GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HLH - Helix-loop-helix DNA-binding domain
Pfam: PF00010 (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: 55
Sequences: 2977
Seq/Len: 54.13
HH_delta: -0.056 (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
9_E12_R0.812332.270
39_S42_S0.752522.103
5_H13_R0.66821.868
46_K49_D0.65261.824
28_P50_Y0.525761.469
21_D25_E0.473661.324
40_K43_I0.466841.305
11_R15_R0.463371.295
16_I48_I0.445261.244
8_R12_R0.438311.225
5_H9_E0.423531.184
5_H8_R0.423211.183
15_R19_C0.408431.142
38_L46_K0.408161.141
41_A45_Q0.407971.140
13_R16_I0.405141.132
19_C46_K0.404981.132
43_I47_A0.401881.123
6_N10_R0.398341.113
48_I52_K0.39351.100
20_F40_K0.392251.096
22_E26_L0.381541.066
11_R14_D0.38111.065
19_C41_A0.380971.065
18_D22_E0.379171.060
51_I54_L0.376631.053
29_S46_K0.376331.052
16_I19_C0.370241.035
21_D24_R0.363241.015
16_I44_L0.360371.007
35_S42_S0.35670.997
30_C36_R0.353070.987
41_A48_I0.352340.985
13_R41_A0.340590.952
3_Q7_E0.333930.933
22_E25_E0.332550.929
19_C22_E0.321290.898
27_L30_C0.319270.892
46_K53_Q0.312060.872
36_R53_Q0.311910.872
19_C39_S0.311520.871
17_N40_K0.31110.870
25_E35_S0.302320.845
49_D53_Q0.301310.842
27_L40_K0.296610.829
19_C45_Q0.296070.827
15_R45_Q0.293340.820
29_S53_Q0.292980.819
50_Y53_Q0.291880.816
21_D29_S0.290330.811
3_Q35_S0.288970.808
17_N20_F0.288860.807
17_N38_L0.28060.784
6_N16_I0.278670.779
40_K51_I0.276310.772
10_R28_P0.275240.769
36_R42_S0.275160.769
14_D29_S0.271830.760
44_L51_I0.27090.757
21_D36_R0.270740.757
24_R38_L0.267070.746
10_R43_I0.264350.739
5_H28_P0.263120.735
3_Q18_D0.263090.735
5_H10_R0.26290.735
9_E17_N0.261390.731
13_R27_L0.260230.727
8_R11_R0.259110.724
45_Q53_Q0.25740.719
9_E13_R0.257310.719
21_D30_C0.255770.715
8_R20_F0.254790.712
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
1a0aA199.1-0.056
1nkpA0.963699.1-0.042
4atiA0.981899.1-0.034
4h10B0.927399.1-0.027
4h10A0.981899-0.022
1nkpB0.945599-0.02
1am9A0.927399-0.018
1nlwA0.963699-0.017
1hloA0.945599-0.011
1an4A199-0.011

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