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leafs_1ptf_fastRelax_25

ID: 1507536403 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 495 (307.3)
Seq/Len: 5.690
Nf(neff/√len): 32.9

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: 5.690).

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
30_E68_R4.1841.00
63_V77_I2.4441.00
9_K85_F2.2391.00
7_L60_L1.9621.00
33_F77_I1.9501.00
1_E70_D1.7221.00
34_W41_I1.7051.00
3_Y64_F1.6040.99
2_V28_L1.5780.99
51_H70_D1.5440.99
11_S28_L1.5330.99
1_E66_R1.4860.99
51_H54_H1.4200.98
28_L70_D1.4140.98
59_L80_E1.4130.98
50_I77_I1.3720.98
39_G44_M1.3040.97
17_Q84_K1.2810.96
81_F86_I1.2720.96
21_A80_E1.2550.95
25_V76_E1.2550.95
9_K18_V1.2130.94
6_F63_V1.2090.94
30_E85_F1.1800.93
5_L71_T1.1730.93
34_W66_R1.1580.92
50_I63_V1.1470.92
12_T82_L1.1460.92
18_V86_I1.1420.91
71_T77_I1.1330.91
68_R85_F1.1300.91
17_Q80_E1.1130.90
70_D78_H1.1090.90
70_D76_E1.1070.90
30_E66_R1.0990.89
6_F50_I1.0890.89
36_D83_R1.0740.88
21_A34_W1.0720.88
40_K52_L1.0560.87
6_F78_H1.0030.82
34_W62_V1.0030.82
5_L17_Q1.0020.82
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  
3le1A20.988595.80.835Contact Map
1ka5A1195.70.835Contact Map
1y51A30.97795.60.837Contact Map
3ihsA20.942595.50.838Contact Map
1kklH30.988595.50.838Contact Map
1pchA10.97795.50.838Contact Map
1sphA20.97795.50.838Contact Map
1ptfA1195.30.84Contact Map
3ccdA20.97795.20.841Contact Map
1u02A10.620713.10.929Contact 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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