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T0814 360-424

ID: 1404852228 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 65 (60)
Sequences: 216 (187.9)
Seq/Len: 3.600
Nf(neff/√len): 24.3

Jackhmmer Results: (2014_04_16)
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: 3.600).

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
43_R50_D3.5621.00
37_S55_V3.0031.00
39_Y52_L2.3311.00
44_P47_A2.3021.00
1_L6_Y2.1611.00
3_Q50_D1.6810.99
5_S25_I1.5340.97
48_R52_L1.4940.97
37_S49_Y1.4250.96
7_N25_I1.4120.95
26_E56_T1.3820.95
46_G49_Y1.3800.94
6_Y46_G1.2560.90
5_S39_Y1.2410.89
23_G28_N1.1650.85
18_S59_R1.1160.81
44_P51_R1.0900.79
26_E52_L1.0780.78
33_Q39_Y1.0690.77
17_S31_Q1.0570.76
5_S49_Y1.0510.75
44_P49_Y1.0410.74
14_P17_S1.0360.74
17_S20_G1.0300.73
14_P18_S1.0270.73
35_E38_I1.0030.70
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: (05Jul14)
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  
3ce2A10.78465.70.919Contact Map
2qr4A20.78464.10.924Contact Map
3hl6A20.23083.70.926Contact Map
1jg7A10.47693.20.928Contact Map
3n2oA40.22.70.931Contact Map
2gzqA10.47692.60.932Contact Map
2e8gA20.56922.50.932Contact Map
1gcyA102.40.933Contact Map
2licA10.49232.30.933Contact Map
3qwnA120.95382.10.935Contact 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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