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blast alignment fixed

ID: 1515171797 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (79)
Sequences: 1714 (1262.4)
Seq/Len: 21.696
Nf(neff/√len): 142.0

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: 21.696).

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
31_V50_K3.2411.00
19_K22_N2.4851.00
59_E79_V2.4531.00
13_A29_R2.3691.00
36_Q46_T2.3671.00
66_P71_K2.2141.00
8_E65_K2.1641.00
37_V43_Y2.1121.00
34_K48_E1.9791.00
66_P69_N1.9721.00
44_Y62_V1.9211.00
44_Y75_E1.7201.00
64_V71_K1.6901.00
33_A58_Y1.5721.00
44_Y64_V1.5181.00
41_T66_P1.4601.00
35_E47_L1.4461.00
33_A50_K1.3780.99
48_E60_A1.3660.99
19_K74_Q1.3620.99
38_V42_M1.3510.99
9_L35_E1.3290.99
13_A47_L1.2710.99
30_V52_G1.2580.99
49_A61_K1.2430.98
27_F51_D1.2260.98
40_G44_Y1.2050.98
14_V18_N1.1960.98
74_Q77_K1.1750.98
12_F65_K1.1740.98
46_T60_A1.1560.97
13_A17_H1.1040.96
10_A14_V1.0910.96
17_H21_E1.0840.96
38_V44_Y1.0810.95
41_T68_E1.0590.95
17_H20_K1.0400.94
51_D59_E1.0250.93
30_V56_K1.0170.93
29_R49_A1.0040.93
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  
3ul5A40.974799.60.067Contact Map
2l4vA1199.60.074Contact Map
1eqkA1199.60.085Contact Map
4lziA1199.60.096Contact Map
3imaB20.936799.50.108Contact Map
5a0oB2099.50.113Contact Map
2kxgA10.96299.50.124Contact Map
4n6tA10.96299.50.124Contact Map
1roaA10.987399.50.128Contact Map
3gaxA20.987399.50.133Contact 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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