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pengfei tian

ID: 1447779671 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 56 (56)
Sequences: 3750 (3750)
Seq/Len: 66.964
Nf(neff/√len): 501.1

HHblits Results: (2015_06)
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: 66.964).

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
32_L53_T1.7691.00
21_V30_F1.6501.00
10_K26_A1.6221.00
17_I30_F1.5071.00
36_A50_K1.4721.00
38_T45_Y1.4481.00
10_K16_A1.4331.00
6_I48_E1.4311.00
33_I44_T1.4251.00
8_N11_Q1.4231.00
7_L44_T1.2840.99
27_E38_T1.2100.98
34_A54_V1.1980.98
26_A46_K1.1920.98
23_A40_E1.1800.98
22_D27_E1.1700.97
14_E44_T1.1660.97
5_L21_V1.1610.97
42_V52_F1.1600.97
20_L54_V1.1550.97
38_T43_W1.1510.97
46_K49_I1.1470.97
8_N52_F1.1260.97
10_K20_L1.1100.96
8_N20_L1.1100.96
11_Q15_E1.0930.96
15_E33_I1.0700.95
17_I32_L1.0670.95
24_G51_T1.0350.94
2_T36_A1.0270.94
38_T47_D1.0180.93
11_Q46_K1.0150.93
15_E44_T1.0040.93
8_N49_I1.0040.93
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  
2jwsA1196.50.241Contact Map
2fs1A1196.50.241Contact Map
2j5yA20.964393.70.367Contact Map
1gjsA10.964392.90.384Contact Map
1pgxA1118.80.676Contact Map
1pn5A1016.40.685Contact Map
1igdA1113.30.698Contact Map
2rpvA11120.704Contact Map
2khuA109.90.715Contact Map
3ui3A20.82147.80.728Contact 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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