GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S15 - Ribosomal protein S15
Pfam: PF00312 (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: 83
Sequences: 1793
Seq/Len: 21.6
HH_delta: -0.018 (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
9_K79_K1.19923.589
30_R54_L1.010833.025
2_R5_K0.935352.799
21_E72_R0.867822.597
70_F74_E0.819582.453
8_K11_Q0.784732.349
10_F79_K0.784632.348
2_R29_E0.776672.324
2_R33_N0.689972.065
75_W79_K0.682252.042
5_K9_K0.656551.965
12_R16_D0.653791.957
29_E33_N0.653361.955
11_Q15_N0.613261.835
28_T32_R0.559961.676
75_W78_K0.55411.658
69_D72_R0.54321.626
45_K48_K0.51361.537
52_L56_S0.491751.472
7_I22_V0.48591.454
4_Q8_K0.452481.354
29_E32_R0.442981.326
59_R63_K0.438611.313
63_K67_R0.438021.311
24_I76_V0.432851.295
49_R53_K0.430781.289
48_K52_L0.41161.232
37_H44_D0.410341.228
36_E39_K0.408711.223
38_L56_S0.392681.175
34_L54_L0.390341.168
21_E65_L0.381231.141
38_L48_K0.380421.139
27_L54_L0.380131.138
46_H50_G0.378811.134
71_E75_W0.378071.132
8_K14_P0.372421.115
73_Y77_L0.365981.095
12_R21_E0.362751.086
47_S50_G0.347791.041
30_R33_N0.34021.018
41_N49_R0.327440.980
38_L45_K0.326370.977
20_P65_L0.318460.953
24_I62_L0.316310.947
36_E40_K0.3160.946
71_E74_E0.310230.928
20_P24_I0.305940.916
35_Q39_K0.305480.914
4_Q71_E0.295210.884
16_D19_S0.29240.875
52_L55_V0.288890.865
32_R35_Q0.283250.848
53_K57_K0.282680.846
63_K66_R0.282230.845
45_K56_S0.275580.825
16_D20_P0.271090.811
4_Q7_I0.264860.793
77_L81_G0.261750.783
24_I61_L0.261150.782
53_K60_R0.259430.776
77_L82_L0.254370.761
16_D58_R0.247790.742
11_Q14_P0.24360.729
66_R73_Y0.243010.727
35_Q59_R0.23710.710
5_K8_K0.236040.706
44_D64_Y0.233430.699
27_L57_K0.23120.692
30_R35_Q0.229280.686
24_I65_L0.229190.686
31_I55_V0.226840.679
55_V82_L0.225570.675
56_S60_R0.225340.674
32_R36_E0.224130.671
43_K49_R0.222850.667
36_E42_K0.222830.667
30_R60_R0.221460.663
33_N36_E0.21250.636
6_S33_N0.211370.633
37_H41_N0.211320.632
41_N46_H0.209520.627
60_R68_K0.207360.621
18_G23_Q0.204960.613
34_L47_S0.204850.613
31_I58_R0.204530.612
20_P72_R0.203960.610
31_I76_V0.203080.608
60_R63_K0.202810.607
66_R70_F0.199340.597
5_K79_K0.199020.596
38_L66_R0.198220.593
52_L59_R0.196560.588
65_L82_L0.195630.585
4_Q60_R0.195490.585
16_D25_A0.194890.583
6_S29_E0.194310.582
10_F22_V0.192870.577
12_R15_N0.192720.577
23_Q44_D0.192080.575
16_D22_V0.191990.575
72_R75_W0.191990.575
64_Y73_Y0.191730.574
22_V26_I0.191450.573
48_K56_S0.191070.572
29_E60_R0.190150.569
53_K56_S0.189610.567
31_I62_L0.189480.567
77_L80_L0.188280.564
3_K7_I0.187990.563
28_T58_R0.186520.558
53_K63_K0.186130.557
17_T25_A0.184880.553
62_L77_L0.184520.552
38_L53_K0.184070.551
14_P36_E0.18350.549
74_E78_K0.182460.546
41_N50_G0.18240.546
6_S26_I0.179280.537
49_R55_V0.178850.535
35_Q51_L0.175430.525
38_L47_S0.173460.519
13_H63_K0.172240.515
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
3ulwA199.9-0.018
2vqeO199.9-0.011
4a5uB199.9-0.01
3r8nO199.9-0.006
1a32A199.9-0.005
3bbnO199.90.031
3j20Q199.70.316
3u5cN199.20.498
2xzmO199.20.519
3zeyG199.10.526

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