GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L27 - Ribosomal L27 protein
Pfam: PF01016 (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: 81
Sequences: 1202
Seq/Len: 14.84
HH_delta: -0.049 (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
24_K30_V1.085313.216
31_K34_N1.082993.209
52_M56_H1.06123.144
20_L40_R0.922852.734
22_V37_V0.89142.641
51_G61_L0.880022.607
24_K34_N0.800172.371
67_K81_V0.754052.234
69_T79_S0.692292.051
50_V58_L0.647521.919
51_G59_F0.628731.863
29_F65_R0.602911.786
24_K28_Q0.591891.754
37_V44_F0.583231.728
69_T81_V0.570491.690
42_T52_M0.554011.642
16_N19_R0.542391.607
44_F76_K0.51661.531
45_H75_R0.51291.520
44_F78_V0.51151.516
53_G57_T0.50531.497
32_A63_D0.494851.466
71_E77_Y0.483631.433
49_N62_V0.482091.428
43_K76_K0.440091.304
24_K66_V0.434141.286
70_K76_K0.42311.254
22_V25_F0.412691.223
6_G9_T0.404961.200
30_V36_I0.385261.142
38_R55_D0.383871.137
40_R56_H0.371721.101
31_K63_D0.362851.075
69_T77_Y0.361181.070
70_K77_Y0.360571.068
36_I58_L0.359491.065
52_M58_L0.358291.062
29_F63_D0.352561.045
26_G67_K0.344961.022
2_H10_K0.336650.997
46_P58_L0.335180.993
42_T56_H0.333250.987
34_N63_D0.331910.983
24_K31_K0.328540.973
22_V68_F0.32530.964
67_K79_S0.320520.950
25_F28_Q0.309850.918
73_R77_Y0.300130.889
72_K75_R0.293110.868
9_T12_G0.29220.866
18_K40_R0.285480.846
48_E81_V0.284030.842
45_H70_K0.28290.838
45_H52_M0.281840.835
20_L56_H0.280010.830
62_V81_V0.276990.821
3_K11_N0.27470.814
74_N77_Y0.273170.809
48_E77_Y0.269970.800
30_V34_N0.263050.779
43_K56_H0.261760.776
69_T73_R0.259050.768
28_Q34_N0.256840.761
24_K36_I0.256220.759
41_G55_D0.252550.748
46_P52_M0.252010.747
2_H6_G0.25140.745
6_G10_K0.247240.733
73_R76_K0.246460.730
32_A61_L0.243930.723
72_K76_K0.243210.721
72_K81_V0.240470.713
50_V80_V0.240380.712
9_T22_V0.240270.712
77_Y81_V0.238490.707
71_E79_S0.236160.700
46_P56_H0.229280.679
38_R57_T0.215430.638
4_K7_G0.214460.635
48_E65_R0.2140.634
2_H5_G0.209870.622
5_G77_Y0.20710.614
48_E69_T0.205490.609
70_K74_N0.204230.605
27_G59_F0.204090.605
42_T45_H0.202940.601
65_R81_V0.20260.600
71_E74_N0.202430.600
58_L78_V0.202350.600
44_F68_F0.200960.595
60_A80_V0.199910.592
22_V26_G0.19960.591
18_K56_H0.197150.584
6_G25_F0.196670.583
58_L61_L0.194410.576
43_K52_M0.191850.568
4_K8_S0.18990.563
53_G59_F0.189490.561
20_L41_G0.189350.561
25_F37_V0.188220.558
48_E61_L0.187230.555
38_R41_G0.186620.553
48_E67_K0.185290.549
32_A60_A0.184640.547
48_E74_N0.184440.546
36_I50_V0.183510.544
5_G10_K0.182910.542
72_K79_S0.182620.541
74_N81_V0.182520.541
36_I66_V0.180520.535
6_G17_P0.179340.531
11_N15_S0.177920.527
26_G68_F0.177890.527
76_K80_V0.176740.524
31_K80_V0.175170.519
48_E79_S0.174760.518
14_D17_P0.171530.508
2_H7_G0.17090.506
29_F48_E0.170780.506
75_R78_V0.170370.505
50_V60_A0.168970.501
48_E71_E0.168890.500
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
3bboX1100-0.049
2zjrT1100-0.024
3v2d01100-0.018
2ftcO0.83951000.086
3r8sW0.90121000.089
2xhcA0.703793.80.852
2nn6I0.864293.50.854
2xhaA0.728492.10.861
3m7nA0.580288.30.872
2ba0A0.580287.60.873

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