Leucine Zipper Pattern
Scan every seventh residue for leucine-zipper runs.
Description
A leucine-zipper screen looks for consecutive leucines along every seventh residue.
A leucine-zipper screen looks for consecutive leucines along every seventh residue. Register describes the sequence offset of that periodic scan.1
Scan every seventh residue for leucine-zipper runs.
When to use Leucine Zipper Pattern
Use this tool to scan every seventh residue for leucine-zipper runs.
Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
How to use Leucine Zipper Pattern and understand its results
- Prepare the canonical sequence, peptide assignments, fitted assay parameters or upstream measurements requested. Keep corresponding entries aligned, use the stated mass and signal units, and remove FASTA headers before entering sequence text.
- Enter sequence, minimumLeucines using the field table and calculation rules, then run the tool.
- Read bestRegister, longestRun, candidate. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| sequence | Sequence | string | Required |
| minimumLeucines | Minimum leucines | number | Required |
Enter a canonical sequence and finite minimum leucines of at least two. Return best zero-based register, longest run and inclusive candidate flag. The minimum need not be an integer.
The shared sequence helper trims outer whitespace and uppercases the sequence. It requires at least one residue from ACDEFGHIKLMNPQRSTVWY. Internal whitespace, FASTA headers, ambiguous letters and modified-residue notation are rejected. Sequence indexes refer to the normalized sequence; individual tools may preserve original strings in their returned lists as explained above.
longestRun=max consecutive L values in each offset 0…6 sampled every seven residues Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| bestRegister | Best register | number |
| longestRun | Longest run | number |
| candidate | Candidate | boolean |
{
"input": {
"sequence": "LAAAAAALAAAAAAL",
"minimumLeucines": 3
},
"output": {
"bestRegister": 0,
"longestRun": 3,
"candidate": true
}
}Limitations and assumptions
Only L is counted. Strict improvements select the first encountered tied run; without any L the register stays zero. Coiled-coil structure and interaction are not established.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Coiled Coil Register: Score coiled-coil heptad register by hydrophobic a/d positions. For a complementary task, use Heptad Hydrophobicity: Score a/d heptad hydrophobicity as a coiled-coil candidate feature.
References
-
Leucine Zipper Pattern — tool.io
Similar or alternative tools
- Coiled Coil Register
Score coiled-coil heptad register by hydrophobic a/d positions.
- Heptad Hydrophobicity
Score a/d heptad hydrophobicity as a coiled-coil candidate feature.