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Fti4_1

ID: 1516554484 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 74 (57)
Sequences: 304 (247.1)
Seq/Len: 5.333
Nf(neff/√len): 32.7

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: 5.333).

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
52_R57_Q3.2311.00
21_T24_E2.4671.00
50_G54_L1.9401.00
20_L24_E1.8451.00
42_L47_I1.7791.00
43_N46_D1.5330.99
32_I42_L1.5150.99
32_I47_I1.5040.99
32_I35_Y1.4330.98
39_N42_L1.4220.98
28_I54_L1.3860.98
53_I68_K1.3390.97
45_D56_G1.2310.94
35_Y40_M1.2200.94
49_A66_K1.2060.93
35_Y43_N1.1720.92
62_E65_L1.1440.91
34_N38_E1.1270.90
33_G42_L1.1120.89
48_L52_R1.0780.87
40_M46_D1.0770.87
61_Q65_L1.0690.86
49_A58_A1.0430.84
53_I58_A1.0260.83
30_S34_N1.0210.83
27_S65_L1.0130.82
25_Y32_I1.0130.82
49_A63_E1.0020.81
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  
3shgB10.810898.10.596Contact Map
4ociA10.797336.50.85Contact Map
3cucA20.945932.90.854Contact Map
4mzjA10.918930.20.857Contact Map
4m70R10.0811230.865Contact Map
2h2kA20.97320.90.867Contact Map
1ggwA10.878418.50.87Contact Map
3j04B20.905417.50.872Contact Map
2kz2A10.905417.50.872Contact Map
3a1kA10.716217.10.872Contact 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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