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AntF_3

ID: 1515667909 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 35 (35)
Sequences: 85 (52.1)
Seq/Len: 2.429
Nf(neff/√len): 8.8

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: 2.429).

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
10_A13_R1.9160.99
1_S9_A1.5890.96
13_R19_A1.4040.90
13_R23_L1.3340.87
1_S4_T1.3220.86
2_L8_Y1.3100.86
16_N21_L1.2940.85
7_A26_F1.2740.83
4_T18_A1.2610.83
12_T33_G1.2450.81
19_A26_F1.2230.80
13_R21_L1.2120.79
1_S28_V1.2100.79
17_Y35_R1.2010.78
27_K34_E1.1350.72
2_L18_A1.1340.72
15_S22_R1.1210.71
29_T34_E1.1200.71
10_A17_Y1.1050.70
17_Y30_F1.1020.69
11_R33_G1.0900.68
31_A34_E1.0850.67
14_R18_A1.0490.64
17_Y21_L1.0480.64
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  
3shgB10.942925.90.775Contact Map
3cucA2117.60.792Contact Map
4u04A215.80.833Contact Map
3eqxA215.10.837Contact Map
4ggoA414.90.838Contact Map
2lzfA20.45714.40.842Contact Map
1t4wA114.30.842Contact Map
1zoqC20.57143.20.852Contact Map
1oz2A112.90.856Contact Map
3ut1A112.80.856Contact 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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