OPENSEQ.org
brca2

ID: 1517368517 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 35 (35)
Sequences: 95 (37.5)
Seq/Len: 2.714
Nf(neff/√len): 6.3

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: 2.714).

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
20_K26_V2.2181.00
21_E27_K1.8910.99
5_L27_K1.6620.98
5_L16_V1.6400.97
24_D31_D1.6130.97
3_P31_D1.5320.95
1_K18_I1.4720.94
2_E22_S1.3560.90
15_K23_L1.2930.87
18_I23_L1.2920.87
10_T26_V1.2880.87
12_S26_V1.2490.84
9_H28_N1.2150.82
10_T15_K1.1580.78
19_A33_K1.1340.75
1_K9_H1.0510.67
2_E26_V1.0160.63
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  
1n0wB10.942999.50.115Contact Map
2mtnA10.542929.90.809Contact Map
4mfkA1115.20.833Contact Map
2zjrR10.714311.20.843Contact Map
4tp9U10.742911.10.843Contact Map
3bboW10.771410.30.846Contact Map
4g06A20.942910.30.846Contact Map
4rb6Y10.68579.20.849Contact Map
2zjrC10.88.90.849Contact Map
3terA20.82866.90.857Contact 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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