GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TetR_C_9 - Transcriptional regulator TetR C-terminal
Pfam: PF14514 (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: CL0174
Length: 129
Sequences: 8343
Seq/Len: 64.67
HH_delta: 0.254 (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
7_K62_E1.416473.093
61_E65_A1.23492.697
3_S6_E1.124792.456
63_G69_F1.074572.347
9_R114_E1.035022.260
3_S68_V0.953442.082
5_V9_R0.923412.017
61_E64_V0.919022.007
57_R75_R0.918262.005
63_G68_V0.90431.975
57_R61_E0.901321.968
119_L123_G0.89281.950
122_N125_L0.858291.874
13_A114_E0.821541.794
61_E74_P0.806451.761
64_V71_P0.800651.749
5_V125_L0.768881.679
62_E66_A0.711591.554
76_L115_H0.700591.530
64_V72_V0.690071.507
13_A110_E0.691.507
59_I63_G0.664021.450
83_G87_F0.660051.442
118_D122_N0.653771.428
4_P66_A0.649741.419
10_R13_A0.623751.362
113_A117_V0.619681.353
60_L74_P0.618961.352
32_L35_E0.614711.342
62_E65_A0.602881.317
80_S84_L0.587091.282
4_P68_V0.583391.274
17_R113_A0.579391.265
6_E10_R0.575851.258
9_R13_A0.573911.253
53_V75_R0.568591.242
17_R21_D0.56281.229
13_A113_A0.546231.193
70_R122_N0.545851.192
12_I81_I0.543751.188
18_Y22_F0.542771.185
50_S54_D0.541831.183
5_V118_D0.537831.175
64_V74_P0.535371.169
5_V121_L0.529531.156
54_D58_R0.529521.156
9_R118_D0.526211.149
56_L78_Y0.521731.139
11_H59_I0.519271.134
57_R74_P0.515831.127
117_V121_L0.51551.126
16_I113_A0.512651.120
77_F124_L0.506651.106
9_R117_V0.492041.075
73_D76_L0.477421.043
7_K59_I0.47271.032
80_S119_L0.470911.028
10_R14_G0.468211.023
58_R62_E0.467551.021
55_A58_R0.465931.018
72_V77_F0.45891.002
111_R115_H0.453450.990
58_R61_E0.451940.987
14_G17_R0.451930.987
81_I120_I0.451630.986
5_V68_V0.450240.983
76_L112_Y0.436520.953
110_E114_E0.413010.902
105_S111_R0.408730.893
60_L81_I0.407320.890
41_A44_L0.406520.888
43_R46_E0.404960.884
53_V57_R0.402580.879
42_R46_E0.40120.876
6_E9_R0.397460.868
11_H56_L0.397090.867
15_V19_Y0.395270.863
84_L120_I0.389450.851
4_P7_K0.386820.845
114_E118_D0.382050.834
17_R110_E0.379990.830
70_R118_D0.379560.829
4_P63_G0.375810.821
115_H118_D0.374290.817
63_G67_G0.371730.812
73_D115_H0.369310.807
54_D57_R0.368060.804
53_V79_I0.36720.802
15_V52_L0.364650.796
17_R106_D0.364120.795
9_R121_L0.362330.791
51_P54_D0.361840.790
4_P69_F0.361670.790
64_V67_G0.358950.784
59_I62_E0.358080.782
40_R43_R0.357370.780
30_N33_L0.350710.766
31_R34_H0.348990.762
73_D111_R0.348780.762
12_I117_V0.345450.754
80_S115_H0.344920.753
5_V69_F0.343520.750
64_V69_F0.341910.747
64_V70_R0.340950.745
35_E38_H0.34010.743
8_L121_L0.33670.735
112_Y116_V0.335940.734
85_C116_V0.328420.717
60_L64_V0.327460.715
79_I112_Y0.326070.712
14_G18_Y0.325870.712
12_I113_A0.324410.708
56_L59_I0.31870.696
86_Y90_S0.314750.687
26_N32_L0.313250.684
13_A17_R0.312210.682
82_I86_Y0.311360.680
121_L125_L0.311160.680
28_L32_L0.31090.679
110_E113_A0.309460.676
7_K63_G0.307120.671
12_I116_V0.305520.667
119_L124_L0.305430.667
44_L47_Q0.304750.666
26_N82_I0.303880.664
48_F52_L0.302950.662
22_F25_L0.301120.658
45_I48_F0.301040.657
12_I16_I0.299830.655
23_P27_R0.299030.653
30_N86_Y0.297710.650
76_L79_I0.2960.646
13_A117_V0.294310.643
51_P55_A0.293960.642
82_I87_F0.29250.639
15_V18_Y0.291180.636
76_L80_S0.289760.633
32_L36_A0.28680.626
15_V82_I0.286690.626
73_D77_F0.285340.623
26_N86_Y0.283290.619
11_H15_V0.28310.618
28_L88_Y0.282630.617
24_Y28_L0.282440.617
15_V85_C0.282080.616
60_L63_G0.280060.612
12_I15_V0.278560.608
12_I85_C0.277610.606
104_L112_Y0.277180.605
30_N88_Y0.276840.605
114_E117_V0.27640.604
118_D121_L0.275950.603
47_Q51_P0.273110.596
79_I82_I0.269360.588
116_V119_L0.269060.588
17_R20_F0.268580.587
84_L116_V0.26810.586
57_R78_Y0.267120.583
41_A45_I0.264150.577
19_Y82_I0.263850.576
19_Y29_L0.262870.574
87_F90_S0.262690.574
31_R35_E0.260340.569
79_I87_F0.258770.565
29_L83_G0.258150.564
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
1pb6A0.976798.60.254
3locA0.976798.60.258
2qtqA0.984598.50.265
3npiA198.50.287
3dewA0.96998.40.307
3nrgA0.976798.30.318
3s5rA0.976798.30.32
1vi0A0.930298.30.324
3vprA0.922598.30.326
3gziA0.992298.30.327

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