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leafs_1ptf_fastRelax_7

ID: 1507536227 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 505 (377.6)
Seq/Len: 5.805
Nf(neff/√len): 40.5

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: 5.805).

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_R68_D3.2181.00
44_I77_V2.2411.00
2_A71_R2.1941.00
38_D56_Y2.0451.00
79_I83_S1.8421.00
25_L83_S1.7401.00
34_L77_V1.7291.00
7_V60_V1.6280.99
14_P66_F1.6020.99
8_V80_A1.5710.99
44_I61_L1.5470.99
10_L18_F1.5390.99
33_F70_A1.5170.99
21_I47_W1.4570.99
40_Y54_P1.4370.98
20_A47_W1.3750.98
4_D21_I1.3670.98
54_P62_L1.3570.98
46_I49_D1.3320.97
14_P85_L1.2410.95
7_V53_F1.2170.95
36_H40_Y1.2100.94
4_D78_R1.1870.94
33_F83_S1.1810.93
46_I84_H1.1640.93
25_L39_S1.1610.93
33_F40_Y1.1450.92
6_F24_R1.1300.91
70_A82_L1.1130.90
29_H83_S1.0970.89
18_F83_S1.0880.89
25_L84_H1.0860.89
46_I82_L1.0580.87
14_P84_H1.0470.86
11_L48_L1.0380.86
78_R82_L1.0310.85
29_H81_F1.0290.85
25_L28_L1.0290.85
3_L23_A1.0260.85
42_I71_R1.0240.85
25_L36_H1.0180.84
60_V78_R1.0090.83
15_L29_H1.0030.83
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  
1pchA10.988570.90.886Contact Map
1kklH3170.90.886Contact Map
1ka5A1163.40.892Contact Map
1ptfA11620.893Contact Map
1sphA20.988557.30.896Contact Map
3ccdA20.97756.90.896Contact Map
1y51A30.988555.70.897Contact Map
3ihsA20.90849.40.9Contact Map
3le1A20.988542.10.904Contact Map
2q8nA30.9772.30.948Contact 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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