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Adhiron2

ID: 1515340367 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 79 (79)
Sequences: 1820 (1328.4)
Seq/Len: 23.038
Nf(neff/√len): 149.5

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: 23.038).

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_E3.3121.00
34_K44_Y2.2011.00
42_M61_K2.0661.00
16_E19_K2.0451.00
58_Y78_P2.0411.00
35_E41_T2.0151.00
47_L60_A1.9971.00
42_M63_W1.9211.00
10_A27_F1.8341.00
65_K70_F1.8221.00
32_K46_T1.7931.00
10_A45_L1.7571.00
65_K68_E1.7201.00
36_Q42_M1.6521.00
17_H60_A1.6271.00
33_A45_L1.6151.00
6_I33_A1.4981.00
5_E64_V1.4581.00
63_W70_F1.4441.00
28_V50_K1.4321.00
42_M74_Q1.3910.99
17_H21_E1.3750.99
25_L49_A1.3650.99
31_V57_L1.3580.99
16_E73_L1.3450.99
49_A58_Y1.3160.99
38_V42_M1.2940.99
64_V71_K1.2880.99
27_F47_L1.2620.99
31_V48_E1.2240.98
46_T59_E1.2090.98
25_L58_Y1.1760.98
45_L62_V1.1720.98
9_L62_V1.1570.97
14_V18_N1.1510.97
9_L64_V1.1160.96
10_A14_V1.1100.96
44_Y59_E1.1020.96
45_L60_A1.0880.96
12_F73_L1.0870.96
13_A60_A1.0810.95
37_V41_T1.0380.94
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  
2l4vA1199.7-0.056Contact Map
3ul5A4199.6-0.045Contact Map
1eqkA1199.6-0.029Contact Map
3imaB20.974799.6-0.014Contact Map
4lziA1199.6-0.007Contact Map
4n6tA1199.6-0.005Contact Map
5a0oB2099.60.015Contact Map
2kxgA10.974799.50.048Contact Map
3gaxA2199.50.063Contact Map
4n6oB1199.50.071Contact 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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