GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MerR_2 - MerR HTH family regulatory protein
Pfam: PF13591 (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: CL0123
Length: 84
Sequences: 8591
Seq/Len: 102.27
HH_delta: -0 (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
38_S41_D2.296983.378
19_E23_E1.795562.641
58_N61_G1.496822.201
15_E22_E1.413152.078
14_P18_R1.359411.999
6_F45_L1.201011.766
2_S36_Y1.137831.673
7_C14_P1.112711.636
21_V35_W1.100261.618
6_F42_L1.082741.592
4_E8_E1.059681.558
6_F41_D1.02731.511
5_E8_E0.97761.438
10_C45_L0.96781.423
48_I62_I0.935511.376
2_S5_E0.924041.359
9_A46_R0.901321.326
63_A67_D0.869181.278
52_H59_L0.861841.267
13_E16_F0.839261.234
44_R66_L0.83041.221
10_C42_L0.823591.211
23_E63_A0.809751.191
28_P37_F0.799871.176
52_H62_I0.770611.133
2_S34_E0.768131.130
21_V37_F0.76481.125
3_L18_R0.763591.123
4_E14_P0.73751.085
29_E41_D0.711641.047
25_L48_I0.701451.032
47_R51_L0.69561.023
9_A42_L0.692041.018
17_L21_V0.689181.014
46_R49_R0.689081.013
29_E38_S0.686751.010
49_R52_H0.669780.985
17_L45_L0.662990.975
16_F20_L0.653850.962
23_E60_E0.640620.942
61_G64_L0.635990.935
39_E43_A0.630320.927
17_L37_F0.628320.924
50_R54_D0.626070.921
12_I16_F0.600840.884
7_C17_L0.596340.877
60_E63_A0.594410.874
47_R50_R0.587750.864
16_F19_E0.586020.862
40_E43_A0.573760.844
43_A46_R0.569120.837
9_A39_E0.565750.832
15_E18_R0.563460.829
3_L7_C0.560180.824
49_R54_D0.551690.811
21_V27_E0.549550.808
64_L67_D0.549450.808
47_R65_I0.547630.805
41_D44_R0.547610.805
10_C49_R0.547510.805
57_I65_I0.542080.797
3_L14_P0.537760.791
27_E44_R0.536270.789
10_C46_R0.533640.785
20_L25_L0.528450.777
32_E36_Y0.514520.757
51_L57_I0.493850.726
3_L21_V0.49350.726
15_E19_E0.490960.722
44_R67_D0.490420.721
42_L46_R0.480520.707
26_I48_I0.474340.698
4_E34_E0.473670.697
12_I45_L0.469380.690
57_I61_G0.44980.661
27_E41_D0.44740.658
18_R21_V0.447380.658
23_E59_L0.446790.657
50_R55_L0.446340.656
6_F10_C0.438390.645
20_L48_I0.433460.637
27_E31_E0.432590.636
10_C17_L0.432380.636
59_L63_A0.4310.634
55_L65_I0.428540.630
12_I49_R0.418390.615
5_E9_A0.411920.606
46_R50_R0.409660.602
51_L65_I0.407850.600
20_L59_L0.407690.600
15_E34_E0.402210.592
43_A50_R0.400630.589
44_R47_R0.399050.587
62_I66_L0.399030.587
24_G27_E0.392030.577
19_E59_L0.388760.572
51_L61_G0.387670.570
52_H56_G0.386790.569
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
3ucsA199.6-0
3qaoA0.988199.50.073
3gpvA0.988199.50.076
3gp4A0.988199.50.084
1r8eA0.988199.50.087
2zhgA0.988199.50.093
3hh0A0.988199.50.099
1q06A0.988199.50.108
2vz4A0.988199.50.124
1r8dA0.988199.50.13

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