GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TPP_enzyme_C - Thiamine pyrophosphate enzyme C-terminal TPP binding domain
Pfam: PF02775 (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: CL0254
Length: 153
Sequences: 12286
Seq/Len: 80.3
HH_delta: 0.076 (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
115_A118_E2.645463.907
81_N152_E2.082233.076
125_A141_E1.965662.903
125_A149_A1.747022.580
112_D115_A1.490682.202
37_A51_A1.489622.200
123_K147_G1.414752.090
126_R152_E1.390212.053
142_A151_I1.354742.001
32_Y36_A1.314831.942
129_T133_E1.23161.819
44_R47_R1.192031.761
125_A138_A1.180511.744
136_E140_R1.179871.743
129_T134_E1.178241.740
127_V138_A1.164571.720
114_A126_R1.12831.667
79_V150_V1.127251.665
74_P146_G1.118961.653
30_M60_M1.09881.623
114_A124_G1.086761.605
48_P143_L1.046531.546
39_G43_A1.037871.533
137_E141_E0.997561.473
123_K141_E0.98621.457
114_A118_E0.950511.404
123_K149_A0.944421.395
50_V76_V0.90221.333
116_L119_A0.901631.332
117_A150_V0.882381.303
128_T134_E0.871651.287
76_V149_A0.870911.286
41_A74_P0.870271.285
76_V142_A0.863281.275
69_V122_I0.860141.270
63_Q120_F0.85531.263
134_E137_E0.847741.252
140_R144_E0.839711.240
50_V143_L0.83511.233
137_E140_R0.828231.223
41_A48_P0.827661.222
42_L73_L0.816881.207
134_E138_A0.803951.187
78_V153_V0.789651.166
114_A152_E0.771811.140
58_F62_L0.771641.140
56_G85_Y0.768141.135
142_A149_A0.76441.129
48_P74_P0.763471.128
41_A73_L0.760761.124
51_A77_I0.759621.122
68_A75_V0.75891.121
135_L139_L0.74991.108
37_A49_V0.748241.105
135_L153_V0.747861.105
78_V139_L0.742081.096
33_A51_A0.740211.093
62_L116_L0.739881.093
62_L120_F0.732891.083
53_T57_S0.723341.068
59_L120_F0.716921.059
66_A70_R0.71281.053
78_V151_I0.709691.048
138_A142_A0.697171.030
65_L117_A0.689221.018
123_K145_S0.687591.016
38_I68_A0.687141.015
49_V75_V0.679781.004
25_G36_A0.677891.001
83_G110_N0.677241.000
127_V135_L0.676871.000
68_A122_I0.668350.987
54_G57_S0.657140.971
69_V148_P0.652140.963
127_V134_E0.649830.960
138_A151_I0.64550.953
145_S149_A0.644620.952
48_P76_V0.643870.951
74_P147_G0.629390.930
139_L143_L0.609590.900
116_L120_F0.603080.891
38_I67_T0.601110.888
122_I150_V0.587530.868
40_A49_V0.585680.865
117_A124_G0.58460.863
65_L122_I0.583820.862
124_G150_V0.574270.848
53_T61_S0.569430.841
38_I73_L0.563950.833
88_T91_Q0.559450.826
41_A49_V0.553250.817
138_A141_E0.553240.817
76_V143_L0.550490.813
74_P145_S0.548950.811
140_R143_L0.546320.807
84_G89_G0.543340.803
117_A122_I0.542430.801
122_I148_P0.533150.787
58_F77_I0.530310.783
133_E136_E0.52610.777
141_E144_E0.523330.773
118_E123_K0.517860.765
72_G146_G0.516670.763
125_A151_I0.515110.761
52_I80_L0.512730.757
87_M91_Q0.508590.751
59_L63_Q0.507450.750
67_T71_Y0.50650.748
59_L62_L0.498560.736
30_M87_M0.496940.734
37_A75_V0.493760.729
53_T77_I0.492180.727
68_A77_I0.483880.715
144_E147_G0.483330.714
82_N152_E0.475980.703
34_L65_L0.475910.703
53_T78_V0.470060.694
123_K144_E0.464150.686
92_Q96_G0.462980.684
68_A148_P0.462520.683
89_G93_T0.458460.677
26_G32_Y0.4580.676
141_E145_S0.452270.668
72_G147_G0.451460.667
133_E137_E0.45140.667
66_A120_F0.448650.663
56_G108_F0.446890.660
76_V146_G0.442240.653
85_Y88_T0.441150.652
35_P64_E0.438550.648
146_G149_A0.435520.643
76_V151_I0.435110.643
72_G109_P0.434920.642
75_V148_P0.431550.637
77_I148_P0.431550.637
53_T79_V0.428710.633
29_S32_Y0.428170.632
62_L66_A0.427220.631
79_V139_L0.427030.631
139_L151_I0.423560.626
41_A46_D0.42230.624
118_E124_G0.421530.623
58_F79_V0.418510.618
48_P51_A0.415230.613
36_A40_A0.415150.613
86_G89_G0.411420.608
65_L150_V0.40470.598
51_A57_S0.403090.595
70_R109_P0.402670.595
85_Y90_G0.402170.594
38_I65_L0.400330.591
118_E126_R0.399040.589
68_A73_L0.398890.589
60_M64_E0.398320.588
34_L53_T0.395560.584
115_A119_A0.395510.584
34_L77_I0.39550.584
93_T96_G0.395220.584
87_M90_G0.39480.583
50_V78_V0.394550.583
70_R110_N0.393540.581
69_V72_G0.391430.578
141_E149_A0.391010.578
69_V121_G0.383850.567
30_M57_S0.382290.565
139_L142_A0.381910.564
69_V109_P0.375610.555
112_D126_R0.37560.555
59_L111_P0.373850.552
124_G152_E0.371270.548
41_A45_P0.370030.547
79_V113_F0.367760.543
52_I78_V0.366860.542
86_G90_G0.366740.542
33_A53_T0.364750.539
27_F33_A0.362010.535
91_Q95_F0.361740.534
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
1t9bA0.96731000.076
2pgnA0.96081000.094
1ybhA0.98691000.096
1ozhA0.96081000.098
2uz1A0.96731000.099
3eyaA0.96081000.099
1v5eA0.95421000.101
2ihtA0.96081000.104
2panA0.98691000.108
4kgdA0.96731000.108

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