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ID: 1504785048 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 46 (46)
Sequences: 61 (33)
Seq/Len: 1.326
Nf(neff/√len): 4.9

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: 1.326).

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
7_D30_L1.7560.93
25_T31_T1.6600.91
1_P33_E1.5880.88
11_K31_T1.5810.88
12_C16_A1.5290.85
26_K46_P1.4950.83
20_L45_S1.4830.83
22_R29_K1.4370.80
42_P45_S1.4220.79
9_N30_L1.3810.76
6_C40_E1.3290.72
5_I9_N1.2420.64
4_E8_I1.2130.62
19_E34_R1.2090.61
15_A33_E1.2000.61
6_C16_A1.1750.58
1_P41_T1.1610.57
6_C20_L1.1220.53
41_T45_S1.0730.48
4_E44_F1.0680.47
8_I44_F1.0640.47
19_E24_T1.0600.47
8_I43_A1.0590.47
20_L46_P1.0550.46
27_E46_P1.0370.44
40_E44_F1.0340.44
2_K46_P1.0170.42
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  
2eroA20.391380.879Contact Map
3k7lA10.39137.70.88Contact Map
2dw0A20.39137.30.881Contact Map
3k7nA10.39137.20.881Contact Map
2ks0A20.80435.80.887Contact Map
4g6iA30.97834.50.892Contact Map
1i8dA30.93484.30.893Contact Map
1t60C80.89134.30.894Contact Map
4phxB80.73914.20.894Contact Map
1oigA10.30434.10.894Contact 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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