bsubt.embl complete entry in EMBL format (DNA and Features) bsubt.embl.Z

1. The role SWISS-PROT and TrEMBL play in the Research Environment • Vivien Junker, Rolf Apweiler, Sergio Contrino, Wolfgang Fleischmann, Henning Hermjakob, Fiona Lang, • Michele Magrane, Maria Jesus Martin, Nicoletta Mitaritonna. • EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, U.K. bsubt.embl complete entry in EMBL format (DNA and Features) bsubt.embl.Z bsubt.fasta complete DNA sequence in Fasta format bsubt.fasta.Z bsubt.con construct information EBI homepage http://www.ebi.ac.uk Webin http://www.ebi.ac.uk/submission/webin.html Datasubmissions http://www.ebi.ac.uk/subs/allsubs.html Genome MOT http://www.ebi.ac.uk/~sterk/genome-MOT Anonymous FTP server ftp.ebi.ac.uk Genome FTP server ftp.ebi.ac.uk/pub/databases/embl/genomes General inquiries datalib@ebi.ac.uk Datasubmissions datasubs@ebi.ac.uk Updates update@ebi.ac.uk Telephone +44(0)1223494444 Telefax +44(0)1223494468 • SWISS-PROT Protein Sequence Data Bank • SWISS-PROT is a curated protein sequence database which strives to provide • a high level of annotation (such as the description of the function • of a protein, its domain structure, post-translational modifications, • variants, etc) • a minimal level of redundancy • a high level of integration with other biomolecular databases. • TrEMBL • TrEMBL (Translation of EMBL) is a computer-annotated protein sequence database supplementing SWISS-PROT. It was introduced to deal with the increased data flow from genome projects. It consists of computer-annotated entries in SWISS-PROT-like format which are derived from the translation of all coding sequences (CDS) in the EMBL Nucleotide Sequence Database, except for those CDS already included in SWISS-PROT. • Model Organisms in SWISS-PROT & TrEMBL • A. thaliana H. sapiens • B. subtilis M. genitalium • C.albicans M. tuberculosis • C. elegans S. cerevisiae • D. discoideum S. typhimurium • D. melanogaster S. pombe • E.coli S. solfataricus • H. infulenzae M. jannaschii • For each of the model organisms our aims are: • to be complete as possible, in SWISS-PROT and TrEMBL for all sequences available at any given time • to provide a higher level of annotation • to provide cross-references to specialized database(s) that contain, among other data, some genetic information about the genes that code for these proteins • to provide specific indices or documents • Schizosaccharomyces pombe Genome Project Data • S. pombe is a unicellular yeast that replicates via a process of fission. Its haploid genome is 14 million base pairs (Mb) long which contains an estimated 4,000 genes on 3 chromosomes. The genome • sequencing project is a collaborative one between a number of laboratories world-wide. • Chromosome 1 is the largest of S. pombe's three chromosomes at 5.7 Mb. Approximately 3.8 Mb of unique chromosome 1 sequence is currently in the EMBL database. Most of this was sequenced at the Sanger Centre during the pilot sequencing project. • Chromosome 2 is being sequenced as part of the European S. pombe genome sequencing project. Its size is estimated at 4.6 Mb. • Chromosome 3 is the smallest of S. pombe's three chromosomes. Its size is estimated at 3.5 Mb. Sequencing of chromosome 3 was started in early 1998. • Status of S. pombe data • There are approximately 1315 S. pombe protein sequence entries in • SWISS-PROT. • SP-TrEMBL contains approximately 1574 S. pombe protein • sequence databases. These will be annotated by a curator and added • into the SWISS-PROT database. Many more cosmids are being submitted daily and so this number will increase drastically. • S. pombe textfiles in SWISS-PROT • POMBE.TXT - Index of S. pombe entries in SWISS-PROT • and their corresponding gene designations. Example of a SWISS-PROT S.pombe entry with data from the genome project and other sources. ID KPYK_SCHPO STANDARD; PRT; 509 AA. AC Q10208; DT 01-OCT-1996 (REL. 34, CREATED) DT 01-OCT-1996 (REL. 34, LAST SEQUENCE UPDATE) DT 01-OCT-1996 (REL. 34, LAST ANNOTATION UPDATE) DE PYRUVATE KINASE (EC 2.7.1.40). GN PYK1 OR SPAC4H3.10C. OS SCHIZOSACCHAROMYCES POMBE (FISSION YEAST). OC EUKARYOTA; FUNGI; ASCOMYCOTINA; HEMIASCOMYCETES. RN [1] RP SEQUENCE FROM N.A. RX MEDLINE; 96102864. RA NAIRN J., SMITH S., ALLISON P.J., RIGDEN D., RA FOTHERGILL-GILMORE L.A., PRICE N.C.; RL FEMS MICROBIOL. LETT. 134:221-226(1995). RN [2] RP SEQUENCE FROM N.A. RC STRAIN=972; RA MURPHY L., HARRIS D., BARRELL B.G., RAJANDREAM M.A., WALSH S.V.; RL SUBMITTED (FEB-1996) TO EMBL/GENBANK/DDBJ DATA BANKS. CC -!- CATALYTIC ACTIVITY: ATP + PYRUVATE = ADP + PHOSPHOENOLPYRUVATE. CC -!- COFACTOR: REQUIRES MAGNESIUM AND POTASSIUM. CC -!- PATHWAY: FINAL STEP IN GLYCOLYSIS. CC -!- SUBUNIT: HOMOTETRAMER (BY SIMILARITY). CC -!- SIMILARITY: BELONGS TO THE PYRUVATE KINASE FAMILY. DR EMBL; X91008; E196863; -. DR EMBL; Z69380; E221947; -. DR PROSITE; PS00110; PYRUVATE_KINASE; 1. KW TRANSFERASE; KINASE; GLYCOLYSIS; MAGNESIUM; PHOSPHORYLATION. FT MOD_RES 29 29 PHOSPHORYLATION (POTENTIAL). FT ACT_SITE 247 247 BY SIMILARITY. FT METAL 249 249 MAGNESIUM (POTENTIAL). FT METAL 270 270 MAGNESIUM (POTENTIAL). FT METAL 271 271 MAGNESIUM (POTENTIAL). FT BINDING 344 344 ADP (POTENTIAL). FT CONFLICT 391 391 A -> R (IN REF. 1). SQ SEQUENCE 509 AA; 55514 MW; 975A0526 CRC32; MSSSAVSPKQ WVAGLNSELD IPAVNRRTSI ICTIGPKSNN VETLCKLRDA GMNIVRMNFS HGSYEYHQSV IDNARKASAT NPLFPLAIAL DTKGPEIRTG LTVGGTDYPI SSGHEMIFTT DDAYAEKCND KVMYIDYKNI TKVIQPGRII YVDDGILSFT VIEKVDDKNL KVRVNNNGKI SSKKGVNLPK TDVDLPALSE KDKADLRFGV KNGVDMIFAS FIRRAEDVIH IREVLGEEGK NIKIICKIEN QQGVNNFDSI LDVTDGIMVA RGDLGIEIPA SQVFVAQKMM IAKCNIAGKP VACATQMLES MTYNPRPTRA EVSDVGNAVL DGADLVMLSG ETTKGSYPVE AVTYMAETAR VAEASIPYGS LYQEMFGLVR RPLECATETT AVAAIGASIE SDAKAIVVLS TSGNTARLCS KYRPSIPIVM VTRCPQRARQ SHLNRGVYPV IYEKEPLSDW QKDVDARVAY GCQQAYKMNI LKKGDKIIVL QGAVGGKGHT SIFRLTVAE // How to contact us: WWW (EBI homepage): http://www.ebi.ac.uk E-Mail (submissions): datasubs@ebi.ac.uk E-Mail: junker@ebi.ac.uk FTP: ftp.ebi.ac.uk Telephone: ++44(0) 1223 494462 Fax: ++44(0) 1223 494468