GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TetR_C_2 - MAATS-type transcriptional repressor C-terminal region
Pfam: PF08361 (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: 121
Sequences: 11273
Seq/Len: 93.17
HH_delta: 0.176 (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
5_R64_R1.472573.061
59_E78_R1.409082.929
63_R67_A1.230252.557
59_E63_R1.11752.323
63_R77_P1.114352.316
63_R66_Q1.093962.274
65_A71_L1.027032.135
65_A70_Q1.001682.082
5_R61_L0.979562.036
11_I109_E0.937641.949
7_R109_E0.93431.942
83_M87_L0.928131.929
66_Q77_P0.921781.916
55_L82_I0.836221.738
7_R11_I0.835861.737
64_R68_R0.819561.703
103_D106_E0.808291.680
86_A90_G0.775081.611
2_P68_R0.753991.567
79_L110_A0.74981.558
66_Q73_A0.740971.540
3_L7_R0.70811.472
62_L77_P0.704011.463
8_E11_I0.680191.414
4_E8_E0.647561.346
52_R56_A0.645621.342
64_R67_A0.64221.335
76_D79_L0.626241.302
56_A60_R0.618191.285
11_I105_A0.606341.260
57_R60_R0.596241.239
61_L65_A0.593341.233
59_E77_P0.585451.217
2_P70_Q0.574291.194
55_L59_E0.564081.172
10_L84_L0.557711.159
55_L78_R0.555791.155
62_L84_L0.555791.155
77_P81_A0.55221.148
44_R48_R0.549341.142
16_R20_D0.54871.140
10_L88_L0.543421.129
59_E81_A0.536391.115
40_M43_V0.535391.113
108_A112_V0.535281.113
61_L64_R0.527331.096
15_R19_E0.517121.075
41_A45_E0.509581.059
12_E15_R0.499481.038
7_R112_V0.490941.020
45_E49_E0.489021.016
11_I108_A0.48891.016
66_Q74_D0.471080.979
66_Q69_G0.465720.968
58_I81_A0.455910.948
105_A109_E0.454860.945
50_A54_A0.448660.933
4_E7_R0.437020.908
9_A58_I0.436830.908
25_R28_E0.43230.899
62_L80_A0.431010.896
3_L70_Q0.430610.895
73_A76_D0.428310.890
28_E31_F0.427890.889
83_M86_A0.427150.888
60_R64_R0.423990.881
62_L66_Q0.421410.876
89_S93_Q0.415330.863
10_L13_A0.410630.853
87_L111_L0.407050.846
60_R63_R0.404770.841
7_R10_L0.403290.838
76_D110_A0.401640.835
66_Q71_L0.401160.834
13_A89_S0.401040.834
8_E12_E0.400290.832
53_E57_R0.400120.832
13_A85_H0.399180.830
86_A94_N0.394730.820
76_D80_A0.393390.818
15_R18_A0.387990.806
11_I15_R0.384790.800
65_A69_G0.38040.791
49_E53_E0.379280.788
49_E52_R0.37830.786
85_H89_S0.37690.783
106_E110_A0.375180.780
13_A54_A0.374610.779
41_A44_R0.374610.779
62_L65_A0.371020.771
2_P61_L0.370550.770
2_P65_A0.369510.768
46_R49_E0.368340.766
94_N97_L0.367620.764
79_L83_M0.367410.764
90_G94_N0.366720.762
82_I94_N0.365510.760
21_E25_R0.364320.757
3_L71_L0.3630.754
26_V96_L0.362550.754
66_Q76_D0.361340.751
13_A17_L0.360210.749
48_R52_R0.354410.737
51_Q89_S0.353730.735
96_L99_P0.352140.732
56_A59_E0.351580.731
51_Q55_L0.351250.730
13_A88_L0.350820.729
103_D107_Q0.349140.726
20_D23_Q0.348760.725
100_E103_D0.347040.721
30_L89_S0.345930.719
78_R82_I0.344110.715
27_F31_F0.34370.714
14_L108_A0.343260.713
15_R105_A0.34320.713
107_Q111_L0.342690.712
10_L112_V0.342610.712
26_V31_F0.341680.710
26_V29_I0.340670.708
43_V46_R0.337920.702
45_E48_R0.333960.694
106_E109_E0.333930.694
14_L91_L0.333370.693
3_L65_A0.333110.692
9_A61_L0.333010.692
79_L82_I0.328310.682
86_A89_S0.327810.681
39_E42_P0.325670.677
55_L85_H0.324980.675
63_R78_R0.323390.672
24_R28_E0.323120.672
53_E56_A0.3210.667
80_A84_L0.320810.667
94_N98_D0.320750.667
66_Q80_A0.315650.656
27_F30_L0.315450.656
31_F36_Y0.312660.650
2_P6_L0.310370.645
6_L84_L0.308540.641
62_L73_A0.301420.626
95_W98_D0.300740.625
91_L107_Q0.298280.620
51_Q85_H0.296620.617
36_Y40_M0.293920.611
109_E112_V0.291790.606
80_A83_M0.291350.606
58_I62_L0.291050.605
56_A78_R0.290120.603
18_A105_A0.289810.602
15_R108_A0.289160.601
62_L81_A0.286910.596
87_L91_L0.285060.592
37_V40_M0.284240.591
9_A13_A0.28360.589
4_E109_E0.283460.589
105_A108_A0.282030.586
77_P80_A0.280830.584
26_V92_I0.280820.584
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
3lhqA198.60.176
3vibA198.60.184
2xdnA198.50.196
1vi0A0.958798.40.223
2w53A0.991798.40.224
4gfkA0.958798.30.253
4gckA0.958798.30.256
3nxcA0.958798.30.259
3anpC0.950498.20.284
2genA0.958798.20.288

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