GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPR_21 - Tetratricopeptide repeat
Pfam: PF09976 (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: 145
Sequences: 63466
Seq/Len: 437.7
HH_delta: -0.097 (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
133_D136_E4.126722.503
63_D66_E4.100552.488
100_Q103_E3.947292.395
121_A140_A3.864182.344
88_R107_T3.815412.315
51_A70_A3.748142.274
26_D29_K3.63372.204
55_A71_L3.384622.053
91_L107_T3.322582.016
54_L70_A3.225251.957
92_A108_L3.175181.926
109_Q124_L3.133081.901
72_E91_L3.129621.899
124_L140_A3.119061.892
58_A66_E2.957811.794
58_A70_A2.941471.784
125_G141_Y2.887221.751
35_E54_L2.875531.744
95_L107_T2.85481.732
34_A53_Q2.794751.695
128_Y140_A2.794291.695
128_Y136_E2.469561.498
95_L103_E2.43891.480
105_L109_Q2.427241.472
68_K72_E2.394241.452
31_E35_E2.384091.446
108_L123_L2.243161.361
71_L90_R2.172641.318
105_L128_Y2.113331.282
31_E58_A2.082381.263
88_R110_Q2.069581.255
31_E61_Q2.055671.247
95_L100_Q2.043611.240
51_A73_K2.03421.234
128_Y133_D2.031491.232
138_R142_Q2.020541.226
58_A63_D2.013261.221
105_L131_Q1.995961.211
41_Y44_S1.951531.184
121_A143_K1.949371.183
68_K98_Q1.942371.178
37_L50_A1.914441.161
93_R123_L1.879011.140
38_A51_A1.82621.108
68_K95_L1.816251.102
64_Y94_I1.77191.075
27_P57_A1.765011.071
89_L123_L1.762641.069
91_L95_L1.719851.043
33_A36_Q1.718651.043
75_L88_R1.714111.040
48_A74_A1.700351.031
74_A87_A1.699021.031
54_L58_A1.683291.021
101_Y127_I1.662171.008
68_K91_L1.659671.007
89_L120_A1.659671.007
37_L40_D1.638310.994
73_K77_N1.625210.986
66_E69_A1.623880.985
103_E106_A1.617910.981
96_L123_L1.614770.980
56_K90_R1.614490.979
59_Y94_I1.596690.969
96_L127_I1.595450.968
81_P87_A1.591710.966
105_L124_L1.590540.965
44_S50_A1.577220.957
123_L126_D1.574860.955
124_L128_Y1.566220.950
136_E139_A1.561640.947
92_A104_A1.517340.920
31_E54_L1.516350.920
65_D98_Q1.511950.917
129_L134_Y1.496550.908
129_L141_Y1.494010.906
94_I98_Q1.493180.906
102_D131_Q1.486120.902
118_A144_A1.484780.901
57_A61_Q1.469140.891
125_G144_A1.462950.887
101_Y130_A1.441190.874
52_L90_R1.439720.873
75_L87_A1.41670.859
55_A74_A1.413350.857
29_K32_A1.411750.856
122_E126_D1.408480.854
140_A143_K1.398150.848
56_K60_E1.389890.843
107_T110_Q1.380410.837
38_A50_A1.366110.829
70_A73_K1.363590.827
125_G137_A1.360310.825
48_A78_A1.352050.820
52_L56_K1.34640.817
59_Y90_R1.344190.815
117_K120_A1.343560.815
36_Q40_D1.340080.813
29_K33_A1.336860.811
73_K76_A1.328890.806
28_A61_Q1.307710.793
126_D129_L1.294170.785
51_A77_N1.291740.784
59_Y97_Q1.288370.782
52_L87_A1.278190.775
114_E117_K1.26960.770
127_I131_Q1.263280.766
64_Y98_Q1.262770.766
96_L130_A1.261990.766
101_Y131_Q1.256690.762
68_K94_I1.252340.760
105_L127_I1.237910.751
121_A144_A1.232640.748
55_A67_A1.220050.740
64_Y97_Q1.21860.739
31_E57_A1.216670.738
44_S49_L1.212260.735
139_A143_K1.204040.730
96_L101_Y1.203920.730
78_A81_P1.200960.729
111_I114_E1.19820.727
129_L137_A1.197040.726
126_D130_A1.189250.721
51_A74_A1.187220.720
96_L126_D1.186130.720
89_L93_R1.1860.719
74_A77_N1.175150.713
33_A37_L1.174010.712
72_E76_A1.173670.712
59_Y64_Y1.170450.710
59_Y67_A1.162270.705
68_K100_Q1.159170.703
93_R96_L1.146180.695
75_L91_L1.142370.693
106_A110_Q1.141550.692
27_P30_A1.139250.691
59_Y71_L1.138030.690
56_K59_Y1.133050.687
104_A127_I1.129320.685
93_R97_Q1.127240.684
35_E70_A1.126860.684
38_A54_L1.121920.681
103_E107_T1.118050.678
105_L133_D1.109690.673
69_A73_K1.091140.662
53_Q56_K1.075610.652
64_Y68_K1.074380.652
52_L86_L1.073990.652
49_L53_Q1.064190.646
128_Y131_Q1.056290.641
32_A36_Q1.048920.636
66_E70_A1.038540.630
96_L108_L1.020950.619
30_A57_A1.014140.615
36_Q39_K1.012560.614
35_E58_A1.010070.613
27_P60_E1.00980.613
27_P61_Q1.004950.610
89_L117_K0.999170.606
86_L119_L0.997820.605
90_R93_R0.996130.604
111_I121_A0.987870.599
108_L127_I0.982940.596
72_E107_T0.977410.593
48_A81_P0.971210.589
31_E63_D0.957530.581
134_Y138_R0.956760.580
109_Q140_A0.955650.580
96_L104_A0.953370.578
30_A34_A0.948180.575
72_E75_L0.934360.567
37_L41_Y0.932950.566
136_E140_A0.931580.565
113_D116_F0.926480.562
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
4gywA0.944899.6-0.097
4gywA0.958699.5-0.069
2pziA0.951799.5-0.029
2pl2A0.917299.40.005
2pl2A0.958699.40.015
3qkyA199.40.023
2h6fA0.958699.40.036
1wao10.924199.40.038
4abnA0.951799.40.042
2vsyA0.958699.40.046

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