org.Sc.sgdENZYME {org.Sc.sgd.db} | R Documentation

## Map between ORF IDs and Enzyme Commission (EC) Numbers

### Description

org.Sc.sgdENZYME is an R object that provides mappings between ORF identifiers and EC numbers.

### Details

Each ORF identifier maps to a named vector containing the EC number that corresponds to the enzyme produced by that gene. The name corresponds to the ORF identifier. If this information is unknown, the vector will contain an `NA`.

Enzyme Commission numbers are assigned by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology http://www.chem.qmw.ac.uk/iubmb/enzyme/ to allow enzymes to be identified.

An Enzyme Commission number is of the format EC x.y.z.w, where x, y, z, and w are numeric numbers. In org.Sc.sgdENZYME2ORF, EC is dropped from the Enzyme Commission numbers.

Enzyme Commission numbers have corresponding names that describe the functions of enzymes in such a way that EC x is a more general description than EC x.y that in turn is a more general description than EC x.y.z. The top level EC numbers and names are listed below:

EC 1 oxidoreductases

EC 2 transferases

EC 3 hydrolases

EC 4 lyases

EC 5 isomerases

EC 6 ligases

The EC name for a given EC number can be viewed at http://www.chem.qmul.ac.uk/iupac/jcbn/index.html#6

Mappings between ORF identifiers and enzyme identifiers were obtained using files provided by: KEGG GENOME ( ftp://ftp.genome.jp/pub/kegg/genomes ) on 2008-Sep2

For the reverse map, each EC number maps to a named vector containing the ORF identifier that corresponds to the gene that produces that enzyme. The name of the vector corresponds to the EC number.

### References

ftp://ftp.genome.ad.jp/pub/kegg/pathways

### Examples

        x <- org.Sc.sgdENZYME
        # Get the ORF identifiers that are mapped to an EC number
        mapped_genes <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_genes])
        if(length(xx) > 0) {
          # Get the ENZYME id for the first five genes
          xx[1:5]
          # Get the first one
          xx[[1]]
        }
        # For the reverse map:
        # Convert to a list
        xx <- as.list(org.Sc.sgdENZYME2ORF)
        if(length(xx) > 0){
           # Gets the ORF identifiers for the first five enzyme
           #commission numbers
           xx[1:5]
           # Get the first one
           xx[[1]]
        }

[Package org.Sc.sgd.db version 2.2.6 Index]