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FYVE

ID: 1511986310 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 98 (82)
Sequences: 1204 (823)
Seq/Len: 14.683
Nf(neff/√len): 90.9

Jackhmmer Results: (2016_04)
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: 14.683).

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
60_S76_R3.5751.00
34_G55_F2.9951.00
29_G54_L2.8941.00
55_F60_S2.0661.00
62_F79_Q2.0591.00
26_D45_R2.0121.00
26_D47_H1.9971.00
24_V33_S1.9931.00
45_R54_L1.8761.00
50_N77_V1.7881.00
44_R47_H1.7011.00
26_D44_R1.6571.00
46_H76_R1.5231.00
46_H49_R1.4691.00
39_F44_R1.4511.00
34_G80_N1.3110.99
44_R49_R1.2730.99
37_V43_E1.2490.99
33_S53_Q1.2440.98
41_L44_R1.2190.98
26_D46_H1.2150.98
75_V83_Y1.1740.98
67_K70_K1.1590.97
49_R76_R1.1470.97
57_Q76_R1.1350.97
39_F46_H1.1160.96
11_V14_Q1.0980.96
18_S25_K1.0920.96
17_R21_D1.0840.96
14_Q18_S1.0670.95
29_G33_S1.0590.95
37_V58_K1.0520.95
71_I74_P1.0440.94
63_Q67_K1.0280.94
13_D21_D1.0200.93
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  
3t7lA10.755199.80.365Contact Map
1jocA20.857199.80.368Contact Map
1z2qA10.857199.80.368Contact Map
3zyqA10.857199.80.371Contact Map
1dvpA10.857199.80.374Contact Map
2yw8A10.622499.80.375Contact Map
1x4uA10.795999.80.378Contact Map
3mpxA1099.80.38Contact Map
1vfyA10.683799.80.391Contact Map
1wfkA10.785799.70.423Contact 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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