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OPENSEQ.org

gremlin_e2

ID: 1480923193 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 40 (40)
Sequences: 2228 (2217)
Seq/Len: 55.700
Nf(neff/√len): 350.5

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: 55.700).

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
18_G24_A2.2581.00
1_G25_C1.6421.00
34_T37_C1.5501.00
27_A31_C1.5031.00
14_G17_T1.4991.00
12_C15_C1.4981.00
36_A39_G1.4651.00
22_T26_A1.4151.00
13_G28_T1.4010.99
7_G40_C1.4010.99
5_T17_T1.3730.99
11_A20_T1.3110.99
34_T40_C1.3060.99
27_A30_C1.2770.99
4_T34_T1.2320.98
24_A31_C1.2020.98
5_T38_T1.1980.98
18_G39_G1.1640.97
21_C39_G1.1620.97
2_A23_T1.1470.97
20_T34_T1.1340.97
21_C24_A1.1290.97
13_G29_A1.1060.96
2_A30_C1.0340.94
26_A30_C1.0240.93
3_C6_T1.0180.93
31_C34_T1.0050.93
2_A10_T1.0030.93
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  
2pk2A400.50.458Contact Map
4kblA200.50.475Contact Map
1cn3F10.2750.20.681Contact Map
2aanA100.20.681Contact Map
2wolA10.250.20.681Contact Map
1s58A10.1250.10.709Contact Map
4aenA100.10.737Contact Map
4ladB10.0750.10.799Contact Map
3n44F100.10.816Contact Map
1airA10.60.10.816Contact 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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