GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SeleniumBinding - Selenium binding protein
Pfam: PF11524 (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: CL0522
Length: 81
Sequences: 880
Seq/Len: 10.86
HH_delta: 0.047 (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_L72_K0.862393.253
50_M73_A0.834873.149
50_M72_K0.697352.630
9_I55_F0.645672.435
16_P22_Y0.543182.049
44_V49_G0.528561.994
28_E40_L0.492671.858
21_Y72_K0.474311.789
11_T54_G0.470261.774
37_I57_I0.434851.640
49_G70_A0.423771.598
28_E36_L0.420451.586
10_T15_I0.381011.437
18_I73_A0.372641.405
33_V63_K0.368931.391
38_K41_E0.368731.391
14_E19_E0.358191.351
20_L53_I0.357181.347
42_E45_K0.344681.300
43_K47_K0.342221.291
30_S35_E0.329591.243
41_E45_K0.326061.230
57_I66_G0.311911.176
15_I18_I0.303421.144
26_V40_L0.298571.126
34_D38_K0.295221.113
37_I66_G0.294871.112
27_S43_K0.293591.107
43_K46_A0.29251.103
56_K67_Y0.287541.085
40_L66_G0.280351.057
35_E38_K0.272631.028
23_L50_M0.265261.000
15_I73_A0.260080.981
29_A59_A0.259340.978
14_E53_I0.256820.969
29_A58_T0.252150.951
13_N54_G0.252070.951
11_T69_T0.242460.914
12_T53_I0.241840.912
9_I41_E0.236340.891
40_L52_I0.23440.884
27_S62_G0.233750.882
59_A67_Y0.233060.879
24_G51_G0.232580.877
58_T65_M0.229830.867
38_K42_E0.226130.853
39_K63_K0.22530.850
13_N53_I0.221660.836
34_D42_E0.217680.821
19_E24_G0.217180.819
7_F41_E0.216520.817
63_K67_Y0.216040.815
32_N63_K0.214460.809
27_S65_M0.213070.804
20_L32_N0.210470.794
27_S67_Y0.209430.790
51_G73_A0.205610.775
25_I55_F0.204220.770
42_E46_A0.197130.744
8_I15_I0.196880.743
59_A64_L0.194790.735
16_P19_E0.194660.734
12_T54_G0.194530.734
10_T53_I0.193140.728
9_I35_E0.191810.723
20_L73_A0.191550.722
30_S39_K0.191480.722
12_T15_I0.19140.722
10_T22_Y0.189280.714
12_T22_Y0.18860.711
26_V47_K0.18650.703
41_E52_I0.18490.697
19_E61_D0.184660.696
35_E42_E0.183320.691
29_A39_K0.178540.673
14_E54_G0.178520.673
54_G69_T0.176570.666
34_D45_K0.17410.657
39_K43_K0.171470.647
58_T64_L0.168980.637
48_G52_I0.1660.626
26_V70_A0.163930.618
24_G41_E0.163030.615
32_N60_G0.161670.610
12_T16_P0.161580.609
39_K67_Y0.159420.601
37_I41_E0.159310.601
57_I65_M0.157640.595
37_I65_M0.157510.594
23_L70_A0.155550.587
31_E69_T0.155270.586
25_I29_A0.155020.585
23_L47_K0.15480.584
27_S57_I0.153990.581
28_E64_L0.153760.580
21_Y34_D0.153750.580
19_E50_M0.15280.576
36_L66_G0.152470.575
27_S30_S0.15120.570
33_V59_A0.151090.570
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
2jz7A199.90.047
1y2iA0.950699.80.277
1vr4A0.827299.70.315
3qkbA0.888999.40.47
2y1bA198.80.602
2m2jA0.913674.60.864
2jnaA0.9383380.89
4evuA0.851934.10.893
2wqpA0.975326.50.899
2nocA0.925919.20.905

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