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OPENSEQ.org

5t1y

ID: 1504882499 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 118 (86)
Sequences: 5140 (3482.3)
Seq/Len: 59.767
Nf(neff/√len): 375.5

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: 59.767).

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 > 50% 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
46_I58_S3.3961.00
43_A62_L3.2381.00
36_K66_E2.8071.00
62_L66_E2.4411.00
8_N11_P2.3261.00
39_E62_L2.1071.00
84_Q87_G1.9771.00
40_S59_Q1.8001.00
47_K57_D1.7331.00
83_V86_D1.7081.00
72_Y76_D1.6971.00
39_E66_E1.6531.00
39_E65_D1.6491.00
35_G39_E1.5671.00
40_S62_L1.3510.99
22_K25_K1.3370.99
34_L74_I1.3080.99
48_I64_A1.3080.99
15_E19_E1.2970.99
30_N33_D1.2920.99
33_D37_E1.2020.98
72_Y75_E1.1710.98
47_K58_S1.1600.97
52_P55_Q1.1120.96
20_E24_H1.0920.96
60_D63_W1.0730.95
19_E22_K1.0610.95
27_V81_F1.0500.94
37_E40_S1.0450.94
12_K15_E1.0420.94
21_F24_H1.0350.94
63_W67_V1.0130.93
31_I37_E1.0100.93
8_N12_K1.0090.93
17_L20_E1.0050.93
80_K84_Q1.0040.93
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  
3qflA10.932299.5-0.035Contact Map
4btfA10.82222.20.794Contact Map
2msvA10.8397.60.833Contact Map
4m70A50.83055.60.843Contact Map
3a7pA20.74585.40.844Contact Map
4k1pA80.64413.50.858Contact Map
4qkwA30.83930.862Contact Map
4qkvA30.80512.70.865Contact Map
1vcsA10.78812.20.872Contact Map
3wqyA20.584720.875Contact 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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