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non45

ID: 1501607812 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 25 (23)
Sequences: 6471 (4905.5)
Seq/Len: 281.348
Nf(neff/√len): 1022.9

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: 281.348).

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
17_R20_E2.8601.00
5_K20_E2.4521.00
2_E9_A2.4491.00
4_K20_E2.4041.00
15_N18_F1.9481.00
12_Y15_N1.8771.00
13_V17_R1.6881.00
6_C19_H1.6621.00
11_R15_N1.6471.00
2_E7_G1.2020.98
18_F21_R1.1830.98
1_Y9_A1.1670.97
14_Q18_F1.1660.97
14_Q22_T1.1170.96
18_F22_T1.0980.96
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  
1ej6B20.9293.2-0.121Contact Map
2eluA10.9692.9-0.111Contact Map
1zr9A1192.5-0.1Contact Map
3zmsC1090.9-0.063Contact Map
4ijdA20.9690.4-0.051Contact Map
2eppA10.9289-0.022Contact Map
2wbtA20.9687.60.001Contact Map
2en3A10.9287.40.004Contact Map
1f2iG60.9287.40.004Contact Map
3w5kB10.9287.20.009Contact 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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