GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
TetR_C - Tetracyclin repressor C-terminal all-alpha domain
Pfam: PF02909 (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: 139
Sequences: 1454
Seq/Len: 10.46
HH_delta: 0.338 (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
13_R129_D0.792844.920
74_F127_G0.739254.587
9_R136_E0.524223.253
17_R125_E0.500023.103
9_R133_D0.428552.659
60_S63_E0.424572.635
58_G64_A0.37762.343
67_A135_I0.362342.249
9_R132_L0.31341.945
16_A75_V0.308731.916
16_A71_L0.303051.881
20_R82_E0.290741.804
11_R56_D0.287451.784
20_R124_F0.284641.766
52_R107_H0.280841.743
48_E106_P0.277391.721
127_G131_L0.275771.711
8_W136_E0.266321.653
63_E138_R0.263361.634
126_F130_L0.262441.629
20_R24_L0.26191.625
55_R110_A0.259131.608
133_D138_R0.255451.585
75_V79_A0.253671.574
48_E52_R0.253291.572
7_D10_E0.244541.518
61_P110_A0.228391.417
20_R121_D0.227751.413
48_E107_H0.224821.395
70_A131_L0.224331.392
13_R132_L0.221331.373
13_R17_R0.220221.367
57_A64_A0.219351.361
16_A128_L0.211641.313
63_E126_F0.205641.276
87_P91_F0.199131.236
20_R79_A0.196611.220
61_P64_A0.195871.215
17_R124_F0.19161.189
74_F78_F0.191031.185
15_L46_L0.189161.174
10_E13_R0.188331.169
73_S77_G0.187511.164
50_M68_Y0.179711.115
71_L75_V0.178261.106
126_F138_R0.177741.103
79_A82_E0.176161.093
48_E108_L0.174921.085
12_L50_M0.173631.077
18_A21_A0.171661.065
107_H110_A0.171531.064
124_F128_L0.170651.059
8_W59_F0.169831.054
28_W134_G0.169311.051
66_R126_F0.169111.049
24_L79_A0.168571.046
28_W83_Q0.16831.044
125_E129_D0.167491.039
12_L54_L0.165991.030
11_R15_L0.162891.011
55_R107_H0.162591.009
55_R61_P0.158960.986
130_L135_I0.158640.984
119_D122_E0.157810.979
21_A25_R0.155150.963
44_L108_L0.153750.954
32_L35_A0.153080.950
23_L30_A0.149870.930
29_L35_A0.149560.928
29_L83_Q0.149450.927
24_L82_E0.148410.921
28_W39_P0.144210.895
55_R64_A0.143650.891
89_A92_S0.142350.883
51_L64_A0.141680.879
133_D137_A0.141390.877
62_E122_E0.141250.877
70_A77_G0.141030.875
79_A83_Q0.13970.867
102_A105_P0.138940.862
70_A127_G0.138020.856
47_M68_Y0.137910.856
130_L134_G0.137330.852
66_R123_R0.137030.850
22_A25_R0.135770.843
23_L33_L0.135680.842
24_L121_D0.135510.841
30_A83_Q0.134940.837
15_L50_M0.134580.835
17_R21_A0.133230.827
106_P110_A0.130840.812
28_W36_R0.130650.811
36_R81_E0.130450.810
15_L49_A0.130140.808
12_L83_Q0.130060.807
31_E83_Q0.129930.806
31_E80_L0.129590.804
29_L36_R0.129260.802
28_W40_G0.129210.802
19_Y72_S0.129140.801
71_L131_L0.128610.798
19_Y23_L0.128310.796
59_F135_I0.128290.796
109_A112_V0.126830.787
64_A107_H0.126490.785
19_Y22_A0.126460.785
11_R53_A0.126390.784
96_E100_D0.126160.783
78_F82_E0.125540.779
74_F77_G0.12540.778
94_S116_A0.125340.778
52_R56_D0.124690.774
40_G130_L0.124650.774
131_L135_I0.124150.770
77_G127_G0.124050.770
47_M65_A0.123870.769
40_G81_E0.122750.762
33_L84_A0.121910.757
59_F67_A0.12180.756
9_R13_R0.121270.753
55_R65_A0.120930.750
18_A80_L0.120540.748
101_E104_D0.119750.743
45_R48_E0.119550.742
15_L22_A0.119490.742
98_R101_E0.119090.739
117_E121_D0.118310.734
8_W57_A0.118250.734
18_A22_A0.118080.733
132_L136_E0.118030.732
10_E14_A0.117690.730
74_F131_L0.117070.726
18_A117_E0.116760.725
81_E84_A0.115780.718
49_A52_R0.115650.718
10_E117_E0.115570.717
12_L53_A0.115560.717
41_P44_L0.114870.713
99_L102_A0.114240.709
54_L67_A0.114010.708
23_L134_G0.113880.707
80_L123_R0.113880.707
51_L68_Y0.113050.702
60_S133_D0.112640.699
11_R14_A0.112090.696
28_W69_A0.111920.695
74_F128_L0.111720.693
121_D124_F0.111170.690
23_L79_A0.110980.689
12_L69_A0.110560.686
10_E44_L0.110540.686
133_D136_E0.110530.686
30_A79_A0.110360.685
5_G11_R0.110210.684
10_E136_E0.110030.683
86_L100_D0.109270.678
21_A121_D0.10850.673
50_M67_A0.10850.673
88_A91_F0.10810.671
51_L55_R0.107940.670
6_D14_A0.107730.669
36_R68_Y0.10650.661
70_A74_F0.106460.661
87_P90_D0.106340.660
19_Y68_Y0.105580.655
72_S81_E0.105410.654
14_A18_A0.105040.652
27_P35_A0.104860.651
74_F124_F0.104260.647
68_Y72_S0.104050.646
98_R103_L0.103990.645
58_G68_Y0.103530.642
5_G18_A0.103460.642
66_R70_A0.103330.641
38_P84_A0.102890.638
6_D10_E0.102760.638
23_L76_L0.102680.637
69_A79_A0.102290.635
31_E36_R0.102250.635
73_S127_G0.101890.632
11_R126_F0.101790.632
36_R83_Q0.101470.630
15_L19_Y0.100950.626
54_L71_L0.100940.626
26_H77_G0.100560.624
38_P69_A0.100320.623
129_D133_D0.100280.622
46_L72_S0.100060.621
60_S64_A0.09920.616
89_A103_L0.09880.613
62_E114_A0.098550.612
32_L78_F0.097920.608
69_A73_S0.09760.606
95_Q99_L0.097510.605
9_R129_D0.097450.605
6_D45_R0.097290.604
47_M61_P0.097270.604
37_P43_A0.097210.603
24_L83_Q0.097120.603
63_E66_R0.096910.601
61_P111_A0.096870.601
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
4ac0A0.96499.60.338
2optA199.50.388
3bqyA199.50.389
2vprA0.971299.40.405
2hxoA199.40.408
2y2zA199.40.41
2xpwA0.956899.40.424
2hxiA199.40.429
2g7lA199.40.433
1z0xA199.20.472

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