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T0829

ID: 1403547195 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 70 (70)
Sequences: 266 (212.7)
Seq/Len: 3.800
Nf(neff/√len): 25.4

HHblits Results: (2013_03)
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: 3.800).

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
3_R24_E3.2171.00
45_N55_F2.3501.00
42_A55_F2.1871.00
3_R13_S2.0481.00
24_E34_Q1.9371.00
56_F61_K1.8471.00
8_S53_G1.5200.98
23_L60_I1.4770.97
37_G65_L1.4070.96
42_A64_F1.3550.94
53_G61_K1.3110.93
3_R26_Q1.2890.92
27_F53_G1.2830.92
23_L35_Y1.2750.92
14_I46_F1.2590.91
23_L36_L1.2580.91
26_Q34_Q1.2570.91
43_H47_M1.2560.91
14_I63_K1.2250.89
57_D61_K1.1910.87
39_P42_A1.1840.87
22_M48_S1.1810.87
6_V15_G1.1770.87
6_V14_I1.1620.86
53_G57_D1.1620.86
15_G26_Q1.1460.85
16_Y42_A1.1350.84
25_I68_K1.1140.82
36_L67_R1.1100.82
37_G67_R1.0890.80
11_I56_F1.0730.79
34_Q67_R1.0320.75
25_I37_G1.0160.73
13_S24_E1.0050.72
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: (21Jun14)
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  
3k8rA20.857118.90.884Contact Map
2x8nA10.942917.10.886Contact Map
3nv7A10.514315.60.888Contact Map
1f9aA60.614310.10.897Contact Map
1n9wA20.42869.80.898Contact Map
2ji4A10.842990.899Contact Map
4j15A20.51438.50.9Contact Map
4f3rA30.58.10.901Contact Map
2qmeI10.34298.10.901Contact Map
1wydA20.92867.80.902Contact 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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