GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ThiS-like - ThiS-like ubiquitin
Pfam: PF14453 (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: 57
Sequences: 6304
Seq/Len: 110.6
HH_delta: 0.169 (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
35_N49_D1.882213.007
33_I52_F1.62352.594
18_L32_V1.573372.514
46_K49_D1.319832.109
33_I38_P1.307762.089
34_L43_I1.297512.073
34_L49_D1.221321.951
39_T43_I1.214581.940
19_F23_K1.110931.775
34_L51_V1.083491.731
17_T20_E1.04411.668
36_G50_E0.923671.476
15_N44_E0.853591.364
21_L45_L0.845661.351
16_T20_E0.801691.281
19_F41_E0.788911.260
10_I25_S0.779461.245
20_E23_K0.777181.242
16_T24_E0.746821.193
10_I24_E0.736051.176
52_F55_K0.724371.157
33_I54_I0.715261.143
22_R53_L0.665631.063
12_T16_T0.654421.045
38_P54_I0.651521.041
22_R26_K0.621360.993
13_E16_T0.619470.990
21_L25_S0.605250.967
12_T24_E0.599470.958
31_I54_I0.590050.943
34_L39_T0.561870.898
32_V53_L0.549560.878
21_L51_V0.532570.851
35_N47_E0.532220.850
13_E24_E0.532110.850
18_L39_T0.524670.838
18_L34_L0.510950.816
34_L46_K0.509570.814
12_T21_L0.504520.806
27_P30_D0.488680.781
31_I38_P0.459210.734
22_R41_E0.454790.727
20_E24_E0.433770.693
40_K43_I0.429910.687
43_I46_K0.428070.684
17_T44_E0.427170.682
33_I55_K0.424470.678
43_I49_D0.406740.650
12_T20_E0.391560.626
26_K30_D0.385090.615
23_K26_K0.383510.613
25_S55_K0.375460.600
31_I40_K0.372150.595
19_F22_R0.3680.588
45_L51_V0.360830.576
33_I36_G0.358950.573
22_R25_S0.355640.568
27_P31_I0.349620.559
26_K40_K0.34260.547
36_G54_I0.337860.540
16_T44_E0.332720.532
9_E42_D0.327140.523
9_E46_K0.325170.519
30_D42_D0.319980.511
23_K27_P0.301480.482
33_I50_E0.287840.460
32_V41_E0.28720.459
15_N20_E0.285560.456
18_L22_R0.283660.453
19_F42_D0.283330.453
29_A55_K0.282410.451
28_D31_I0.280660.448
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
1tygB198.20.169
2kl0A0.982598.20.182
2k5pA198.20.189
1f0zA198.20.189
1ryjA198.10.203
1rwsA198.10.219
2cu3A0.9649980.234
2kmmA197.70.296
2l32A0.982597.40.344
1tkeA197.30.356

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