\HeaderA{PFAMCAZY2AC}{Mappings from an ID to a PFAM Accession number}{PFAMCAZY2AC}
\aliasA{PFAMDE2AC}{PFAMCAZY2AC}{PFAMDE2AC}
\aliasA{PFAMHOMSTRAD2AC}{PFAMCAZY2AC}{PFAMHOMSTRAD2AC}
\aliasA{PFAMID2AC}{PFAMCAZY2AC}{PFAMID2AC}
\aliasA{PFAMINTERPRO2AC}{PFAMCAZY2AC}{PFAMINTERPRO2AC}
\aliasA{PFAMLOAD2AC}{PFAMCAZY2AC}{PFAMLOAD2AC}
\aliasA{PFAMMEROPS2AC}{PFAMCAZY2AC}{PFAMMEROPS2AC}
\aliasA{PFAMMIM2AC}{PFAMCAZY2AC}{PFAMMIM2AC}
\aliasA{PFAMPFAMB2AC}{PFAMCAZY2AC}{PFAMPFAMB2AC}
\aliasA{PFAMPRINTS2AC}{PFAMCAZY2AC}{PFAMPRINTS2AC}
\aliasA{PFAMPROSITE2AC}{PFAMCAZY2AC}{PFAMPROSITE2AC}
\aliasA{PFAMPROSITEPROFILE2AC}{PFAMCAZY2AC}{PFAMPROSITEPROFILE2AC}
\aliasA{PFAMRM2AC}{PFAMCAZY2AC}{PFAMRM2AC}
\aliasA{PFAMSMART2AC}{PFAMCAZY2AC}{PFAMSMART2AC}
\aliasA{PFAMTC2AC}{PFAMCAZY2AC}{PFAMTC2AC}
\aliasA{PFAMTP2AC}{PFAMCAZY2AC}{PFAMTP2AC}
\aliasA{PFAMURL2AC}{PFAMCAZY2AC}{PFAMURL2AC}
\keyword{datasets}{PFAMCAZY2AC}
\begin{Description}\relax
This is an R object that contains mapppings from an ID to its
PFAM Accession number (AC)
\end{Description}
\begin{Details}\relax
For each of the aliases listed above, there is a mapping object that
corresponds which will map you from the ID type in the environments
name to the appropriate PFAM accession number.  So for example
PFAMCAZY2AC will map from CAZY IDs to PFAM IDs while
PFAMDE2AC will map from Descriptions to PFAM IDs.

Details on supported things that are mapped to:

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.
\end{Details}
\begin{References}\relax
\url{http://www.sanger.ac.uk/Software/Pfam/} and
\url{ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/userman.txt}
\end{References}
\begin{Examples}
\begin{ExampleCode}
        #To map from CAZY to PFAM IDs:
        x <- PFAMCAZY2AC
        # Get the CAZY identifiers that are mapped to a PFAM ID
        mapped_keys <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_keys])
        if(length(xx) > 0) {
          # Get the PFAM ID for the first five CAZYs
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

        #Or to use the DE2AC mapping:
        x <- PFAMDE2AC
        # Get the Descriptions that are mapped to a PFAM ID
        mapped_keys <- mappedkeys(x)
        # Convert to a list
        xx <- as.list(x[mapped_keys])
        if(length(xx) > 0) {
          # Get the PFAM ID for the first five DEs
          xx[1:5]
          # Get the first one
          xx[[1]]
        }

        #etc.
\end{ExampleCode}
\end{Examples}

