GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HHH_6 - Helix-hairpin-helix motif
Pfam: PF14579 (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: 90
Sequences: 2811
Seq/Len: 31.23
HH_delta: 0.025 (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_D81_S1.242563.296
3_K24_A1.173293.112
46_E49_N0.885912.350
57_D61_R0.855262.269
46_E52_F0.815592.163
19_E26_R0.797952.117
5_L26_R0.787262.088
73_L78_A0.771282.046
46_E61_R0.759642.015
16_F27_L0.728231.932
32_I76_A0.721981.915
11_K19_E0.712851.891
5_L24_A0.687211.823
13_D17_T0.665631.766
58_F79_F0.611071.621
20_D23_N0.60151.596
16_F31_A0.558931.483
19_E24_A0.556731.477
14_A30_S0.551281.462
74_I90_L0.548191.454
86_R89_A0.538371.428
37_E41_E0.532211.412
55_L74_I0.529781.405
40_A43_I0.521311.383
41_E45_E0.520681.381
77_G80_D0.520591.381
36_G39_V0.513861.363
35_L69_Q0.499911.326
13_D48_E0.487931.294
11_K51_P0.478451.269
44_V47_R0.464881.233
34_G68_R0.463551.230
42_K45_E0.460251.221
38_E41_E0.45731.213
42_K46_E0.457011.212
14_A41_E0.456981.212
34_G72_A0.439491.166
10_N52_F0.421711.119
45_E48_E0.411091.090
58_F70_L0.395811.050
67_K71_E0.392091.040
50_G53_K0.385031.021
11_K26_R0.383821.018
83_G89_A0.380751.010
53_K57_D0.378891.005
46_E62_L0.373950.992
56_E60_Q0.372020.987
8_D11_K0.3640.966
42_K64_K0.362650.962
14_A37_E0.358340.951
87_R90_L0.353050.936
43_I58_F0.342080.907
68_R72_A0.340780.904
49_N61_R0.338480.898
51_P61_R0.336610.893
15_D30_S0.335980.891
80_D87_R0.330930.878
56_E59_I0.330640.877
65_I69_Q0.326190.865
14_A44_V0.325640.864
84_K89_A0.324510.861
39_V69_Q0.323450.858
66_N69_Q0.321920.854
59_I70_L0.320320.850
32_I72_A0.313620.832
5_L19_E0.312090.828
79_F82_F0.303970.806
35_L40_A0.303840.806
7_P29_L0.301870.801
52_F61_R0.296890.788
58_F62_L0.293520.779
27_L31_A0.286560.760
35_L72_A0.284980.756
59_I74_I0.282910.750
17_T26_R0.282020.748
8_D26_R0.278680.739
10_N50_G0.276710.734
34_G69_Q0.274570.728
44_V48_E0.267930.711
14_A40_A0.264180.701
20_D24_A0.262750.697
28_G44_V0.261750.694
2_I25_I0.260490.691
16_F25_I0.257640.683
32_I35_L0.251590.667
39_V65_I0.251180.666
10_N51_P0.24980.663
83_G90_L0.24580.652
40_A44_V0.243770.647
7_P76_A0.239770.636
46_E50_G0.239690.636
12_S26_R0.239360.635
17_T28_G0.23930.635
7_P32_I0.239180.634
81_S84_K0.236920.628
12_S29_L0.236860.628
31_A36_G0.23440.622
13_D44_V0.233810.620
12_S47_R0.232010.615
6_P75_K0.231290.614
26_R81_S0.228090.605
36_G71_E0.225870.599
50_G61_R0.224960.597
29_L43_I0.223880.594
16_F77_G0.223040.592
65_I70_L0.221020.586
13_D60_Q0.218560.580
59_I67_K0.218350.579
83_G86_R0.218160.579
42_K62_L0.216890.575
12_S27_L0.216060.573
7_P74_I0.215550.572
3_K23_N0.215020.570
14_A34_G0.214380.569
9_I78_A0.212710.564
29_L72_A0.209940.557
3_K45_E0.209020.554
66_N71_E0.208440.553
11_K81_S0.205060.544
28_G87_R0.204660.543
9_I40_A0.20210.536
11_K20_D0.201010.533
9_I58_F0.200210.531
56_E88_Q0.200170.531
33_K71_E0.199240.529
54_S57_D0.197490.524
49_N53_K0.196020.520
57_D82_F0.19480.517
18_V67_K0.193820.514
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
2hnhA0.977899.90.025
2hpiA0.966799.90.03
3f2bA0.966799.90.033
2eduA0.898.60.586
2i5hA0.911197.40.707
3bzcA0.833396.10.764
3arcU0.811195.80.771
1s5lU0.895.80.771
3psfA0.888995.60.774
3psiA0.888995.40.778

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