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d3zijb_

ID: 1447475755 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 73 (73)
Sequences: 16603 (9281.9)
Seq/Len: 227.438
Nf(neff/√len): 1086.4

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: 227.438).

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
6_T29_E2.9141.00
16_V54_V2.5741.00
17_K29_E2.2891.00
56_I72_L1.8521.00
65_Q68_K1.7821.00
32_V51_T1.7381.00
22_H66_I1.6821.00
9_D33_K1.6761.00
55_V60_V1.6371.00
8_P31_D1.6201.00
3_E28_E1.5891.00
66_I70_Q1.5781.00
61_V65_Q1.5681.00
23_N70_Q1.5301.00
68_K71_Q1.4701.00
31_D34_K1.4701.00
21_K27_Y1.4561.00
46_Y55_V1.4451.00
16_V64_F1.4381.00
3_E30_F1.3850.99
2_I56_I1.3740.99
20_L27_Y1.3620.99
48_S53_T1.3610.99
19_F23_N1.3410.99
10_C13_C1.3330.99
12_P15_I1.3320.99
16_V69_L1.3320.99
19_F22_H1.3000.99
38_A41_R1.2300.98
8_P33_K1.2110.98
5_Y55_V1.2010.98
61_V72_L1.1790.98
4_V29_E1.1700.97
41_R45_D1.1610.97
53_T60_V1.1320.97
19_F66_I1.1060.96
18_E22_H1.0950.96
68_K72_L1.0640.95
7_Q51_T1.0630.95
5_Y32_V1.0530.95
19_F64_F1.0480.94
35_D38_A1.0340.94
4_V54_V1.0250.93
67_E71_Q1.0150.93
7_Q33_K1.0150.93
15_I64_F1.0130.93
41_R44_Y1.0060.93
16_V65_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  
4k8mA10.986399.30.085Contact Map
1u6tA1199.30.087Contact Map
2wciA2199.30.098Contact Map
3l4nA1199.30.109Contact Map
4mjeA1199.30.111Contact Map
2ht9A2199.20.119Contact Map
2ct6A1199.20.12Contact Map
3zitA2199.20.121Contact Map
2jadA1199.20.122Contact Map
2ltkA1199.20.127Contact 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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