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OPENSEQ.org

HAB_-17_-16

ID: 1447310980 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 56 (56)
Sequences: 990 (990)
Seq/Len: 17.679
Nf(neff/√len): 132.3

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: 17.679).

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
44_T51_T1.7081.00
12_A43_W1.6821.00
33_I52_F1.6181.00
1_T18_K1.2980.99
31_K34_A1.2860.99
33_I56_E1.2170.98
25_I52_F1.1960.98
3_Y19_E1.1870.98
46_K54_V1.1780.98
17_I38_T1.1640.97
3_Y47_D1.1640.97
38_T52_F1.1590.97
14_E21_V1.1560.97
24_G28_K1.1410.97
30_F35_N1.1140.96
27_E39_V1.1140.96
36_A44_T1.1030.96
2_T42_V1.0960.96
7_L15_E1.0900.96
1_T46_K1.0760.95
13_K35_N1.0750.95
4_K44_T1.0690.95
29_Y45_Y1.0660.95
50_K55_T1.0660.95
31_K35_N1.0620.95
12_A29_Y1.0600.95
32_L49_I1.0520.95
22_D40_E1.0450.94
19_E54_V1.0400.94
5_L46_K1.0300.94
6_I16_A1.0270.94
2_T10_K1.0110.93
10_K54_V1.0100.93
10_K15_E1.0040.93
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  
2fs1A1178.2-0.043Contact Map
2jwsA1143.10.169Contact Map
1gjsA10.964335.40.209Contact Map
2j5yA20.964327.60.249Contact Map
2es9A10.82140.60.687Contact Map
1pn5A100.50.706Contact Map
3jszA10.94640.50.712Contact Map
2dgjA20.94640.40.721Contact Map
1vx7L10.46430.40.727Contact Map
1s2xA110.40.727Contact 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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