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RB_cyclinD

ID: 1504665409 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 26 (26)
Sequences: 60 (33.4)
Seq/Len: 2.308
Nf(neff/√len): 6.6

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: 2.308).

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
20_E25_S1.7950.98
6_L10_D1.7200.97
16_L23_R1.6440.96
2_M6_L1.4920.93
2_M13_D1.4560.92
6_L13_D1.4470.91
10_D13_D1.3300.86
17_D21_E1.2370.80
18_F22_F1.2180.78
15_L25_S1.1880.76
2_M10_D1.1830.75
17_D26_Q1.1460.72
21_E25_S1.1270.70
16_L25_S1.0580.63
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  
1c9bA50.88469.70.678Contact Map
3g33B216.10.707Contact Map
1f5qB20.96155.60.712Contact Map
2w96A115.20.717Contact Map
1w98B115.10.717Contact Map
1g3nC214.80.72Contact Map
3n2zB10.88464.80.72Contact Map
2f2cA114.70.722Contact Map
4ebbA214.20.728Contact Map
2b9rA20.96154.20.728Contact 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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