GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_18 - Tetratricopeptide repeat
Pfam: PF13512 (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: CL0020
Length: 142
Sequences: 32570
Seq/Len: 229.37
HH_delta: -0.018 (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
25_N28_E3.570682.557
62_D65_E3.53232.530
50_Q69_A3.337312.390
54_A70_Y3.259142.334
13_L32_Q3.184682.281
71_D90_R3.153952.259
17_A33_L3.095352.217
20_A28_E2.70781.939
34_E53_L2.703961.936
57_Y65_E2.688911.926
53_L69_A2.683691.922
16_E32_Q2.630221.884
57_Y69_A2.615121.873
87_Y121_D2.551131.827
99_E117_Q2.509771.797
20_A32_Q2.431571.741
33_L52_D2.311541.655
70_Y89_M2.27471.629
90_R121_D2.219651.590
91_G122_F2.209361.582
94_Y121_D2.125621.522
67_I71_D2.012241.441
119_F123_E1.99521.429
67_I94_Y1.933431.385
30_I34_E1.927681.380
30_I60_Q1.907811.366
67_I97_Q1.887721.352
73_F86_A1.831711.312
57_Y62_D1.758871.260
74_I87_Y1.749311.253
13_L35_A1.658991.188
94_Y117_Q1.640651.175
64_E97_Q1.635071.171
37_D50_Q1.633781.170
50_Q72_R1.610511.153
30_I57_Y1.608291.152
20_A25_N1.596311.143
65_E68_A1.574281.127
16_E20_A1.570121.124
94_Y99_E1.556891.115
55_Y89_M1.54411.106
19_E23_K1.540531.103
129_Y132_S1.530161.096
63_Y93_S1.525031.092
88_Y92_L1.51911.088
124_Q128_R1.508221.080
27_E60_Q1.504641.078
67_I90_R1.486591.065
124_Q127_R1.477761.058
10_P36_L1.472961.055
53_L57_Y1.465361.049
98_D115_A1.450241.039
90_R94_Y1.415311.014
35_A39_R1.378770.987
121_D124_Q1.349080.966
63_Y96_E1.342680.962
93_S97_Q1.341380.961
13_L36_L1.339560.959
117_Q120_R1.338070.958
40_Y43_G1.320750.946
72_R75_R1.320380.946
80_H86_A1.320010.945
36_L49_A1.315460.942
30_I56_A1.310120.938
30_I53_L1.308660.937
17_A36_L1.301770.932
77_H80_H1.301380.932
72_R76_L1.296920.929
26_Y56_A1.279090.916
37_D49_A1.274930.913
67_I93_S1.220060.874
28_E31_K1.216130.871
87_Y124_Q1.209230.866
21_L52_D1.208540.865
21_L56_A1.201990.861
74_I86_A1.189680.852
51_L89_M1.185360.849
18_Q22_Q1.183570.848
58_Y93_S1.181660.846
12_E19_E1.175710.842
69_A72_R1.164750.834
14_Y18_Q1.16230.832
56_A60_Q1.149290.823
92_L95_Y1.146680.821
10_P40_Y1.136550.814
18_Q52_D1.134990.813
92_L96_E1.12660.807
14_Y52_D1.106660.793
73_F76_L1.100110.788
21_L33_L1.094530.784
58_Y96_E1.092950.783
125_L132_S1.089830.780
55_Y59_K1.068540.765
63_Y97_Q1.065540.763
35_A38_T1.063780.762
58_Y63_Y1.062770.761
74_I90_R1.062180.761
13_L39_R1.058590.758
66_A70_Y1.051140.753
89_M92_L1.048870.751
32_Q35_A1.047230.750
58_Y89_M1.042990.747
125_L128_R1.039330.744
58_Y70_Y1.030160.738
55_Y58_Y1.025150.734
58_Y66_A1.023390.733
16_E19_E1.021230.731
87_Y125_L1.017150.728
115_A119_F1.008180.722
12_E16_E1.004730.720
26_Y59_K0.989820.709
18_Q21_L0.973570.697
28_E32_Q0.972130.696
70_Y93_S0.971280.696
50_Q73_F0.962040.689
117_Q121_D0.959950.687
54_A73_F0.955750.684
52_D55_Y0.950730.681
14_Y49_A0.949790.680
51_L80_H0.941240.674
21_L29_A0.934850.669
51_L86_A0.931610.667
123_E127_R0.928490.665
21_L26_Y0.922820.661
67_I99_E0.922360.661
51_L55_Y0.917770.657
95_Y122_F0.911520.653
17_A29_A0.904560.648
30_I62_D0.901090.645
65_E69_A0.898140.643
54_A66_A0.895190.641
31_K35_A0.891290.638
58_Y92_L0.881970.632
95_Y115_A0.881890.632
36_L39_R0.879370.630
73_F80_H0.874990.627
68_A71_D0.873340.625
34_E69_A0.872750.625
26_Y60_Q0.857090.614
10_P43_G0.849240.608
121_D125_L0.847640.607
37_D53_L0.847130.607
123_E126_V0.8470.607
88_Y125_L0.84650.606
91_G125_L0.844280.605
66_A93_S0.835290.598
43_G49_A0.834040.597
68_A72_R0.831880.596
95_Y118_A0.831710.596
34_E38_T0.830220.595
15_Q19_E0.821540.588
12_E15_Q0.818560.586
116_R120_R0.818010.586
120_R124_Q0.815290.584
27_E30_I0.814790.583
20_A23_K0.814640.583
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
4gywA0.845199.6-0.018
4gywA0.852199.50.021
4i2zA0.859299.50.024
4ga2A0.852199.50.035
3gyzA0.852199.50.035
2h6fA0.852199.40.079
3qkyA0.950799.40.081
2pziA0.957799.40.088
1kt0A0.873299.40.091
2pziA0.950799.40.092

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