GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PEGA - PEGA domain
Pfam: PF08308 (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: CL0287
Length: 71
Sequences: 4895
Seq/Len: 68.94
HH_delta: 0.349 (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
41_V65_V1.873123.484
49_Y65_V1.353812.518
38_T50_T1.245042.316
40_T50_T1.225242.279
47_E68_E1.185772.206
18_D40_T1.169482.176
36_E54_T1.133492.109
40_T48_P1.115462.075
36_E52_T1.099932.046
14_E42_E1.011891.882
35_G55_V0.956421.779
42_E48_P0.951011.769
18_D50_T0.896851.668
16_Y40_T0.887131.650
27_L64_N0.853121.587
13_A41_V0.841171.565
18_D38_T0.818361.522
10_P13_A0.809041.505
56_K59_E0.782331.455
38_T52_T0.759151.412
17_V29_L0.702971.308
10_P43_K0.692681.289
32_L37_H0.690631.285
16_Y42_E0.687671.279
32_L35_G0.686021.276
13_A43_K0.675551.257
18_D37_H0.603971.124
17_V32_L0.591841.101
51_K65_V0.57631.072
12_G43_K0.570371.061
17_V37_H0.562831.047
15_V27_L0.555921.034
41_V49_Y0.548621.021
16_Y21_Y0.539951.004
46_Y67_L0.527610.981
44_P69_P0.527020.980
12_G44_P0.525950.978
43_K46_Y0.518990.965
11_S43_K0.496610.924
32_L55_V0.477070.887
14_E23_G0.466030.867
10_P46_Y0.444850.828
51_K63_V0.441260.821
49_Y68_E0.432780.805
14_E21_Y0.429480.799
15_V41_V0.397350.739
37_H55_V0.382580.712
21_Y36_E0.382370.711
17_V39_V0.374170.696
55_V61_T0.363110.675
22_I29_L0.346450.644
34_P37_H0.343690.639
39_V51_K0.337830.628
46_Y69_P0.337120.627
22_I32_L0.32980.614
28_T60_T0.327730.610
10_P44_P0.325810.606
10_P26_P0.323260.601
39_V53_V0.321770.599
23_G27_L0.31560.587
51_K54_T0.308770.574
56_K62_T0.30650.570
16_Y23_G0.300830.560
56_K61_T0.299720.558
34_P57_P0.289840.539
29_L64_N0.277090.515
10_P25_T0.275740.513
37_H53_V0.275720.513
53_V63_V0.273370.509
14_E24_T0.271870.506
14_E44_P0.269330.501
18_D22_I0.269080.501
10_P67_L0.269020.500
55_V59_E0.268950.500
20_K52_T0.263760.491
41_V67_L0.262960.489
62_T66_T0.261920.487
63_V66_T0.260920.485
30_K57_P0.257090.478
20_K23_G0.256640.477
26_P57_P0.254070.473
12_G25_T0.252360.469
24_T33_P0.249840.465
26_P30_K0.249270.464
20_K38_T0.244650.455
34_P52_T0.234650.437
21_Y24_T0.231220.430
57_P61_T0.229170.426
22_I27_L0.229080.426
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
1uwyA0.985997.60.349
3mn8A0.985997.50.351
1h8lA0.971897.50.361
2nsmA0.971897.10.414
1nkgA0.9718960.491
1ti6B0.887382.80.642
3kcpA0.957765.60.687
1xpnA0.943765.50.687
3irpX0.929646.80.719
3qecA0.943743.60.725

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