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Geovibrio sp L21-Ace-BES -force run

ID: 1513959379 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 147 (124)
Sequences: 114 (97.1)
Seq/Len: 0.919
Nf(neff/√len): 8.7

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: 0.919).

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
38_A41_T1.8550.91
42_T46_D1.7940.89
16_V19_I1.7920.89
14_L21_G1.7710.89
20_I79_D1.5920.80
33_K37_R1.5740.79
26_V37_R1.5640.79
27_A34_F1.5460.77
11_I19_I1.4920.74
55_E105_C1.4850.73
69_A100_N1.4840.73
17_V25_A1.4630.72
33_K36_A1.3880.66
82_N100_N1.3810.65
8_F11_I1.3530.63
17_V59_G1.3390.62
9_T21_G1.3370.62
45_S77_L1.3230.61
18_A34_F1.2970.58
42_T80_G1.2880.57
25_A40_N1.2820.57
38_A124_S1.2810.57
121_K125_P1.2780.57
24_A105_C1.2730.56
20_I125_P1.2560.55
48_S53_E1.2410.53
14_L34_F1.2360.53
9_T24_A1.2170.51
63_R121_K1.2110.51
62_D89_S1.1900.49
15_V25_A1.1840.48
10_L24_A1.1840.48
37_R48_S1.1760.47
31_Y35_R1.1750.47
104_S121_K1.1660.46
20_I126_A1.1540.45
22_I119_T1.1520.45
45_S98_T1.1490.45
84_S108_G1.1460.45
105_C109_V1.1430.44
122_T125_P1.1430.44
46_D124_S1.1350.44
108_G123_P1.1310.43
15_V33_K1.1310.43
67_P97_K1.1310.43
17_V50_F1.1070.41
66_D80_G1.1060.41
17_V34_F1.0940.40
21_G31_Y1.0910.40
26_V117_I1.0690.38
15_V121_K1.0620.37
11_I16_V1.0590.37
57_F68_F1.0590.37
63_R92_T1.0550.37
26_V112_M1.0520.36
111_S119_T1.0450.36
9_T95_G1.0420.36
74_T77_L1.0410.36
14_L50_F1.0360.35
6_K119_T1.0350.35
74_T105_C1.0280.34
35_R40_N1.0150.33
41_T60_E1.0070.33
92_T121_K1.0040.32
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  
2hi2A10.904899.70.634Contact Map
3sokA20.857199.70.646Contact Map
1oqwA20.850399.60.665Contact Map
2m7gA10.41599.50.686Contact Map
3g20A20.761998.70.784Contact Map
4noaA10.659998.40.807Contact Map
2m3kA10.7143980.825Contact Map
3jyzA10.755197.50.843Contact Map
1x6zA10.680396.80.858Contact Map
1qveA20.734796.70.859Contact 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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