An ontology describing enzyme sequence-structure-function relationships Links an FDGroup to the ConservedChemicalCapability common to the FunctionalDomains in the group. Links a FunctionalDomain to an FDSchemeAssociation. Links a FunctionalDomain to an FDStructureAssociation. Links an FDGroup to a literature Reference describing the group. For FunctionalDomains that are linked to a Family, this link specifies the Reference that the Family assignment was based on. Links an AminoAcidResidue to the Reference used to determine its functional importance. Links an FDGroup to the Structure used to create the image in the image_file data property for that group. Links an Association to a Reference. This link specifies the Reference that the Superfamily assignment of the associated FunctionalDomain was based on. Links a ReactionScheme to an FDSchemeAssociation. Links a Structure to an FDStructureAssociation. Links a Structure to the literature Reference describing it. Links a FunctionalDomain to a Structure. Relates a parent subgroup to a child subgroup, allowing an arbitrary number of subgroups to be nested (with top level subgroups more general and bottom level subgroups more specific) according to the needs of the sequence group in question. Relates a subfamily to a parent family, allowing an arbitrary number of families to be nested (with top level families more general and bottom level families more specific) according to the needs of the sequence group in question. Links a ConservedChemicalCapability with the ReactionScheme(s) that include this capability. For example, the ConservedChemicalCapability of the Enolase Superfamily, abstraction of a proton alpha to a carboxylic acid, would be linked to all ReactionScheme(s) catalyzed by FunctionalDomains in the Enolase superfamily. Links functionally important amino acids to the FDGroup the group they're conserved by. Links an Enzyme to the Organism it's from. Links a FunctionalDomain to the Enzyme it's a part of. Links a Reaction to a particular mechanism of that Reaction, as implemented by a specific FDGroup. Links a FunctionalDomain to a Family, Subgroup, Superfamily, or Suprafamily to which it has been classified. FunctionalDomains can be assigned to all of these groups, some of these groups, or none of these groups. However, if a FunctionalDomain is classified into a given group, it MUST be classified into all groups above that group in the functional hierarchy. For example, if a FunctionalDomain is classified into a particular Subgroup, it must also be classified into the Superfamily to which the Subgroup belongs. However, it does not have to be assigned to a Family. Links a Family to the Subgroup under which it is classified. Links a Subgroup to the Superfamily under which it is classified. Links a Superfamily to the Suprafamily under which it is classified. Links functionally important amino acid residues to the FunctionalDomain that they're a part of. Links a Molecule to the Reaction it participates in. Links a SuperfamilyDomain to the Superfamily to which it corresponds. Links a SuperfamilyDomain to the Enzyme that it's a part of. Links a SuperfamilyDomain to the FunctionalDomain its a part of. Links a Cofactor to a Superfamily whose member enzymes utilize the Cofactor in catalyzing reactions. Links a ReactionScheme to the Cofactor(s) it utilizes. Abstract from paper Text description of the structure used in the active site image specified in active_site_img and active_site_session Name of PNG format file containing image of active site for an example member of the group. File name for the chimera session used to create the active site image specified by active_site_img. An integer specifying a position within a multiple alignment. Stockholm format sequence alignment for a representative set of sequences in the group. Amino acid type (one letter amino acid code) CFM FSM ICR ICS IDA IEA IES IGS IME ISS An evidence code associated with the linkage between two classes. A comma delimited list of authors BLAST e-value for the match between a FunctionalDomain sequence and a Structure sequence. BLAST percent aligned for the match between a FunctionalDomain sequence and a Structure sequence. BLAST e-value for the match between a FunctionalDomain sequence and a Structure sequence. Specifies whether the residue is conserved across the corresponding subgroup or family. Allowed values: "subgroup," or "family." A string giving a text description of the ConservedChemicalCapability. The accession number of a compound in the ChEBI database. Classification status of a record. Allowed values: "public," "private," or "staff." Records with a classification of "staff" are only showed to members of the Babbitt lab when they are logged in to the SFLD. Records with a classification of "private" are only showed to users with an SFLD login when they are logged in to the SFLD. Records with a classification of "public" are showed to everyone. A string specifying the name of a PNG or GIF format file containing an image of the corresponding cofactor's chemical structure. A string specifying the name of a cofactor. A string specifying the type of cofactor corresponding to the record. Valid entries include: "coenzyme or prosthetic group," "prosthetic group," "complex," "coenzyme," "Metal," and "Organic Cofactor (PTM)." NCBI COG identifier (http://www.ncbi.nlm.nih.gov/COG/) A text string specifying the name of a compound. A text string specifying the source database from which the compound information was obtained. The date/time a record was created SFLD login or automated protocol name for the curator/protocol who last edited a record. The curation status of a record. Allowed values: "valid," "invalid," and "pending. A free-text field specifying curator notes for a given record. A text description for a given group. backward forward reversible unknown A string specifying the directionality of a reaction. Accepted values are: backward, forward, reversible, unknown. A string specifying the NCBI Taxonomy division in which the corresponding organism has been classified. Digital object identifier for a given literature reference A string specifying the NCBI Taxonomy domain in which the corresponding organism has been classified. Enzyme commission number The amino acid residue number that specifies the end of the segment corresponding to a given FunctionalDomain. This number is in reference to the corresponding full-length enzyme sequence. The final page of the corresponding reference An integer specifying a position in an enzyme sequence. An identifier from the EzCatDB database (http://ezcatdb.cbrc.jp/EzCatDB/). A three letter code specifying the type of evidence used to classify a given FunctionalDomain into a given Family. Allowed values are specified here: http://sfld.rbvi.ucsf.edu/django/web/ecodes/#Family%20Assignment A string specifying the name of a Functional Domain. This name is generally based on the name of the most specific level of the Family-Subgroup-Superfamily hierarchy to which the FD has been classified. An integer specifying an amino acid residue position in a Functional Domain sequence. A string specifying the name of an FDGroup record. FIG identifier from TheSEED database (http://theseed.org/wiki/Main_Page) A free text field specifying the function of an amino acid residue. A three letter code specifying the type of evidence used to determine the function of a given amino acid residue. Allowed values are specified here: http://sfld.rbvi.ucsf.edu/django/web/ecodes/#Conserved%20Residue%20Assignment An accession number from the NCBI Genbank database (http://www.ncbi.nlm.nih.gov/genbank) for a given enzyme. extended superfamily A text value specifying the type of superfamily. Allowed values: "superfamily," "extended." Records with a group_type of "superfamily" are part of the core SFLD, while records with a group_type of "extended" are part of the extended SFLD. An MD5 hash of the corresponding enzyme sequence. A string specifying the chemical name of a compound (from the HETNAM record of the corresponding PDB file). An HMM generated with the HMMER3 package using as input the alignment in the alignment3 field. A string specifying the name of a JPG or PNG format file containing an image of an example structure from the appropriate group. Text description of the structure used in the image specified in the image_file field. The issue number of the corresponding reference. The journal name for the corresponding reference. A string specifying the identifier from the KEGG database (Kyoto Encyclopedia of Genes and Genomes) corresponding to a given Reaction. A string specifying the NCBI Taxonomy kingdom in which the corresponding organism has been classified. An identifier from the MACiE (Mechanism, Annotation and Classification In Enzymes) database (http://www.ebi.ac.uk/thornton-srv/databases/MACiE/). An identifer from the MACiE database (http://www.ebi.ac.uk/thornton-srv/databases/MACiE/). TRUE if the associated FunctionalDomain has been mapped to the associated Structure by Uniprot. FALSE if not. A locus identifier from the Microbes OnLine database (http://www.microbesonline.org/). 0 1 An integer specifying whether a PDB structure is wild type or mutant. Allowed values: 0, 1. A value of 0 indicates that the structure is wild type, and a value of 1 indicates that the structure is a mutant. The noise cutoff for sequence searches using the corresponding group-specific HMM to search against domain sequences. The noise cutoff for sequence searches using the corresponding group-specific HMM to search against full-length sequences. A string specifying an organism name. An integer specifying an identifier from the PATRIC (Pathosystems Resource Integration Center) database (http://www.patricbrc.org). An identifier from the Protein Databank (http://www.rcsb.org/pdb/home/home.do) A string specifying an amino acid sequence corresponding to a given structure. A string specifying the title from the corresponding PDB record. A string specifying the NCBI Taxonomy phylum in which the corresponding organism has been classified. A string specifying the name of a protein (from the MOLECULE field of the corresponding PDB record). An integer specifying an identifier from the NCBI PubMed database (http://www.ncbi.nlm.nih.gov/pubmed). The UniProt Proteome ID for the corresponding organism for organisms that are part of the Quest for Orthologs project (http://questfororthologs.org/) A string specifying the name of a reaction. cognate generic other unknown A string specifying a reaction type. Accepted values are: cognate, other, unknown, generic. A string specifying the title of the corresponding reference. A string specifying an NCBI RefSeq accession number (http://www.ncbi.nlm.nih.gov/refseq/). A string specifying the resolution of a PDB structure. A string specifying an identifier from the RHEA database (http://www.rhea-db.org/home) corresponding to a given Reaction. product substrate Describes the role of a Compound in a Reaction. Accepted values are: substrate, product. ICR IDA IEA IGS IMP ISS A three letter code specifying the type of evidence used to classify a given FunctionalDomain into a given Family. Allowed values are specified here: http://sfld.rbvi.ucsf.edu/django/web/ecodes/#Reaction%20Assignment A text string describing a Reaction Scheme. A string specifying the name of a Reaction Scheme. A string specifying the amino acid sequence of an enzyme in one letter code. An integer specifying the amino acid position on the corresponding full-length sequence at which the superfamily domain ends. An integer specifying the amino acid position on the corresponding full-length sequence at which the superfamily domain begins. A SMILES string representing the structure of the Cofactor. The amino acid residue number that specifies the beginning of the segment corresponding to a given FunctionalDomain. This number is in reference to the corresponding full-length enzyme sequence. The initial page of the corresponding reference The number of copies of the Molecule used / produced in the Reaction. A three letter code specifying the type of evidence used to classify a given FunctionalDomain into a given Superfamily. Allowed values are specified here: http://sfld.rbvi.ucsf.edu/django/web/ecodes/#Superfamily Assignment An identifier from the Swiss-Prot section of UniProtKB (http://www.uniprot.org/). A sequence name from the SwissProt database. A string specifying an additional name for an organism. An identifier from the NCBI taxon database (http://www.ncbi.nlm.nih.gov/taxonomy). The trusted cutoff for sequence searches using the corresponding group-specific HMM to search against domain sequences. The trusted cutoff for sequence searches using the corresponding group-specific HMM to search against full-length sequences. A FIG identifier from The SEED database (http://www.theseed.org/wiki/Main_Page). A string specifying the title of the corresponding reference. An identifier from the TrEMBL section of UniProtKB (http://www.uniprot.org/). A string specifying an accession number from UniProtKB (http://www.uniprot.org/). An Enzyme Commission number parsed from the UniProt record for a given enzyme. A string specifying a protein name from UniProtKB (http://www.uniprot.org/). The UniProt Proteome ID for the corresponding organism for organisms that are part of the Uniprot Reference Proteomes set (http://www.uniprot.org/help/reference_proteome) A string specifying a secondary accession number from UniProtKB (http://www.uniprot.org/). The date/time a record was most recently updated. For records that are no longer valid, the date/time the record was found to be obsolete. A NULL value indicates the record is still valid. A string specifying the volume of the corresponding reference. An integer specifying the year of publication of the corresponding reference. Describes the location and function of amino acid residue. Describes a complex cofactor. A chemical capability common to an FDGroup. Depending on the group in question, the capability may be quite general or quite specific. For example, FunctionalDomains in the enolase superfamily all catalyze reactions involving the abstraction of a proton alpha to a carboxylic acid. Describes the location and function of an amino acid residue found in an individual sequence. Describes a full-length enzyme. Describes the location and function of an amino acid residue conserved by a group of sequences. Describes a group of evolutionarily-related FunctionalDomains. Associates an evidence code and Reference with a linkage between a FunctionalDomain and a ReactionScheme. Associates BLAST e-value, BLAST alignment length, BLAST percent aligned, and uniprot mapping Data Properties with a linkage between a FunctionalDomain and a Structure An evolutionarily related group of FunctionalDomains thought to catalyze the same overall reaction via the same mechanism. A region of an Enzyme required for catalysis of a particular reaction. An organism. An overall reaction. Contains information on substrate(s) / product(s) in a Reaction. A specific mechanism by which a Reaction is catalyzed, as implemented by one or more specific FunctionalDomain(s). Note that while the same Reaction may be catalyzed by FunctionalDomains from multiple FDGroups, a ReactionScheme contains the complete description of the reaction mechanism, and thus is unique to FunctionalDomains from a particular FDGroup. A literature reference. A 3-dimensional protein structure. An evolutionarily related group of FunctionalDomains which catalyze reactions sharing some conserved aspect of chemistry. This group of FunctionalDomains is more diverse than the associated Family(s) but less diverse than the parent Superfamily. An evolutionarily related group of FunctionalDomains which catalyze reactions sharing some conserved aspect of chemistry. This group of FunctionalDomains is more diverse than the associated Subgroup(s) and Family(s) but less diverse than the parent Suprafamily (if it exists). A region of an Enzyme common to a particular Superfamily. This region may be identical to the associated FunctionalDomain, or it may be a subset of the FunctionalDomain. An evolutionarily related group of FunctionalDomains which share conserved active site residues, but may use these residues in different ways. This group of FunctionalDomains is more diverse than the associated Family(s), Subgroup(s), and Superfamily(s). owl:Thing An ontology describing enzyme sequence-structure-function relationships