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NIa-pro cleavage site-active site coupling

ID: 1500927777 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 33 (33)
Sequences: 651 (133.4)
Seq/Len: 19.727
Nf(neff/√len): 23.2

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: 19.727).

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
26_D32_Q2.5041.00
26_D30_V2.3371.00
28_V33_A1.9051.00
30_V33_A1.8721.00
26_D33_A1.6681.00
29_V32_Q1.6091.00
27_E33_A1.6071.00
27_E30_V1.4751.00
28_V31_H1.4331.00
26_D31_H1.3610.99
28_V32_Q1.2730.99
29_V33_A1.2110.98
1_R16_N1.1680.97
1_R24_E1.0690.95
27_E31_H1.0330.94
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  
3n40F10.96976.60.733Contact Map
1i9wA10.84856.40.734Contact Map
3n44F10.96976.20.736Contact Map
3muuA60.96975.40.743Contact Map
3j0fE40.96975.40.743Contact Map
3j0cA40.96975.40.743Contact Map
2v33A20.96973.60.765Contact Map
4h9jA10.78792.90.775Contact Map
2yewB40.90912.40.784Contact Map
3obkA812.30.788Contact 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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