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contact-prediction-test

ID: 1506308976 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 63 (63)
Sequences: 2100 (1325.3)
Seq/Len: 33.333
Nf(neff/√len): 167.0

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: 33.333).

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
8_Y56_A2.8031.00
16_L59_V2.2411.00
12_V59_V2.2281.00
9_N22_P2.2211.00
9_N21_E1.9651.00
10_N13_R1.9561.00
9_N23_A1.7671.00
13_R19_D1.7401.00
7_E53_L1.5111.00
38_I42_L1.4931.00
32_G41_V1.3940.99
2_R42_L1.3770.99
16_L63_A1.3210.99
58_Q62_K1.2910.99
8_Y52_Y1.2860.99
29_D42_L1.2760.99
1_R54_D1.2650.99
6_A10_N1.2230.98
25_N55_A1.2130.98
1_R7_E1.1950.98
2_R29_D1.1840.98
58_Q61_A1.1620.97
27_P48_L1.1560.97
51_K54_D1.1370.97
4_N36_D1.1210.97
44_V49_V1.1210.97
32_G43_S1.0950.96
47_L50_E1.0820.96
57_E60_A1.0790.95
25_N58_Q1.0580.95
9_N26_F1.0490.94
5_R28_S1.0240.93
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  
2ijaA10.555621.90.82Contact Map
4nv8A20.571410.80.843Contact Map
3lnbA10.30169.10.848Contact Map
4guzA40.55568.10.851Contact Map
3pukA20.984180.852Contact Map
3ayfA10.88897.60.853Contact Map
4h0nA40.79376.90.856Contact Map
3d9wA40.57146.20.859Contact Map
1e2tA80.6196.10.86Contact Map
1xrsA10.41275.50.862Contact 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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