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Adhiron2

ID: 1515599285 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (79)
Sequences: 1797 (1316.4)
Seq/Len: 22.747
Nf(neff/√len): 148.1

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: 22.747).

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
29_R48_E3.1141.00
34_K44_Y2.5691.00
16_E19_K2.1861.00
32_K46_T2.1701.00
65_K70_F2.0821.00
35_E41_T2.0201.00
42_M61_K2.0161.00
65_K68_E2.0011.00
58_Y78_P1.9321.00
10_A27_F1.8391.00
42_M63_W1.6591.00
10_A45_L1.6531.00
33_A45_L1.6481.00
28_V50_K1.6311.00
5_E64_V1.5741.00
63_W70_F1.5401.00
6_I33_A1.5031.00
42_M74_Q1.5001.00
31_V57_L1.4791.00
36_Q42_M1.4791.00
25_L49_A1.4681.00
64_V71_K1.4311.00
47_L60_A1.4251.00
17_H21_E1.3580.99
46_T59_E1.3510.99
31_V48_E1.2830.99
27_F47_L1.2560.99
17_H60_A1.2460.98
38_V42_M1.2400.98
16_E73_L1.2250.98
25_L58_Y1.2190.98
10_A14_V1.1930.98
49_A60_A1.1710.98
14_V18_N1.1590.97
6_I9_L1.1130.96
39_A65_K1.0980.96
3_S7_E1.0810.95
16_E20_K1.0640.95
44_Y59_E1.0550.95
12_F73_L1.0350.94
61_K75_E1.0100.93
28_V55_K1.0080.93
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  
2l4vA1199.7-0.037Contact Map
3ul5A4199.7-0.023Contact Map
1eqkA1199.6-0.009Contact Map
3imaB20.974799.60.005Contact Map
4n6tA1199.60.012Contact Map
4lziA1199.60.02Contact Map
5a0oB2099.60.038Contact Map
2kxgA10.974799.50.075Contact Map
3gaxA2199.50.081Contact Map
4n6oB1199.50.087Contact 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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