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TssG

ID: 1515509246 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 66 (66)
Sequences: 294 (175.9)
Seq/Len: 4.455
Nf(neff/√len): 21.7

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: 4.455).

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
35_R65_T1.9341.00
46_M58_P1.8721.00
31_W34_D1.7000.99
18_L32_H1.5800.99
5_M66_D1.5660.99
43_P50_H1.4630.98
8_P23_A1.4080.97
48_V60_M1.3600.96
37_R63_H1.3590.96
3_P49_H1.3430.96
5_M40_L1.3140.95
1_L66_D1.2970.94
1_L14_G1.2810.94
16_T29_R1.2400.92
12_A25_G1.2360.92
57_R60_M1.2230.92
2_L25_G1.2100.91
2_L22_L1.2100.91
7_L46_M1.1980.90
5_M36_R1.1950.90
1_L22_L1.1640.89
4_L19_V1.1600.89
18_L24_P1.1410.87
16_T30_V1.1090.85
28_A38_I1.1090.85
47_R62_D1.1090.85
24_P28_A1.1040.85
53_S58_P1.1030.85
43_P53_S1.0850.84
42_T50_H1.0790.83
23_A44_L1.0560.81
46_M57_R1.0320.79
27_Q42_T1.0160.78
42_T53_S1.0150.78
33_H66_D1.0070.77
48_V51_P1.0000.76
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  
3c9pA1115.20.87Contact Map
1ocxA30.86368.40.884Contact Map
3fttA10.87887.30.887Contact Map
4n6aA20.95457.10.888Contact Map
3nz2A120.87886.50.89Contact Map
3hjjA30.87886.20.891Contact Map
1krrA30.87886.10.892Contact Map
3srtA20.87885.80.892Contact Map
2p2oA60.87885.50.893Contact Map
4rxvA10.68185.40.894Contact 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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