1 / 14

Mus musculus - a model organism in SWISS-PROT

Mus musculus - a model organism in SWISS-PROT. SWISS-PROT. Curated protein sequence data bank established in 1986 by Amos Bairoch in Geneva and maintained collaboratively with EMBL since 1987 Contains currently >74 000 protein sequence entries (Release 36). Distinguishing features.

nicole
Download Presentation

Mus musculus - a model organism in SWISS-PROT

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Mus musculus - a model organism in SWISS-PROT

  2. SWISS-PROT • Curated protein sequence data bank established in 1986 by Amos Bairoch in Geneva and maintained collaboratively with EMBL since 1987 • Contains currently >74 000 protein sequence entries (Release 36)

  3. Distinguishing features • High level of annotation • Minimal redundancy • High level of integration with other databases

  4. TrEMBL • Computer-annotated supplement to SWISS-PROT • Consists of entries in SWISS-PROT format • Contains translations of all coding sequences in EMBL Nucleotide Sequence Database which are not yet in SWISS-PROT • Consists of SP-TrEMBL and REM-TrEMBL

  5. Model organisms in SWISS-PROT • Target of genome sequencing and/or mapping • Priority annotation • incorporate new sequences/updates as quickly as possible • high level of annotation • cross-references to specialised databases • additional information in form of specific documents

  6. Current status of mouse sequences • Total of 7006 entries in SWISS-PROT and TrEMBL • 3264 entries in SWISS-PROT • 3742 in SP-TrEMBL

  7. Citation information Taxonomic data Sequence data Function(s) of the protein Post-translational modification(s) Domains and sites Secondary and quaternary structure Similarities to other proteins Disease(s) associated with deficiencie(s) in the protein Sequence variants, conflicts Annotation

  8. Annotation sources • Publications reporting sequence data • Review articles • External experts

  9. Integration with other databases • Sequence • EMBL Nucleotide Sequence Database • Structure • Protein Data Bank (PDB)

  10. Integration • Specialised data collections • e.g. ENZYME, PROSITE • Mouse Genome Database (MGD) • Index of MGD entries referenced in SWISS-PROT: http://www.expasy.ch/cgi-bin/lists?mgdtosp.txt

  11. ID GCDH_MOUSE STANDARD; PRT; 438 AA. • AC Q60759; • DT 01-NOV-1997 (REL. 35, CREATED) • DT 01-NOV-1997 (REL. 35, LAST SEQUENCE UPDATE) • DT 01-NOV-1997 (REL. 35, LAST ANNOTATION UPDATE) • DE GLUTARYL-COA DEHYDROGENASE PRECURSOR (EC 1.3.99.7). • GN GCDH. • OS MUS MUSCULUS (MOUSE). • OC EUKARYOTA; METAZOA; CHORDATA; VERTEBRATA; TETRAPODA; MAMMALIA; EUTHERIA; RODENTIA. • RN [1] • RP SEQUENCE FROM N.A. • RC STRAIN=129/SV; TISSUE=LIVER; • RX MEDLINE; 96039264. • RA KOELLER D.M., DIGIULIO K.A., ANGELONI S.V., DOWLER L.L., FRERMAN F.E., WHITE R.A., GOODMAN S.I.; • RL GENOMICS 28:508-512(1995). • CC -!- CATALYTIC ACTIVITY: GLUTARYL-COA + ACCEPTOR = CROTONOYL-COA + CO(2) + REDUCED ACCEPTOR. • CC -!- COFACTOR: FAD FLAVOPROTEIN. • CC -!- PATHWAY: DEGRADATIVE PATHWAY OF L-LYSINE, L-HYDROXYLYSINE, AND L-TRYPTOPHAN METABOLISM. • CC -!- SUBUNIT: HOMOTETRAMER. • CC -!- SUBCELLULAR LOCATION: MITOCHONDRIAL MATRIX. • CC -!- SIMILARITY: BELONGS TO THE ACYL-COA DEHYDROGENASES FAMILY. • DR EMBL; U18992; G1439521; -. • DR MGD; MGI:104541; GCDH. • DR PROSITE; PS00072; ACYL_COA_DH_1; FALSE_NEG. • DR PROSITE; PS00073; ACYL_COA_DH_2; 1. • KW OXIDOREDUCTASE; FLAVOPROTEIN; FAD; MITOCHONDRION; TRANSIT PEPTIDE. • FT TRANSIT 1 44 MITOCHONDRION (POTENTIAL). • FT CHAIN 45 438 GLUTARYL-COA DEHYDROGENASE. • SQ SEQUENCE 438 AA; 48646 MW; 8C9149C3 CRC32;

  12. Summary • Complete with minimal redundancy • As much up-to-date information as possible on each sequence • Priority annotation of mouse sequences • MGD cross-refererences

  13. Rolf Apweiler Sergio Contrino Wolfgang Fleischmann Henning Hermjakob Vivien Junker Stephanie Kappus Fiona Lang Michele Magrane Maria Jesus Martin Nicoletta Mitaritonna Steffen Moeller Claire O’Donovan SWISS-PROT at EBI

  14. Some ways to access SWISS-PROT + TREMBL • ftp.ebi.ac.uk/pub/databases • http://srs.ebi.ac.uk:5000/ • http://www2.ebi.ac.uk/fasta3/ • http://www2.ebi.ac.uk/blast2/ • http://www2.ebi.ac.uk/bic_sw/

More Related