From: BAIROCH@CMU.UNIGE.CH (Amos Bairoch)
Newsgroups: bionet.molbio.proteins
Subject: Annotated yeast chromosome III protein sequences.
Date: 6 Apr 92 15:56:00 GMT
Distribution: bionet


SWISS-PROT ANNOTATED YEAST CHROMOSOME 3 SEQUENCES
=================================================

Like everyone we are eagerly waiting for an official annotated version of the
yeast chromosome 3 protein sequences.   As a  preliminary  measure we decided
to use all the information that  was available in the sequence data banks and
in the literature to annotate the  maximum  number of proteins encoded on the
yeast chromosome III (YCIII).

To do  that  we  used  data  from  the  current  release  of  SWISS-PROT, the
unannotated sections of PIR (PIR2 and PIR3), EMBL and GenBank including daily
updates up to April 2, 1992, Medline abstracts,  as  well  as  all the papers
published  from  1990 to 1992  in the journal Yeast which deal with the YCIII
sequence data.

We have  used  an  ORF library  prepared  by  Peter Rice,  from the EMBL Data
Library, which has translated YCIII in  the six potential frames and kept all
sequences >=100 residues,  he  has run FASTA searches  on  these  ORF against
SWISS-PROT and PIR, as well as scanned them  for PROSITE motifs using the GCG
program MOTIF.

Some additional analyses  were  carried out  with the PC/Gene package: signal
sequence prediction according  to  von Heijne; mitochondrial transit peptides
according  to Gavel and  von Heijne, transmembrane regions according to three
different methods (Eisenberg et al, Rao and Argos, Klein, et al.).

We decided to annotated only two groups of proteins:

   - The proteins for which there is at least one published report.
     Total: 61 entries.

   - The ORFS which are highly similar to an  existing sequence or
     protein family.
     Total: 12 entries.

In each cases we have added a "CC" comment  line that  indicates the position
of the protein coding sequence on YCIII.

Two files have  been  deposited on  a number of FTP and Email servers.  These
files are:

 yc3_sprot.seq : The 73 sequence entries (61 + 12).
 yc3_sprot.doc : This documentation file.

You can get these two files from the following FTP servers  (you should login
as user = anonymous, password: your name or email address).

    Organism : GenBank On-line Service (GOS)
    Address  : genbank.bio.net (or 134.172.1.160)
    Directory: /pub/db/swiss-prot

    Organism : National Center for Biotechnology Information (NCBI)
    Address  : ncbi.nlm.nih.gov (or 130.14.20.1)
    Directory: /repository/swiss-prot

    Organism : Basel Biozentrum Biocomputing server (EMBnet SWISS node)
    Address  : bioftp.unibas.ch (or 131.152.1.7)
    Directory: /biology/database/yeast3

    Organism : ExPASy (Geneva University Expert Protein Analysis System)
    Address  : expasy.hcuge.ch  (or 129.195.254.61)
    Directory: /databases/swiss-prot

--------------------------------------------------------------------------

a) The 61 YCIII sequence entries that correspond to at least one published
   report:

ABP1_YEAST  ACTIN BINDING PROTEIN (GENE: ABP1).
ADP1_YEAST  PROBABLE ATP-DEPENDENT PERMEASE PRECURSOR (GENE ADP1 OR YCR105).
APA1_YEAST  5',5'''-P-1,P-4-TETRAPHOSPHATE PHOSPHORYLASE I (AP-4-A
            PHOSPHORYLASE) (ATP ADENYLYLTRANSFERASE (EC 2.7.7.53))
            (ADP-SULFURYLASE (EC 2.7.7.5)) (GENE: APA1 OR DTP).
BIK1_YEAST  NUCLEAR FUSION PROTEIN BIK1 (GENE: BIK1).
BUD5_YEAST  BUD SITE SELECTION PROTEIN BUD5 (GENE: BUD5).
CD10_YEAST  CELL DIVISION CONTROL PROTEIN 10 (GENE: CDC10).
CISZ_YEAST  CITRATE SYNTHASE, CYTOPLASMIC (EC 4.1.3.7) (GENE: CIT2).
CYPR_YEAST  PEPTIDYL-PROLYL CIS-TRANS ISOMERASE C PRECURSOR (EC 5.2.1.8)
            (PPIASE) (ROTAMASE) (GENE: SCC3).
ERS1_YEAST  TRANSMEMBRANE PROTEIN ERS1 (ERD SUPPRESSOR) (GENE: ERS1).
FUS1_YEAST  NUCLEAR FUSION PROTEIN FUS1 (GENE: FUS1).
G10_YEAST   G10-LIKE PROTEIN (GENE: YCR903).
HIS2_YEAST  PHOSPHORIBOSYL-AMP CYCLOHYDROLASE (EC 3.5.4.19) / PHOSPHORIBOSYL-
            ATP PYROPHOSPHOHYDROLASE (EC 3.6.1.31) / HISTIDINOL DEHYDROGENASE
            (EC 1.1.1.23) (HDH) (GENE: HIS4).
HXKG_YEAST  GLUCOKINASE (GLK) (EC 2.7.1.2) (GENE: GLK1).
KCR1_YEAST  PROBABLE SERINE/THREONINE-PROTEIN KINASE YCR101 (EC 2.7.1.-)
            (GENE: YCR101 OR YCR046).
KI82_YEAST  PROBABLE SERINE/THREONINE-PROTEIN KINASE KIN82 (EC 2.7.1.-)
            (GENE: KIN82).
LEU3_YEAST  3-ISOPROPYLMALATE DEHYDROGENASE (EC 1.1.1.85) (BETA-IPM
            DEHYDROGENASE) (IMDH) (GENE: LEU2).
MIBP_YEAST  PUTATIVE MISMATCH BINDING PROTEIN (MBP) (GENE: YCR1152).
MK31_YEAST  MAK31 PROTEIN (GENE: MAK31).
MK32_YEAST  MAK32 PROTEIN (GENE: MAK32).
MAT1_YEAST  MATING HORMONE ALPHA-1 (GENE: MAT ALPHA-1).
MTA2_YEAST  MATING-TYPE PROTEIN ALPHA-2 (GENE: MAT ALPHA-2).
PGK_YEAST   PHOSPHOGLYCERATE KINASE (EC 2.7.2.3) (GENE: PGK1).
PDI_YEAST   PROBABLE PROTEIN DISULPHIDE ISOMERASE PRECURSOR (PDI) (EC 5.3.4.1).
            (GENE: PDI1 OR MFP1 OR YCL313).
R137_YEAST  PROBABLE METABOLITE TRANSPORT PROTEIN YCR137 (GENE: YCR137).
RA18_YEAST  DNA REPAIR PROTEIN RAD18 (GENE: RAD18).
RBSK_YEAST  PROBABLE RIBOKINASE (EC 2.7.1.15) (GENE: RBK1 OR YCR523).
RS14_YEAST  40S RIBOSOMAL PROTEIN S14 (RP59) (GENE: CRY1).
RVS1_YEAST  REDUCED VIABILITY UPON STARVATION PROTEIN 161 (GENE: RVS161).
ST50_YEAST  STE50 PROTEIN (GENE: STE50).
STDH_YEAST  CATABOLIC L-SERINE DEHYDRATASE (EC 4.2.1.13) / L-THREONINE
            DEHYDRATASE (EC 4.2.1.16) (L-SERINE DEAMINASE) (THREONINE
            DEAMINASE) (GENE: CHA1).
SYN_YEAST   PUTATIVE ASPARAGINYL-TRNA SYNTHETASE (EC 6.1.1.22) (ASPARAGINE--
            TRNA LIGASE) (GENE: YCR242).
THRC_YEAST  THREONINE SYNTHASE (EC 4.2.99.2) (GENE: THR4).
TSM1_YEAST  TSM1 PROTEIN (GENE: TSM1 OR YCR724).
TUP1_YEAST  GLUCOSE REPRESSION REGULATORY PROTEIN TUP1 (FLOCCULATION
            SUPPRESSOR PROTEIN) (REPRESSOR AER2) (GENE: TUP1 OR AER2 OR SFL2
            OR CYC9).
YC21_YEAST  HYPOTHETICAL 12.5 KD PROTEIN IN CDC10 5'REGION (GENE: YCR021).
YC41_YEAST  HYPOTHETICAL 21.4 KD PROTEIN IN CDC10-CIT2 INTERGENIC REGION.
            YCR041.
YC42_YEAST  HYPOTHETICAL 26.4 KD PROTEIN IN CDC10-CIT2 INTERGENIC REGION.
            YCR042.
YC44_YEAST  HYPOTHETICAL 18.3 KD PROTEIN IN CIT2 5'REGION (GENE: YCR044).
YC45_YEAST  HYPOTHETICAL 27.6 KD PROTEIN IN SUF20 5'REGION (GENE: YCR045).
YC86_YEAST  HYPOTHETICAL 65.2 KD PROTEIN IN THR4 3'REGION (GENE: CTR86).
YCA1_YEAST  HYPOTHETICAL 41.6 KD PROTEIN IN HMR REGION (GENE: YCR131).
YCB1_YEAST  HYPOTHETICAL 69.2 KD PROTEIN IN PGK1-CRY1 INTERGENIC REGION (GENE:
            YCR241).
YCB4_YEAST  HYPOTHETICAL 16.0 KD PROTEIN IN PGK1-CRY1 INTERGENIC REGION (GENE:
            YCR244).
YCB6_YEAST  HYPOTHETICAL 84.9 KD PROTEIN IN PGK1-CRY1 INTERGENIC REGION (GENE:
            YCR246).
YCE1_YEAST  HYPOTHETICAL 40.0 KD PROTEIN IN CRY1-MAT INTERGENIC REGION (GENE:
            YCR521).
YCE2_YEAST  HYPOTHETICAL 44.1 KD PROTEIN IN RBK1 5'REGION (GENE: YCR522).
YCE3_YEAST  HYPOTHETICAL 102.5 KD PROTEIN IN RBK1 3'REGION (GENE: YCR524).
YCE4_YEAST  HYPOTHETICAL 251 KD PROTEIN IN CRY1-MAT INTERGENIC REGION (GENE:
            YCR591 OR YCR601).
YCE5_YEAST  HYPOTHETICAL 138.5 KD PROTEIN IN CRY1-MAT INTERGENIC REGION (GENE:
            YCR592).
YCG5_YEAST  HYPOTHETICAL 14.8 KD PROTEIN IN TSM1 5'REGION (GENE: YCR725).
YH26_YEAST  HYPOTHETICAL 26 KD PROTEIN IN CHROMOSOME III RIGHT ARM
            TRANSCRIPTION HOT-SPOT.
YCI1_YEAST  HYPOTHETICAL 114.1 KD PROTEIN IN RAD18 3'REGION (GENE: YCR901).
YCI2_YEAST  HYPOTHETICAL 60.6 KD PROTEIN IN RAD18 5'REGION (GENE: YCR902).
YCI4_YEAST  HYPOTHETICAL 13.8 KD PROTEIN IN SUP61 5'REGION (GENE: YCR904).
YCL1_YEAST  HYPOTHETICAL 42.6 KD PROTEIN IN BIK1-FUS1 INTERGENIC REGION (GENE:
            YCL181).
YCL4_YEAST  HYPOTHETICAL 34.5 KD PROTEIN IN HIS4-STE50 INTERGENIC REGION
            (GENE: YCL184).
YCL6_YEAST  HYPOTHETICAL 23.6 KD PROTEIN IN STE50 5'REGION (GENE: YCL186).
YCL7_YEAST  HYPOTHETICAL 64.9 KD PROTEIN IN STE50 5'REGION (GENE: YCL187).
YCMK_YEAST  HYPOTHETICAL 25.2 KD PROTEIN IN MAK31 3'REGION.
YTYA_YEAST  TRANSPOSON TY1-17 50 KD HYPOTHETICAL PROTEIN (GENE: TYA).
YTYB_YEAST  TRANSPOSON TY1-17 154 KD HYPOTHETICAL PROTEIN (GENE: TYB).


b) The ORFS which are highly similar to an existing sequence or protein
   family.

YAAP_YEAST  HYPOTHETICAL AMINO ACID PERMEASE IN CHROMOSOME III.
YADH_YEAST  HYPOTHETICAL ZINC-TYPE ALCOHOL DEHYDROGENASE-LIKE PROTEIN IN
            CHROMOSOME III (EC 1.1.1.-).
YGLP_YEAST  HYPOTHETICAL GUANINE NUCLEOTIDE-BINDING PROTEIN BETA SUBUNIT-LIKE
            PROTEIN IN CHROMOSOME III.
YGLR_YEAST  HYPOTHETICAL GLUTAREDOXIN LIKE-PROTEIN IN CHROMOSOME III.
YKI1_YEAST  HYPOTHETICAL SERINE/THREONINE-PROTEIN KINASE IN CHROMOSOME III
            (EC 2.7.1.-).
YKI2_YEAST  HYPOTHETICAL SERINE/THREONINE-PROTEIN KINASE IN CHROMOSOME III
            (EC 2.7.1.-).
YNIS_YEAST  HYPOTHETICAL NIFS-LIKE PROTEIN IN CHROMOSOME III.
YRAS_YEAST  HYPOTHETICAL RAS-RELATED PROTEIN IN CHROMOSOME III.
YSPS_YEAST  HYPOTHETICAL SPS2-LIKE PROTEIN IN CHROMOSOME III.
YSUB_YEAST  HYPOTHETICAL SUBTILASE TYPE PROTEINASE IN CHROMOSOME III PRECURSOR
            (EC 3.4.24.-).
YTHI_YEAST  HYPOTHETICAL THIOREDOXIN-LIKE PROTEIN IN CHROMOSOME III.
YZNP_YEAST  HYPOTHETICAL ZINC METALLOPROTEINASE IN CHROMOSOME III
            (EC 3.4.24.-).