GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
ParB_Ct

ID: 1515153819 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 69 (55)
Sequences: 302 (201.1)
Seq/Len: 5.491
Nf(neff/√len): 27.1

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: 5.491).

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
32_F64_L2.1161.00
56_D59_R1.9511.00
49_I64_L1.8921.00
30_N52_F1.6651.00
37_N42_K1.5240.99
59_R63_L1.5090.99
24_R53_S1.4210.98
28_L51_F1.3530.97
48_E52_F1.3190.97
52_F56_D1.2930.96
27_Y37_N1.2600.95
44_K50_E1.2460.95
40_R51_F1.2380.95
14_E68_E1.2020.93
33_G56_D1.2010.93
21_L61_L1.1540.92
44_K59_R1.1470.91
21_L40_R1.1420.91
27_Y46_K1.0900.88
25_E54_N1.0840.88
24_R57_L1.0730.87
22_K54_N1.0680.87
34_T59_R1.0680.87
22_K25_E1.0680.87
35_T52_F1.0360.84
50_E59_R1.0140.83
25_E51_F1.0060.82
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  
3mkyB20.246493.80.713Contact Map
2cu1A10.97149.40.818Contact Map
4g08A10.811648.80.818Contact Map
2jrhA10.956544.40.823Contact Map
1zx4A20.927543.70.824Contact Map
2c60A10.869642.70.825Contact Map
4y5oB1040.90.827Contact Map
2nptB20.956540.30.827Contact Map
4ar0A10.94225.50.844Contact Map
3cjlA20.594222.80.848Contact 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 0.0106 seconds.