GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S8 - Ribosomal protein S8
Pfam: PF00410 (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: 129
Sequences: 1857
Seq/Len: 14.4
HH_delta: -0.022 (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
107_K118_L0.872923.654
37_K44_G0.85773.591
88_Y119_N0.780833.269
8_T11_R0.762933.194
34_K38_K0.686072.872
38_K114_E0.60722.542
22_I58_W0.604572.531
31_S34_K0.567862.377
114_E118_L0.549972.302
112_H116_R0.531662.226
6_L33_L0.526542.204
73_K129_W0.467471.957
7_L126_C0.463041.938
3_L32_I0.461351.931
5_D9_R0.446391.869
6_L23_I0.425151.780
42_I45_F0.423651.774
13_A21_V0.398211.667
20_F60_E0.380461.593
36_L128_V0.37171.556
33_L59_I0.36681.536
22_I56_R0.36641.534
26_S29_N0.360181.508
2_P29_N0.359371.504
20_F58_W0.348641.460
34_K45_F0.343551.438
109_I125_L0.327931.373
14_S69_P0.325041.361
28_L125_L0.320931.344
25_Y30_L0.318261.332
87_S90_E0.317921.331
3_L28_L0.317851.331
17_R67_G0.317661.330
49_D52_R0.309771.297
65_R68_K0.307431.287
46_E60_E0.306161.282
23_I59_I0.301751.263
82_R127_Y0.297211.244
48_I52_R0.294061.231
86_I103_L0.290091.214
30_L47_I0.288331.207
75_K127_Y0.288191.206
35_I109_I0.286831.201
48_I58_W0.286731.200
107_K120_V0.285681.196
101_L127_Y0.283421.186
17_R69_P0.283341.186
68_K72_K0.272061.139
85_Y123_E0.268021.122
2_P26_S0.266991.118
65_R69_P0.261431.094
114_E117_K0.261331.094
34_K37_K0.257581.078
95_K129_W0.253641.062
50_D55_K0.251151.051
37_K42_I0.250231.048
30_L57_I0.249161.043
91_L112_H0.247691.037
83_R123_E0.247611.037
52_R55_K0.243111.018
91_L103_L0.242941.017
35_I100_I0.24041.006
46_E58_W0.237180.993
110_M114_E0.235740.987
25_Y55_K0.235130.984
30_L55_K0.232190.972
77_I84_V0.229170.959
86_I124_V0.229030.959
47_I55_K0.228030.955
52_R56_R0.227370.952
30_L34_K0.226710.949
40_G62_K0.222420.931
1_D76_R0.222060.930
9_R13_A0.219580.919
94_V101_L0.214530.898
7_L11_R0.213110.892
43_S55_K0.212620.890
92_P98_L0.211910.887
73_K127_Y0.205130.859
92_P101_L0.204740.857
10_I71_I0.203470.852
49_D55_K0.202320.847
13_A16_A0.201090.842
28_L109_I0.200310.839
35_I102_I0.20010.838
50_D56_R0.197940.829
78_S85_Y0.197910.829
23_I57_I0.194260.813
108_G121_G0.194090.813
100_I128_V0.192340.805
51_N55_K0.191460.802
38_K110_M0.190780.799
31_S38_K0.18990.795
33_L36_L0.188850.791
17_R114_E0.186840.782
23_I29_N0.185130.775
32_I109_I0.184740.773
92_P127_Y0.18460.773
78_S123_E0.183840.770
25_Y47_I0.183330.767
91_L124_V0.183320.767
6_L59_I0.182050.762
4_A29_N0.181150.758
102_I128_V0.180580.756
124_V127_Y0.179930.753
45_F59_I0.1790.749
37_K45_F0.178550.747
14_S129_W0.178470.747
100_I125_L0.178020.745
76_R83_R0.177440.743
6_L29_N0.177310.742
110_M118_L0.17660.739
104_S123_E0.175420.734
14_S65_R0.17490.732
10_I63_Y0.174530.731
88_Y120_V0.17370.727
43_S60_E0.172520.722
48_I56_R0.172380.722
5_D115_A0.171050.716
38_K117_K0.169260.709
99_G108_G0.169120.708
49_D56_R0.168680.706
32_I126_C0.168620.706
27_K30_L0.168420.705
33_L42_I0.167480.701
18_K57_I0.166870.699
72_K129_W0.166840.698
104_S109_I0.165380.692
25_Y110_M0.164190.687
14_S70_V0.164040.687
43_S58_W0.162730.681
86_I91_L0.161230.675
48_I60_E0.160740.673
82_R86_I0.160010.670
36_L77_I0.159920.669
65_R70_V0.157970.661
24_P29_N0.157490.659
23_I47_I0.15660.656
105_T110_M0.154870.648
62_K71_I0.154680.648
1_D4_A0.153390.642
41_Y100_I0.153390.642
87_S103_L0.152810.640
14_S79_K0.152760.640
110_M120_V0.152530.639
20_F46_E0.152220.637
32_I35_I0.151320.633
86_I90_E0.151270.633
5_D45_F0.149360.625
90_E93_K0.148130.620
30_L45_F0.14810.620
104_S108_G0.147760.619
19_R117_K0.147680.618
81_G85_Y0.147520.618
33_L72_K0.147480.617
66_N129_W0.146610.614
95_K104_S0.145560.609
4_A8_T0.145120.608
81_G123_E0.144150.603
19_R43_S0.144130.603
106_S120_V0.143990.603
92_P116_R0.143320.600
22_I44_G0.14330.600
6_L32_I0.143150.599
9_R18_K0.142940.598
122_G125_L0.142580.597
35_I126_C0.142010.594
20_F30_L0.141650.593
23_I51_N0.14160.593
3_L129_W0.141540.593
26_S41_Y0.141320.592
11_R104_S0.140750.589
94_V97_G0.139060.582
8_T40_G0.1390.582
67_G70_V0.137330.575
43_S91_L0.1370.574
83_R99_G0.136820.573
77_I127_Y0.136790.573
6_L39_E0.136340.571
48_I55_K0.136250.570
41_Y98_L0.135650.568
38_K87_S0.135570.568
71_I120_V0.13470.564
36_L80_P0.134340.562
66_N69_P0.134080.561
105_T121_G0.133790.560
21_V124_V0.133640.559
87_S95_K0.133510.559
37_K60_E0.133320.558
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
2vqeH0.9922100-0.022
1seiA0.9845100-0.016
3bbnH0.9767100-0.01
3rf2A1100-0.009
1s03H0.9767100-0.006
2xzmH0.92251000.105
1i6uA0.92251000.109
3u5cW0.92251000.141
3k1jA0.651225.60.931
2zrrA0.496124.30.931

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