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leafs_1ptf_fastRelax_1

ID: 1507536175 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 493 (337.1)
Seq/Len: 5.667
Nf(neff/√len): 36.1

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: 5.667).

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
4_Y78_L2.4481.00
79_E83_F2.3081.00
22_L25_L2.0951.00
36_L41_I2.0091.00
38_R60_E1.8391.00
72_D75_R1.8101.00
48_E63_I1.7591.00
34_W43_L1.7131.00
55_V71_R1.6551.00
8_V15_D1.6040.99
27_D32_P1.5430.99
35_L42_I1.5390.99
10_E58_D1.4540.99
5_W62_L1.4460.98
56_D86_L1.4240.98
65_V74_L1.4050.98
3_F48_E1.4020.98
37_Y58_D1.4000.98
2_L84_E1.3460.97
32_P39_G1.3210.97
10_E51_R1.3020.96
15_D54_D1.2710.96
42_I75_R1.2410.95
10_E56_D1.2130.94
37_Y59_I1.2090.94
20_I24_R1.2050.94
1_D66_T1.1720.93
50_L53_L1.1540.92
33_L54_D1.1180.90
17_R35_L1.1040.89
19_A74_L1.1000.89
33_L74_L1.0840.88
21_A79_E1.0620.87
29_F63_I1.0620.87
24_R64_V1.0610.87
81_L85_R1.0500.86
7_V23_I1.0490.86
4_Y48_E1.0460.86
17_R60_E1.0430.86
17_R45_L1.0420.85
38_R52_R1.0370.85
70_A74_L1.0340.85
21_A77_T1.0270.84
62_L70_A1.0200.84
46_V66_T1.0100.83
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  
1ka5A11980.761Contact Map
1kklH31980.763Contact Map
1ptfA1197.90.764Contact Map
1sphA20.988597.90.767Contact Map
1y51A30.988597.90.769Contact Map
1pchA10.988597.80.77Contact Map
3ccdA20.97797.80.773Contact Map
3ihsA20.896697.70.775Contact Map
3le1A20.988597.60.783Contact Map
1vhfA10.32185.70.937Contact 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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