GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L28 - Ribosomal L28 family
Pfam: PF00830 (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: 61
Sequences: 1275
Seq/Len: 20.9
HH_delta: -0.039 (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
14_N24_K1.284073.193
16_V22_K1.0572.629
33_K46_R1.021622.541
15_N23_T0.971142.415
6_T53_A0.970922.415
13_G27_W0.880332.189
50_S53_A0.801621.994
35_R44_K0.747171.858
10_P26_R0.699861.740
17_S21_N0.65121.619
31_L48_R0.644921.604
16_V20_N0.637911.586
32_Q51_T0.629181.565
36_L47_V0.62841.563
12_F24_K0.622591.548
6_T50_S0.611131.520
37_W42_G0.610131.517
37_W44_K0.597341.486
10_P29_P0.588681.464
2_R9_K0.585061.455
36_L57_I0.582021.447
10_P28_K0.548661.364
18_H21_N0.536191.333
36_L54_L0.47981.193
52_R56_T0.475851.183
33_K48_R0.458361.140
3_C53_A0.441331.098
17_S20_N0.429481.068
4_L47_V0.429431.068
2_R48_R0.390090.970
49_V57_I0.38420.955
3_C6_T0.378820.942
53_A56_T0.371690.924
34_K54_L0.358010.890
38_S45_I0.351230.873
5_I53_A0.341860.850
49_V54_L0.322720.803
14_N20_N0.314920.783
15_N21_N0.311920.776
8_K52_R0.309960.771
11_M27_W0.300730.748
12_F26_R0.290970.724
1_R12_F0.290070.721
12_F28_K0.282960.704
34_K37_W0.280150.697
38_S44_K0.272950.679
37_W43_K0.26780.666
11_M52_R0.265140.659
18_H23_T0.259150.644
1_R28_K0.252450.628
52_R55_R0.248020.617
2_R43_K0.247680.616
30_N51_T0.247230.615
3_C50_S0.246090.612
32_Q54_L0.241230.600
2_R31_L0.240790.599
1_R48_R0.240580.598
47_V57_I0.23880.594
34_K45_I0.234390.583
5_I57_I0.233750.581
24_K27_W0.224860.559
34_K57_I0.22370.556
28_K48_R0.223530.556
51_T54_L0.223250.555
8_K51_T0.223030.555
29_P50_S0.222820.554
4_L50_S0.222090.552
34_K56_T0.217580.541
8_K30_N0.216280.538
38_S57_I0.214770.534
8_K11_M0.211750.527
45_I48_R0.20740.516
35_R46_R0.203050.505
39_E43_K0.197040.490
14_N22_K0.196590.489
21_N24_K0.195210.485
33_K37_W0.191510.476
53_A57_I0.190830.475
28_K31_L0.190360.473
12_F27_W0.189010.470
8_K50_S0.18740.466
13_G16_V0.18410.458
4_L48_R0.181420.451
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
3r8sX199.8-0.039
3bboY199.8-0.039
2jl610.967299.80.035
2zjrU0.950899.70.048
2jz6A0.983699.70.06
3v2d10.967299.70.086
3mpxA0.967212.70.879
2l8eA0.459110.882
3ny5A0.786910.80.883
1dvpA0.96729.90.884

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