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Annotazione Sequenze + informazioni Manuale Automatica.

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Presentation on theme: "Annotazione Sequenze + informazioni Manuale Automatica."— Presentation transcript:

1 Annotazione Sequenze + informazioni Manuale Automatica

2 Attendibilità di una sequenza proteica In ordine decrescente - Proteina nota - mRNA noto (tradotto?) - Gene noto (splicing alternativi?) - Gene predetto per omologia con proteine note - Gene predetto con altri metodi

3 Attendibilità di una funzione In ordine decrescente - Informazioni ottenute dalla letteratura con metodi manuali - Per similarità con proteine a funzione nota - Con altri metodi bioinformatici

4 UNIPROT TrEMBL Swiss- Prot proteine Annotate manualmente Annotate automaticamente





9 Description Protein name Annexin A5 Synonyms Annexin V, Lipocortin V, Endonexin II Ec number EC Contains Prodotti di taglio contenuti Includes Domini funzionali contenuti

10 Gene Name Primary Phospholipase A2 Synonym cPLA2 Locus name Nome ordinato sul genoma Es: XAC2464 ORF name Nome temporaneo su genoma Es: ACAM_3000_MVA_081

11 Organism Common name Eggplant Scientific Solanum melongea Synonym Aubergine Classification Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; a sterids; lamiids; Solanales; Solanaceae; Solanum Taxonomy NCBI_TaxID=9606

12 Date DD-MMM-YYYY Es. 01-Gen-2001 Integrated Data di creazione Entry modified Ultima modifica alla descrizione Sequence modified Ultima modifica alla sequenza

13 References Position Nuleotide/protein sequence Genomic dna/rna, X-ray crystallography, variant Comment Strain, Tissue, Plasmid, Species, Transposon Es. STRAIN=Liver Type Journal Article, Thesis, Submission, Unpublished Author, Title, Year, Journal title, Volume Dati bibliografici

14 Keywords Es: 3D-structure; Alternative splicing; Alzheimer disease; Amyloid;Apoptosis; Cell adhesion; Coated pits; Copper;Direct protein sequencing; Disease mutation; Endocytosis;Glycoprotein; Heparin- binding; Iron; Metal-binding; Notch signaling pathway; Phosphorylation; Polymorphism; Protease inhibitor; Proteoglycan; Serine protease inhibitor; Signal;Transmembrane; Zinc. Iron Bind

15 Organelle Es: Hydrogenosome Mitochondrion Nucleomorph Plasmid Plastid

16 Comments FUNCTION: Binds to actin and affects the structure of the cytoskeleton. At high concentrations, profilin prevents the polymerization of actin, whereas it enhances it at low concentrations. By binding to PIP2, it inhibits the formation of IP3 and DG. ALLERGEN: Causes an allergic reaction in human. Minor allergen of bovine dander. ALTERNATIVE PRODUCTS: Event=Alternative initiation; Comment=2 isoforms, Alpha and Beta, are produced by alternative initiation; BIOPHYSICOCHEMICAL PROPERTIES: Kinetic parameters: KM=98 uM for ATP; KM=688 uM for pyridoxal; Vmax=1.604 mmol/min/mg enzyme; pH dependence: Optimum pH is 6.0. Active from pH 4.5 to 10.5; CATALYTIC ACTIVITY: ATP + L-glutamate + NH(3) = ADP + phosphate + L-glutamine. COFACTOR: Pyridoxal phosphate. DEVELOPMENTAL STAGE: Expressed early during conidial (dormant spores) differentiation. DISEASE: Defects in PHKA1 are linked to X-linked muscle glycogenosis [MIM:311870]. It is a disease characterized by slowly progressive, predominantly distal muscle weakness and atrophy. DOMAIN: Contains a coiled-coil domain essential for vesicular transport and a dispensable C-terminal region. PATHWAY: Porphyrin biosynthesis by the C5 pathway; second step. PHARMACEUTICAL: Available under the name Proleukin (Chiron). Used in patients with renal cell carcinoma or metastatic melanoma. POLYMORPHISM: The allelic form of the enzyme with Gln-191 (Allozyme A) hydrolyzes paraoxon with a low turnover number and the one with Arg-191 (Allozyme B) with a high turnover number. PTM: N- glycosylated and probably also O-glycosylated. RNA EDITING: Modified_positions=393, 431, 452, 495. TISSUE SPECIFICITY: Shoots, roots, and cotyledon from dehydrating seedlings. TOXIC DOSE: PD(50) is 1.72 mg/kg by injection in blowfly larvae.

17 Comments ALLERGENInformation relevant to allergenic proteins ALTERNATIVE PRODUCTS Description of the existence of related protein sequence(s) produced by alternative splicing of the same gene or by the use of alternative initiation codons; see BIOPHYSICOCHEMICAL PROPERTIES Description of the information relevant to biophysical and physicochemical data and information on pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption; see BIOTECHNOLOGYDescription of the use of a specific protein in a biotechnological process CATALYTIC ACTIVITYDescription of the reaction(s) catalyzed by an enzyme [1][1] COFACTORDescription of any non-protein substance required by an enzyme for its catalytic activity DEVELOPMENTAL STAGEDescription of the developmentally-specific expression of mRNA or protein DISEASEDescription of the disease(s) associated with a deficiency of a protein DOMAINDescription of the domain structure of a protein ENZYME REGULATIONDescription of an enzyme regulatory mechanism FUNCTIONGeneral description of the function(s) of a protein INDUCTIONDescription of the compound(s) or condition(s) that regulate gene expression INTERACTIONConveys information relevant to binary protein-protein interaction MASS SPECTROMETRYReports the exact molecular weight of a protein or part of a protein as determined by mass spectrometric methods; see PATHWAYDescription of the metabolic pathway(s) with which a protein is associated PHARMACEUTICALDescription of the use of a protein as a pharmaceutical drug POLYMORPHISMDescription of polymorphism(s) RNA EDITINGDescription of any type of RNA editing that leads to one or more amino acid changes SIMILARITYDescription of the similaritie(s) (sequence or structural) of a protein with other proteins SUBCELLULAR LOCATIONDescription of the subcellular location of the mature protein SUBUNITDescription of the quaternary structure of a protein and any kind of interactions with other proteins or protein complexes; except for receptor- ligand interactions, which are described in the topic FUNCTION. TISSUE SPECIFICITYDescription of the tissue-specific expression of mRNA or protein TOXIC DOSEDescription of the lethal dose (LD), paralytic dose (PD) or effective dose of a protein

18 Features Feature type Start-End range Description Dipende dal tipo INIT_MET - Initiator methionine.SIGNAL - Extent of a signal sequence (prepeptide). PROPEP - Extent of a propeptideTRANSIT - Extent of a transit peptide (mitochondrion, chloroplast, thylakoid) CHAIN - Extent of a polypeptide chain in the mature protein.PEPTIDE - Extent of a released active peptide. TOPO_DOM - Topological domain.TRANSMEM - Extent of a transmembrane region. DOMAIN - Specific combination of secondary structures. NON_TER - The residue at an extremity of the sequence is not the terminal residue. REPEAT - Extent of an internal sequence repetition.CA_BIND - Extent of a calcium-binding region. ZN_FING - Extent of a zinc finger region.DNA_BIND - Extent of a DNA-binding re NP_BIND - Extent of a nucleotide phosphate-binding region.REGION - Extent of a region of interest in the sequen Hydrophobic. COILED - Extent of a coiled-coil region.MOTIF - Short (up to 20 amino acids) sequence motif of biological interest. COMPBIAS - Extent of a compositionally biased region.ACT_SITE - Amino acid(s) involved in the activity of an enzyme. METAL - Binding site for a metal ion.BINDING - Binding site for any chemical group (co-enzyme, prosthetic group, etc.). SITE - Any interesting single amino-acid site, not defined. SE_CYS - Selenocysteine MOD_RES - Posttranslational modification of a residue.LIPID - Lipid binding CARBOHYD - Glycosylation site.DISULFID - Disulfide bond. CROSSLNK - Posttranslationally formed amino acid bonds.VARSPLIC - Description of sequence variants produced by alternative splicing. VARIANT - Authors report that sequence variants exist.MUTAGEN - Site which has been experimentally altered. UNSURE - Uncertainties in the sequenceCONFLICT - Different sources report differing sequences. NON_CONS - Non-consecutive residues.HELIX - Secondary structure STRAND - Secondary structureTURN - Secondary structure

19 Identificativi Entry name Swissprot: Sigla + specie Es. B2MG_HUMAN TrEMBL: Accessionnumber + specie Es. O95417_MOUSE Accession Number Es: Q1AAA9 Primary : Quello da utilizzare Secondary : Elenco dei precedenti numeri non più usati

20 Cross references 70 Banche dati Altri Id altre informazioni Id identificativo primario della bancadati Es. EMBL; AJ297977; CAC ; -; Genomic_DNA. Database nome banca dati

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