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AntF_4

ID: 1515687455 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 56 (55)
Sequences: 98 (57.5)
Seq/Len: 1.782
Nf(neff/√len): 7.8

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: 1.782).

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
5_S8_T1.9740.98
21_Y25_L1.9520.98
45_E52_T1.8540.97
17_R25_L1.6860.95
14_A17_R1.5410.91
40_K50_A1.5040.89
30_F40_K1.4350.86
4_V12_Y1.4080.85
13_A51_F1.2580.75
14_A21_Y1.2480.74
43_T55_R1.2360.73
8_T22_A1.2230.72
10_K21_Y1.2110.70
33_T53_Q1.2050.70
6_L22_A1.1740.67
38_E43_T1.1740.67
3_N21_Y1.1450.64
4_V28_E1.1270.62
11_A19_S1.1240.62
2_G7_E1.1030.60
43_T53_Q1.0940.59
5_S13_A1.0940.59
34_F48_L1.0810.58
17_R23_A1.0680.56
48_L52_T1.0580.55
47_V51_F1.0570.55
49_K53_Q1.0220.51
2_G55_R1.0200.51
19_S23_A1.0120.50
9_K12_Y1.0100.50
43_T46_E1.0060.50
12_Y16_T1.0040.49
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  
3shgB10.928615.20.862Contact Map
3cucA2110.70.871Contact Map
3zs9C20.57146.20.884Contact Map
1o1zA10.57145.60.886Contact Map
2avuE20.96435.50.887Contact Map
3hc1A10.3754.70.891Contact Map
2m09A10.98214.50.892Contact Map
2hepA10.39294.40.893Contact Map
1zdaA10.33934.30.893Contact Map
1w4tA10.73214.20.893Contact 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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