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PYY91-36

ID: 1513659467 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 36 (36)
Sequences: 49 (19.4)
Seq/Len: 1.361
Nf(neff/√len): 3.2

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: 1.361).

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
21_Y24_L1.7250.93
15_E29_N1.7120.93
23_S28_L1.4720.83
15_E36_Y1.4560.82
18_S28_L1.4070.79
29_N36_Y1.3880.77
29_N32_T1.3530.75
29_N33_R1.3530.75
10_E21_Y1.3220.72
10_E17_L1.2740.68
25_R30_L1.2300.64
1_Y24_L1.2120.62
1_Y4_K1.2050.62
10_E26_H1.1980.61
4_K34_Q1.1860.60
2_P27_Y1.1520.57
12_A35_R1.1470.56
20_Y25_R1.0980.51
4_K30_L1.0490.46
1_Y16_E1.0290.44
10_E16_E1.0220.44
14_P35_R1.0200.43
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  
1bbaA1199.70.04Contact Map
2bf9A10.972299.70.046Contact Map
1f8pA1199.60.076Contact Map
2l60A1199.60.08Contact Map
1qbfA1199.60.091Contact Map
1k8vA10.972278.30.756Contact Map
2faoA2135.90.815Contact Map
2iruA2133.90.817Contact Map
2a26A30.7510.50.856Contact Map
4c5wA1110.20.857Contact 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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