GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
Tatiana Brailovskaya

ID: 1500661939 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 81 (81)
Sequences: 112 (108)
Seq/Len: 1.383
Nf(neff/√len): 12.0

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: 1.383).

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
14_F22_Q2.4321.00
38_P54_P2.4201.00
22_Q30_F2.3470.99
14_F54_P2.2750.99
22_Q54_P2.2650.99
14_F30_F2.2470.99
30_F54_P2.2220.99
20_F28_I1.9810.97
6_F14_F1.9010.97
6_F30_F1.8470.96
16_A32_A1.7720.94
6_F38_P1.7700.94
6_F22_Q1.7040.93
30_F38_P1.6960.92
14_F38_P1.6420.91
6_F54_P1.6140.90
12_I52_S1.6100.89
22_Q38_P1.5860.89
44_I47_Q1.4810.83
20_F68_G1.3380.74
4_I20_F1.2490.66
28_I68_G1.1980.62
34_F42_E1.1680.59
12_I36_I1.1270.55
20_F52_S1.1260.55
36_I52_S1.1250.54
20_F36_I1.1160.54
8_S27_H1.1020.52
4_I36_I1.1000.52
28_I36_I1.0890.51
28_I44_I1.0870.51
24_N58_D1.0430.46
28_I52_S1.0410.46
4_I28_I1.0370.46
4_I68_G1.0260.44
40_G60_L1.0130.43
51_T78_I1.0090.43
12_I20_F1.0080.43
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  
4xtkA80.39512.10.927Contact Map
1wthA111.90.928Contact Map
4bouA10.51851.70.931Contact Map
3syaA10.3211.60.932Contact Map
3spcA10.2841.20.936Contact Map
3mmgA20.88891.10.938Contact Map
3zfpA10.691410.94Contact Map
2gixA40.3580.90.94Contact Map
1ho8A10.34570.90.94Contact Map
1fizL10.13580.80.942Contact 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.

Page generated in 0.21 seconds.