3.1.1.2.1.5. etfl.core.expression

ME-related Reaction subclasses and methods definition

3.1.1.2.1.5.1. Module Contents

3.1.1.2.1.5.1.1. Functions

build_trna_charging(model, aa_dict, atp='atp_c', amp='amp_c', ppi='ppi_c', h2o='h2o_c', h='h_c')

Build th tRNA charging reactions, based on the amino acid dictionary

get_trna_charging_id(aa_id)

make_stoich_from_aa_sequence(sequence, aa_dict, trna_dict, gtp, gdp, pi, h2o, h)

Makes the stoichiometry of the peptide synthesis reaction based on the

make_stoich_from_nt_sequence(sequence, nt_dict, ppi)

Makes the stoichiometry of the RNA synthesis reaction based on the

degrade_peptide(peptide, aa_dict, h2o)

Degrades a peptide in amino acids, based on its sequence

degrade_mrna(mrna, nt_dict, h2o, h)

Degrades a mRNA in nucleotides monophosphate, based on its sequence

is_me_compatible(reaction)

Check if a Cobra reaction has sufficient information to add expression coupling

enzymes_to_gpr(rxn)

Builds a Gene to Protein to Reaction association rules from the enzymes of

enzymes_to_gpr_no_stoichiometry(rxn)

Builds a Gene to Protein to Reaction association rules from the enzymes of

_extract_trna_from_reaction(aa_stoichiometry, rxn)

Read a stoichiometry dictionary, and replaces free aminoacids with tRNAs
ETFL.build_trna_charging(model, aa_dict, atp='atp_c', amp='amp_c', ppi='ppi_c', h2o='h2o_c', h='h_c')

Build th tRNA charging reactions, based on the amino acid dictionary

Parameters

  • model (etfl.core.memodel.MEModel) – An ETFL Model

  • aa_dict –

    A dictionary of aminoacid letter to amicoacid met id

    Example :

    aa_dict = {
            'A':'ala__L_c',
            'R':'arg__L_c',
            ...
        }

  • atp – metabolite ID of the cytosolic ATP

  • amp – metabolite ID of the cytosolic AMP

  • ppi – metabolite ID of the cytosolic diphosphate

  • h2o – metabolite ID of the cytosolic water

  • h – metabolite ID of the cytosolic hydrogen ions

Returns

A dictionary of tRNAs, keys are the aminoacido letters, values the charging reactions

ETFL.get_trna_charging_id(aa_id)
ETFL.make_stoich_from_aa_sequence(sequence, aa_dict, trna_dict, gtp, gdp, pi, h2o, h)

Makes the stoichiometry of the peptide synthesis reaction based on the amino acid sequence

Parameters

  • sequence (Bio.Seq or str) – sequence of aminoacids (letter form)

  • aa_dict –

    A dictionary of aminoacid letter to amicoacid met id

    Example :

    aa_dict = {
            'A':'ala__L_c',
            'R':'arg__L_c',
            ...
        }

  • trna_dict – the dict returned by etfl.core.expression.build_trna_charging()

  • gtp – metabolite ID for GTP

  • gdp – metabolite ID for GDP

  • pi – metabolite ID for phosphate

  • h2o – metabolite ID for water

  • h – metabolite ID for H+

Returns

ETFL.make_stoich_from_nt_sequence(sequence, nt_dict, ppi)

Makes the stoichiometry of the RNA synthesis reaction based on the nucleotides sequence

Parameters

  • sequence (Bio.Seq or str) – sequence of RNA nucleotides

  • nt_dict –

    A dictionary of RNA nucleotide triphosphate

    letter to nucleotideTP met id

    Example :

    rna_nucleotides = {
            'A':'atp_c',
            'U':'utp_c',
            ...
        }

  • ppi – metabolite ID for diphosphate

Returns

ETFL.degrade_peptide(peptide, aa_dict, h2o)

Degrades a peptide in amino acids, based on its sequence

Parameters

  • peptide (etfl.core.enzyme.Peptide) – The peptide

  • aa_dict –

    A dictionary of aminoacid letter to amicoacid met id

    ** Example : **

    aa_dict = {
            'A':'ala__L_c',
            'R':'arg__L_c',
            ...
        }

  • h2o – metabolite ID for water

Returns

ETFL.degrade_mrna(mrna, nt_dict, h2o, h)

Degrades a mRNA in nucleotides monophosphate, based on its sequence

Parameters

  • mrna (etfl.core.rna.mRNA) – The peptide

  • nt_dict –

    A dictionary of RNA nucleotide monophosphate letter to nucleotideMP met id

    Example :

    rna_nucleotides_mp = {
            'A':'amp_c',
            'U':'ump_c',
            ...
        }

  • h2o – metabolite ID for water

  • h – metabolite ID for H+

Returns

ETFL.is_me_compatible(reaction)

Check if a Cobra reaction has sufficient information to add expression coupling

Parameters

reaction (cobra.core.Reaction) –

Returns

ETFL.enzymes_to_gpr(rxn)

Builds a Gene to Protein to Reaction association rules from the enzymes of an enzymatic reaction

Parameters

rxn –

Returns

ETFL.enzymes_to_gpr_no_stoichiometry(rxn)

Builds a Gene to Protein to Reaction association rules from the enzymes of an enzymatic reaction

Parameters

rxn –

Returns

ETFL._extract_trna_from_reaction(aa_stoichiometry, rxn)

Read a stoichiometry dictionary, and replaces free aminoacids with tRNAs

Parameters

  • aa_stoichiometry ((dict) {cobra.core.Metabolite: Number}) – the stoichiometry dict to edit

  • rxn (cobra.core.Reaction) – the reaction whose stoichiometry is inspected

Returns