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SH3

ID: 1518203456 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 68 (60)
Sequences: 7942 (4551.2)
Seq/Len: 132.367
Nf(neff/√len): 587.6

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: 132.367).

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
13_A20_T3.3261.00
39_L48_K2.7971.00
40_G51_F2.7851.00
7_A21_F2.7841.00
10_D22_K2.4951.00
28_I41_E2.4071.00
31_E39_L2.3921.00
41_E48_K2.2991.00
51_F56_V2.2331.00
3_P32_F2.1531.00
25_D42_L2.1101.00
4_W26_K1.9741.00
6_T57_S1.7291.00
4_W28_I1.7251.00
21_F27_I1.5151.00
38_W53_S1.4201.00
42_L45_D1.3870.99
10_D23_E1.3860.99
6_T26_K1.3760.99
5_A58_L1.3730.99
22_K25_D1.3550.99
8_L57_S1.3550.99
27_I40_G1.3510.99
42_L47_S1.3320.99
5_A29_N1.3090.99
49_G52_P1.2590.99
3_P58_L1.1850.98
26_K59_G1.1310.97
52_P55_Y1.0860.96
5_A56_V1.0800.95
19_L40_G1.0760.95
12_D20_T1.0600.95
30_I41_E1.0530.95
32_F38_W1.0520.95
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  
4n78F1099.2-0.069Contact Map
1fmkA1199.2-0.036Contact Map
2h8hA10.955999.1-0.028Contact Map
2dvjA10.985399.1-0.021Contact Map
1mv3A10.882499.1-0.016Contact Map
4xi2A10.985399.1-0.015Contact Map
3pvlA10.955999.1-0.013Contact Map
1ri9A10.838299.1-0.01Contact Map
4mt7A1099.1-0.009Contact Map
2pz1A10.882499.1-0.008Contact 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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