GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S3_C - Ribosomal protein S3 C-terminal domain
Pfam: PF00189 (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: 85
Sequences: 1090
Seq/Len: 12.82
HH_delta: -0.072 (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
73_K78_V0.860764.110
18_K22_R0.6453.080
71_H78_V0.600042.865
52_K55_K0.45962.194
35_Q48_T0.379451.812
1_F4_Q0.367161.753
10_I15_I0.358031.710
35_Q50_K0.355931.699
2_I19_I0.34821.663
11_S22_R0.322271.539
36_I79_I0.314341.501
2_I34_I0.310541.483
23_I85_I0.308061.471
23_I32_I0.303421.449
21_R27_K0.30041.434
57_S63_S0.288641.378
8_K50_K0.284581.359
6_L12_F0.283221.352
7_E72_A0.281481.344
2_I15_I0.280941.341
52_K56_I0.275071.313
30_K55_K0.274581.311
4_Q8_K0.268771.283
23_I29_I0.26551.268
45_R50_K0.265061.266
4_Q35_Q0.26411.261
3_A70_S0.260221.242
1_F5_K0.24511.170
50_K56_I0.239371.143
38_G77_G0.23731.133
10_I14_R0.2281.089
15_I29_I0.223461.067
29_I51_F0.221981.060
67_Y84_W0.219161.046
17_K41_N0.217811.040
16_I36_I0.217311.038
15_I51_F0.21691.036
35_Q52_K0.215731.030
37_S48_T0.21461.025
35_Q84_W0.214111.022
37_S45_R0.21211.013
33_K58_L0.208620.996
18_K21_R0.206470.986
56_I59_Q0.206340.985
29_I85_I0.204210.975
50_K55_K0.202790.968
34_I50_K0.199470.952
12_F40_L0.199140.951
67_Y82_K0.194680.930
22_R26_N0.193440.924
20_I36_I0.19160.915
25_M29_I0.189460.905
11_S41_N0.189390.904
44_E55_K0.189250.904
68_A83_V0.188570.900
43_A83_V0.18840.900
32_I85_I0.187910.897
3_A7_E0.18630.890
20_I53_K0.186090.889
7_E70_S0.184110.879
21_R53_K0.182880.873
8_K45_R0.182860.873
34_I51_F0.180590.862
20_I50_K0.179210.856
46_A78_V0.178070.850
1_F25_M0.177460.847
6_L19_I0.176190.841
4_Q18_K0.172790.825
5_K10_I0.172630.824
30_K64_N0.171690.820
8_K44_E0.170050.812
11_S18_K0.167770.801
1_F51_F0.16630.794
77_G80_G0.163940.783
14_R43_A0.163740.782
43_A72_A0.161950.773
20_I32_I0.161210.770
57_S65_I0.158480.757
20_I51_F0.158130.755
22_R27_K0.157650.753
12_F49_E0.15710.750
45_R48_T0.157030.750
72_A81_I0.156880.749
44_E49_E0.156010.745
8_K76_Y0.155530.743
6_L84_W0.15480.739
20_I34_I0.154770.739
31_G38_G0.154360.737
69_S73_K0.15380.734
18_K78_V0.152910.730
1_F10_I0.151590.724
75_K78_V0.151360.723
17_K76_Y0.150790.720
39_R67_Y0.150550.719
16_I51_F0.149210.712
16_I34_I0.149090.712
4_Q22_R0.149040.712
23_I27_K0.148610.710
40_L62_K0.14730.703
35_Q41_N0.145580.695
57_S74_T0.14410.688
47_R60_T0.142870.682
17_K46_A0.141940.678
34_I55_K0.141320.675
42_G74_T0.141020.673
6_L13_R0.140810.672
33_K43_A0.140250.670
60_T66_D0.139850.668
3_A81_I0.138830.663
8_K22_R0.138750.663
33_K39_R0.138730.662
60_T84_W0.138450.661
19_I68_A0.138420.661
34_I44_E0.138090.659
8_K27_K0.137880.658
21_R75_K0.137790.658
68_A75_K0.137390.656
8_K35_Q0.136260.651
28_G80_G0.136060.650
4_Q56_I0.1360.649
21_R26_N0.135940.649
39_R58_L0.135630.648
26_N40_L0.135230.646
8_K48_T0.135070.645
35_Q73_K0.134290.641
26_N30_K0.133120.636
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
3bbnC0.988299.9-0.072
2vqeC0.988299.9-0.07
3i1mC0.988299.9-0.067
3r8nC0.988299.9-0.066
3j20C0.976599.9-0.038
3iz6B0.976599.9-0.02
3u5cD0.976599.9-0.017
2zkqc0.964799.9-0.017
2xzmC0.964799.9-0.01
3j3aD0.964799.9-0.003

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