GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_DeoR - DeoR-like helix-turn-helix domain
Pfam: PF08220 (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: 57
Sequences: 48270
Seq/Len: 846.84
HH_delta: 0.036 (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
8_L23_E2.702452.137
16_S19_E2.672162.113
17_V32_R2.276641.800
4_Q8_L2.199861.740
21_A28_E2.185391.728
39_E46_R2.167631.714
17_V28_E1.965731.554
29_M32_R1.848061.461
19_E23_E1.728031.366
12_K15_V1.684851.332
18_K28_E1.684331.332
32_R36_N1.622661.283
15_V23_E1.613651.276
18_K22_E1.578961.249
28_E32_R1.56381.237
6_L43_L1.535121.214
37_K41_Q1.526161.207
26_V30_T1.516461.199
8_L24_F1.488321.177
27_S30_T1.465461.159
34_D37_K1.376921.089
15_V19_E1.374131.087
4_Q7_E1.354011.071
8_L15_V1.330231.052
30_T34_D1.316811.041
8_L12_K1.308031.034
9_L15_V1.304661.032
5_I20_L1.298011.026
29_M33_R1.295041.024
39_E44_I1.288961.019
14_K47_T1.275681.009
36_N39_E1.252380.990
36_N40_K1.233190.975
19_E22_E1.199310.948
20_L31_I1.188080.939
5_I34_D1.184730.937
33_R36_N1.175860.930
30_T33_R1.172660.927
21_A31_I1.169030.924
8_L11_E1.104610.873
4_Q24_F1.099770.870
26_V31_I1.075470.850
17_V35_L1.055660.835
33_R37_K1.030280.815
12_K23_E1.023830.810
5_I31_I1.012250.800
6_L10_K0.991490.784
10_K13_G0.929180.735
35_L39_E0.919350.727
7_E10_K0.855550.677
18_K32_R0.854340.676
24_F31_I0.844110.667
9_L44_I0.843320.667
17_V21_A0.838670.663
37_K40_K0.833710.659
20_L35_L0.81820.647
18_K21_A0.816160.645
38_L43_L0.798510.631
17_V31_I0.790840.625
35_L44_I0.740420.585
9_L14_K0.7250.573
6_L38_L0.72140.570
17_V46_R0.708340.560
7_E11_E0.706250.558
27_S33_R0.705970.558
8_L20_L0.690920.546
41_Q45_K0.669940.530
21_A26_V0.665850.527
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
2o0mA198.10.036
1stzA197.90.091
2jt1A197.90.092
1j5yA197.90.095
1biaA197.80.114
2wteA197.80.116
2g7uA197.70.129
1mkmA197.70.131
2ia2A197.70.134
3r4kA197.70.139

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