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OPENSEQ.org

3966_2

ID: 1433411302 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 40 (40)
Sequences: 739 (450.8)
Seq/Len: 18.475
Nf(neff/√len): 71.3

HHblits Results: (2013_03)
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: 18.475).

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
28_S31_A3.6881.00
13_T31_A3.1741.00
18_V29_K2.9971.00
13_T28_S2.6921.00
25_E34_A2.4891.00
19_L37_I2.3431.00
20_S23_K1.7681.00
15_G30_Q1.3650.99
4_L14_K1.3080.99
19_L24_T1.2730.99
9_A14_K1.2300.98
33_L38_R1.1820.98
10_C28_S1.1260.97
8_L16_P1.1220.97
4_L7_I1.0910.96
25_E36_P1.0580.95
27_I34_A1.0340.94
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: (31Jan15)
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  
2js4A1199.30.057Contact Map
2hf1A2199.30.057Contact Map
2jr6A1199.30.058Contact Map
2pk7A20.97599.30.059Contact Map
2jnyA1199.30.061Contact Map
2k5rA1199.30.092Contact Map
2kpiA10.9599.10.15Contact Map
3q87A10.997.60.454Contact Map
1dl6A1197.60.454Contact Map
1pftA10.9597.40.472Contact 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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