Enzyme & EC data#

MATLAB functions in GECKO/src/get_enzyme_data of the GECKO toolbox.

Functions#

Function	Summary
`applyECcodes`	Copy EC numbers from ecModel.ec.eccodes to ecModel.eccodes.
`calculateMW`	Calculate the molecular weight of a protein.
`findECInDB`	Look up EC numbers for a reaction's gene set in a UniProt or KEGG index.
`getECfromDatabase`	Populate model.ec.eccodes from UniProt and KEGG databases.
`getECfromGEM`	Populate model.ec.eccodes from the model.eccodes field.
`getECstring`	Build a single string of EC numbers for a protein.

Reference#

applyECcodes#

function ecModel = applyECcodes(ecModel, varargin)

Copy EC numbers from ecModel.ec.eccodes to ecModel.eccodes.

Copies the EC numbers stored in the ecModel.ec structure across to the top-level ecModel.eccodes field.

Parameters

ecModel : struct: an ecModel in GECKO 3 format (with ecModel.ec structure).

Name-Value Arguments

overwrite : logical: whether existing (non-empty) ecModel.eccodes entries should be overwritten by a non-empty ecModel.ec.eccodes entry. Empty ecModel.eccodes entries are always overwritten if possible (default false). An empty ecModel.ec.eccodes source entry is never copied, so it can never erase an existing annotation.

Returns

ecModel : struct: ecModel with populated model.eccodes.

Examples

% optional arguments may be given positionally or as name-value pairs:
ecModel = applyECcodes(ecModel, true);
ecModel = applyECcodes(ecModel, 'overwrite', true);

calculateMW#

function MW = calculateMW(sequence)

Calculate the molecular weight of a protein.

Calculates the molecular weight of a protein from its amino acid sequence. Matching is case-insensitive. Sequences with no recognized residue (including an empty sequence) return NaN, rather than being mistaken for an 18 Da protein.

Parameters

sequence : char: the amino acid sequence (can include extra things such as spaces or numbers, which are ignored).

Returns

MW : double: the molecular weight in Da, or NaN if no residue was recognized.

findECInDB#

function [EC,conflicts] = findECInDB(gene_set, DBecNum, DBMW, geneIndex, geneHashMap)

Look up EC numbers for a reaction's gene set in a UniProt or KEGG index.

For each gene, finds its matching database entries and takes the EC number of the lightest-weight matching protein when a single EC number applies to that gene; genes with several distinct EC numbers among their matches are also reported as conflicts (the first match is still used for EC). Genes without an EC number are left out. When gene_set has more than one gene (an enzyme complex), the numbers found for each gene are combined by intersection where they share a match (a wildcard such as "1.1.1.-" matches the specific codes of its prefix), otherwise by union. The EC set of every gene set, one gene or a complex, is cleaned of a wildcard code such as "1.1.1.-" when a more specific code of the same prefix ("1.1.1.4") is present; only codes with four levels take part, and empty codes are removed.

Parameters

gene_set : cell: genes from a given metabolic reaction.
DBecNum : cell: array of EC numbers.
DBMW : double: array of molecular weights in Da.
geneIndex : cell: as generated by getECfromDatabase.
geneHashMap : containers.Map: as generated by getECfromDatabase.

Returns

EC : char: EC numbers that apply to gene_set, each prefixed with "EC" and separated by ";" (e.g. "EC1.1.1.1;EC1.1.1.2").
conflicts : cell: genes with multiple protein matches.

Examples

[EC, conflicts] = findECInDB(gene_set, DBecNum, DBMW, geneIndex, geneHashMap);

See also

getECfromDatabase, getECstring

getECfromDatabase#

function model = getECfromDatabase(model, varargin)

Populate model.ec.eccodes from UniProt and KEGG databases.

Populates the model.ec.eccodes field with enzyme codes that are extracted from UniProt and KEGG databases, as assigned to the proteins that catalyze the specific reactions.

Parameters

model : struct: an ecModel in GECKO 3 format (with ecModel.ec structure).

Name-Value Arguments

ecRxns : logical

of length model.ec.rxns that specifies which model.ec.eccodes entries should be queried. Existing values in model.ec.eccodes will be wiped. Entries that are indicated by false will be kept and not modified by this function, and are not searched for multiplicities. An empty logical array selects no entry, and the model is returned unchanged. When ecRxns is omitted or [], all model.ec.eccodes entries are populated by this function.

action : char

response action if multiple proteins with different EC numbers are found for a given gene in a metabolic reaction (default 'display'):

'display' gives a warning that lists all found multiplicities and uses the protein with the lowest index in the database.
'ignore' ignores multiplicities and uses the protein with the lowest index in the database.

Any other action raises getECfromDatabase:unsupportedAction.

modelAdapter : ModelAdapter

a loaded model adapter (default: the current default model adapter).

Returns

model : struct: ecModel with populated model.ec.eccodes.

Examples

% optional arguments may be given positionally or as name-value pairs:
model = getECfromDatabase(model, ecRxns, action, modelAdapter);
model = getECfromDatabase(model, 'action', 'ignore');

See also

getECfromGEM, findECInDB, loadDatabases

getECfromGEM#

function [model, invalidEC, invalidECpos] = getECfromGEM(model, varargin)

Populate model.ec.eccodes from the model.eccodes field.

Uses the model.eccodes to populate the model.ec.eccodes field. EC numbers must be formatted as four numbers separated by periods, possibly with trailing wildcards; incorrectly formatted EC numbers are skipped. A model without a model.eccodes field gives a warning and every EC number is empty.

Parameters

model : struct: an ecModel in GECKO 3 format (with ecModel.ec structure).

Name-Value Arguments

ecRxns : logical: of length model.ec.rxns that specifies for which reactions the existing model.ec.eccodes entry should be kept and not modified by this function (by default all model.ec.eccodes entries are populated by this function).

Returns

model : struct: ecModel with populated model.ec.eccodes.
invalidEC : cell: incorrectly formatted EC numbers.
invalidECpos : double: position of invalidEC in model.eccodes.

Notes

Valid EC numbers are e.g. 1.2.3.4 or 1.2.3.-, while invalid EC numbers are 1.2.3 or 1_2_3_4. Multiple EC numbers are separated by ; for instance 1.2.3.4;1.2.3.5 not 1.2.3.4|1.2.3.5.

Examples

% optional arguments may be given positionally or as name-value pairs:
[model, invalidEC, invalidECpos] = getECfromGEM(model, ecRxns);
[model, invalidEC, invalidECpos] = getECfromGEM(model, 'ecRxns', ecRxns);

See also

getECfromDatabase, applyECcodes

getECstring#

function EC_set = getECstring(EC_set,ecNumbers)

Build a single string of EC numbers for a protein.

Provides a single string with all the EC numbers associated to a given protein, according to the following format: "ECX.X.X.X ECX.X.X.X ECX.X.X.X".

Parameters

EC_set : char: existing EC string to which the EC numbers are appended.
ecNumbers : char: EC numbers associated to the protein, separated by white space and/or semicolons.

Returns

EC_set : char: a single string with all the EC numbers, each prefixed with "EC".

Examples

EC_set = getECstring(EC_set, ecNumbers);

See also

findECInDB In case of several ec numbers for the same protein