GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HHH_2 - Helix-hairpin-helix motif
Pfam: PF12826 (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: CL0198
Length: 64
Sequences: 8543
Seq/Len: 133.48
HH_delta: -0.062 (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
52_Y56_Q1.997372.794
15_T47_I1.693962.369
33_S36_E1.607622.249
34_V49_Q1.518632.124
38_S45_P1.415451.980
38_S48_A1.240671.735
45_P49_Q1.191231.666
23_F32_A1.184481.657
25_S28_A1.116561.562
10_G50_S1.113961.558
34_V52_Y1.091221.526
49_Q53_E0.9631.347
36_E39_A0.961731.345
43_I47_I0.925191.294
34_V38_S0.918521.285
18_L40_I0.89121.247
15_T18_L0.883041.235
27_E31_N0.873961.222
18_L41_P0.852421.192
30_M55_F0.846781.184
11_V18_L0.836091.169
14_K17_K0.814421.139
22_H40_I0.792351.108
28_A31_N0.779321.090
14_K18_L0.772971.081
44_G47_I0.767561.074
24_G28_A0.757481.059
22_H39_A0.754891.056
23_F36_E0.739441.034
47_I50_S0.725781.015
10_G46_K0.722241.010
11_V16_A0.717391.003
18_L21_K0.680410.952
25_S32_A0.665560.931
34_V45_P0.661090.925
50_S54_F0.646510.904
48_A52_Y0.643670.900
18_L42_G0.601270.841
9_P54_F0.600250.840
28_A32_A0.568880.796
43_I48_A0.565950.792
16_A30_M0.559310.782
8_I54_F0.55890.782
7_G54_F0.553550.774
50_S53_E0.544020.761
7_G16_A0.526610.737
12_G15_T0.526170.736
37_L48_A0.510660.714
27_E30_M0.504960.706
46_K50_S0.504070.705
17_K21_K0.485420.679
19_L40_I0.484730.678
29_L51_I0.482610.675
40_I43_I0.47410.663
29_L37_L0.464670.650
13_E17_K0.464640.650
28_A36_E0.456980.639
35_E38_S0.456480.638
16_A20_A0.426990.597
46_K49_Q0.425860.596
26_L30_M0.421760.590
12_G47_I0.420320.588
33_S52_Y0.415890.582
11_V15_T0.413490.578
43_I51_I0.413290.578
8_I13_E0.413070.578
9_P50_S0.412940.578
29_L32_A0.408310.571
23_F29_L0.406850.569
17_K20_A0.403640.565
52_Y55_F0.403020.564
16_A44_G0.400280.560
29_L55_F0.397590.556
8_I11_V0.390420.546
19_L51_I0.389880.545
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
3sgiA198.8-0.062
4glxA198.7-0.02
2owoA198.7-0.019
1dgsA198.70.001
2bgwA0.937598.20.156
3c1yA198.20.157
2a1jB0.968898.10.17
3c65A0.87598.10.186
1x2iA1980.189
1kftA0.8906980.195

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