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

ID: 1500381169 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 65 (64)
Sequences: 941 (761.5)
Seq/Len: 14.703
Nf(neff/√len): 95.2

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: 14.703).

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
43_I46_I3.2541.00
44_E54_R2.5211.00
50_H61_R2.3031.00
8_L19_A2.2441.00
43_I51_V1.9771.00
44_E59_I1.9511.00
42_V54_R1.8831.00
8_L11_I1.8471.00
10_G20_V1.7761.00
41_A51_V1.7321.00
4_L60_E1.5351.00
47_N50_H1.4411.00
21_I51_V1.3630.99
55_Y60_E1.3570.99
52_M61_R1.3080.99
7_V22_E1.3070.99
6_V21_I1.2740.99
46_I51_V1.2200.98
40_N55_Y1.1570.97
11_I19_A1.1210.97
47_N52_M1.1090.96
54_R59_I1.0880.96
30_Y34_E1.0690.95
22_E39_H1.0630.95
32_Q45_E1.0540.95
17_P32_Q1.0530.95
21_I41_A1.0400.94
8_L51_V1.0260.94
54_R57_G1.0140.93
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  
3ossC11990.033Contact Map
2lnvA1198.90.057Contact Map
4av2M12196.70.433Contact Map
2ivwA1194.30.525Contact Map
2lc4A1194.30.525Contact Map
2y4xA20.984694.10.529Contact Map
1vw4N10.876916.80.768Contact Map
2zjrO10.610.20.789Contact Map
4rb6V10.66157.90.8Contact Map
3j3wR10.67697.60.801Contact 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 0.0309 seconds.