GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L17 - Ribosomal protein L17
Pfam: PF01196 (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: 97
Sequences: 1362
Seq/Len: 14.04
HH_delta: -0.063 (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
11_R53_D0.878392.918
13_E59_K0.870492.892
19_L92_A0.794292.639
25_L94_I0.786672.614
10_I29_A0.709132.356
14_R95_E0.688462.287
6_V29_A0.616392.048
33_I96_L0.604972.010
76_T94_I0.584321.941
42_H46_Q0.550131.828
13_E67_R0.540641.796
9_L29_A0.529861.760
58_K62_K0.51041.696
16_E93_I0.509471.693
47_A61_F0.508241.689
1_L21_K0.502991.671
1_L5_L0.500091.661
77_R95_E0.471361.566
48_L57_V0.466781.551
4_N8_S0.461441.533
17_T22_A0.454311.509
46_Q50_W0.442481.470
35_L47_A0.439361.460
83_P88_A0.436361.450
10_I96_L0.436171.449
40_D43_A0.433621.441
6_V32_L0.424311.410
14_R93_I0.422721.404
19_L80_K0.408361.357
78_I92_A0.398341.323
71_R97_V0.393821.308
7_T56_L0.390211.296
6_V28_Y0.390151.296
51_L56_L0.387191.286
3_R7_T0.382451.271
24_E27_P0.382411.270
39_G43_A0.380171.263
3_R52_R0.378891.259
11_R56_L0.362791.205
59_K63_E0.361011.199
62_K66_P0.358541.191
38_K43_A0.356011.183
81_L93_I0.343591.142
1_L8_S0.341911.136
41_L45_R0.336341.117
35_L46_Q0.326671.085
13_E68_Y0.326461.085
30_E78_I0.32571.082
46_Q49_S0.325561.082
19_L90_P0.322161.070
13_E64_L0.31891.059
44_R61_F0.316281.051
5_L8_S0.309191.027
10_I56_L0.308181.024
68_Y96_L0.307581.022
7_T51_L0.303481.008
2_L5_L0.298930.993
32_L60_L0.292550.972
26_R78_I0.281950.937
27_P31_R0.280740.933
16_E81_L0.276310.918
2_L28_Y0.274650.912
54_K58_K0.27080.900
47_A57_V0.270240.898
7_T52_R0.268520.892
81_L91_M0.260730.866
59_K68_Y0.258220.858
26_R30_E0.257060.854
7_T53_D0.253980.844
39_G44_R0.253320.842
27_P30_E0.252740.840
25_L28_Y0.251310.835
36_A60_L0.25090.834
18_T89_A0.249610.829
28_Y50_W0.24910.828
33_I68_Y0.248180.825
11_R55_E0.245120.814
38_K42_H0.244160.811
8_S11_R0.24070.800
43_A46_Q0.23730.788
36_A65_A0.237250.788
44_R57_V0.229930.764
26_R29_A0.223650.743
38_K69_A0.220010.731
84_R87_D0.217210.722
2_L21_K0.214480.713
35_L61_F0.212030.704
2_L25_L0.211540.703
13_E63_E0.210640.700
83_P90_P0.208850.694
84_R89_A0.208230.692
34_T73_G0.207830.690
31_R35_L0.206470.686
6_V25_L0.205520.683
54_K88_A0.205490.683
16_E91_M0.202170.672
63_E66_P0.202150.672
48_L52_R0.201940.671
34_T75_Y0.201410.669
82_G90_P0.201150.668
3_R24_E0.199790.664
86_G96_L0.199630.663
47_A51_L0.198910.661
59_K64_L0.198860.661
29_A76_T0.198120.658
34_T37_K0.192760.640
71_R74_G0.192210.639
64_L68_Y0.191150.635
32_L35_L0.190840.634
7_T48_L0.19020.632
20_A90_P0.189220.629
16_E82_G0.188030.625
4_N52_R0.185090.615
53_D56_L0.184550.613
10_I60_L0.183410.609
32_L50_W0.183320.609
41_L44_R0.18160.603
8_S12_H0.181180.602
82_G91_M0.180950.601
1_L24_E0.17850.593
48_L58_K0.177860.591
14_R94_I0.175810.584
55_E59_K0.174710.580
1_L4_N0.173550.577
44_R60_L0.173190.575
14_R81_L0.168840.561
76_T97_V0.168650.560
1_L15_I0.168180.559
10_I36_A0.16520.549
12_H21_K0.163650.544
79_I97_V0.162260.539
53_D57_V0.162230.539
30_E51_L0.161060.535
58_K81_L0.160410.533
20_A92_A0.159870.531
84_R91_M0.159750.531
8_S53_D0.159430.530
24_E93_I0.15920.529
81_L85_R0.158570.527
41_L48_L0.157730.524
55_E69_A0.156730.521
6_V50_W0.156710.521
3_R48_L0.15580.518
9_L94_I0.155580.517
9_L15_I0.155430.516
45_R73_G0.154920.515
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
3bboP1100-0.063
2zjrK1100-0.047
3j3wN1100-0.046
3r8sN1100-0.046
1gd8A1100-0.042
2cqmA1100-0.029
3qmlC0.8763430.916
3mv2B0.649538.40.918
1t6sA0.783531.30.922
2z99A0.835123.30.926

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