GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ubiquitin - Ubiquitin family
Pfam: PF00240 (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. )
Clan: CL0072
Length: 69
Sequences: 5358
Seq/Len: 77.65
HH_delta: -0.112 (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
22_K47_D2.049534.509
49_K53_D1.069482.353
16_D24_K0.991692.182
16_D20_D0.923192.031
49_K54_Y0.922492.029
50_T53_D0.830771.828
46_D49_K0.822191.809
19_A23_Q0.796771.753
19_A47_D0.793491.746
13_D16_D0.721961.588
14_P52_S0.705121.551
26_A33_P0.70321.547
26_A36_Q0.677291.490
20_D23_Q0.677021.489
57_K60_S0.648961.428
36_Q64_L0.639531.407
17_T20_D0.625661.376
25_I38_L0.623531.372
24_K28_E0.607961.337
39_I65_V0.591681.302
19_A48_D0.586911.291
39_I63_H0.555271.222
31_I36_Q0.549211.208
24_K27_E0.542751.194
39_I44_E0.534921.177
51_L56_I0.521411.147
33_P36_Q0.513291.129
32_P36_Q0.512821.128
12_V16_D0.505741.113
22_K36_Q0.494331.087
8_F29_T0.488021.074
18_V51_L0.477271.050
50_T54_Y0.468041.030
15_D52_S0.456411.004
23_Q27_E0.4551.001
21_L51_L0.436910.961
37_R44_E0.436290.960
15_D50_T0.430630.947
38_L62_I0.42180.928
40_Y45_L0.413790.910
39_I43_K0.404890.891
18_V45_L0.402330.885
21_L29_T0.392210.863
6_K29_T0.380780.838
16_D21_L0.369420.813
23_Q30_G0.36580.805
42_G63_H0.365770.805
50_T55_G0.362820.798
40_Y43_K0.362470.797
45_L54_Y0.354830.781
18_V54_Y0.353860.778
7_T61_T0.350850.772
12_V56_I0.341280.751
21_L62_I0.335430.738
20_D24_K0.328560.723
56_I62_I0.323470.712
40_Y60_S0.323430.712
19_A33_P0.321240.707
6_K9_T0.319140.702
10_L25_I0.318820.701
37_R41_N0.317450.698
10_L21_L0.312690.688
26_A32_P0.312010.686
31_I64_L0.303720.668
13_D20_D0.293970.647
40_Y56_I0.293540.646
26_A31_I0.293360.645
51_L54_Y0.29110.640
25_I36_Q0.29050.639
12_V21_L0.287970.634
31_I35_Q0.283510.624
37_R65_V0.276140.607
32_P35_Q0.271920.598
27_E34_E0.271430.597
31_I44_E0.2670.587
35_Q46_D0.255430.562
38_L51_L0.254130.559
9_T13_D0.254060.559
20_D48_D0.252880.556
18_V38_L0.251610.554
11_E24_K0.248030.546
9_T59_G0.247950.545
10_L28_E0.247190.544
10_L64_L0.243540.536
12_V51_L0.241970.532
38_L64_L0.241480.531
5_G8_F0.238420.525
8_F61_T0.237130.522
25_I54_Y0.236150.520
56_I60_S0.234880.517
12_V24_K0.234440.516
26_A34_E0.234420.516
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
4k95A199.2-0.112
2lrwA199.1-0.073
3u5cf199.1-0.072
3v6cB199.1-0.071
3u5em199.1-0.069
3l0wB199.1-0.068
3q3fA199.1-0.066
4fbjB199.1-0.062
3phxB199.1-0.062
4hcnB199.1-0.056

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