_D138_E0.12290.643
57_P60_I0.122650.642
18_N58_I0.122540.641
7_Y10_K0.122460.641
20_P66_E0.122440.641
108_R115_F0.122050.639
78_K82_K0.121920.638
4_K66_E0.121290.635
5_G111_K0.12090.632
115_F141_H0.120430.630
24_K27_N0.120420.630
77_I85_Q0.120150.629
49_I55_K0.120120.628
16_K54_N0.120110.628
52_K79_K0.120090.628
10_K23_K0.119910.627
52_K142_K0.119440.625
8_K15_P0.119360.624
94_R98_L0.119290.624
25_F30_M0.119190.624
28_R104_L0.119020.623
82_K90_I0.1190.623
129_N138_E0.118270.619
6_R130_K0.117850.617
127_S137_K0.117820.616
3_R7_Y0.117310.614
126_A133_A0.117310.614
6_R100_I0.116550.610
23_K35_K0.115590.605
72_V109_K0.115470.604
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
3i1mG1100-0.035
3bbnG1100-0.022
3r8nG0.9932100-0.013
1husA0.9932100-0.004
3gtyS0.95951000.013
1rssA0.9731000.015
2xzmG0.98651000.054
2zkqg0.98651000.06
3u5cF0.98651000.076
1iqvA0.98651000.082

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