GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DSL - Delta serrate ligand
Pfam: PF01414 (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: CL0001
Length: 63
Sequences: 3051
Seq/Len: 48.43
HH_delta: 0.305 (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
33_F48_S1.26793.619
47_D53_V0.863072.463
50_G62_N0.856812.446
17_I29_N0.831582.374
34_C46_C0.754472.153
40_S52_K0.64851.851
43_H55_L0.644111.838
60_G63_C0.548281.565
19_V25_Y0.520661.486
25_Y58_W0.507121.447
26_Y32_K0.501971.433
21_C30_C0.488681.395
42_G55_L0.468461.337
23_E56_P0.465591.329
26_Y59_T0.455661.301
19_V44_Y0.428341.223
45_T55_L0.409351.168
54_C63_C0.401661.146
28_P61_P0.387891.107
44_Y52_K0.386571.103
42_G58_W0.364631.041
36_P41_F0.364211.040
36_P40_S0.346090.988
41_F61_P0.345280.986
22_D25_Y0.339380.969
49_N61_P0.334150.954
15_Y18_R0.333420.952
15_Y37_R0.331980.948
27_G31_S0.323730.924
27_G30_C0.322250.920
24_N52_K0.313370.894
17_I50_G0.306860.876
31_S48_S0.303680.867
47_D50_G0.303410.866
15_Y48_S0.296120.845
41_F62_N0.294420.840
17_I28_P0.279160.797
15_Y19_V0.278320.794
25_Y33_F0.276860.790
17_I36_P0.260850.745
33_F36_P0.250690.716
20_V28_P0.240860.687
54_C60_G0.236240.674
16_R19_V0.235060.671
37_R42_G0.23450.669
16_R20_V0.234110.668
23_E28_P0.232350.663
30_C46_C0.23130.660
22_D55_L0.231280.660
46_C54_C0.230810.659
21_C27_G0.230330.657
18_R51_N0.223080.637
50_G58_W0.22180.633
45_T56_P0.219310.626
23_E35_K0.217770.622
35_K62_N0.215650.616
21_C57_G0.212810.607
45_T53_V0.211070.602
48_S51_N0.210070.600
29_N56_P0.208820.596
54_C57_G0.205690.587
19_V26_Y0.201950.576
23_E55_L0.201540.575
15_Y57_G0.200670.573
27_G60_G0.200540.572
20_V51_N0.200350.572
19_V40_S0.199150.568
23_E60_G0.198480.567
15_Y41_F0.195330.558
23_E53_V0.194870.556
51_N59_T0.19420.554
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
4k0vA0.936598.30.305
2vj2A198.20.319
2gy5A0.936598.10.328
2wg3C0.968398.10.339
2gy5A198.10.341
4k0vA198.10.346
2ygqA0.968397.90.376
2ygqA0.968397.90.383
2e26A0.952497.80.394
3k6sB0.984197.80.398

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