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gremlin inefficient 001

ID: 1480919024 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 40 (40)
Sequences: 234 (234)
Seq/Len: 5.850
Nf(neff/√len): 37.0

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: 5.850).

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
13_C34_A1.6301.00
10_G13_C1.5820.99
9_C15_A1.5520.99
4_A12_G1.5280.99
17_C23_G1.5120.99
1_C9_C1.3890.98
8_C40_G1.3830.98
26_A29_C1.3430.97
25_C39_A1.3060.97
3_C18_G1.2930.97
29_C34_A1.2520.96
13_C31_A1.2510.96
11_G36_G1.2040.94
16_C22_C1.1980.94
22_C27_A1.1560.92
20_G27_A1.1290.91
22_C25_C1.1260.91
14_A40_G1.1190.91
14_A26_A1.1190.91
26_A38_G1.0910.89
3_C6_T1.0890.89
19_T37_T1.0850.89
27_A37_T1.0460.86
14_A30_G1.0140.84
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  
1cn3F10.250.20.661Contact Map
4kblA200.20.672Contact Map
2pk2A400.10.72Contact Map
1s58A10.1250.10.742Contact Map
1t2yA10.40.10.747Contact Map
1airA10.60.10.758Contact Map
2qy1A20.4750.10.774Contact Map
2wolA10.4250.10.779Contact Map
2aanA100.10.822Contact Map
4ma7A10.3250.10.822Contact 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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