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Adhiron

ID: 1515596981 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 73 (73)
Sequences: 1525 (1115.9)
Seq/Len: 20.890
Nf(neff/√len): 130.6

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: 20.890).

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
28_E47_K3.1611.00
33_T43_E2.6761.00
34_Q40_F2.3401.00
60_K65_E2.3061.00
41_I58_W2.1911.00
9_F26_F2.1691.00
15_L18_Q1.9921.00
9_F44_G1.9271.00
31_T45_V1.6621.00
60_K63_N1.6431.00
35_Q41_I1.6171.00
24_L48_T1.5981.00
5_V32_A1.5401.00
32_A44_G1.5281.00
27_V49_N1.4030.99
54_K72_E1.4010.99
4_H59_C1.3930.99
26_F46_V1.3550.99
9_F13_V1.3350.99
5_V8_A1.3250.99
30_I47_K1.3160.99
41_I56_K1.3060.99
41_I69_Q1.3040.99
58_W65_E1.2800.99
36_V40_F1.2750.99
37_V41_I1.2730.99
16_A20_N1.2560.99
59_C66_K1.2280.98
8_A59_C1.2100.98
15_L68_L1.1880.98
13_V17_N1.1670.97
56_K72_E1.0860.96
39_G58_W1.0860.96
11_D68_L1.0530.95
30_I52_D1.0370.94
4_H8_A1.0340.94
27_V47_K1.0180.93
2_D6_I1.0120.93
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  
3ul5A4199.50.011Contact Map
2l4vA1199.50.012Contact Map
1eqkA1199.50.017Contact Map
5a0oB2099.40.047Contact Map
4n6tA1199.40.053Contact Map
3imaB20.986399.40.055Contact Map
4lziA1199.40.056Contact Map
2kxgA10.972699.40.085Contact Map
3gaxA2199.30.12Contact Map
4n6oB1199.30.121Contact 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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