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ID: 1518193630 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 56 (48)
Sequences: 1501 (1219.1)
Seq/Len: 31.271
Nf(neff/√len): 176.0

Jackhmmer Results: (2016_04)
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: 31.271).

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
15_L29_I3.0071.00
11_F33_K2.9771.00
21_N24_Q2.3021.00
26_N30_Q2.2801.00
22_A26_N2.2691.00
30_Q34_D2.1631.00
31_S45_E1.7051.00
14_V32_L1.6761.00
19_N50_N1.6141.00
37_S40_A1.5551.00
27_G31_S1.5511.00
8_Q12_Y1.4701.00
28_F49_L1.4491.00
27_G30_Q1.3750.99
6_A38_Q1.3170.99
13_Q47_Q1.3130.99
28_F42_V1.3090.99
44_G48_K1.3060.99
5_E9_N1.2980.99
41_N44_G1.2820.99
12_Y16_N1.1290.97
42_V45_E1.0680.95
9_N12_Y1.0650.95
43_L47_Q1.0500.94
5_E8_Q1.0210.93
11_F29_I1.0160.93
10_A43_L1.0130.93
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  
4gwpC1098.50.266Contact Map
2kziA1198.20.312Contact Map
3qwoC20.9464980.349Contact Map
4npfY2197.90.372Contact Map
2lr2A1197.80.379Contact Map
4npdA1197.70.392Contact Map
4kjmA20.910797.20.447Contact Map
1zxgA1197.10.452Contact Map
2dgjA20.892994.60.561Contact Map
1zdaA10.62589.90.622Contact 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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