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pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor§

class pypath.core.enz_sub.EnzymeSubstrateOrthologyProcessor(ncbi_tax_id, input_param=None, input_method=None, map_by_orthology_from=None, trace=False, id_type_enzyme=None, id_type_substrate=None, name=None, orthology_only_swissprot=True, ptm_orthology_strict=False, **kwargs)[source]§

Bases: PtmOrthology, EnzymeSubstrateProcessor, Logger

__init__(ncbi_tax_id, input_param=None, input_method=None, map_by_orthology_from=None, trace=False, id_type_enzyme=None, id_type_substrate=None, name=None, orthology_only_swissprot=True, ptm_orthology_strict=False, **kwargs)[source]§

Unifies a pypath.core.enz_sub.EnzymeSubstrateProcessor and a pypath.utils.orthology.PtmOrthology object to build a set of enzyme-substrate interactions from a database and subsequently translate them by orthology to one different organism. Multiple organism can be chosen as the source of the enzyme-substrate interactions. For example if you want mouse interactions, you can translate them from human and from rat. To get the original mouse interactions themselves, use an other instance of the EnzymeSubstrateProcessor. To have both the original and the orthology translated set, and also from multiple databases, whatmore all these merged into a single set, use the EnzymeSubstrateAggregator.

Parameters:

  • input_method (str) – Data source for EnzymeSubstrateProcessor.

  • ncbi_tax_id (int) – The NCBI Taxonomy ID the interactions should be translated to.

  • orthology_only_swissprot (bool) – Use only SwissProt (i.e. not Trembl) at orthology translation.

  • ptm_orthology_strict (bool) – Use only those homologous PTM pairs which are in PhosphoSite data, i.e. do not look for residues with same offset in protein sequence.

See further options at EnzymeSubstrateProcessor.

Methods

__init__(ncbi_tax_id[, input_param, ...])

Unifies a pypath.core.enz_sub.EnzymeSubstrateProcessor and a pypath.utils.orthology.PtmOrthology object to build a set of enzyme-substrate interactions from a database and subsequently translate them by orthology to one different organism.

get_seq(protein[, taxon])

get_taxon(protein[, only_swissprot])

get_taxon_trembl(protein)

has_protein(protein)

input_is(i[, op])

is_swissprot(protein)

load_data()

Loads the data by the defined input method.

load_enz_sub()

load_proteome(taxon[, only_swissprot])

load_seq(taxon)

load_taxonomy()

ptm_orthology()

Load PTM orthology data from PhosphoSite.

reload()

reset_ptmprocessor([seq, ncbi_tax_id])

set_inputargs(**inputargs)

Sets the arguments to be provided for the input method.

set_method()

Selects the input method.

set_taxon(ncbi_tax_id)

setup()

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.
load_data()§

Loads the data by the defined input method.

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.

set_inputargs(**inputargs)§

Sets the arguments to be provided for the input method.

set_method()§

Selects the input method.

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.

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