PFAMCAZY {PFAM.db} | R Documentation

## Mappings from a PFAM Accession number to another kind of ID

### Description

This is an R object that always contains mappings from a PFAM ID to the other ID type named by the object

### Details

For each of the aliases listed above, there is a mapping object that corresponds which will map you from the appropriate PFAM accession number to the ID type that is in the environments name. So for example PFAMCAZY will map from PFAM IDs to CAZY IDs while PFAMDE will map from PFAM IDs to Descriptions.

CAZY: The CAZy database (<URL: http://afmb.cnrs-mrs.fr/CAZY/>) describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

DE: Definition for all the Accession number in the database.

ID: Associated Identification for all the Accession number in the database.

HOMSTRAD: HOMSTRAD (HOMologous STRucture Alignment Database, <URL: http://www-cryst.bioc.cam.ac.uk/homstrad/>) is a curated database of structure-based alignments for homologous protein families. Reference: Mizuguchi K, Deane CM, Blundell TL, Overington JP. (1998) HOMSTRAD: a database of protein structure alignments for homologous families. Protein Science 7:2469-2471.

INTERPRO: Associated INTERPRO ID for all the Accession number in the database. <URL: http://www.ebi.ac.uk/interpro/>

LOAD: LOAD ID for all the Accession number in the database.

MEROPS: The MEROPS database (<URL: http://merops.sanger.ac.uk/>) is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. Reference: Rawlings, N.D., Tolle, D.P. & Barrett, A.J. (2004) MEROPS: the peptidase database. Nucleic Acids Res. 32 Database issue, D160-D164

MIM: MIM (a.k.a. OMIM, <URL: http://www.ncbi.nlm.nih.gov/omim/>) is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere. Reference: <MIM> MIM: McKusick, V.A.: Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th edition). <OMIM> Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), 2000

PFAMB: Pfam-B is an automatic clustering of the rest of SWISSPROT and TrEMBL derived from the PRODOM database.

PRINTS: PRINTS (<URL: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/>) is a compendium of protein fingerprints.

PROSITEPROFILE: A list of associated PROSITE PROFILE ID.

RM: Reference Medline (<URL: http://www.ncbi.nlm.nih.gov/PubMed/>)

SMART: SMART (a Simple Modular Architecture Research Tool, <URL: http://smart.embl-heidelberg.de/>) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. Reference: (1) Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864. (2) Letunic et al. (2004) Nucleic Acids Res 32, D142-D144

TC: Trusted cutoff for all the Accession number in the database.

TP: A list of associated Type field for the given Accession.

URL: A list of associated URL for all the Accession number in the database.

### References

http://www.sanger.ac.uk/Software/Pfam/ and ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt

### Examples

            #To map from PFAM to CAZYs:
            x <- PFAMCAZY
            # Get the PFAM identifiers that are mapped to a CAZY
            mapped_keys <- mappedkeys(x)
            # Convert to a list
            xx <- as.list(x[mapped_keys])
            if(length(xx) > 0) {
              # Get the CAZY for the first five PFAM IDs
              xx[1:5]
              # Get the first one
              xx[[1]]
            }

            #Or to use the DE mapping:
            x <- PFAMDE
            # Get the PFAM identifiers that are mapped to a DE
            mapped_keys <- mappedkeys(x)
            # Convert to a list
            xx <- as.list(x[mapped_keys])
            if(length(xx) > 0) {
              # Get the DE for the first five PFAM IDs
              xx[1:5]
              # Get the first one
              xx[[1]]
            }

            #etc.

[Package PFAM.db version 2.2.5 Index]