GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S5 - Ribosomal protein S5 N-terminal domain
Pfam: PF00333 (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. )
Clan: CL0196
Length: 67
Sequences: 1150
Seq/Len: 17.16
HH_delta: -0.061 (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
3_E33_G0.996043.672
32_N36_L0.703462.594
49_D52_R0.687962.536
28_V54_A0.611152.253
36_L62_L0.591912.182
2_L36_L0.591532.181
15_M22_F0.570712.104
55_K59_K0.564172.080
15_M20_R0.547852.020
25_R41_V0.513471.893
26_A50_A0.414191.527
10_K25_R0.411731.518
36_L64_Y0.407641.503
1_D34_N0.403331.487
16_T21_I0.38261.411
57_K61_N0.378021.394
26_A47_V0.37441.380
24_F47_V0.356471.314
6_V9_V0.339491.252
21_I45_K0.337021.243
2_L62_L0.328131.210
3_E57_K0.327331.207
41_V54_A0.326841.205
12_V23_S0.322921.191
11_R22_F0.319751.179
63_I66_P0.302311.115
27_L39_F0.299021.102
13_S22_F0.292231.077
8_E41_V0.285451.052
8_E25_R0.284231.048
11_R18_G0.283561.045
4_E55_K0.280971.036
40_G57_K0.279721.031
30_V58_A0.269110.992
2_L34_N0.267830.987
52_R56_R0.263930.973
8_E49_D0.263130.970
43_K53_K0.260980.962
6_V23_S0.258860.954
26_A51_I0.253260.934
6_V51_I0.247540.913
15_M18_G0.243070.896
10_K59_K0.237830.877
59_K63_I0.237530.876
9_V46_E0.234880.866
14_K18_G0.233070.859
47_V51_I0.232540.857
28_V55_K0.231980.855
31_G38_G0.22860.843
27_L48_P0.227480.839
1_D8_E0.221590.817
23_S41_V0.218490.806
10_K27_L0.217580.802
10_K56_R0.211750.781
23_S66_P0.211550.780
23_S45_K0.206250.760
12_V42_G0.203450.750
7_L17_K0.195350.720
23_S44_A0.19020.701
3_E8_E0.188420.695
57_K63_I0.187240.690
39_F54_A0.183890.678
2_L21_I0.181680.670
6_V39_F0.181260.668
42_G50_A0.18090.667
11_R24_F0.180720.666
58_A65_V0.180650.666
27_L43_K0.180470.665
20_R56_R0.180130.664
55_K63_I0.179740.663
48_P51_I0.176910.652
6_V26_A0.176660.651
6_V28_V0.172710.637
40_G61_N0.172140.635
9_V47_V0.16940.625
46_E53_K0.168740.622
18_G22_F0.1680.619
45_K54_A0.165990.612
42_G53_K0.165150.609
7_L57_K0.16470.607
27_L56_R0.164230.605
11_R53_K0.163510.603
6_V48_P0.16130.595
1_D33_G0.160990.594
33_G62_L0.160960.593
30_V38_G0.160770.593
3_E6_V0.15820.583
24_F51_I0.155650.574
3_E52_R0.155520.573
39_F57_K0.155090.572
35_G40_G0.154910.571
2_L59_K0.154280.569
3_E62_L0.154210.569
41_V49_D0.153770.567
32_N64_Y0.151090.557
9_V26_A0.150840.556
42_G61_N0.14960.552
12_V66_P0.149240.550
3_E55_K0.149080.550
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
3bbnE199.9-0.061
2xzmE199.9-0.053
3j38C199.9-0.052
3j3aC199.8-0.049
3r8nE199.8-0.047
2vqeE199.8-0.047
3j20F199.8-0.045
3u5cC199.8-0.044
3iz6E199.8-0.042
3i1mE199.8-0.042

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