GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L11_N - Ribosomal protein L11 N-terminal domain
Pfam: PF03946 (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: 60
Sequences: 979
Seq/Len: 16.32
HH_delta: -0.071 (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
30_K34_D1.320384.665
37_K40_K0.921263.255
26_I54_V0.800542.828
19_P23_P0.692682.447
1_V51_K0.60362.133
2_I54_V0.565611.998
34_D38_A0.542781.918
43_K46_I0.477311.686
42_Y47_P0.46861.656
7_P10_K0.451431.595
29_K33_K0.425791.504
10_K43_K0.420231.485
2_I24_L0.403441.425
12_T32_C0.398821.409
6_V17_L0.358421.266
6_V47_P0.336751.190
31_F35_F0.33581.186
10_K40_K0.323831.144
29_K60_F0.313921.109
7_P47_P0.312251.103
22_G25_G0.303891.074
1_V56_N0.302911.070
24_L54_V0.295721.045
33_K37_K0.295011.042
23_P28_I0.294151.039
16_P19_P0.284851.006
11_A18_G0.276470.977
34_D43_K0.273920.968
35_F47_P0.273550.966
35_F56_N0.267890.946
27_N30_K0.266540.942
21_L26_I0.255030.901
8_A46_I0.254650.900
1_V46_I0.250630.886
42_Y46_I0.246070.869
6_V35_F0.244480.864
24_L47_P0.24210.855
42_Y48_V0.232980.823
10_K45_G0.230690.815
1_V24_L0.230080.813
43_K47_P0.226110.799
25_G58_K0.222770.787
29_K37_K0.221950.784
34_D37_K0.221720.783
34_D60_F0.220980.781
17_L20_A0.219480.775
30_K33_K0.218940.774
35_F51_K0.218190.771
7_P46_I0.214390.757
24_L50_V0.213590.755
3_K13_P0.212190.750
12_T28_I0.211540.747
19_P54_V0.207370.733
26_I59_S0.206180.728
39_T48_V0.203790.720
13_P57_D0.202960.717
6_V42_Y0.20260.716
7_P21_L0.201970.714
28_I55_Y0.201880.713
5_R35_F0.200340.708
1_V47_P0.198080.700
13_P36_N0.193860.685
18_G49_P0.193490.684
12_T55_Y0.189930.671
29_K34_D0.188660.667
31_F59_S0.187260.662
8_A42_Y0.186580.659
49_P52_I0.186080.657
16_P36_N0.185740.656
2_I26_I0.185570.656
10_K56_N0.181260.640
38_A48_V0.178970.632
29_K32_C0.178850.632
10_K46_I0.177550.627
2_I9_G0.176260.623
6_V38_A0.176140.622
8_A31_F0.174770.617
31_F36_N0.173560.613
23_P50_V0.173220.612
23_P26_I0.173040.611
55_Y59_S0.17180.607
51_K60_F0.170610.603
49_P58_K0.167590.592
5_R51_K0.164180.580
12_T27_N0.164160.580
43_K48_V0.163410.577
18_G36_N0.163180.577
16_P28_I0.163040.576
4_L50_V0.159090.562
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
2ftcG199.9-0.071
3r8sI199.9-0.069
3bboK0.983399.9-0.066
1mmsA0.983399.9-0.062
1vq8I0.983399.9-0.061
3egvB0.983399.9-0.052
3j21H0.983399.8-0.046
3cjsB0.983399.8-0.037
3j3bK0.983399.8-0.034
2zkri0.966799.8-0.03

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