GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S14 - Ribosomal protein S14pS29e
Pfam: PF00253 (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: 55
Sequences: 1366
Seq/Len: 24.84
HH_delta: -0.087 (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_C22_T1.086722.822
29_I39_F0.988032.566
17_N28_V0.920372.390
22_T38_C0.851632.211
22_T35_S0.807162.096
20_V33_G0.801172.080
41_E45_K0.7852.038
48_L51_V0.753991.958
39_F51_V0.745161.935
16_K26_R0.697281.811
43_A51_V0.602821.565
35_S38_C0.578451.502
42_L47_L0.578221.501
9_N15_I0.535021.389
17_N30_R0.485421.261
44_S47_L0.48021.247
16_K25_S0.424911.103
37_I44_S0.4221.096
32_F51_V0.416011.080
18_R25_S0.407851.059
21_I42_L0.396511.030
21_I34_L0.389021.010
14_R24_R0.3790.984
29_I32_F0.378370.983
31_K47_L0.370830.963
25_S37_I0.362130.940
38_C41_E0.354650.921
19_C38_C0.349830.908
42_L45_K0.347810.903
8_R11_S0.346780.900
14_R26_R0.343260.891
10_S22_T0.325860.846
21_I41_E0.322420.837
20_V28_V0.320850.833
12_P15_I0.32010.831
43_A48_L0.315530.819
32_F39_F0.315240.819
9_N14_R0.311630.809
17_N27_G0.309670.804
31_K48_L0.29550.767
21_I38_C0.290730.755
18_R23_G0.285060.740
18_R54_S0.284610.739
10_S14_R0.272220.707
44_S53_K0.270370.702
26_R44_S0.260020.675
39_F43_A0.25980.675
34_L42_L0.255390.663
14_R18_R0.246430.640
18_R34_L0.239340.622
39_F48_L0.237940.618
25_S41_E0.237550.617
24_R37_I0.236640.614
44_S52_K0.235230.611
31_K52_K0.234840.610
40_R50_G0.23270.604
40_R53_K0.228380.593
34_L39_F0.224840.584
15_I33_G0.222790.579
13_T16_K0.219120.569
25_S44_S0.219040.569
21_I52_K0.217420.565
37_I52_K0.215470.560
24_R27_G0.215310.559
49_P54_S0.215060.558
32_F52_K0.210260.546
40_R43_A0.209880.545
39_F44_S0.209330.544
27_G55_S0.206310.536
32_F43_A0.205550.534
34_L38_C0.204820.532
37_I41_E0.202280.525
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
3r8nN199.8-0.087
3bbnN199.7-0.082
2vqeN199.60.052
2xzmN0.927399.10.279
3iz6N0.9273990.317
3u5cd0.9273990.323
3j3ad0.9273990.324
3j20P0.927398.90.346
3zey80.945598.30.477
1bw3A0.854517.30.854

Page generated in 0.0273 seconds.