GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Death - Death domain
Pfam: PF00531 (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: CL0041
Length: 83
Sequences: 1489
Seq/Len: 17.94
HH_delta: 0.029 (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
19_A29_I0.723983.454
16_K33_E0.633513.022
18_L70_I0.405981.937
22_L66_A0.382011.822
68_R80_E0.375331.790
24_L49_R0.348081.660
24_L32_I0.340411.624
55_G58_A0.337171.608
20_R26_E0.327771.564
68_R73_N0.326331.557
14_D17_R0.319541.524
21_K69_D0.317881.516
65_Q69_D0.31541.505
19_A46_M0.304051.450
50_W58_A0.302111.441
18_L22_L0.298091.422
36_N45_E0.287561.372
21_K70_I0.268641.281
49_R52_Q0.263951.259
72_R75_L0.257611.229
16_K41_E0.251691.201
30_E33_E0.251271.199
18_L63_L0.249511.190
35_E39_L0.247731.182
20_R29_I0.242321.156
15_W19_A0.238381.137
46_M51_R0.235971.126
60_V64_I0.23381.115
45_E76_A0.232641.110
8_A43_T0.225231.074
24_L53_R0.225151.074
75_L78_K0.220341.051
13_S71_G0.219581.047
26_E30_E0.216751.034
28_E53_R0.215551.028
14_D72_R0.214781.025
35_E45_E0.212891.016
38_D42_Q0.209290.998
8_A11_L0.206290.984
73_N77_E0.206230.984
64_I73_N0.20370.972
76_A79_I0.202160.964
39_L42_Q0.200660.957
62_Q65_Q0.198920.949
57_N69_D0.197980.944
8_A12_G0.193450.923
67_L70_I0.190790.910
76_A80_E0.18790.896
26_E48_Q0.186830.891
62_Q69_D0.185970.887
25_S28_E0.184030.878
33_E41_E0.18370.876
15_W58_A0.182730.872
45_E48_Q0.18140.865
33_E42_Q0.181360.865
38_D41_E0.180550.861
18_L43_T0.179970.858
32_I49_R0.178640.852
17_R34_E0.175520.837
35_E42_Q0.174770.834
33_E36_N0.173720.829
19_A32_I0.173050.825
71_G78_K0.171030.816
62_Q66_A0.169660.809
68_R76_A0.167970.801
17_R44_Y0.167360.798
13_S40_R0.16560.790
56_P62_Q0.164530.785
37_P42_Q0.163340.779
41_E44_Y0.16320.779
60_V78_K0.162970.777
28_E49_R0.162350.774
34_E37_P0.162240.774
15_W59_T0.160820.767
38_D66_A0.159840.762
56_P61_D0.158550.756
35_E40_R0.158040.754
45_E49_R0.15750.751
51_R56_P0.157490.751
47_L63_L0.156110.745
11_L15_W0.155430.741
27_S37_P0.153020.730
40_R44_Y0.147790.705
17_R40_R0.147620.704
43_T47_L0.147440.703
44_Y70_I0.14670.700
26_E44_Y0.145920.696
23_G57_N0.145020.692
31_N40_R0.143760.686
31_N61_D0.143140.683
50_W63_L0.142220.678
31_N35_E0.141880.677
11_L74_D0.141810.676
10_D41_E0.141730.676
64_I68_R0.141320.674
8_A18_L0.139770.667
49_R53_R0.13970.666
27_S33_E0.138050.659
28_E70_I0.136030.649
14_D31_N0.134880.643
20_R41_E0.132750.633
14_D30_E0.132320.631
26_E78_K0.131730.628
32_I42_Q0.131430.627
13_S79_I0.131290.626
53_R64_I0.130370.622
39_L43_T0.130060.620
74_D78_K0.130010.620
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
3ezqB199.60.029
1wxpA199.50.049
1fadA199.50.051
4d8oA199.50.06
2gf5A199.50.062
2yqfA199.50.072
2of5H199.50.084
1ichA199.40.095
2ib1A0.951899.40.144
3ezqA199.40.144

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