GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trns_repr_metal - Metal-sensitive transcriptional repressor
Pfam: PF02583 (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. )
Length: 85
Sequences: 1438
Seq/Len: 16.92
HH_delta: -0.009 (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
15_E19_R1.396674.952
12_K22_E0.927693.289
5_K9_N0.745262.642
23_R27_E0.722582.562
18_V41_V0.641832.276
21_I41_V0.584612.073
14_I18_V0.552781.960
9_N13_R0.476571.690
30_D33_D0.453011.606
8_L22_E0.410291.455
4_K28_D0.409871.453
3_D6_D0.398531.413
10_R44_A0.379881.347
14_I48_V0.37641.335
6_D9_N0.373441.324
41_V45_L0.371021.315
42_R46_D0.364821.293
38_I49_G0.361471.282
32_E77_E0.356221.263
11_L25_I0.355491.260
8_L26_E0.354261.256
11_L18_V0.341421.210
37_Q40_A0.338691.201
31_C60_C0.338571.200
13_R44_A0.334781.187
14_I44_A0.332481.179
13_R17_Q0.331831.176
67_D70_D0.32681.159
30_D77_E0.325271.153
76_E80_K0.323431.147
20_G24_M0.320271.136
15_E22_E0.312971.110
17_Q20_G0.311451.104
74_A77_E0.300341.065
29_R33_D0.300271.065
11_L48_V0.299361.061
75_I78_L0.298411.058
24_M29_R0.297521.055
45_L49_G0.29241.037
65_I69_E0.291391.033
49_G85_Y0.28871.024
55_D59_H0.287171.018
38_I45_L0.285261.011
38_I48_V0.283691.006
7_L25_I0.283141.004
14_I41_V0.280010.993
79_I83_D0.279750.992
38_I52_V0.279520.991
17_Q41_V0.278320.987
10_R16_G0.271720.963
19_R23_R0.269870.957
62_V66_Q0.268310.951
72_E76_E0.264670.938
54_E58_E0.264410.937
10_R13_R0.257540.913
7_L48_V0.256560.910
75_I79_I0.25180.893
59_H63_E0.246070.872
63_E67_D0.243190.862
17_Q36_Q0.241940.858
63_E66_Q0.241550.856
35_L49_G0.241180.855
6_D51_L0.23760.842
69_E80_K0.237170.841
43_S47_K0.23590.836
39_A46_D0.234690.832
78_L85_Y0.233950.829
58_E76_E0.232760.825
15_E18_V0.227570.807
81_L84_K0.225060.798
69_E72_E0.219040.777
33_D36_Q0.2180.773
48_V51_L0.217750.772
62_V65_I0.214580.761
29_R34_I0.213130.756
24_M37_Q0.210940.748
4_K26_E0.202990.720
10_R14_I0.202080.716
32_E36_Q0.200850.712
49_G53_L0.198640.704
43_S46_D0.198210.703
75_I82_I0.196140.695
51_L54_E0.195720.694
53_L82_I0.194290.689
71_R75_I0.193110.685
47_K50_K0.192010.681
70_D73_E0.191330.678
20_G23_R0.190660.676
42_R50_K0.190520.675
10_R35_L0.190010.674
64_A71_R0.188730.669
30_D56_H0.186470.661
11_L38_I0.18560.658
54_E79_I0.185540.658
54_E83_D0.185250.657
50_K83_D0.185030.656
78_L81_L0.184980.656
39_A49_G0.184910.656
36_Q85_Y0.182670.648
47_K52_V0.181920.645
30_D59_H0.181470.643
80_K84_K0.181160.642
46_D57_L0.180520.640
46_D72_E0.179740.637
31_C56_H0.179180.635
49_G52_V0.179130.635
78_L83_D0.179130.635
73_E77_E0.179080.635
66_Q70_D0.178080.631
9_N12_K0.178070.631
39_A42_R0.178040.631
30_D61_L0.176740.627
17_Q81_L0.175990.624
25_I46_D0.174560.619
46_D49_G0.174450.619
12_K17_Q0.174020.617
25_I34_I0.173290.614
11_L37_Q0.172680.612
32_E74_A0.171870.609
35_L85_Y0.17180.609
79_I82_I0.171720.609
19_R22_E0.1710.606
56_H59_H0.169980.603
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
2hh7A0.976599.9-0.009
4adzA199.90.002
3aaiA0.976599.90.016
2fb5A0.894139.50.879
3frtA0.988221.20.893
3ggoA0.541219.10.895
1gaxA0.741216.80.898
2gd5A0.988216.10.899
1h7cA0.6150.9
3bj4A0.482413.90.901

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