GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ub-Mut7C - Mut7-C ubiquitin
Pfam: PF14451 (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: 81
Sequences: 2472
Seq/Len: 30.52
HH_delta: 0.149 (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
55_N69_D1.63714.328
8_F25_F1.130232.988
34_T37_D0.822972.176
66_K69_D0.819652.167
38_V71_V0.711371.881
56_G70_R0.705741.866
9_Y72_A0.683561.807
53_L58_P0.638781.689
54_V63_Y0.620551.641
5_T26_T0.619411.638
8_F16_L0.610661.614
33_A37_D0.607361.606
4_I68_G0.599071.584
59_V63_Y0.598781.583
38_V65_L0.588011.555
32_G41_S0.579131.531
8_F73_V0.547391.447
54_V71_V0.540861.430
58_P74_Y0.531631.405
5_T70_R0.531481.405
35_V52_I0.484191.280
11_E15_F0.48061.271
52_I73_V0.46741.236
39_I61_F0.447291.183
7_R70_R0.443331.172
36_K40_E0.439271.161
43_G48_E0.425171.124
8_F18_P0.42481.123
36_K62_D0.424341.122
53_L56_G0.415421.098
36_K61_F0.40421.069
53_L72_A0.392641.038
11_E74_Y0.382951.012
7_R72_A0.379971.005
9_Y76_V0.377280.997
8_F11_E0.371480.982
6_F38_V0.369640.977
33_A64_R0.365640.967
39_I73_V0.356420.942
41_S44_V0.355510.940
54_V66_K0.354110.936
33_A41_S0.350250.926
13_N19_E0.334460.884
9_Y74_Y0.327290.865
53_L76_V0.326360.863
7_R56_G0.319340.844
25_F28_P0.317830.840
14_D72_A0.312570.826
45_P48_E0.311750.824
30_D33_A0.309650.819
35_V63_Y0.308650.816
54_V59_V0.305620.808
37_D40_E0.305580.808
14_D53_L0.304570.805
10_A76_V0.303350.802
4_I67_D0.303110.801
9_Y75_P0.301060.796
13_N75_P0.299490.792
72_A76_V0.295530.781
35_V71_V0.283910.751
9_Y53_L0.281660.745
12_L73_V0.280150.741
51_L74_Y0.279330.738
7_R53_L0.269280.712
34_T64_R0.267070.706
10_A75_P0.266580.705
41_S45_P0.264390.699
56_G72_A0.258470.683
40_E43_G0.257730.681
31_G41_S0.252640.668
30_D37_D0.250150.661
44_V47_T0.248870.658
40_E50_G0.248390.657
38_V43_G0.247850.655
15_F51_L0.245040.648
8_F15_F0.243480.644
12_L74_Y0.239220.632
25_F46_H0.236520.625
10_A14_D0.235980.624
11_E51_L0.226770.600
45_P49_V0.226630.599
6_F41_S0.226550.599
16_L46_H0.223510.591
51_L60_D0.222170.587
34_T38_V0.219620.581
56_G74_Y0.21830.577
65_L71_V0.218160.577
6_F27_H0.217460.575
18_P25_F0.213480.564
12_L49_V0.211580.559
55_N68_G0.210660.557
35_V38_V0.210640.557
7_R74_Y0.210560.557
14_D75_P0.210320.556
10_A53_L0.209690.554
37_D41_S0.209690.554
61_F64_R0.209550.554
44_V48_E0.209310.553
11_E52_I0.207610.549
33_A45_P0.206620.546
31_G44_V0.206370.546
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
2qjlA0.938399.60.149
1vjkA0.938399.60.161
3po0A0.925999.60.164
2l52A0.901299.50.189
3dwgC0.901299.50.19
2q5wD0.901299.50.21
1fm0D0.901299.50.21
2g1eA0.888999.40.251
1wgkA0.96399.40.256
3rpfC0.839599.40.264

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