Yeast Protein Database (YPD)

[James I. Garrels]

Dear Yeastnetters,

This is an update on the Yeast Protein Database (YPD).

--- YPD is found on the Web at http://www.proteome.com/YPDhome.html

--- YPD contains information on all yeast proteins of known sequence,
       There are presently 5185 proteins in YPD.

--- YPD specializes in protein properties including physical properties,
       function, modification, localization, mutant phenotypes, and
       relatedness to other proteins.

--- YPD contains extensive annotations extracted from the yeast literature.
      There are presently over 20000 annotations.

--- YPD has direct links to sequence databases, to SGD, and to Medline.
       There are presently over 8200 references cited in YPD.

--- YPD is updated daily with new sequences released to GenBank.

YPD keeps a current tabulation of all the yeast proteins by many categories
     of function, localization, modification, and genetic properties.
     The current table of contents is found below.

Comments and corrections are always welcome.

Jim Garrels

---------------------------------------------------------------
James I. Garrels, Ph.D.                 Tel (508) 922-1643
PROTEOME INC.                           FAX (508) 922-3971
181 Elliott St.,  Suite 909             Email jg at proteome.com
Beverly, MA 01915                       WWW http://www.proteome.com
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YPD SUMMARY REPORT for Feb. 21, 1996

TOTAL PROTEINS   = 5185
TOTAL REFERENCES = 8288

PROTEINS CHARACTERIZED BY GENETICS OR BIOCHEMISTRY   = 2280
PROTEINS KNOWN BY HOMOLOGY TO CHARACTERIZED PROTEINS =  880
PROTEINS OF UNKNOWN FUNCTION                         = 2025

PROTEINS BY MAJOR LOCALIZATION CATEGORY(documentation)
    536  Nuclear proteins
    418  Cytoplasmic proteins
    271  Mitochondrial proteins
    110  Plasma membrane proteins
     77  Endoplasmic reticulum proteins
     51  Cytoskeletal proteins
     50  Extracellular and cell wall proteins
     51  Vacuolar proteins
     31  Golgi proteins
     23  Peroxisomal proteins
     28  Vesicular proteins of the secretory system
    137  Unspecified membrane proteins
   3420  Proteins of unknown localization

PROTEINS BY MINOR LOCALIZATION CATEGORY(documentation)
     91  Mitochondrial inner membrane proteins
     10  Mitochondrial outer membrane proteins
     17  Nucleolar proteins
     23  Nuclear pore proteins
     10  Spindle pole body proteins
     17  Cell wall proteins

PROTEINS BY MOLECULAR ENVIRONMENT (documentation)
    195  Soluble proteins
    546  Integral membrane proteins
     98  Peripheral membrane proteins
     24  Actin-associated proteins
     16  Tubulin-associated proteins
    165  Ribosomal proteins
     43  Protein synthesis factors
    383  DNA-associated proteins
    104  RNA-associated proteins

PROTEINS BY FUNCTIONAL CATEGORY (documentation)
    107  Protein kinases
     35  Protein phosphatases
    152  Transcription factors
     20  Cyclins
     34  Heat shock proteins
     33  tRNA synthetases
     16  Glucose metabolism
     68  Amino acid metabolism
     24  Serine-rich protein family
     22  Conserved ATPase domain (AAA) proteins
     20  ATP-binding cassette (ABC) proteins
     37  Proteases (non-proteasomal)
     50  GTPases
      8  Guanine nucleotide exchange factors
     11  GTPase-activating proteins
     11  Ubiquitin-conjugating proteins
     14  Proteasome subunits

PROTEINS BY POST-TRANSLATIONAL MODIFICATION(documentation)
    147  Phosphorylated proteins
     51  N-glycosylated proteins
     22  O-glycosylated proteins
     86  N-acetylated proteins
      8  N-myristylated proteins
    107  N-unmodified proteins
     15  C-farnesylated proteins
     11  C-geranylgeranylated proteins
     15  C-gpi anchor proteins
    273  Proteins with N-terminal precursor

PROTEINS BY GENETIC PROPERTIES(documentation)
    407  Essential proteins
    219  Coded from gene with intron
     98  Coded from Chromosome I
    409  Coded from Chromosome II
    202  Coded from Chromosome III
    597  Coded from Chromosome IV
    267  Coded from Chromosome V
    127  Coded from Chromosome VI
    247  Coded from Chromosome VII
    271  Coded from Chromosome VIII
    216  Coded from Chromosome IX
    381  Coded from Chromosome X
    332  Coded from Chromosome XI
    359  Coded from Chromosome XII
    444  Coded from Chromosome XIII
    283  Coded from Chromosome XIV
    312  Coded from Chromosome XV
    342  Coded from Chromosome XVI

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