GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_16 - Helix-turn-helix domain
Pfam: PF12645 (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: 65
Sequences: 11622
Seq/Len: 178.8
HH_delta: 0.087 (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
17_E21_H1.979082.196
16_E20_K1.925022.136
60_A63_K1.899892.108
6_A11_D1.564351.736
26_I53_L1.527411.695
19_L23_E1.473321.635
30_S49_L1.465491.626
56_K60_A1.464771.625
26_I50_K1.349691.498
15_M62_L1.332661.479
55_I59_E1.323091.468
25_Y29_L1.319011.464
34_L49_L1.303181.446
51_Q55_I1.266591.406
11_D14_A1.264021.403
15_M58_I1.237841.374
29_L33_T1.19151.322
27_S31_T1.129041.253
23_E27_S1.112941.235
31_T46_D1.099681.220
22_Y54_E1.097251.218
50_K54_E1.087561.207
30_S46_D1.037851.152
28_K32_R1.014351.126
31_T35_Y1.013051.124
12_P16_E1.010251.121
30_S50_K0.997171.107
27_S46_D0.985121.093
19_L54_E0.977271.084
28_K31_T0.977091.084
27_S50_K0.96881.075
6_A14_A0.947351.051
24_P28_K0.923121.024
13_E16_E0.910671.011
53_L57_L0.886030.983
5_K8_K0.876110.972
54_E58_I0.850420.944
27_S47_E0.850330.944
5_K9_Q0.833160.925
48_D51_Q0.831130.922
6_A9_Q0.811960.901
4_I61_I0.808190.897
29_L32_R0.801960.890
23_E54_E0.799940.888
34_L46_D0.791420.878
17_E20_K0.770050.855
46_D50_K0.735470.816
18_I22_Y0.732060.812
7_A61_I0.726330.806
50_K53_L0.72160.801
10_G14_A0.704180.781
20_K23_E0.682240.757
56_K59_E0.663690.737
13_E17_E0.662060.735
4_I8_K0.659970.732
58_I61_I0.622640.691
24_P27_S0.601390.667
30_S34_L0.592460.657
31_T34_L0.590730.656
34_L45_V0.58780.652
23_E50_K0.585320.650
10_G61_I0.579540.643
30_S33_T0.578880.642
25_Y28_K0.572420.635
26_I54_E0.559050.620
7_A15_M0.555470.616
9_Q14_A0.552870.614
52_R55_I0.5480.608
6_A10_G0.54450.604
22_Y25_Y0.541930.601
7_A14_A0.534930.594
30_S53_L0.533440.592
7_A18_I0.519860.577
35_Y46_D0.516140.573
19_L58_I0.5120.568
53_L56_K0.5110.567
15_M19_L0.503320.559
32_R35_Y0.499020.554
19_L51_Q0.493220.547
7_A58_I0.48090.534
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
3vdoA0.907798.70.087
4kn7X0.907798.70.087
3iydF0.907798.70.09
1sigA0.907798.70.106
2q1zA0.907798.60.114
1l0oC0.907798.60.12
1or7A0.892398.60.122
2o7gA0.892398.60.124
3n0rA0.907798.60.131
3ugoA0.907798.50.146

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