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leafs_1ptf_fastRelax_28

ID: 1507536426 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 452 (201.8)
Seq/Len: 5.195
Nf(neff/√len): 21.6

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: 5.195).

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
23_A49_E2.4241.00
1_P41_R2.2591.00
42_V65_I1.9361.00
30_E68_P1.8781.00
21_L84_F1.8131.00
4_Y78_I1.7661.00
4_Y36_D1.6730.99
32_L81_Y1.6170.99
34_L44_V1.5990.99
34_L42_V1.5930.99
36_D41_R1.5550.99
72_E75_T1.4610.98
10_A57_P1.4440.98
3_I12_R1.4400.98
4_Y8_V1.4150.98
8_V55_L1.3970.98
10_A36_D1.3830.97
4_Y40_I1.3490.97
25_T52_L1.3310.96
34_L66_S1.3260.96
18_Y59_V1.3080.96
10_A17_E1.2740.95
53_L60_I1.2560.95
1_P10_A1.2470.94
38_D53_L1.2140.93
11_E77_L1.2110.93
25_T65_I1.1630.91
3_I83_Y1.1530.91
70_A74_L1.1510.91
36_D85_Q1.1350.90
20_M61_V1.1250.89
37_L60_I1.1200.89
24_I29_Y1.1180.89
1_P64_L1.1170.89
7_T10_A1.1170.89
10_A41_R1.1020.88
10_A81_Y1.0970.88
53_L59_V1.0850.87
9_R68_P1.0840.87
29_Y32_L1.0820.87
32_L74_L1.0720.86
2_L74_L1.0560.85
29_Y71_E1.0410.84
10_A44_V1.0210.82
8_V38_D1.0180.82
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  
3ccdA20.97794.40.849Contact Map
1ka5A1194.30.85Contact Map
1ptfA1194.30.85Contact Map
1kklH3194.10.851Contact Map
3ihsA20.942593.90.852Contact Map
1y51A30.988593.30.856Contact Map
1sphA20.988592.90.858Contact Map
3le1A20.988592.20.861Contact Map
1pchA10.988589.40.87Contact Map
1u02A10.59773.60.946Contact 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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