GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
4rng

ID: 1500382174 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 82 (82)
Sequences: 572 (460.3)
Seq/Len: 6.976
Nf(neff/√len): 50.8

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: 6.976).

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
30_S33_D3.7671.00
4_N58_E2.2311.00
11_G64_A2.0421.00
29_K82_Y2.0261.00
43_A72_I2.0261.00
14_T45_G1.9221.00
25_I31_A1.6401.00
18_L38_M1.6171.00
47_T69_L1.5470.99
8_I59_I1.4320.99
18_L42_M1.3750.99
78_M82_Y1.3590.98
22_A75_I1.3550.98
10_A48_L1.3530.98
26_Y78_M1.3420.98
15_T68_S1.3340.98
59_I63_L1.3250.98
43_A69_L1.2950.98
50_F54_V1.2530.97
18_L39_F1.2500.97
56_I61_V1.2490.97
31_A82_Y1.1940.96
39_F72_I1.1860.95
46_I68_S1.1820.95
36_L79_K1.1810.95
14_T68_S1.1700.95
42_M68_S1.1630.95
4_N8_I1.1460.94
6_I11_G1.1300.94
14_T42_M1.1260.93
70_I74_L1.1130.93
31_A34_V1.1080.93
42_M46_I1.1010.92
39_F75_I1.1000.92
9_I48_L1.0700.91
2_L5_L1.0660.91
34_V75_I1.0550.90
18_L68_S1.0440.89
19_I71_L1.0370.89
3_N62_I1.0170.88
34_V39_F1.0160.88
50_F61_V1.0090.87
51_F70_I1.0050.87
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  
4rngA6199.70.314Contact Map
4x5mA3199.70.326Contact Map
4qncA20.987899.70.33Contact Map
4qndA1199.70.353Contact Map
3ne5A10.3784.80.915Contact Map
3dh4A40.95122.30.928Contact Map
3l1lA10.963420.93Contact Map
3j27A30.68291.90.931Contact Map
4cbfA30.68291.90.931Contact Map
4cctA30.68291.80.932Contact 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 0.0304 seconds.