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leafs_1ptf_fastRelax_13

ID: 1507536308 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 487 (268.7)
Seq/Len: 5.598
Nf(neff/√len): 28.8

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: 5.598).

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
15_D54_K3.9351.00
8_P59_D3.4371.00
5_T60_T2.0641.00
30_V68_E2.0551.00
2_L74_F2.0011.00
36_D77_L1.9081.00
10_A18_F1.6801.00
33_I73_T1.6451.00
22_L44_M1.6270.99
52_S55_V1.5920.99
5_T71_A1.5620.99
8_P61_L1.5490.99
46_V49_Q1.4410.98
25_E38_K1.4390.98
48_D52_S1.3690.98
2_L71_A1.3620.97
20_H47_K1.3170.97
36_D41_I1.2920.96
65_V74_F1.2600.95
25_E76_R1.2400.95
33_I44_M1.2400.95
6_L48_D1.1960.93
29_Y58_G1.1930.93
55_V83_R1.1110.90
59_D66_I1.1100.90
73_T84_L1.0910.89
60_T74_F1.0800.88
79_L83_R1.0800.88
49_Q68_E1.0740.87
3_R12_N1.0610.87
28_L51_A1.0450.85
72_D75_R1.0400.85
10_A35_L1.0320.84
3_R7_V1.0320.84
44_M66_I1.0160.83
6_L22_L1.0160.83
1_P41_I1.0130.83
25_E75_R1.0120.83
17_H55_V1.0050.82
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  
3ccdA20.97798.20.77Contact Map
1kklH3198.10.774Contact Map
1ka5A10.9885980.777Contact Map
1ptfA11980.779Contact Map
3ihsA20.931980.781Contact Map
1pchA10.988597.90.784Contact Map
1y51A30.988597.90.786Contact Map
1sphA20.988597.90.786Contact Map
3le1A20.97797.70.793Contact Map
3n6rA60.89668.90.936Contact 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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