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2VXF

ID: 1515674961 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 88 (83)
Sequences: 322 (191.5)
Seq/Len: 3.880
Nf(neff/√len): 21.0

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: 3.880).

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
33_D36_N2.7771.00
22_E76_K2.7261.00
51_D54_T2.1591.00
26_E75_I2.0911.00
49_T52_R1.4860.97
67_Y73_S1.4660.97
12_G17_L1.4540.97
40_A69_I1.4380.96
45_R64_T1.3890.95
15_I78_L1.3650.95
65_F68_I1.3590.95
39_V81_C1.3470.94
42_A61_R1.3410.94
68_I74_D1.3110.93
44_V48_G1.2940.93
29_L77_D1.2310.90
39_V78_L1.2300.90
62_D66_E1.1960.88
51_D57_P1.1800.87
48_G52_R1.1580.86
42_A66_E1.1390.85
44_V50_E1.1340.84
9_P34_T1.1270.84
16_S23_I1.1080.82
43_K53_P1.1080.82
39_V79_T1.1060.82
37_S65_F1.1050.82
18_I23_I1.0950.81
12_G24_R1.0900.81
46_S60_P1.0890.81
19_S24_R1.0700.79
23_I46_S1.0660.79
21_A71_R1.0610.78
46_S71_R1.0610.78
75_I81_C1.0560.78
40_A67_Y1.0520.77
38_T41_L1.0420.77
66_E74_D1.0290.75
9_P80_V1.0180.74
30_Y81_C1.0140.74
15_I24_R1.0040.73
30_Y69_I1.0030.73
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  
2fb7A10.90911000.019Contact Map
2vxeA10.98861000.069Contact Map
4a53A10.772799.60.539Contact Map
2vc8A10.784199.20.639Contact Map
2rm4A10.8636970.798Contact Map
3pgwB20.965995.70.822Contact Map
1y96A20.829595.10.83Contact Map
3pggA20.8636930.845Contact Map
4emkA10.806892.50.847Contact Map
4c92E10.931892.10.85Contact 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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