pypath.utils.orthology.PtmOrthology

class pypath.utils.orthology.PtmOrthology(target: str | int, source: str | int | None = None, only_swissprot: bool = True, strict: bool = True, orthology_args: dict | None = None)

Bases: Proteomes, SequenceContainer

__init__(target: str | int, source: str | int | None = None, only_swissprot: bool = True, strict: bool = True, orthology_args: dict | None = None)

This is an object to store sequences of multiple organisms and select the appropriate one.

Methods

__init__(target[, source, only_swissprot, ...])	This is an object to store sequences of multiple organisms and select the appropriate one.
get_seq(protein[, taxon])
get_taxon(protein[, only_swissprot])
get_taxon_trembl(protein)
has_protein(protein)
is_swissprot(protein)
load_proteome(taxon[, only_swissprot])
load_seq(taxon)
load_taxonomy()
ptm_orthology()	Load PTM orthology data from PhosphoSite.
reload()
translate(x[, return_strings])	Translates anything: string notation, intera objects, tuples.
translate_domain(domain)
translate_domain_motif(dmotif)
translate_ptm(ptm)
translate_residue(residue)
translate_site(protein, res, offset[, ...])	Translates one PTM site.

ptm_orthology()

Load PTM orthology data from PhosphoSite.

Creates an orthology translation dict of phosphosites based on phosphorylation sites table from PhosphoSitePlus. In the result all PTMs represented by a tuple of the following 6 elements: UniProt ID, isoform (int), residue one letter code, residue number (int), NCBI Taxonomy ID (int), modification type.

translate(x, return_strings=False, **kwargs)

Translates anything: string notation, intera objects, tuples.

• one PTM provided as tuple of (UniProt, amino acid, offest)

• one PTM provided as string (e.g. P00533_S231)

• instance from pypath.intera: DomainMotif, Domain or Ptm

Additional arguments can be isoform and typ (modification type).

translate_site(protein: str | intera.Protein, res: str, offset: int, isoform: int = 1, typ: str = 'phosphorylation', source_organism: str | int | None = None) → set[tuple]

Translates one PTM site.

Parameters:

• protein – A protein identifier or an intera.Protein object.

• res – Single letter code of the residue.

• offset – Sequence offset of the site.

• isoform – Sequence isoform.

• typ – Modification type.

• source_organism – Name or NCBI Taxonomy ID of the source organism.

Returns:

A list of tuples with the identifier, isoform, residue, offset, taxon and modification type of the orthologous PTM sites.