GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HHH_3 - Helix-hairpin-helix motif
Pfam: PF12836 (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: 65
Sequences: 7304
Seq/Len: 112.37
HH_delta: -0.018 (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
12_S15_E1.641042.453
33_Y37_N1.375672.056
17_Q27_A1.365382.041
26_Q56_T1.292581.932
26_Q29_A1.289351.927
44_E47_K1.202391.797
53_G56_T1.20181.796
13_A28_K1.187831.775
13_A17_Q1.154641.726
28_K32_E1.127041.685
17_Q24_P1.11591.668
47_K54_P1.08381.620
24_P28_K1.028551.537
42_S45_D1.025131.532
47_K57_Y1.020111.525
33_Y49_V0.969681.449
33_Y48_E0.944161.411
41_K45_D0.933781.396
54_P58_E0.929751.390
45_D48_E0.925721.384
33_Y40_F0.914431.367
6_I11_A0.835881.249
25_K28_K0.778531.164
13_A31_V0.777061.161
31_V34_R0.774271.157
56_T59_K0.771091.153
43_L61_K0.748031.118
55_K59_K0.734611.098
29_A32_E0.708311.059
43_L57_Y0.686071.025
7_D10_T0.680771.018
58_E62_P0.66740.998
13_A18_A0.664860.994
23_G26_Q0.662110.990
22_I26_Q0.658130.984
57_Y61_K0.657140.982
20_P60_L0.622820.931
32_E36_K0.605520.905
27_A31_V0.603980.903
14_E17_Q0.592320.885
26_Q52_I0.576160.861
11_A15_E0.565270.845
55_K58_E0.5640.843
46_L57_Y0.563160.842
25_K29_A0.554620.829
21_G59_K0.551360.824
13_A24_P0.54990.822
29_A51_G0.536220.801
43_L47_K0.52520.785
13_A27_A0.518140.774
22_I27_A0.512960.767
19_L23_G0.512760.766
15_E18_A0.50280.752
33_Y50_P0.494820.740
35_E38_G0.494770.740
59_K62_P0.48950.732
35_E39_P0.484740.725
9_N40_F0.472140.706
33_Y36_K0.46850.700
8_I46_L0.466570.697
44_E57_Y0.465670.696
45_D49_V0.45670.683
6_I15_E0.45150.675
56_T60_L0.450440.673
31_V35_E0.450260.673
14_E18_A0.444870.665
25_K51_G0.439650.657
6_I19_L0.419840.628
32_E35_E0.41570.621
52_I56_T0.407840.610
26_Q53_G0.406830.608
19_L60_L0.402740.602
20_P59_K0.380930.569
58_E61_K0.380110.568
52_I57_Y0.367590.549
22_I56_T0.364720.545
43_L58_E0.354910.530
19_L22_I0.352410.527
50_P53_G0.349930.523
20_P23_G0.349250.522
27_A30_I0.348340.521
36_K39_P0.345960.517
21_G55_K0.34360.514
26_Q51_G0.34220.511
29_A50_P0.342080.511
10_T41_K0.340910.510
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
3bzcA199.2-0.018
3psfA1990.072
3psiA198.90.079
3arcU0.938598.90.09
1s5lU0.938598.90.101
2duyA0.938598.80.136
2eduA198.60.186
2i5hA0.969298.40.262
3f2bA0.984698.10.32
3ci0K0.9846980.338

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