GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ribosomal_L31 - Ribosomal protein L31
Pfam: PF01197 (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: 69
Sequences: 1475
Seq/Len: 21.38
HH_delta: 0.013 (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
11_E24_E1.266694.250
13_K24_E0.703292.360
19_C39_C0.667952.241
15_T22_T0.661142.218
9_Y26_R0.636052.134
21_N41_N0.613692.059
39_C42_C0.595381.997
2_K6_H0.572981.922
15_T35_K0.530681.780
13_K22_T0.530311.779
11_E26_R0.490521.646
19_C42_C0.482111.617
14_V23_F0.474541.592
10_R30_E0.456841.533
29_K34_I0.445351.494
19_C41_N0.436611.465
52_V59_V0.421281.413
17_S35_K0.412331.383
16_C39_C0.409161.373
16_C42_C0.405291.360
60_E64_K0.397551.334
52_V55_T0.365641.227
63_N68_K0.360441.209
64_K67_G0.352771.184
16_C19_C0.336971.131
14_V25_T0.316991.063
24_E31_Y0.314091.054
15_T20_G0.312051.047
4_G8_E0.305731.026
12_V29_K0.301191.010
63_N67_G0.295940.993
14_V31_Y0.295060.990
49_K52_V0.28870.969
3_K8_E0.274410.921
21_N39_C0.272490.914
12_V30_E0.270780.908
55_T60_E0.268920.902
2_K5_I0.265460.891
16_C31_Y0.263890.885
12_V31_Y0.260420.874
53_V63_N0.25420.853
10_R29_K0.251480.844
64_K68_K0.250570.841
63_N66_F0.249230.836
58_R65_K0.247070.829
52_V63_N0.246030.825
19_C46_Y0.244790.821
27_S47_T0.243720.818
13_K16_C0.238240.799
12_V26_R0.23790.798
49_K56_A0.234840.788
13_K31_Y0.234750.788
58_R66_F0.233140.782
44_P52_V0.23270.781
52_V65_K0.229460.770
55_T59_V0.22690.761
52_V56_A0.222770.747
56_A60_E0.217980.731
56_A63_N0.21750.730
61_K65_K0.214380.719
53_V59_V0.212980.715
55_T58_R0.212870.714
3_K29_K0.209060.701
17_S36_V0.203080.681
17_S39_C0.2030.681
62_F65_K0.201430.676
1_M42_C0.200960.674
1_M9_Y0.199890.671
56_A61_K0.199210.668
17_S46_Y0.198720.667
12_V27_S0.19770.663
54_D59_V0.196510.659
43_H48_G0.196260.658
57_G66_F0.194920.654
49_K54_D0.193230.648
10_R28_T0.192080.644
20_G39_C0.188960.634
14_V24_E0.188760.633
58_R61_K0.187310.628
41_N67_G0.187290.628
60_E63_N0.184560.619
40_S63_N0.18340.615
54_D61_K0.180160.604
10_R35_K0.179940.604
23_F40_S0.179290.602
20_G36_V0.179160.601
53_V68_K0.179010.601
15_T19_C0.178020.597
38_I57_G0.177840.597
51_K54_D0.177750.596
7_P62_F0.176710.593
44_P64_K0.176470.592
41_N52_V0.176330.592
51_K56_A0.174910.587
47_T51_K0.172080.577
28_T34_I0.171580.576
10_R26_R0.170510.572
9_Y51_K0.16920.568
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
3f1f40.956599.90.013
3v2d40.956599.90.019
1nkwY0.956599.90.032
1vs6Z0.97199.90.037
3bbo10.97199.90.058
3a1bA0.884184.40.85
2pv0B0.884181.50.855
2lbmA0.97145.60.885
3ql9A0.855139.90.889
2d2aA0.347825.30.899

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