GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_S6 - Ribosomal protein S6
Pfam: PF01250 (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: 92
Sequences: 1543
Seq/Len: 16.77
HH_delta: -0.041 (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
29_I34_G1.059764.066
8_I57_G0.923883.545
35_V65_D0.901263.458
27_K31_K0.735472.822
26_K30_E0.545852.094
73_E76_R0.533392.046
75_E87_Y0.443441.701
12_D54_Q0.442381.697
6_M61_L0.437751.679
46_R56_E0.437741.679
51_I86_R0.435151.670
37_R65_D0.434871.668
23_E27_K0.430181.650
64_F89_I0.427321.639
50_P55_K0.426171.635
26_K39_V0.42351.625
74_L78_L0.392011.504
5_L64_F0.391021.500
9_L21_L0.387251.486
41_N58_H0.371661.426
66_A71_I0.370511.422
76_R80_L0.367231.409
10_R83_D0.356971.370
23_E26_K0.351931.350
27_K30_E0.349531.341
44_K56_E0.343131.316
14_S17_E0.341721.311
5_L78_L0.336671.292
2_K65_D0.334191.282
68_P72_K0.333171.278
66_A70_A0.331631.272
21_L83_D0.330271.267
5_L89_I0.325181.248
54_Q85_L0.322461.237
75_E79_R0.312471.199
19_K41_N0.309621.188
18_I58_H0.307641.180
67_S70_A0.305341.171
10_R54_Q0.286591.100
47_L85_L0.285731.096
69_S72_K0.280971.078
19_K23_E0.274621.054
30_E35_V0.272631.046
24_R81_D0.269281.033
11_P54_Q0.265511.019
41_N60_F0.264291.014
32_N70_A0.264121.013
24_R82_E0.263221.010
38_S63_N0.260791.001
28_I77_K0.257030.986
75_E89_I0.255530.980
9_L13_L0.253230.972
5_L74_L0.24560.942
42_W61_L0.243710.935
7_F62_F0.243330.934
40_E61_L0.242410.930
44_K58_H0.235010.902
28_I32_N0.23460.900
20_K23_E0.234370.899
9_L84_V0.225120.864
71_I89_I0.223040.856
6_M88_L0.222620.854
68_P89_I0.217390.834
20_K83_D0.214160.822
18_I41_N0.214150.822
36_V90_V0.21390.821
6_M42_W0.213510.819
7_F22_I0.210230.807
45_R59_Y0.210220.807
34_G73_E0.209750.805
28_I73_E0.20490.786
29_I70_A0.204890.786
15_E19_K0.200890.771
39_V62_F0.200760.770
77_K89_I0.200370.769
50_P53_K0.196750.755
25_V46_R0.194980.748
72_K76_R0.192690.739
28_I76_R0.191130.733
26_K62_F0.188010.721
44_K59_Y0.187760.720
6_M90_V0.187330.719
11_P50_P0.186090.714
25_V81_D0.185780.713
40_E44_K0.184840.709
64_F71_I0.184250.707
32_N69_S0.182160.699
47_L57_G0.181210.695
37_R63_N0.180020.691
68_P75_E0.179510.689
42_W59_Y0.176140.676
25_V78_L0.175110.672
78_L84_V0.174830.671
7_F60_F0.173870.667
71_I79_R0.173160.664
21_L24_R0.171580.658
69_S73_E0.169840.652
35_V55_K0.168980.648
68_P71_I0.168950.648
39_V60_F0.164660.632
67_S72_K0.164030.629
50_P85_L0.162630.624
29_I74_L0.160840.617
7_F78_L0.158860.609
15_E44_K0.157710.605
28_I31_K0.157480.604
51_I85_L0.156890.602
73_E77_K0.156670.601
24_R27_K0.156380.600
8_I51_I0.156250.599
7_F26_K0.15410.591
64_F78_L0.154090.591
16_E90_V0.153770.590
20_K24_R0.153570.589
17_E21_L0.153240.588
53_K66_A0.152120.584
28_I46_R0.151970.583
9_L22_I0.151120.580
39_V55_K0.149880.575
18_I53_K0.14970.574
77_K81_D0.148970.572
79_R87_Y0.146210.561
48_A82_E0.14580.559
30_E76_R0.145080.557
52_K69_S0.144590.555
60_F64_F0.143730.551
32_N67_S0.142180.545
82_E88_L0.140510.539
11_P47_L0.140380.539
23_E30_E0.139460.535
2_K37_R0.139260.534
33_G70_A0.138990.533
7_F29_I0.13890.533
38_S55_K0.137530.528
14_S56_E0.136330.523
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
1vmbA199.9-0.041
1cqmA199.9-0.033
3r3tA199.9-0.033
2j5aA199.9-0.029
3bbnF199.9-0.025
3i1mF0.989199.9-0.024
3r8nF0.989199.9-0.017
2kjwA0.576199.40.392
3zzpA0.434898.60.592
2kjwA0.434898.60.594

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