GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L6 - Ribosomal protein L6
Pfam: PF00347 (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: 77
Sequences: 3516
Seq/Len: 45.66
HH_delta: 0 (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
72_K76_E1.645783.144
68_N72_K1.630573.115
17_K22_E1.275082.436
27_I33_V1.257272.402
34_E45_S1.115972.132
25_R63_Y1.055692.017
48_S53_Q0.967941.849
6_K17_K0.939491.795
12_N26_P0.939251.795
62_T65_S0.918521.755
25_R70_M0.913311.745
17_K63_Y0.910781.740
15_T22_E0.854871.633
15_T24_S0.801631.532
13_I26_P0.746281.426
9_I27_I0.727461.390
34_E48_S0.713931.364
46_V60_I0.713811.364
14_I24_S0.711391.359
18_G21_G0.710891.358
12_N24_S0.686381.311
44_V67_I0.673761.287
30_G53_Q0.666311.273
13_I24_S0.665811.272
9_I14_I0.651291.244
32_K45_S0.633561.210
10_K14_I0.581081.110
62_T66_L0.555791.062
64_R68_N0.542051.036
2_P5_V0.537411.027
17_K74_V0.53681.026
32_K48_S0.520210.994
50_N53_Q0.514390.983
52_K55_A0.513210.981
25_R59_M0.509160.973
32_K47_L0.493560.943
31_V47_L0.48880.934
54_K60_I0.48310.923
59_M63_Y0.478930.915
25_R33_V0.475330.908
46_V49_G0.470890.900
34_E43_T0.462310.883
41_K44_V0.457390.874
25_R66_L0.4570.873
67_I70_M0.449510.859
12_N27_I0.44760.855
8_T15_T0.443370.847
8_T16_V0.441030.843
11_G26_P0.440550.842
23_L74_V0.438870.838
49_G55_A0.437280.835
19_P23_L0.434950.831
61_G66_L0.427330.816
10_K13_I0.423530.809
47_L55_A0.421860.806
8_T14_I0.420620.804
46_V54_K0.40870.781
64_R71_I0.408090.780
47_L53_Q0.40640.776
28_P59_M0.382970.732
16_V70_M0.380530.727
9_I33_V0.380360.727
23_L63_Y0.370470.708
14_I22_E0.368810.705
59_M62_T0.367790.703
52_K59_M0.366040.699
55_A59_M0.365990.699
14_I67_I0.363830.695
49_G60_I0.356220.681
51_K54_K0.354820.678
47_L60_I0.350840.670
23_L70_M0.347720.664
28_P31_V0.343070.655
28_P52_K0.324490.620
17_K21_G0.324150.619
61_G76_E0.319290.610
30_G51_K0.316660.605
44_V62_T0.314990.602
46_V53_Q0.312590.597
20_K76_E0.306720.586
31_V53_Q0.306150.585
30_G52_K0.305010.583
16_V75_T0.301220.576
54_K59_M0.295040.564
30_G48_S0.294740.563
21_G74_V0.294350.562
33_V47_L0.293870.561
30_G54_K0.292420.559
13_I45_S0.292360.559
42_I67_I0.286720.548
34_E46_V0.285620.546
51_K55_A0.281410.538
10_K15_T0.277690.531
55_A65_S0.277630.530
29_P54_K0.274590.525
4_G73_G0.273540.523
66_L71_I0.271890.519
68_N76_E0.27040.517
4_G7_V0.269840.516
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
3r8sG0.935199.70
3bboI0.935199.70
3v2dH0.935199.70.001
2cqlA0.935199.70.002
1nkwE0.935199.70.004
1rl6A0.935199.70.004
2zjrE0.935199.70.006
3j39H0.935199.70.007
4a17E0.935199.70.012
2zkre0.935199.70.015

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