OPENSEQ.org
merF

ID: 1518459242 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 81 (74)
Sequences: 101 (78.8)
Seq/Len: 1.365
Nf(neff/√len): 9.2

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: 1.365).

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_G50_A1.6940.92
6_T9_R1.6280.90
7_L61_A1.5540.87
15_T20_L1.5440.86
17_L28_V1.4980.84
54_F60_Y1.4900.84
19_A23_F1.4820.83
28_V43_L1.4710.83
20_L39_L1.4580.82
14_G31_L1.3900.77
4_P29_I1.3600.75
17_L64_R1.3460.74
44_D51_L1.3090.71
54_F58_T1.2820.69
56_G59_I1.2730.68
55_I69_D1.2580.67
33_V37_S1.2560.67
28_V38_A1.2350.65
10_V53_I1.2280.64
55_I65_K1.2120.63
41_G60_Y1.1960.61
42_Y65_K1.1610.58
45_Y52_A1.1530.57
24_T44_D1.1520.57
5_K9_R1.1480.56
38_A65_K1.1350.55
30_L50_A1.1260.54
48_L52_A1.1230.54
3_D9_R1.1210.54
57_L64_R1.1180.53
39_L56_G1.1150.53
3_D6_T1.1040.52
38_A45_Y1.1010.52
46_V54_F1.1010.52
5_K18_V1.0860.50
16_T37_S1.0800.50
31_L55_I1.0770.49
42_Y67_Q1.0640.48
14_G28_V1.0490.46
3_D45_Y1.0490.46
15_T58_T1.0350.45
48_L59_I1.0230.44
13_I40_T1.0230.44
47_L51_L1.0180.43
3_D10_V1.0070.42
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  
2m67A1199.80.381Contact Map
1wazA10.567999.70.465Contact Map
2h3oA10.543299.60.504Contact Map
2a65A10.827220.30.911Contact Map
3l1lA10.790117.20.914Contact Map
1rzhH10.469115.40.916Contact Map
2l2tA20.543215.20.916Contact Map
1eysH10.4198150.917Contact Map
2ks1B10.506213.30.918Contact Map
2wjnH10.493812.50.919Contact 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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