Phosphorylation Sites

Count potential Ser/Thr/Tyr phosphorylation positions.

Description

Serine, threonine and tyrosine enumeration provides a basic phosphorylation-candidate list.

Serine, threonine and tyrosine enumeration provides a basic phosphorylation-candidate list. A possible residue is distinct from an observed modification site.^[1]

Count potential Ser/Thr/Tyr phosphorylation positions.

When to use Phosphorylation Sites

Use this tool to count potential Ser/Thr/Tyr phosphorylation positions.

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 Phosphorylation 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 candidateIndexes, serineCount, threonineCount, tyrosineCount. 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 ascending zero-based candidate indexes and separate serine, threonine and tyrosine counts.

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:residue_i in STY}

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

Output field	Meaning	Value type
candidateIndexes	Candidate indexes	list of number
serineCount	Serine count	number
threonineCount	Threonine count	number
tyrosineCount	Tyrosine count	number

json

{
  "input": {
    "sequence": "ASTY"
  },
  "output": {
    "candidateIndexes": [
      1,
      2,
      3
    ],
    "serineCount": 1,
    "threonineCount": 1,
    "tyrosineCount": 1
  }
}

Limitations and assumptions

No kinase preference, occupancy, localization confidence or phosphoproteomic data is evaluated.

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 Phosphoserine Adapter Motifs: Match RS-X-pS-X-P adapter motifs against measured phosphoserine positions. For a complementary task, use Methionine Oxidation Screen: Screen exposed methionines as oxidation candidates, not measured modifications.

References

Phosphorylation Sites — tool.io

Similar or alternative tools

Phosphoserine Adapter Motifs
Match RS-X-pS-X-P adapter motifs against measured phosphoserine positions.
Methionine Oxidation Screen
Screen exposed methionines as oxidation candidates, not measured modifications.