GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
student

ID: 1504548454 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 71 (68)
Sequences: 607 (529.6)
Seq/Len: 8.926
Nf(neff/√len): 64.2

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: 8.926).

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
17_S49_S4.2671.00
21_V53_G3.2821.00
23_L55_L3.1121.00
24_K56_K2.4331.00
25_R57_R2.4191.00
28_L60_L2.2161.00
18_T50_T1.9551.00
10_N16_N1.8911.00
4_K38_N1.8051.00
29_R61_K1.7891.00
39_A47_V1.7521.00
20_A59_I1.4841.00
11_D35_N1.4541.00
56_K60_L1.3510.99
22_A54_I1.3270.99
43_E66_L1.2250.98
40_D44_D1.1940.97
63_I66_L1.1870.97
15_V58_Y1.1790.97
52_L56_K1.1670.97
26_Y36_T1.1650.97
15_V55_L1.1620.97
9_V23_L1.1470.96
27_V59_I1.1400.96
57_R62_E1.1220.96
66_L69_K1.1220.96
20_A24_K1.1170.96
20_A52_L1.1050.95
34_I38_N1.1050.95
14_K46_R1.1010.95
27_V52_L1.0870.95
16_N48_N1.0590.94
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  
1daqA1199.7-0.002Contact Map
2yikA1099.60.031Contact Map
4cj0A1099.60.065Contact Map
4fl4A40.901499.50.098Contact Map
4uypB20.971899.50.104Contact Map
2y3nB20.845199.50.107Contact Map
4dh2B20.957799.50.11Contact Map
2vn6B10.901499.50.13Contact Map
3kcpA10.929699.30.203Contact Map
2cclB20.845199.30.214Contact 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 0.0221 seconds.