Lysine Acetylation Context

Inspect lysine acetylation candidates and nearby acidic residues.

Description

Lysine acetylation-context inspection summarizes nearby acidic residues around every lysine.

Lysine acetylation-context inspection summarizes nearby acidic residues around every lysine. It supplies positional context rather than predicting modification.^[1]

Inspect lysine acetylation candidates and nearby acidic residues.

When to use Lysine Acetylation Context

Use this tool to inspect lysine acetylation candidates and nearby acidic residues.

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 Lysine Acetylation Context 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, contextRadius using the field table and calculation rules, then run the tool.
Read lysineIndexes, acidicNeighborCounts. 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
contextRadius	Context radius	number	Required

Enter a canonical sequence and nonnegative safe-integer radius. Return zero-based lysine indexes and aligned D/E counts in inclusive neighborhoods clipped to sequence ends. Radius zero gives zero acidic neighbors.

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.

acidicCount_i=count(D/E within clipped [i−radius,i+radius])

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
lysineIndexes	Lysine indexes	list of number
acidicNeighborCounts	Acidic neighbor counts	list of number

json

{
  "input": {
    "sequence": "AEKAA",
    "contextRadius": 2
  },
  "output": {
    "lysineIndexes": [
      2
    ],
    "acidicNeighborCounts": [
      1
    ]
  }
}

Limitations and assumptions

No threshold, enzyme specificity or acetylation evidence is used. The window includes the lysine position, which cannot itself contribute a D/E count.

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.

Alternative or Complementary methods

Use Ubiquitination Sites: Count lysine residues as potential ubiquitination sites, not confirmed sites. For a complementary task, use Methionine Oxidation Screen: Screen exposed methionines as oxidation candidates, not measured modifications.

References

Lysine Acetylation Context — tool.io

Similar or alternative tools

Ubiquitination Sites
Count lysine residues as potential ubiquitination sites, not confirmed sites.
Methionine Oxidation Screen
Screen exposed methionines as oxidation candidates, not measured modifications.