]> Properties and classes used for protein annotation. name A synonym of the recommended name. Attaches an annotation to a resource. based on The sequence on which the description of a modified sequence is based. 1 1 1 A publication from which data was extracted, or which contains additional information. classified with A concept that classifies this resource. A component of a protein. A domain of a protein. encoded by The gene by which a protein is encoded. encoded in The subcellular location where a protein is encoded. enzyme The catalytic activity associated with a protein. or part of a protein. An erratum for a publication. erratum for The publication which an erratum refers to. 1 1 1 located on The molecule a this resource is located on. One of several similar resources. member of The experimental method that was used. A modification of a sequence. The organism in which a protein occurs. 1 1 1 A protein that participates in a protein-protein interaction. A range of amino acids. The rank of a taxon. The name recommended by the UniProt consortium. replaced by A resource that replaces this resource. A resource that is replaced by this resource. An amino acid sequence. sequence for A resource that describes this sequence. The reliability of a statement. A name provided by the submitter of the underlying nucleotide sequence. 1 1 1 True if the class does not have any direct instances. catalytic activity The description of a catalytic activity. An alternative name used in the flat text format. See http://www.expasy.org/cgi-bin/lists?allergen.txt True if the protein is divergent in sequence or has mutated functional sites. The author of a publication. The first position of a range. A name used in a biotechnological context. A name from the Human Cell Differentiation Molecules (HCDM) nomenclature. False if there is any uncertainty about a statement. Maps a series of symbols representing chains of a protein to a range of amino acids. An caclulated value that is used to detect if there are errors in the sequence as shown due to among others IO errors. Both the crc64 and md5sum have collisions in UniProt data and cannot be used as unique keys. cofactor A cofactor required for a catalytic activity. common name The date a resource was created. The number of domains in a protein that correspond to a family. This is almost always 1, but may be 2 if two identical domains are fused. The editor of a publication. The last position of a range. false negative True if a statement is true even though it was not predicted. Indicates if a sequence is complete or consists of one or more fragments. multiple single True if a sequence modification causes a frameshift. The full name. True if the rule on which the membership of a protein to a family is based does not cover the entire protein. The group or consortium that authored a publication. The number of hits found in a sequence. The level of sequence identity in a cluster. 0.5 0.9 1.0 True if existance of this resource can be inferred. The institution at which a thesis was written. The international nonproprietary name: A generic name for a pharmaceutical substance or active pharmaceutical ingredient that is globally recognized and is a public property. True if the range does not extend beyond the specified endpoint. locus name The mass of a sequence in Daltons. A maximum value. measured activity The maximum velocity, Vmax. measured affinity The Michaelis-Menten constant, Km. measured error The magnitude of the error of a value that was measured. measured value A value that was measured. The date a resource was last modified. name obsolete True if this resource has been replaced or deleted. ORF name other name The first and last page for a chapter or article. part of lineage True for taxa that can appear as part of an organism's lineage. True if the pattern or profile on which the domain assignment is based did not detect the sequence because the sequence is not complete and lacks the region on which the pattern or profile is based. A URL pattern, used to generate links by substituting an identifier. The place where a publication was published. This usually includes a country name. A position on a sequence. The publisher of a book. The resolution of an experiment, in Angstrom. Indicates whether a resource has been reviewed by a curator. scientific name The extent of the work carried out by the authors of a publication. An abbreviation of the full name or an acronym. The database a resource was submitted to. A replacement sequence. The title of a publication. The volume a publication is part of. Absorption Indicates the wavelength in nm at which photoreactive proteins such as opsins and DNA photolyases show maximal absorption. Active Site Amino acid(s) involved in the activity of an enzyme. Allergen Information relevant to allergenic proteins. Alternative Initiation Alternative Products Description of the existence of related protein sequences produced by alternative splicing of the same gene or by the use of alternative initiation codons. Alternative Promoter Usage Splice Variant Description of sequence variants produced by alternative splicing. Alternative Splicing Description of a resource on a specific topic. Entity used to attach evidence or provenance to a rdf statement via reification. Strand Binding Site Binding site for any chemical group (co-enzyme, prosthetic group, etc.). Biophysicochemical Property Biophysical and physicochemical data such as pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption. Biotechnology Description of the use of a specific protein in a biotechnological process. Book Citation 1 A chapter from a book. Calcium Binding Extent of a calcium-binding region. Catalytic Activity Description of the reactions catalyzed by an enzyme. Caution Warning about possible errors and/or grounds for confusion. Cellular Component Chain Extent of a polypeptide chain in the mature protein. Description of a publication from which data was obtained. Citation Statement The relationship between a resource and a citation. Cluster of proteins with similar sequences. Cofactor Description of an enzyme cofactor. Coiled-Coil Extent of a coiled-coil region. Compositionally Biased Region Extent of a compositionally biased region. Concept A concept used to classify resources. Crosslink Posttranslationally formed amino acid bonds. Metadata for a life science database. Developmental Stage Description of the developmentally-specific expression of a protein. Disease Description of the diseases associated with a deficiency of a protein. Disruption Phenotype Disulfide Bond Describes residues which are linked by an intra-chain disulfide bond. If the endpoints are identical, the disulfide bond is an interchain one. Domain Description of the domain structure of a protein. Domain Assignment Statement The relationship between a protein and a protein domain. Domain Extent Extent of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold. Electronic Citation 1 An electronic publication. Endpoint Statement Metadata for an endpoint of a range on a sequence. Enzyme A specific catalytic activity, defined by the Enzyme Commission of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB). http://www.expasy.org/enzyme/ Enzyme Regulation Description of an enzyme regulatory mechanism. Erroneous Gene Model Prediction Erroneous Initiation Erroneous Termination Erroneous Translation Experimental Information External Sequence Family Membership Statement The relationship between a protein and a protein family. Frameshift Function General description of the functions of a protein. 1 Genomic DNA Genomic RNA Glycosylation Site Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein. Helix Induction Description of the compounds or conditions that stimulate the synthesis of a protein. Initiator Methionine Indicates that the initiator methionine has been cleaved off and is not shown in the sequence. Description of a protein-protein interaction. Journal Citation 1 An article published in a journal. Kinetics Mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes. Known Sequence Lipid Binding Covalent binding of a lipid moiety. mRNA Mass Measurement An experimental method for measuring the mass of a molecule. iki:Mass_spectrometry Mass 1 Indicates the mass of a sequence determined by mass spectrometry. Metal Ion Binding Site Binding site for a metal ion. An experimental method. Modification Describes amino acid modifications, post pre- and post-translational. Modified Residue Posttranslational modification of a residue. Modified Sequence A biological molecule. Molecule Processing Motif Short (<=20 amino acids) sequence motif of biological interest. Mutagenesis Site Site which has been experimentally altered. Nucleotide Phosphate Binding Extent of a nucleotide phosphate-binding region. Sequence Variant Authors report that sequence variants exist. Natural Variation Non-consecutive Residues Indicates that two residues in a sequence are not consecutive and that there are a number of unsequenced residues between them. Non standard residue Describes the occurrence of a non standard residue in the sequence record. Non-terminal Residue The residue at an extremity of the sequence is not the terminal residue. false 1 1 DNA Binding Extent of a DNA-binding region. Nucleotide Mapping Statement The relationship between a protein and a nucleotide sequence. Nucleotide Resource 1 A resource that descripes a nucleotide sequence. Observation Citation Citation of an unpublished result. true Organelle Orientation Other DNA Other RNA pH Dependence Describes the optimum pH for enzyme activity and/or the variation of enzyme activity with pH variation. PTM Description of a posttranslational modification. Description of a part of a protein. Patent Citation A patent application. Pathway Description of the metabolic pathways with which a protein is associated. Peptide Extent of a released active peptide. Pharmaceutical Description of the use of a protein as a pharmaceutical drug. Polymorphism Description of polymorphisms. Propeptide Extent of a propeptide. Protein Description of a protein. Protein Family Desription of a set of related proteins. Published Citation RNA Editing Description of any type of RNA editing that leads to one or more amino acid changes. 1 1 1 1 A range of amino acids on a protein sequence. A rank of a taxon. Redox Potential Reports the value of the standard (midpoint) oxido-reduction potential(s) for electron transport proteins. Region Repeat Extent of an internal sequence repetition. 1 A life science resource. Ribosomal Frameshifting Secondary Structure Describes the secondary structure of proteins whose tertiary structure is known experimentally. An amino acid sequence. Sequence Annotation Description of a special region or site in a protein sequence. Sequence Caution Sequence Conflict Different sources report differing sequences. Unsure Residue Used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment. Signal Peptide Extent of a signal sequence (prepeptide). Similarity Description of the similarities (sequence or structural) of a protein with other proteins. Simple Sequence Site Any interesting single amino-acid site on the sequence, that is not defined by another feature key. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. Indicator for the reliability of a piece of information. Strain A strain of a species. Structure Determination An experimental method for determining the 3D structure of a protein. Structure Mapping Statement The relationship between a protein and a 3D structure. Structure Resource 1 A resource that describes the 3D structure of a protein. Subcellular Location Subcellular Location Description of the subcellular location of the mature protein. Submission Citation 1 Data that was submitted directly to a database. Subunit Description of the quaternary structure of a protein. 1 An element of a taxonomy for classifying life forms. http://www.ebi.ac.uk/newt/ Temperature Dependence Indicates the optimum temperature for enzyme activity and/or the variation of enzyme activity with temperature variation; the thermostability/thermolability of the enzyme is also mentioned when it is known. Thesis Citation 1 A Ph.D. thesis. Tissue A tissue such as lung or heart. Tissue Specificity Description of the tissue specificity of a protein. Topological Domain A topological domain. Topology Toxic Dose Information on the LD(50). LD stands for "Lethal Dose". LD(50) is the amount of a toxin, given all at once, which causes the death of 50% (one half) of a group of test animals. Transcribed RNA Transcript Resource Transit Peptide Extent of a transit peptide (mitochondrion, chloroplast, thylakoid, cyanelle or microbody). Transmembrane Extent of a transmembrane region. Transposon A transposon Turn Unassigned DNA Unassigned RNA Unknown Sequence Unpublished Citation Viral cRNA Positive cRNA molecule that is made from from a single stranded genomic RNA. Zinc Finger Extent of a zinc finger region. Atmospheric Pressure Ionization Mass measurement using Atmospheric Pressure Ionization Apicoplast By Similarity Chloroplast Taxonomy rank Class Cyanelle Electrospray Ionization iki:Electrospray_ionization Electron Microscopy The electron microscope is a microscope that can magnify very small details with high resolving power due to the use of electrons rather than light to scatter off material, magnifying at levels up to 500,000 times. iki:Electron_microscopy Evidence at protein level Evidence at transcript level Indicates that the existence of a protein has not been strictly proven but that expression data (such as existence of cDNA(s), RT-PCR or Northern blots) indicate the existence of a transcript. Indicates that there is some experimental evidence that the given annotation could apply. Fast Atom Bombardment Taxonomy rank Family Fiber Diffraction Taxonomy rank Forma Taxonomy rank Genus Hydrogenosome Inferred from homology Taxonomy rank Infraclass Taxonomy rank Infraorder Infrared Spectroscopy A type of spectroscopy that uses the Infrared portion of the electromagnetic spectrum. iki:Infrared_spectroscopy Taxonomy rank Kingdom Liquid Secondary Ionization Matrix-Assisted Laser Desorption iki:Matrix-assisted_laser_desorption_ionization Mitochondion NMR Spectroscopy iki:NMR Neutron Diffraction iki:Neutron_diffraction Non-photosyntethic plastid Nuleomorph Taxonomy rank Order Organellar chromatophore Plasma Desorption Taxonomy rank Parvorder Taxonomy rank Phylum Plastid Potential indicates that there is some logical or conclusive evidence that the given annotation could apply. This non-experimental qualifier is often used to present results from protein sequence analysis software tools, which are only annotated if the result makes sense in the biological context of a given protein. A typical example is the annotation of N-glycosylation sites in secreted proteins Predicted This is used for proteins without evidence at protein, transcript, or homology levels. Prediction Probable The status ?Probable? indicates stronger evidence than the qualifier ?Potential?. This qualifier implies that there must be at least some experimental evidence, which indicates, that the information is expected to be found in the natural environment of a protein. Surface Enhanced Laser Desorption Ionization Taxonomic rank Species Taxonomic rank Species Group Taxonomic rank Species Subgroup Taxonomic rank Subclass Taxonomic rank Subfamily Taxonomic rank Subgenus Taxonomic rank Subkingdom Taxonomic rank Suborder Taxonomic rank Subphylum Taxonomic rank Subspecies Taxonomic rank Subtribe Taxonomic rank Superclass Taxonomic rank Superfamily Taxonomic rank Superkingdom Taxonomic rank Superorder Taxonomic rank Superphylum Taxonomic rank Tribe Uncertain Taxonomic rank Varietas X-Ray Crystallography A technique in crystallography in which the pattern produced by the diffraction of x-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. iki:X-ray_crystallography