GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
3oss

ID: 1501759490 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 65 (61)
Sequences: 520 (511)
Seq/Len: 8.525
Nf(neff/√len): 65.4

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: 8.525).

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 > 50% 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
8_L19_A2.3811.00
43_I46_I2.3681.00
44_E54_R2.2851.00
43_I51_V2.1871.00
8_L11_I1.8611.00
50_H61_R1.8611.00
10_G20_V1.8031.00
4_L60_E1.7691.00
7_V22_E1.5931.00
42_V54_R1.4230.99
41_A51_V1.3860.99
40_N55_Y1.3800.99
54_R59_I1.3320.99
45_E52_M1.2710.98
44_E59_I1.2260.98
46_I51_V1.2230.98
29_V41_A1.2220.98
10_G13_F1.1920.97
43_I53_L1.1850.97
47_N50_H1.1810.97
31_L43_I1.1750.97
41_A60_E1.1690.97
36_L51_V1.1530.96
35_R61_R1.1470.96
12_A64_L1.1330.96
55_Y60_E1.1180.95
11_I19_A1.1020.95
42_V57_G1.0830.94
20_V29_V1.0760.94
35_R42_V1.0690.93
5_N45_E1.0610.93
30_Y43_I1.0120.91
6_V57_G1.0100.91
27_Q34_E1.0020.90
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  
3ossC1198.90.079Contact Map
2lnvA1198.80.106Contact Map
4av2M12197.10.406Contact Map
2lc4A1195.50.495Contact Map
2ivwA1195.50.496Contact Map
2y4xA20.984695.20.504Contact Map
1vw4N10.876924.10.752Contact Map
2zjrO10.630818.10.766Contact Map
4rb6V10.661512.20.784Contact Map
3j3wR10.676911.60.786Contact 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 0.0314 seconds.