GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ubiquitin_2 - Ubiquitin-like domain
Pfam: PF14560 (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: 87
Sequences: 3094
Seq/Len: 35.56
HH_delta: 0.092 (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_K63_D1.218733.573
65_A69_S0.878172.575
24_I28_E0.695282.038
58_E61_D0.673241.974
62_D65_A0.64981.905
34_E44_M0.644321.889
27_S31_Q0.63311.856
7_T77_R0.602791.767
27_S63_D0.600031.759
22_K68_G0.528131.548
28_E31_Q0.521611.529
33_L46_L0.520751.527
24_I32_K0.517951.518
21_P24_I0.487441.429
32_K35_K0.483031.416
32_K36_L0.478641.403
73_K76_M0.464111.361
31_Q35_K0.439781.289
34_E41_P0.437461.283
66_T69_S0.434311.273
5_F15_S0.433741.272
41_P44_M0.432731.269
3_K19_R0.432061.267
25_T28_E0.426651.251
44_M80_V0.424691.245
3_K74_D0.423561.242
8_S11_S0.418941.228
65_A70_Y0.411141.205
47_Q60_L0.411131.205
3_K17_E0.408861.199
20_F24_I0.389161.141
30_K44_M0.38371.125
7_T11_S0.381491.118
26_V67_L0.367791.078
47_Q79_H0.361741.061
18_K24_I0.360911.058
16_V37_T0.348721.022
31_Q38_G0.335240.983
23_S68_G0.327680.961
26_V70_Y0.327050.959
46_L78_I0.321780.943
5_F16_V0.317160.930
6_I33_L0.316150.927
4_L20_F0.315990.926
20_F29_L0.294950.865
6_I80_V0.292830.859
18_K33_L0.291960.856
66_T70_Y0.289440.849
61_D70_Y0.288760.847
5_F17_E0.285810.838
28_E32_K0.282880.829
21_P28_E0.281480.825
45_R81_V0.280490.822
26_V61_D0.275550.808
67_L72_I0.273190.801
23_S66_T0.266880.782
35_K42_S0.262970.771
47_Q81_V0.260750.764
6_I18_K0.251890.738
20_F28_E0.249740.732
39_I80_V0.248170.728
8_S16_V0.247590.726
7_T10_N0.246550.723
45_R79_H0.245210.719
40_P44_M0.244030.715
6_I29_L0.242470.711
67_L70_Y0.24020.704
5_F77_R0.239940.703
4_L78_I0.238880.700
5_F74_D0.238680.700
16_V19_R0.236360.693
10_N37_T0.235520.690
29_L78_I0.234440.687
19_R74_D0.234050.686
33_L44_M0.232090.680
31_Q42_S0.230140.675
47_Q59_E0.22990.674
39_I44_M0.228890.671
34_E40_P0.227780.668
29_L37_T0.227180.666
40_P43_D0.224740.659
71_G76_M0.223850.656
8_S17_E0.222160.651
9_S81_V0.219410.643
47_Q77_R0.218930.642
27_S64_D0.218110.639
4_L72_I0.217140.637
24_I29_L0.215750.633
33_L80_V0.215380.631
73_K80_V0.214340.628
16_V36_L0.21390.627
49_K77_R0.212540.623
43_D81_V0.20770.609
31_Q41_P0.202690.594
49_K76_M0.202240.593
31_Q34_E0.202220.593
8_S80_V0.201950.592
4_L61_D0.201430.591
34_E42_S0.199820.586
46_L80_V0.198990.583
46_L67_L0.197580.579
66_T71_G0.19640.576
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
3m62B0.885199.30.092
4hwiB0.862199.30.102
4k95A0.885199.30.103
4b6wA0.97799.20.116
1t0yA0.97799.20.119
1v6eA0.97799.20.128
2kj6A0.965599.20.135
4a20A0.896699.20.136
3m63B0.850699.20.139
3shqA0.873699.20.14

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