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Adhiron2

ID: 1515341267 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (79)
Sequences: 972 (704.5)
Seq/Len: 12.304
Nf(neff/√len): 79.3

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 12.304).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

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] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
29_R48_E2.8131.00
10_A27_F2.4381.00
5_E64_V2.3511.00
16_E73_L2.3221.00
16_E19_K2.2721.00
42_M61_K2.2041.00
65_K70_F2.1671.00
65_K68_E2.0351.00
34_K44_Y1.9761.00
17_H21_E1.9721.00
35_E41_T1.9581.00
33_A45_L1.9401.00
42_M74_Q1.9181.00
63_W70_F1.6481.00
27_F47_L1.4811.00
25_L58_Y1.4791.00
31_V57_L1.4571.00
42_M63_W1.4521.00
61_K75_E1.4331.00
10_A47_L1.4191.00
28_V50_K1.3700.99
6_I33_A1.3470.99
25_L49_A1.2900.99
6_I9_L1.2740.99
49_A58_Y1.2720.99
32_K46_T1.2540.99
37_V41_T1.2190.98
9_L64_V1.1720.98
12_F73_L1.1560.97
38_V42_M1.1550.97
49_A56_K1.1040.96
40_G43_Y1.1020.96
3_S7_E1.0720.95
36_Q39_A1.0660.95
5_E33_A1.0510.94
44_Y59_E1.0290.94
36_Q40_G1.0290.94
9_L71_K1.0170.93
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
2l4vA1199.80.05Contact Map
3ul5A4199.80.058Contact Map
3imaB20.974799.80.072Contact Map
1eqkA1199.80.075Contact Map
4n6tA1199.80.079Contact Map
4lziA1199.80.086Contact Map
5a0oB2099.70.113Contact Map
2kxgA10.974799.70.124Contact Map
4n6oB1199.60.184Contact Map
3gaxA2199.60.188Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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