GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
leafs_1ptf_fastRelax_31

ID: 1507536452 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (87)
Sequences: 467 (232.4)
Seq/Len: 5.368
Nf(neff/√len): 24.9

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: 5.368).

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
38_N59_Q5.9501.00
16_D20_R4.3191.00
29_F76_T3.1391.00
42_I64_V2.5731.00
10_A18_Y2.0581.00
7_I60_T1.7271.00
25_D80_I1.6881.00
64_V80_I1.6661.00
14_I50_I1.6250.99
2_A71_W1.5990.99
3_V62_I1.5880.99
2_A74_F1.4710.98
25_D28_R1.3920.98
41_R64_V1.3140.96
4_L38_N1.2190.94
48_E52_N1.2150.94
21_I84_H1.1900.93
6_I77_L1.1580.91
12_D16_D1.1530.91
50_I64_V1.1410.91
30_K68_K1.1320.90
26_A29_F1.1210.90
78_L82_R1.1020.88
9_I16_D1.1010.88
3_V56_P1.0990.88
15_R40_S1.0900.88
20_R50_I1.0510.85
12_D68_K1.0450.85
38_N42_I1.0450.85
56_P68_K1.0430.84
7_I85_R1.0420.84
3_V51_H1.0240.83
68_K78_L1.0200.83
12_D51_H1.0150.82
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  
3ccdA20.97793.10.868Contact Map
1pchA10.9885930.868Contact Map
1ka5A11930.869Contact Map
1kklH3192.90.869Contact Map
1ptfA1191.80.873Contact Map
3ihsA20.942591.80.873Contact Map
1y51A30.9885910.876Contact Map
1sphA20.988590.80.876Contact Map
3le1A20.988587.20.884Contact Map
4wlrA10.59774.70.947Contact 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.

Page generated in 0.0152 seconds.