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T0809

ID: 1402086345 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 62 (60)
Sequences: 585 (505.3)
Seq/Len: 9.750
Nf(neff/√len): 65.2

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: 9.750).

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
29_V37_Y4.4241.00
47_K50_D3.9861.00
15_D55_K2.3281.00
49_L59_V2.1481.00
5_Y45_D2.0921.00
11_E16_Q2.0831.00
12_V17_V1.8321.00
4_D7_T1.8121.00
13_N51_N1.7451.00
19_E58_K1.6651.00
53_L59_V1.5811.00
19_E60_V1.4931.00
27_I37_Y1.4721.00
41_I49_L1.4571.00
41_I61_G1.3790.99
7_T11_E1.3680.99
4_D58_K1.3090.99
30_T36_R1.2700.99
17_V31_K1.2640.99
50_D53_L1.2190.98
50_D54_T1.2120.98
27_I41_I1.1740.97
27_I39_T1.1520.97
25_R40_Y1.1440.97
23_N26_E1.0490.94
41_I44_Q1.0360.94
20_A59_V1.0260.93
11_E31_K1.0190.93
51_N55_K1.0060.92
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: (29May14)
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  
2lnaA10.983945.50.841Contact Map
3pm6A20.774217.50.871Contact Map
2wlbA20.612914.70.876Contact Map
3q94A20.838711.80.881Contact Map
2y5cA20.612910.50.883Contact Map
3if4A40.77429.80.885Contact Map
2iswA20.83879.70.885Contact Map
3n9rA80.83879.60.885Contact Map
1l5pA30.58069.20.886Contact Map
1qoaA20.59688.30.889Contact 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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