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non24

ID: 1501783843 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 24 (23)
Sequences: 7313 (5625.2)
Seq/Len: 317.957
Nf(neff/√len): 1172.9

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: 317.957).

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
17_Y20_I2.4601.00
2_A9_R2.3951.00
5_W20_I2.2141.00
4_K20_I2.0021.00
15_D18_R1.8841.00
13_S17_Y1.6321.00
11_T15_D1.5981.00
12_Q15_D1.5781.00
6_C19_H1.3460.99
14_G18_R1.2950.99
14_G22_K1.2130.98
2_A7_E1.1370.97
1_H9_R1.1270.97
18_R21_R1.0180.93
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: (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  
2eluA1194-0.131Contact Map
1ej6B20.958393.9-0.129Contact Map
1zr9A10.958393.1-0.101Contact Map
3zmsC1091.9-0.069Contact Map
4ijdA2191.7-0.062Contact Map
2eppA10.958390.3-0.032Contact Map
2wbtA2189.4-0.014Contact Map
2lv2A1188.8-0.002Contact Map
2en3A10.958388.50.003Contact Map
1f2iG60.958388.40.006Contact 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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