GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
SubBPNPro

ID: 1513643764 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 77 (75)
Sequences: 2367 (1920.2)
Seq/Len: 31.560
Nf(neff/√len): 221.7

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: 31.560).

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
13_G67_Y4.4861.00
9_K71_D3.4851.00
15_K66_A3.1851.00
5_N70_E3.0221.00
56_V60_K2.4961.00
13_G66_A2.1011.00
8_K70_E2.0381.00
57_K60_K2.0091.00
9_K50_T2.0091.00
56_V68_V1.9191.00
26_K47_A1.8731.00
52_N55_A1.7681.00
40_Q48_S1.6571.00
71_D74_A1.6521.00
56_V59_L1.5361.00
26_K30_I1.4441.00
9_K38_Q1.4361.00
59_L68_V1.3920.99
19_S22_S1.3890.99
14_F47_A1.3470.99
51_L56_V1.2800.99
9_K48_S1.2510.99
65_V68_V1.2460.98
38_Q48_S1.2170.98
4_S75_H1.2070.98
8_K53_E1.1660.97
13_G44_V1.1070.96
58_E61_K1.0830.96
39_K48_S1.0440.94
57_K61_K1.0320.94
25_K28_D1.0290.94
6_G73_V1.0230.93
13_G16_Q1.0150.93
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  
4nmxA11990.061Contact Map
1v5iB10.9351990.064Contact Map
2w2nP11990.078Contact Map
3cnqP10.896198.90.089Contact Map
2z30B10.844298.70.157Contact Map
3whiA20.935198.70.179Contact Map
2p4eP2198.50.229Contact Map
3afgA20.96197.80.354Contact Map
3wiuA30.857197.70.364Contact Map
3t41A20.870196.90.447Contact 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 0.0414 seconds.