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YOHJ_ECOLI

ID: 1427525149 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 132 (118)
Sequences: 1799 (1379.1)
Seq/Len: 15.246
Nf(neff/√len): 127.0

Jackhmmer Results: (2015_01_07)
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: 15.246).

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
21_C49_L3.7151.00
113_W116_Q2.2641.00
48_V52_L2.2341.00
110_V114_S2.2141.00
112_S116_Q2.0621.00
109_L113_W1.9501.00
102_V106_V1.8291.00
29_A41_I1.8171.00
44_L48_V1.8131.00
20_A24_A1.7161.00
21_C45_I1.6871.00
89_L96_V1.6681.00
24_A49_L1.6561.00
25_G38_G1.6261.00
95_P99_S1.6151.00
83_M86_F1.6101.00
39_S74_L1.5871.00
14_A63_G1.5801.00
92_Q95_P1.5631.00
41_I45_I1.5601.00
26_I30_S1.5011.00
22_L39_S1.4611.00
114_S117_L1.4511.00
56_P59_W1.4491.00
13_R59_W1.4271.00
43_M79_G1.4141.00
22_L26_I1.4020.99
82_V85_Y1.4000.99
45_I49_L1.3510.99
113_W117_L1.3380.99
57_A60_V1.3200.99
27_F31_L1.3040.99
87_D90_R1.2660.99
53_Q56_P1.2620.99
57_A61_N1.2390.98
37_P78_I1.2050.98
28_I31_L1.1870.98
85_Y88_L1.1700.97
115_S119_H1.1620.97
61_N65_Y1.1620.97
43_M115_S1.1590.97
107_V111_V1.1470.97
29_A33_P1.1440.97
98_V102_V1.1280.97
21_C25_G1.1090.96
29_A38_G1.0920.96
87_D91_A1.0860.96
28_I45_I1.0580.95
25_G41_I1.0540.95
29_A32_L1.0530.95
46_L55_L1.0530.95
44_L66_V1.0500.94
86_F90_R1.0410.94
69_R78_I1.0380.94
28_I33_P1.0350.94
118_V121_E1.0310.94
100_C107_V1.0310.94
14_A21_C1.0300.94
27_F30_S1.0300.94
111_V115_S1.0200.93
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: (31Jan15)
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  
4k0jA60.886481.70.887Contact Map
4bwzA10.916768.20.899Contact Map
4cz8A20.931863.40.902Contact Map
3aqpA20.856161.30.903Contact Map
4czbA30.931856.50.906Contact Map
2kncA10.386448.50.91Contact Map
4mt1A10.901547.30.911Contact Map
2kv5A10.2545.90.911Contact Map
2kluA10.333341.40.914Contact Map
4dx5A3140.90.914Contact 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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