OPENSEQ.org
MSMEG_1063

ID: 1516679149 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 108 (100)
Sequences: 242 (180.2)
Seq/Len: 2.420
Nf(neff/√len): 18.0

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: 2.420).

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
28_P32_L2.9061.00
14_N26_R2.1851.00
64_I68_T2.1011.00
28_P31_A1.8880.99
32_L68_T1.7610.98
24_P27_V1.6940.97
27_V30_L1.6590.97
62_V71_M1.5220.94
65_T72_P1.4380.92
85_A91_L1.4350.91
31_A72_P1.4190.91
12_W25_D1.3350.87
35_R76_D1.3350.87
97_G100_P1.3230.86
40_D66_Q1.2820.84
40_D51_K1.2610.83
25_D37_L1.2600.82
51_K67_M1.2560.82
34_T79_R1.2560.82
20_G84_L1.2470.82
25_D89_W1.2470.82
54_H59_D1.2430.81
33_L88_G1.2250.80
58_I62_V1.2200.80
16_G33_L1.2180.79
61_G69_D1.2060.78
51_K86_L1.1950.78
9_I38_T1.1860.77
20_G89_W1.1540.74
21_V25_D1.1280.72
28_P68_T1.1240.71
69_D77_I1.1050.69
20_G25_D1.0970.69
61_G93_D1.0880.68
88_G91_L1.0730.66
12_W82_R1.0720.66
45_I82_R1.0670.65
45_I71_M1.0550.64
82_R92_D1.0530.64
27_V79_R1.0510.64
77_I86_L1.0490.64
84_L88_G1.0460.63
8_K88_G1.0410.63
43_K87_Q1.0310.62
64_I70_E1.0310.62
36_R91_L1.0230.61
83_H87_Q1.0200.60
44_A47_E1.0130.60
25_D84_L1.0120.59
33_L89_W1.0080.59
21_V70_E1.0020.58
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  
2lkyA111000.047Contact Map
2kvcA10.93521000.109Contact Map
3ol3A20.87041000.126Contact Map
2m0nA10.93521000.127Contact Map
4giuA20.768567.50.896Contact Map
2zooA10.592663.60.898Contact Map
4ga6A20.990762.50.899Contact Map
4eadA10.796359.10.901Contact Map
1uouA10.7552.50.905Contact Map
4gtnA10.824150.30.906Contact 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.

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