GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HapK - REDY-like protein HapK
Pfam: PF11639 (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: 104
Sequences: 2838
Seq/Len: 27.29
HH_delta: 0.271 (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
63_D66_A1.484764.122
38_R62_S1.241073.445
15_D18_A1.07252.977
39_S60_D0.938592.606
64_M68_G0.869472.414
21_R25_E0.776672.156
62_S66_A0.751312.086
20_E24_R0.713991.982
3_V60_D0.684191.899
44_R55_Y0.599911.665
65_D68_G0.563981.566
11_K88_E0.560541.556
65_D69_R0.542331.506
13_G16_P0.533021.480
78_R81_A0.532361.478
25_E82_E0.501931.393
33_S75_T0.491741.365
74_E78_R0.482861.340
11_K15_D0.471251.308
10_L19_F0.465881.293
68_G72_A0.450231.250
20_E44_R0.445241.236
18_A21_R0.442851.229
75_T78_R0.440161.222
17_A21_R0.438471.217
4_I67_F0.434891.207
36_S66_A0.434761.207
20_E55_Y0.426891.185
34_L75_T0.423221.175
41_E60_D0.420441.167
28_Y40_F0.415921.155
74_E77_Q0.414371.150
19_F23_V0.411011.141
23_V55_Y0.40831.133
9_R54_H0.399371.109
23_V42_V0.389331.081
7_L54_H0.372561.034
69_R72_A0.370351.028
45_A50_D0.368121.022
16_P20_E0.366411.017
68_G71_M0.365961.016
80_V84_Q0.362731.007
3_V58_I0.357920.994
77_Q80_V0.35550.987
9_R88_E0.342260.950
72_A77_Q0.340990.947
5_V58_I0.339960.944
77_Q81_A0.339760.943
17_A20_E0.334820.929
34_L70_D0.329950.916
82_E85_Q0.318310.884
9_R53_Y0.317330.881
70_D76_F0.317080.880
35_P62_S0.314450.873
9_R51_A0.314140.872
2_T67_F0.313710.871
22_W83_F0.309780.860
5_V56_I0.306040.850
40_F59_I0.305340.848
35_P66_A0.30370.843
66_A69_R0.302870.841
34_L73_T0.301280.836
37_V40_F0.300820.835
16_P53_Y0.300620.835
42_V55_Y0.296990.824
25_E29_P0.29590.821
22_W25_E0.289330.803
2_T64_M0.288440.801
37_V59_I0.283560.787
15_D86_M0.283420.787
7_L56_I0.283010.786
37_V70_D0.282970.786
30_T33_S0.279950.777
73_T76_F0.277030.769
22_W82_E0.271350.753
28_Y32_P0.271190.753
29_P32_P0.266480.740
31_C67_F0.257590.715
32_P37_V0.256430.712
31_C59_I0.254910.708
30_T75_T0.252340.700
10_L55_Y0.252070.700
4_I59_I0.248760.691
45_A52_P0.247880.688
3_V41_E0.245670.682
18_A22_W0.245490.681
31_C40_F0.245280.681
67_F71_M0.245250.681
35_P69_R0.244180.678
16_P44_R0.243540.676
57_E79_L0.243260.675
7_L53_Y0.241350.670
43_H58_I0.241050.669
24_R29_P0.236530.657
36_S69_R0.236170.656
6_H59_I0.234920.652
37_V61_V0.232950.647
43_H46_S0.23270.646
83_F87_A0.223030.619
29_P33_S0.220450.612
59_I70_D0.21880.607
76_F80_V0.218110.605
38_R60_D0.215060.597
3_V71_M0.211850.588
31_C37_V0.211420.587
12_D15_D0.211290.587
24_R33_S0.210460.584
17_A69_R0.210270.584
8_I57_E0.208820.580
10_L54_H0.206620.574
71_M76_F0.205790.571
46_S51_A0.204990.569
79_L83_F0.204830.569
31_C61_V0.202240.561
40_F70_D0.201050.558
61_V67_F0.199760.555
45_A54_H0.198850.552
78_R82_E0.197310.548
23_V57_E0.196940.547
71_M80_V0.196290.545
42_V61_V0.195330.542
42_V57_E0.193920.538
6_H57_E0.190570.529
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
2jdjA199.40.271
3gz7A0.913599.30.314
4hl9A0.923199.30.317
3kg0A0.942399.30.317
3hx9A0.942399.30.324
4dpoA0.894299.30.326
1y0hA0.942399.30.33
2fb0A0.87599.30.33
2gffA0.951999.30.334
3kkfA0.951999.30.338

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