Phosphoserine Adapter Motifs

Match RS-X-pS-X-P adapter motifs against measured phosphoserine positions.

Description

A phosphoserine-adapter screen requires both a residue motif and declared support at its central serine.

A phosphoserine-adapter screen requires both a residue motif and declared support at its central serine. Supplied positions serve as evidence labels rather than measured data read by the tool.^[1]

Match RS-X-pS-X-P adapter motifs against measured phosphoserine positions.

When to use Phosphoserine Adapter Motifs

Use this tool to match RS-X-pS-X-P adapter motifs against measured phosphoserine 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 Phosphoserine Adapter Motifs 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, phosphoserineIndexes using the field table and calculation rules, then run the tool.
Read motifStarts, supportedCount. 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
phosphoserineIndexes	Phosphoserine indexes	list of number	Required

Enter a canonical sequence and phosphoserine position list. Examine six-residue windows and return ascending zero-based motif starts where the fourth residue is included exactly in the supplied set.

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.

match RS-X-S-X-P at i only if phosphoserineIndexes contains i+3

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

Output field	Meaning	Value type
motifStarts	Motif starts	list of number
supportedCount	Supported count	number

json

{
  "input": {
    "sequence": "RSASAP",
    "phosphoserineIndexes": [
      3
    ]
  },
  "output": {
    "motifStarts": [
      0
    ],
    "supportedCount": 1
  }
}

Limitations and assumptions

Position values are finite numbers but are not separately checked for integer, range or serine identity; only matching integer positions contribute. Evidence quality and adapter binding are not evaluated.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. 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 Phosphorylation Sites: Count potential Ser/Thr/Tyr phosphorylation positions. For a complementary task, use SH3 Pxxp Motifs: Locate proline-X-X-proline SH3 ligand motifs.

References

Phosphoserine Adapter Motifs — tool.io

Similar or alternative tools

Phosphorylation Sites
Count potential Ser/Thr/Tyr phosphorylation positions.
SH3 Pxxp Motifs
Locate proline-X-X-proline SH3 ligand motifs.