]> Properties and classes used for protein annotation. A synonym of the recommended name. http://www.uniprot.org/manual/protein_names 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 http://www.uniprot.org/faq/15 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 ecName is the enzyme classification associated with a structured name of the protein. Proteins are often named after their enzymatic activity but can have more than one activity leading to multiple names. 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. http://www.uniprot.org/manual/sequence_status 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. http://www.uniprot.org/manual/entry_name A easy to remember identifier for a UniProtKB entry, but it is not a stable identifier and should not be used by programs to identify entries. The date a resource was last modified. name obsolete True if this resource has been replaced or deleted. A mnemonic that is no longer in use for this entry. 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. http://www.uniprot.org/faq/47 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. http://www.uniprot.org/manual/protein_names All names of the protein, from commonly used to obsolete, to used in the literature.. The database a resource was submitted to. A replacement sequence. The title of a publication. The volume a publication is part of. http://www.uniprot.org/manual/binary_interactions 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. http://www.uniprot.org/manual/act_site Allergen Information relevant to allergenic proteins. http://www.uniprot.org/manual/allergenic_properties 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. http://www.uniprot.org/manual/alternative_products Alternative Promoter Usage Splice Variant Description of sequence variants produced by alternative splicing. http://www.uniprot.org/manual/var_seq Alternative Splicing Description of a resource on a specific topic. Entity used to attach evidence or provenance to a rdf statement via reification. Strand Beta strand regions within the experimentally determined protein structure http://www.uniprot.org/manual/strand Binding Site Binding site for any chemical group (co-enzyme, prosthetic group, etc.). http://www.uniprot.org/manual/binding Biophysicochemical Property Biophysical and physicochemical data such as pH dependence, temperature dependence, kinetic parameters, redox potentials, and maximal absorption. http://purl.uniprot.org/core/biophysicochemical_properties Biotechnology Description of the use of a specific protein in a biotechnological process. http://www.uniprot.org/manual/biotechnological_use Book Citation 1 A chapter from a book. Calcium Binding Extent of a calcium-binding region. http://www.uniprot.org/manual/ca_bind Catalytic Activity Description of the reactions catalyzed by an enzyme. http://www.uniprot.org/manual/catalytic_activity Caution Warning about possible errors and/or grounds for confusion. http://www.uniprot.org/manual/caution Cellular Component Chain Extent of a polypeptide chain in the mature protein. http://www.uniprot.org/manual/chain Description of a publication from which data was obtained. http://www.uniprot.org/manual/references Citation Statement The relationship between a resource and a citation. Cluster of proteins with similar sequences. http://www.uniprot.org/uniref/ Cofactor Description of an enzyme cofactor. http://www.uniprot.org/manual/cofactor Coiled-Coil Extent of a coiled-coil region. http://www.uniprot.org/manual/coiled Compositionally Biased Region Extent of a compositionally biased region. http://www.uniprot.org/manual/compbias Concept A concept used to classify resources. Crosslink Posttranslationally formed amino acid bonds. http://www.uniprot.org/manual/crosslnk Metadata for a life science database. http://www.uniprot.org/manual/cross_references Developmental Stage Description of the developmentally-specific expression of a protein. http://www.uniprot.org/manual/developmental_stage Disease Description of the diseases associated with a deficiency of a protein. http://www.uniprot.org/manual/involvement_in_disease Disruption Phenotype http://www.uniprot.org/manual/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. http://www.uniprot.org/manual/disulfid Domain Description of the domain structure of a protein. http://www.uniprot.org/manual/domain_cc 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. http://www.uniprot.org/manual/domain 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. http://www.uniprot.org/manual/enzyme_regulation Erroneous Gene Model Prediction Erroneous Initiation Erroneous Termination Erroneous Translation Experimental Information External Sequence The protein described in the linked record is an alternative splice form of the same gene product as described in this record. The function between the two isoforms is highly divergent. http://www.uniprot.org/manual/alternative_products Family Membership Statement The relationship between a protein and a protein family. Frameshift Function General description of the functions of a protein. http://www.uniprot.org/manual/function 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. http://www.uniprot.org/manual/carbohyd Helix Helical regions within the experimentally determined protein structure http://www.uniprot.org/manual/helix Induction Description of the compounds or conditions that stimulate the synthesis of a protein. http://www.uniprot.org/manual/induction Initiator Methionine Indicates that the initiator methionine has been cleaved off and is not shown in the sequence. http://www.uniprot.org/manual/init_met Description of a protein-protein interaction. http://www.uniprot.org/manual/binary_interactions INTRAMEM Extent of a region located in a membrane without crossing it http://www.uniprot.org/manual/Intramembrane Journal Citation 1 An article published in a journal. Kinetics Mentions the Michaelis-Menten constant (KM) and maximal velocity (Vmax) of enzymes. Known Sequence http://www.uniprot.org/manual/sequences Lipid Binding Covalent binding of a lipid moiety. http://www.uniprot.org/manual/lipid 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. http://www.uniprot.org/manual/mass_spectrometry Metal Ion Binding Site Binding site for a metal ion. http://www.uniprot.org/manual/metal An experimental method. Modification Describes amino acid modifications, post pre- and post-translational. Modified Residue Posttranslational modification of a residue. http://www.uniprot.org/manual/mod_res Modified Sequence A biological molecule. Molecule Processing Motif Short (<=20 amino acids) sequence motif of biological interest. http://www.uniprot.org/manual/motif Mutagenesis Site Site which has been experimentally altered. http://www.uniprot.org/manual/mutagen Nucleotide Phosphate Binding Extent of a nucleotide phosphate-binding region. http://www.uniprot.org/manual/dna_bind Sequence Variant Authors report that sequence variants exist. http://www.uniprot.org/manual/variant 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. http://www.uniprot.org/manual/non_cons Non standard residue Describes the occurrence of a non standard residue in the sequence record. http://www.uniprot.org/manual/non_std Non-terminal Residue The residue at an extremity of the sequence is not the terminal residue. http://www.uniprot.org/manual/non_ter false A class introduced to group all records that are currently in the database. 1 1 DNA Binding Extent of a DNA-binding region. http://www.uniprot.org/manual/np_bind 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 The class of all obsolete records in the database (i.e. records that where once published but are now removed). http://www.uniprot.org/faq/11 Taxa are occasionally removed from the taxonomy database (particularly internal nodes, during a taxonomic revision) – these taxids are deleted, and are not reused. http://www.ncbi.nlm.nih.gov/books/NBK54428/ 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. http://www.uniprot.org/manual/post-translational_modification Description of a part of a protein. http://www.uniprot.org/manual/protein_names A participant in a protein-protein interaction. http://www.uniprot.org/manual/binary_interactions Patent Citation A patent application. A hierarchical discription of a metabolic pathway. http://www.grenoble.prabi.fr/obiwarehouse/unipathway http://www.uniprot.org/manual/pathway Pathway Description of the metabolic pathways with which a protein is associated. http://www.uniprot.org/manual/pathway Peptide Extent of a released active peptide. http://www.uniprot.org/manual/peptide Pharmaceutical Description of the use of a protein as a pharmaceutical drug. http://www.uniprot.org/manual/pharmaceutical_use Polymorphism Description of polymorphisms. http://www.uniprot.org/manual/polymorphism Propeptide Extent of a propeptide. http://www.uniprot.org/manual/propep Protein Description of a protein. http://www.uniprot.org/help/uniprotkb Protein Family Desription of a set of related proteins. Published Citation http://www.uniprot.org/manual/references RNA Editing Description of any type of RNA editing that leads to one or more amino acid changes. http://www.uniprot.org/manual/rna_editing 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. http://www.uniprot.org/manual/repeat 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. http://www.uniprot.org/help/uniparc http://www.uniprot.org/manual/sequences Sequence Annotation Description of a special region or site in a protein sequence. http://www.uniprot.org/manual/sequence_annotation Sequence Caution Warning about possible errors related to the protein sequence http://www.uniprot.org/manual/sequence_caution Sequence Conflict Different sources report differing sequences. http://www.uniprot.org/manual/conflict Unsure Residue Used to describe region(s) of a sequence for which the authors are unsure about the sequence assignment. http://www.uniprot.org/manual/unsure Signal Peptide Extent of a signal sequence (prepeptide). http://www.uniprot.org/manual/signal Similarity Description of the similarities (sequence or structural) of a protein with other proteins. http://www.uniprot.org/manual/sequence_similarities 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. http://www.uniprot.org/manual/site Indicator for the reliability of a piece of information. http://www.uniprot.org/manual/non_experimental_qualifiers 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. A resource that holds a set of the known names for this protein together. http://www.uniprot.org/manual/protein_names Subcellular Location http://www.uniprot.org/locations/ Subcellular Location Description of the subcellular location of the mature protein. http://www.uniprot.org/manual/subcellular_location Submission Citation 1 Data that was submitted directly to a database. Subunit Description of the quaternary structure of a protein. http://www.uniprot.org/manual/subunit_structure 1 An element of a taxonomy for classifying life forms. http://www.ncbi.nlm.nih.gov/books/NBK54428/ 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. http://www.uniprot.org/docs/tisslist Tissue Specificity Description of the tissue specificity of a protein. http://www.uniprot.org/manual/tissue_specificity Topological Domain A topological domain. http://www.uniprot.org/manual/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. http://www.uniprot.org/manual/toxic_dose Transcribed RNA Transcript Resource Transit Peptide Extent of a transit peptide (mitochondrion, chloroplast, thylakoid, cyanelle or microbody). http://www.uniprot.org/manual/transit Transmembrane Extent of a transmembrane region. http://www.uniprot.org/manual/transmem Transposon A transposon Turn Turns within the experimentally determined protein structure. http://www.uniprot.org/manual/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. http://www.uniprot.org/manual/zn_fing 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