Ubiquitination Sites

Count lysine residues as potential ubiquitination sites, not confirmed sites.

Description

Lysine residues provide a simple candidate list for ubiquitination screening.

Lysine residues provide a simple candidate list for ubiquitination screening. Residue presence alone does not demonstrate modification.^[1]

Count lysine residues as potential ubiquitination sites, not confirmed sites.

When to use Ubiquitination Sites

Use this tool to count lysine residues as potential ubiquitination sites, not confirmed sites.

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 Ubiquitination Sites 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 using the field table and calculation rules, then run the tool.
Read lysineIndexes, candidateCount. 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

Enter a canonical sequence. Return every zero-based lysine index in ascending order and the total candidate count.

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.

candidateIndexes={i:sequence[i]=K}; candidateCount=length(candidateIndexes)

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
candidateCount	Candidate count	number

json

{
  "input": {
    "sequence": "AKK"
  },
  "output": {
    "lysineIndexes": [
      1,
      2
    ],
    "candidateCount": 2
  }
}

Limitations and assumptions

The tool does not evaluate accessibility, enzyme specificity or measured ubiquitin attachment. Other modification sites and atypical ubiquitination are outside this lysine-only screen.

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 Lysine Acetylation Context: Inspect lysine acetylation candidates and nearby acidic residues. For a complementary task, use Phosphorylation Sites: Count potential Ser/Thr/Tyr phosphorylation positions.

References

Ubiquitination Sites — tool.io

Similar or alternative tools

Lysine Acetylation Context
Inspect lysine acetylation candidates and nearby acidic residues.
Phosphorylation Sites
Count potential Ser/Thr/Tyr phosphorylation positions.