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NewPHL

ID: 1502472502 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 136 (132)
Sequences: 430 (340.2)
Seq/Len: 3.258
Nf(neff/√len): 29.6

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: 3.258).

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
40_S44_R3.4691.00
100_L105_A3.4291.00
113_A117_K3.2291.00
27_A30_V3.1581.00
82_R86_R2.6811.00
85_L96_L2.4441.00
107_A125_L2.1151.00
107_A118_F1.9571.00
73_M98_P1.6370.98
111_A115_F1.6090.98
21_R34_T1.5850.98
62_W68_A1.5650.97
115_F129_R1.5570.97
113_A118_F1.5410.97
112_K117_K1.4850.96
40_S101_R1.4790.96
13_A62_W1.4740.96
78_E82_R1.3990.94
119_K123_P1.3990.94
68_A71_I1.3560.93
77_P108_W1.3550.93
83_D118_F1.3340.92
72_V77_P1.3160.91
100_L103_H1.2870.90
110_H122_I1.2820.90
9_P13_A1.2680.89
21_R26_V1.2620.89
45_Y49_L1.2610.89
107_A122_I1.2210.86
28_P31_T1.2130.86
124_A128_R1.2080.85
101_R104_D1.1790.84
116_F119_K1.1730.83
38_L42_C1.1710.83
14_I42_C1.1600.82
19_A59_L1.1600.82
6_A9_P1.1110.78
102_D105_A1.0960.77
66_A95_P1.0830.76
76_T98_P1.0750.75
44_R112_K1.0740.75
103_H107_A1.0680.74
58_D61_A1.0630.74
40_S112_K1.0600.73
32_D37_A1.0600.73
18_A45_Y1.0590.73
34_T84_L1.0330.71
106_A124_A1.0300.70
119_K129_R1.0300.70
14_I38_L1.0280.70
12_T51_P1.0280.70
33_W36_A1.0250.70
32_D40_S1.0200.69
73_M96_L1.0190.69
9_P91_D1.0170.69
60_G92_S1.0090.68
10_L55_A1.0030.67
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  
2xryA10.933863.90.898Contact Map
4gu5A20.970625.90.92Contact Map
4djaA10.992618.30.926Contact Map
1owlA10.9706150.929Contact Map
3umvA20.948512.40.931Contact Map
1dnpA20.970612.30.931Contact Map
2wq7A10.992611.20.932Contact Map
4k0rA10.897110.40.934Contact Map
1xc0A10.14715.70.941Contact Map
4p0gA10.55155.70.941Contact 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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