GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cyt-b5 - Cytochrome b5-like HemeSteroid binding domain
Pfam: PF00173 (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: 76
Sequences: 3175
Seq/Len: 41.78
HH_delta: 0 (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
23_K71_K1.803724.803
71_K74_Y1.285363.423
7_L19_I1.131523.013
10_H15_D1.062612.829
18_V27_V0.998942.660
10_H17_W0.898222.392
23_K74_Y0.713561.900
59_S62_A0.676581.802
4_W19_I0.673381.793
18_V49_A0.645451.719
16_C45_A0.634841.690
44_Y52_A0.604351.609
20_I49_A0.594271.582
6_E9_K0.567531.511
7_L75_L0.567061.510
16_C31_L0.560831.493
20_I53_F0.5371.430
34_H37_G0.524991.398
19_I22_G0.51671.376
2_Y7_L0.489321.303
21_D55_E0.479711.277
5_E9_K0.469951.251
12_K15_D0.462851.232
32_D38_A0.46221.231
21_D50_T0.461021.228
23_K67_E0.449861.198
37_G58_H0.445231.186
4_W8_A0.438641.168
34_H58_H0.424031.129
15_D26_D0.422851.126
2_Y73_G0.404751.078
21_D63_E0.398961.062
44_Y47_R0.397341.058
2_Y17_W0.383811.022
65_C70_Y0.382341.018
40_I43_K0.374250.997
61_W64_K0.37210.991
29_D70_Y0.364620.971
5_E8_A0.356380.949
24_V73_G0.337320.898
16_C41_L0.337260.898
65_C68_K0.33210.884
31_L42_K0.326010.868
43_K57_F0.32290.860
56_A59_S0.313080.834
6_E10_H0.310950.828
34_H41_L0.30460.811
36_G58_H0.294730.785
25_Y66_L0.294190.783
15_D28_T0.293560.782
13_K38_A0.291330.776
19_I75_L0.28340.755
51_D56_A0.281360.749
40_I44_Y0.281210.749
61_W65_C0.277570.739
7_L24_V0.276470.736
30_F65_C0.274420.731
30_F33_R0.271270.722
52_A56_A0.27110.722
4_W7_L0.269310.717
60_W64_K0.262410.699
44_Y61_W0.259520.691
13_K32_D0.258330.688
17_W72_V0.257580.686
43_K51_D0.256510.683
44_Y49_A0.248650.662
24_V75_L0.246780.657
66_L70_Y0.24610.655
49_A52_A0.24360.649
43_K62_A0.242680.646
66_L71_K0.242080.645
53_F57_F0.235910.628
53_F65_C0.235680.628
42_K45_A0.235250.626
3_T6_E0.233710.622
62_A66_L0.232310.619
63_E66_L0.228720.609
8_A11_N0.22820.608
40_I56_A0.227610.606
33_R39_D0.226340.603
25_Y67_E0.226260.602
43_K52_A0.22620.602
32_D42_K0.225580.601
10_H16_C0.225050.599
29_D32_D0.222710.593
20_I50_T0.222150.592
38_A60_W0.221510.590
30_F34_H0.221470.590
16_C27_V0.221430.590
38_A42_K0.220450.587
35_P58_H0.220150.586
30_F57_F0.219580.585
40_I52_A0.217430.579
53_F63_E0.216990.578
10_H13_K0.215710.574
9_K13_K0.215080.573
19_I24_V0.212740.566
49_A53_F0.212170.565
33_R61_W0.211820.564
56_A63_E0.210520.561
25_Y71_K0.209170.557
2_Y70_Y0.207380.552
40_I57_F0.205890.548
33_R38_A0.205340.547
15_D29_D0.204980.546
3_T9_K0.204840.545
51_D55_E0.204630.545
31_L35_P0.203940.543
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
1hkoA0.986899.70
1cyoA0.986899.70.003
1cxyA0.986899.70.004
2keoA0.986899.70.005
2ibjA0.986899.70.007
3nerA0.986899.70.008
1kbiA0.973799.70.023
1soxA0.973799.70.04
3lf5A0.973799.70.041
1x3xA0.973799.70.051

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