PFAMCAZY2AC             package:PFAM.db             R Documentation

_M_a_p_p_i_n_g_s _f_r_o_m _a_n _I_D _t_o _a _P_F_A_M _A_c_c_e_s_s_i_o_n _n_u_m_b_e_r

_D_e_s_c_r_i_p_t_i_o_n:

     This is an R object that contains mapppings from an ID to its PFAM
     Accession number (AC)

_D_e_t_a_i_l_s:

     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.

_R_e_f_e_r_e_n_c_e_s:

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

_E_x_a_m_p_l_e_s:

             #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.

