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1CRN

ID: 1515662834 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 46 (46)
Sequences: 114 (85.8)
Seq/Len: 2.478
Nf(neff/√len): 12.7

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: 2.478).

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
12_N30_T4.8351.00
5_P31_G2.3641.00
41_P45_A1.9630.99
5_P30_T1.7380.98
18_L21_T1.5710.96
14_N17_R1.5430.95
40_C44_Y1.4960.94
12_N15_V1.4080.91
27_A34_I1.3170.86
10_R32_C1.3040.86
15_V42_G1.2990.85
1_T41_P1.2850.85
6_S46_N1.2320.81
4_C10_R1.1670.76
11_S17_R1.1670.76
21_T34_I1.1130.71
40_C43_D1.0890.68
5_P46_N1.0840.68
25_I44_Y1.0780.67
4_C40_C1.0630.66
17_R20_G1.0330.63
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  
2v9bA2199.60.008Contact Map
1nblA1199.60.013Contact Map
1bhpA10.978399.60.025Contact Map
3nirA10.956599.50.068Contact Map
2llrA10.478360.858Contact Map
3q9kA10.43483.90.871Contact Map
1bdsA10.56522.50.883Contact Map
1wxnA10.565220.889Contact Map
1wqkA10.56521.90.89Contact Map
3gf8A10.15221.60.895Contact 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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