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OPENSEQ.org

hdv_gremlin

ID: 1477405816 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 31 (31)
Sequences: 74 (15.9)
Seq/Len: 2.387
Nf(neff/√len): 2.9

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: 2.387).

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
5_I19_A2.0240.99
10_G20_D1.7570.98
22_P27_S1.6440.97
11_F28_C1.6230.96
1_E21_P1.5730.95
6_R9_R1.5280.94
8_N18_P1.5040.94
3_L6_R1.4510.92
6_R18_P1.3840.89
24_S27_S1.3510.88
13_W18_P1.2120.79
6_R11_F1.2090.78
23_F30_P1.1940.77
23_F26_Q1.1920.77
23_F27_S1.1680.75
11_F17_F1.1610.74
8_N13_W1.1010.69
22_P25_P1.0900.67
6_R13_W1.0480.63
1_E13_W1.0160.59
9_R13_W1.0040.58
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  
1ro2A10.8715.20.847Contact Map
3m1mA10.8714.60.851Contact Map
1m1jA20.16133.40.86Contact Map
3swjA10.83872.50.869Contact Map
4a15A10.70972.40.87Contact Map
4bnqA212.40.87Contact Map
3dwlE20.12920.876Contact Map
3sopA20.83871.80.879Contact Map
4l0yA101.80.879Contact Map
1q1qA10.32261.60.883Contact 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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