GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L10 - Ribosomal protein L10
Pfam: PF00466 (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: 100
Sequences: 2174
Seq/Len: 21.74
HH_delta: -0.014 (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
16_L49_K0.87963.146
14_K64_N0.724562.591
14_K18_K0.671982.403
15_E19_K0.599362.144
3_K7_E0.582042.082
19_K85_N0.567962.031
38_E42_E0.566752.027
60_K63_K0.545171.950
11_E15_E0.52861.891
42_E97_K0.498031.781
42_E45_K0.493731.766
89_F93_K0.458751.641
4_E7_E0.454711.626
26_V80_A0.44981.609
53_V58_M0.438231.567
16_L83_F0.436541.561
17_L58_M0.433311.550
13_L53_V0.429361.536
25_V71_L0.421121.506
46_K94_I0.418651.497
36_L50_F0.417961.495
7_E10_V0.411561.472
43_L48_G0.402041.438
3_K6_K0.400871.434
58_M81_L0.39231.403
32_S35_Q0.389061.392
63_K68_E0.363851.301
59_K72_S0.359511.286
5_K8_E0.356391.275
33_A37_Q0.350771.255
29_N78_P0.348871.248
26_V50_F0.341721.222
14_K65_T0.33811.209
15_E18_K0.332271.188
36_L80_A0.331281.185
41_K45_K0.325941.166
20_S83_F0.323861.158
34_N38_E0.322231.152
4_E8_E0.321461.150
39_L98_F0.32071.147
25_V79_T0.315481.128
43_L95_L0.3121.116
27_D79_T0.309451.107
65_T68_E0.309351.106
6_K10_V0.308351.103
43_L94_I0.298281.067
21_K85_N0.294241.052
56_T59_K0.289611.036
46_K90_E0.289321.035
12_E51_K0.289031.034
87_D90_E0.287731.029
28_Y31_L0.282191.009
8_E12_E0.279280.999
17_L62_L0.278330.995
23_V81_L0.271280.970
50_F80_A0.270960.969
8_E11_E0.267860.958
17_L23_V0.266890.955
7_E11_E0.266040.952
63_K72_S0.262920.940
17_L83_F0.262880.940
49_K85_N0.258310.924
70_A73_P0.257740.922
23_V71_L0.25610.916
93_K97_K0.251460.899
10_V60_K0.248780.890
67_F70_A0.247730.886
13_L58_M0.246390.881
20_S85_N0.245070.877
25_V75_L0.243660.871
12_E16_L0.241910.865
50_F82_I0.241030.862
34_N37_Q0.240940.862
11_E14_K0.232940.833
23_V62_L0.225860.808
5_K9_I0.2190.783
31_L39_L0.218360.781
43_L80_A0.218080.780
73_P76_K0.215080.769
84_S91_I0.213840.765
29_N77_G0.211190.755
24_I82_I0.21090.754
92_A95_L0.210840.754
18_K65_T0.207720.743
35_Q38_E0.205610.735
4_E11_E0.20440.731
11_E64_N0.202880.726
75_L81_L0.201690.721
30_G52_V0.201490.721
12_E15_E0.200210.716
10_V55_N0.199650.714
48_G91_I0.199330.713
42_E94_I0.197990.708
25_V81_L0.197640.707
82_I92_A0.196630.703
40_R54_K0.196310.702
28_Y35_Q0.191760.686
88_P92_A0.190040.680
3_K10_V0.189630.678
53_V81_L0.189470.678
46_K86_E0.189120.676
62_L66_G0.189110.676
48_G84_S0.189070.676
48_G82_I0.188840.675
26_V53_V0.187720.671
85_N88_P0.187480.671
86_E90_E0.187440.670
24_I37_Q0.18660.667
51_K83_F0.185970.665
82_I95_L0.185960.665
17_L70_A0.185490.663
55_N79_T0.185060.662
59_K63_K0.180680.646
17_L37_Q0.180340.645
64_N68_E0.179750.643
9_I57_L0.178340.638
10_V61_A0.178060.637
66_G73_P0.177750.636
28_Y33_A0.177110.633
46_K97_K0.176930.633
46_K50_F0.175160.626
91_I95_L0.174360.624
82_I87_D0.169940.608
21_K74_L0.169570.606
24_I95_L0.168110.601
54_K60_K0.165330.591
13_L83_F0.165210.591
37_Q60_K0.164990.590
35_Q55_N0.164550.589
26_V82_I0.164160.587
31_L35_Q0.164010.587
42_E98_F0.163710.586
55_N75_L0.163470.585
50_F58_M0.162930.583
71_L75_L0.16240.581
89_F92_A0.162310.581
28_Y79_T0.161620.578
21_K58_M0.160070.573
48_G53_V0.159790.572
24_I89_F0.15830.566
5_K51_K0.157790.564
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
3sgfH0.9999.9-0.014
1zavA0.9999.90.002
2j01J0.9799.90.016
3a1yG0.9999.90.021
1vq8G0.9899.80.032
3j21k0.9999.80.032
3u5iq0.9899.80.04
2zkrg0.9899.80.052
4hubG0.9899.80.063
3iz5s0.9899.80.065

Page generated in 0.0299 seconds.