The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. This slot is used to indicate which KB classes are logically part of the general GenoPath MetaCyc schema are organism-independent, in contrast to those slots that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions. One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. This slot is used to indicate which KB classes are logically part of the general GenoPath MetaCyc schema are organism-independent, in contrast to those slots that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions. Restricts the cellular compartment to organisms that match one of the values of this slot. One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. The three bases of the tRNA, which make up the anticodon. The direction is 5' to 3' of the tRNA. This is the reverse and complementary to the sequence of the recognized codons. This slot is used to cross-reference a chemical to the one or more binding reactions in which the chemical is a reactant. Binding reactions only explicitly list their reactants, but not their products, so there is no analog of this slot for products of binding reactions. This slot lists all reactions in which this chemical appears in the left side of the reaction as a reactant . This slot lists all reactions in which this chemical appears on the right side as a product . Lists those atoms that participate in aromatic rings for this compound. This slot lists the charges of specific atoms within the compound. Each value of the slot is a list of the form A C where A is the index of an atom in slot Structure-Atoms, and C is the charge of that atom. In analogy to the ATOM-CHARGES slot, this slot can contain multiple values, which are lists of two elements: first the atom number, and second a description of the stereocenter. This slot was used for the \ @atom stereo parity", as documented for the MDL molfile format, but it is currently not used. Instead, this slot could be recycled later for describing stereocenters according to the CIP system. This slot stores the atomic number of a chemical element. This slot stores the atomic weight of a chemical element. This slot is a list of the form (name1 value1 name2 value2 ....). The name-value pairs describe statistics for this object that have been precomputed and cached on this object. This slot points from a protein to an enzymatic-reaction frame that in turn links the protein to a reaction that the protein catalyzes. This slot stores the net charge of a chemical, which must be an integer. Lists the empirical formula for this compound. Each value of this slot is a list of the form ATOM COUNT where ATOM is the ID of a frame for the corresponding element, and COUNT is the number of occurrences of that atom in this compound. For example, water would be represented as two slot values :The first value is the list H 2 . The second value is the list O 1 . This slot applies to both small molecular weight compounds, and to proteins. In the case of proteins, it is used to encode chemical modifications to proteins, such as methylation. In this case, one of the ATOMs would be the ID of a protein frame. When the value of this slot is TRUE it means that the genetic element is a circular as opposed to linear. This slot lists general citations pertaining to the object containing the slot. Citations may or may not have evidence codes attached to them. Each value of the slot is a string of the form either \ @[reference-id]" or "[reference-id:evidence-code:timestamp:curator:probability]", where: reference-id = a PubMed/Medline identifier we prefer the PubMed id or id for a Publication frame w/o the leading \ @PUB-") evidence-code = the frame id of some subclass of |Evidence|, e.g. EV-EXP timestamp = a lisp universal time corresponding to the time the evidence code was assigned curator = the username of the curator who assigned the evidence code probability = a number between 0 and 1 describing the probability that the evidence is correct Any of the above components may be omitted, but it is meaningless to supply a timestamp, curator or probability if the evidence-code is omitted. Trailing colons should be omitted, but if a value contains an evidence-code with no accompanying citation, the leading colon must be present. The square brackets are optional. Examples : [ 123456 ] -- a PubMed or Medline reference [ SMITH95 ] -- a non-PubMed reference [ 123456 :EV-IDA ] -- an evidence code with associated PubMed reference [ :EV-HINF ] -- an evidence code with no associated reference [ 123456 :EV-IGI :9876543 :paley ] -- a time- and user-stamped evidence code with associated reference [ 123456 :EV-AINF :9876543 :paley :0.75 ] -- a fully instantiated evidence code and reference Indicates the base triplets that are recognized by the anticodon of this tRNA. The direction is 5' to 3' on the coding strand of genes. The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slotunit is outdated; it is kept around because it's used in templates, then altered by the template parser. This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. A sorted list of the centisome positions of the componets of the chromosome. This list contains only the positions of the first N components that actually have map positions. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Stores links to information about the same object in other DBs. Each value is a list of the form (DB-NAME DB-UNIQUE-ID) This slot lists coordinates for the display of the chemical structure of this compound in two dimensions. The values of this slot correspond one-to-one to the values of slot Structure-Atoms. Each value of this slot is of the form X Y and consists of the X-Y display coordinate of the corresponding atom in Structure-Atoms. The coordinates are real numbers with no specified minimum or maximum values -- they are re-scaled at display time. For proteins that bind to DNA, the number of base pairs on the DNA strand that the binding protein covers. Lists sites of interest (such as binding sites, modification sites, etc.) on a polypeptide. Used from PathoLogic to record any research done so far or conclusions reached about matching (or not matching) the protein to a reaction. Describes how PathoLogic should treat a polypeptide unassigned to any reaction -- whether an enzyme or not, high-priority or not, etc. Multiple values are possible generally in the case of a probable enzyme that is also marked as flagged or don't-show . Possible values : :PROBABLE-ENZYME -- the user should try to find a reaction to match to this protein :AMBIGUOUS -- multiple reaction assignment possibilities were found by the name matcher :NOT-AN-ENZYME -- even though the function name matches the criteria to be a probable enzyme, the user has decide that it is not :NON-SPECIFIC-ENZYME-NAME -- no reaction can be assigned because the function name is not specific enough :DONT-SHOW -- the user has decided that this protein cannot be assigned to a reaction for the time being reasons can be unspecified or detailed in the FUNCTIONAL-ASSIGNMENT-COMMENT slot :FLAGGED -- this protein should be considered high-priority The gene that encodes the current polypeptide (or RNA). When a polypeptide exists in one or more chemically modified forms, all of those forms of the polypeptide should link to the same gene frame using the Gene slot. The NCBI translation table number (1-15) for the chromosome's genetic code. If no value is supplied, the standard genetic code (1) is assumed. The genetic codes are as follows : 1. Standard 2. Vertebrate Mitochondrial 3. Yeast Mitochondrial 4. Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma 5. Invertebrate Mitochondrial 6. Ciliate, Dasycladacean and Hexamita no tables 7 or 8 9. Echinoderm Mitochondrial 10. Euplotid Nuclear 11. Bacterial same as standard, except for different alternate initiation codons 12. Alternative Yeast Nuclear 13. Ascidian Mitochondrial 14. Flatworm Mitochondrial 15. Blepharisma Nuclear See http ://anatomy.med.unsw.edu.au/CBL/embryo/DNA/Genetic_Codes.htm for more info, including systematic ranges for each code and citations. The standard Gibbs free energy of formation of the compound. The values are in units of kcal/mol, assuming the common state in aqueous solution at pH = 7 and T = 25C. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. This is an own slot on classes that specifies a template for generating a frame id for instances of the class; it may contain a wildcard character * for which a number gets substituted when an instance name is generated. Values are of the form (other-polypeptide YES/NO) Specifies which slot (if any) in a given frame contains a key for indexing that frame. Usually defined on a per-class basis. This slot describes the one or more cellular locations in which this protein is found. This slot indicates proteins that are derived from the current protein by some type of chemical modification. This slot lists the molecular weight of a chemical, in daltons. An experimentally determined molecular weight. When multiple values are stored in this slot they should be treated as alternative observations. Molecular weights for this molecule in kilodaltons. Values of this slot are computed by combining the values of the slots molecular-weight-seq and molecular-weight-exp. When multiple values are stored in this slot they should be treated as alternative observations. A molecular weight as computed from a nucleotide sequence. When multiple values are stored in this slot they should be treated as alternative observations. For a polymeric compound, the name to use when displaying it in its N-1 form For a polymeric compound, the name to use when displaying it in its N form For a polymeric compound, the name to use when displaying it in its N+1 form This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots. This slot lists the Neidhardt Spot Number of the protein, reflecting its electrophoretic behavior in two-dimensional electrophoresis. Describes how an object should be drawn in the overview graph Stores the pI of a protein. When multiple values are stored in this slot they should be treated as alternative observations. Ionization constant of the first site in this compound to ionize. Ionization constant of the second site in this compound to ionize. Ionization constant of the third site in this compound to ionize. This slot is used to indicate which KB classes are logically part of the general GenoPath MetaCyc schema are organism-independent, in contrast to those slots that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions. Filename containing the full chromosome sequence in FASTA fo rmat Length of a genetic element in bases. A smiles string for this compound, computed automatically from the compound structure. This slot is used in three ways: 1 Lists the introns for the splice form of the gene that codes for this particular polypeptide or RNA. Because different splice forms of a given gene will give rise to different proteins or RNAs, the list of introns is associated with the end product of the splice form the protein or RNA rather than with the gene. Each value of this slot is a two-element list start-bp end-bp, containing the start and end position of an intron, respectively. Positions refer to base pair numbers relative to the start of the gene, with the first base pair if the gene is transcribed in the negative direction, this is the first base pair of the reverse complement being number 1. Start-bp and end-bp are included as part of the intron. Introns cannot overlap, start-bp must be less than end-bp, and neither start-bp nor end-bp can be less than 1 or greater than the length of the gene. If a splice form has a different start position than the gene as a whole, then it should specify an intron extending from 1 to its start position. Similarly, if it has a different end position, an extra intron should be specified there. This slot is one of several that are used to encode the chemical structure of a compound. This slot lists all of the distinct atoms in the compound, with multiple entries for atoms of the same element that occur more than once. For example, water could be described as the list H H O . There is no special order in which the atoms are listed. However, other slots refer to the atoms in the compound according to their position in this list, for example, the first hydrogen is atom 0, and the oxygen is atom 2. This slot describes the chemical bonds within a compound. Each bond is encoded as a list of the form A1 A2 B-TYPE where A1 is the index in slot Structure-Atoms of the first atom in the bond, A1 is the index of the second atom in the bond, and B-TYPE encodes the type of the chemical bond. Valid bond types are the numbers 1, 2, and 3 for single, double, and triple bounds, and the symbol :AROMATIC for aromatic bonds. Indicates that part of the compound structure can be replaced by a superatom. The annotations REPLACES-ATOM AND CONNECTED-TO specify which atom by indexing into the STRUCTURE-ATOMS list the superatom replaces, and which atom in the compound structure it is connected to, respectively. Superatoms may only connect at one atom. This slot defines the type of symmetry found in the DNA binding site recognized by a transcription factor. The two possible symmetry types are INVERTED-REPEAT and DIRECT-REPEAT. One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. This slot stores the systematic chemical name of a chemical. This outdated slot stores the template file (an outdated form of input to EcoCyc This slot allows a protein to point to its apo form, which must be another protein. The value of the Unmodified-Form slot is always the completely unmodified \ @base" form of a protein, that is, if a protein can undergo several subsequent stages of modification, each modified form is linked back to the base form, not to the previous form in the pathway. Put another way, no protein should have both an unmodified form and a modified form ; every modified protein should be linked back to the base form of the protein. Valence applies to all-elements because superelements must have a valence. Some elements may have several valence possibilities, due to non-bonding electron pairs that can get oxydized. In such cases, the code that performs valence checking in order to draw hydrogens that fill unsatisfied valences will only fill up to the lowest valence value. This slot specifies a list of gene names or IDs that will be displayed as markers on the lowest-resolution view of the map of this genetic element. This is the version of the database name that is used in links Stores URL for Database home page The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Stores URL format string for dynamic searches. Format string has one arg: the search string. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. The Pathway Tools orgid for databases that are Pathway/Genome Databases e.g. META for MetaCyc, ECOLI for EcoCyc . This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots. True if the database is a Pathway/Genome Database that uses the Pathway Tools schema. This slot is used to indicate which KB classes are logically part of the general GenoPath MetaCyc schema are organism-independent, in contrast to those slots that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions. This slot lists the classes of EcoCyc objects (e.g. Pathways, Genes, Proteins, etc.) that can have unification links to this database via the search URL. Stores URL format string for OID searches. Format string has one arg: the desired OID. One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. The computed set of all activators of the current enzymatic reaction, combined from all of the other activators slots. Allosteric activators increase the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that increases the affinity of the enzyme to its substrates without affecting its VMAX. Nonallosteric activators increase the specified enzyme activity by means other than allosteric. Compounds that activate the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper s curated thus far do not define the mechanism, and a full literature search has yet to be performed. This slot records variability in the cofactors that have been observed for this enzymatic reaction. If, for example, the literature indicates that Mn+2 can substitute for Mg+2 as a cofactor in this reaction, we would list the following as a value : Mg+2 Mn+2 . This slot records variability in the substrates that have been observed for this enzymatic reaction. If, for example, the literature indicates that X can substitute for Y as a substrate in this reaction, we would list the following as a value : Y X, where X and Y are the frame IDs for the corresponding substrates. Records the basis for assignment of the protein to the reaction, whether manually by a curator (the default), or automatically by various means. This slot lists general citations pertaining to the object containing the slot. Citations may or may not have evidence codes attached to them. Each value of the slot is a string of the form either \ @[reference-id]" or "[reference-id:evidence-code:timestamp:curator:probability]", where: reference-id = a PubMed/Medline identifier we prefer the PubMed id or id for a Publication frame w/o the leading \ @PUB-") evidence-code = the frame id of some subclass of |Evidence|, e.g. EV-EXP timestamp = a lisp universal time corresponding to the time the evidence code was assigned curator = the username of the curator who assigned the evidence code probability = a number between 0 and 1 describing the probability that the evidence is correct Any of the above components may be omitted, but it is meaningless to supply a timestamp, curator or probability if the evidence-code is omitted. Trailing colons should be omitted, but if a value contains an evidence-code with no accompanying citation, the leading colon must be present. The square brackets are optional. Examples : [ 123456 ] -- a PubMed or Medline reference [ SMITH95 ] -- a non-PubMed reference [ 123456 :EV-IDA ] -- an evidence code with associated PubMed reference [ :EV-HINF ] -- an evidence code with no associated reference [ 123456 :EV-IGI :9876543 :paley ] -- a time- and user-stamped evidence code with associated reference [ 123456 :EV-AINF :9876543 :paley :0.75 ] -- a fully instantiated evidence code and reference A comment describing cofactor requirements of an enzyme. Cofactors are compounds that are required for an enzyme to catalyze a reaction, but that are unchanged by the reaction, and that are not tightly bound to the enzyme. Compounds that are required for an enzyme to catalyze a reaction, but that are unchanged by the reaction, and whose degree of binding to the enzyme is unknown. The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Stores links to information about the same object in other DBs. Each value is a list of the form (DB-NAME DB-UNIQUE-ID) This slot links an enzymatic reaction to the enzyme whose activity the enzymatic reaction describes. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. The computed set of all inhibitors of this enzymatic reaction as defined in all of the other inhibitors slots. Allosteric inhibitors decrease the specified enzyme activity by binding reversibly to the enzyme and inducing a conformational change that decreases the affinity of the enzyme to its substrates without affecting its VMAX. Allosteric inhibitors can be competitive or noncompetitive inhibitors, therefore, those inhibition categories can be used in conjunction with this category. Competitive inhibitors are compounds that competitively inhibit the specified enzyme activity by binding reversibly to the enzyme and preventing the substrate from binding. Binding of the inhibitor and substrate are mutually exclusive because it is assumed that the inhibitor and substrate can both bind only to the free enzyme. A competitive inhibitor can either bind to the active site of the enzyme, directly excluding the substrate from binding there, or it can bind to another site on the enzyme, altering the conformation of the enzyme such that the substrate can not bind to the active site. Irreversible inhibitors are compounds that irreversibly inhibit the specified enzyme activity by binding to the enzyme and dissociating so slowly that it is considered irreversible. For example, alkylating agents, such as iodoacetamide, irreversibly inhibit the catalytic activity of some enzymes by modifying cysteine side chains. Noncompetitive inhibitors are compounds that noncompetitively inhibit the specified enzyme by binding reversibly to both the free enzyme and to the enzyme-substrate complex. The inhibitor and substrate may be bound to the enzyme simultaneously and do not exclude each other. However, only the enzyme-substrate complex not the enzyme- substrate-inhibitor complex is catalytically active. Compounds that inhibit the specified enzyme activity by a mechanism that has been characterized, but that cannot be clearly classified as irreversible, competitive, noncompetitive, uncompetitive, or allosteric. Uncompetitive inhibitors are compounds that uncompetitively inhibit the specified enzyme activity by binding reversibly to the enzyme-substrate complex but not to the enzyme alone. Compounds that inhibit the specified enzyme activity by an unknown mechanism. The mechanism is defined as unknown, because either the mechanism has yet to be elucidated in the experimental literature, or the paper s curated thus far do not define the mechanism, and a full literature search has yet to be performed. The Michaelis constant (K_M) of an enzyme is equal to the substrate concentration at which the rate of the reaction is at half of its maximum value. The Michaelis constant is an apparent dissociation constant of the enzyme-substrate complex, and thereby is an indicator of the affinity of an enzyme to a given substrate. Values of this slot are two-element lists of the form cpd-frame Km where cpd-frame is the frame id for a substrate of the reaction referred to by this enzymatic-reaction frame and Km is the Michaelis constant, a floating point number. This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots. The pH optimum of an enzyme is the pH at which the rate of reaction is at a maximum. This slot is a companion to all slots that describe activators and inhibitors. It contains a list of those activators and inhibitors whose effects are known to be of physiological relevance. The values of this slot are therefore a possibly empty subset of all values of the activators and inhibitors slots. Prosthetic groups are compounds that are required for an enzyme to catalyze a reaction, but that are unchanged by the reaction, and that are covalently or tightly bound to the enzyme. The value of this slot is the key of a frame from the Reaction class -- the second half of the enzyme/reaction pair that the current frame describes. In fact, this slot can have multiple values corresponding to multiple reactions catalyzed by a single catalytic site of an enzyme. Specifies the directionality of a reaction. This slot is particularly important to fill for reactions that are not part of a pathway, because for such reactions, the direction cannot be computed automatically, whereas for reactions within a pathway, the direction can be inferred from the pathway context. Possible values of this slot are : REVERSIBLE :Reaction occurs in both directions in physiological settings. PHYSIOL-LEFT-TO-RIGHT PHYSIOL-RIGHT-TO-LEFT The reaction occurs in the specified direction in physiological settings, because of several possible factors including the energetics of the reaction, local concentrations of reactants and products, and the regulation of the enzyme or its expression. IRREVERSIBLE-LEFT-TO-RIGHT IRREVERSIBLE-RIGHT-TO-LEFT For all practical purposes, the reaction occurs only in the specified direction in physiological settings, because of chemical properties of the reaction. Some enzymes only catalyze a particular reaction when they are components of a larger protein complex. For such an enzyme, this slot identifies the particular protein complex of which the enzyme must be a component. This slot is used to indicate which KB classes are logically part of the general GenoPath MetaCyc schema are organism-independent, in contrast to those slots that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions. One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. The temperature optimum of an enzyme is the temperature at which the rate of reaction is at a maximum. This outdated slot stores the template file (an outdated form of input to EcoCyc The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. This slot lists the one or more classes that this evidence code pertains to. For example, some evidence codes pertain to promoters only. If no class is listed, we assume the evidence code pertains to all classes of objects. This slot is used to indicate which KB classes are logically part of the general GenoPath MetaCyc schema are organism-independent, in contrast to those slots that are specific to a particular organism. This slot is used by the PathoLogic code that does schema copying, and by the code in kb-update.lisp that does schema mirroring. The general rule is that classes that should be copied from MetaCyc to a new organism by PathoLogic are considered schema classes. Examples include the hierarchies of compounds and pathways, and general classes like Genes and Proteins and All-ACPs. Examples of classes to exclude are classes for specific modified proteins that occur as substrates in reactions, such as Thioredoxin. The problem with copying Theoredoxin is that the reactions it appears as a substrate in are not copied when the class is copied, causing bad references to those reactions. One or more secondary names for an object -- names that a scientist might attempt to use to retrieve the object. The Synonyms should include any name a user might use to try to retrieve an object. Values of this slot are tuples containing a transcription factor and a DNA binding site. Presence of the transcription factor bound to the DNA binding site activates this RNA-Polymerase binding reaction, and therefore activates transcription. This slot is used to cross-reference a chemical to the one or more binding reactions in which the chemical is a reactant. Binding reactions only explicitly list their reactants, but not their products, so there is no analog of this slot for products of binding reactions. This slot lists all reactions in which this chemical appears in the left side of the reaction as a reactant . This slot lists all reactions in which this chemical appears on the right side as a product . Lists those atoms that participate in aromatic rings for this compound. This slot lists the charges of specific atoms within the compound. Each value of the slot is a list of the form A C where A is the index of an atom in slot Structure-Atoms, and C is the charge of that atom. In analogy to the ATOM-CHARGES slot, this slot can contain multiple values, which are lists of two elements: first the atom number, and second a description of the stereocenter. This slot was used for the \ @atom stereo parity", as documented for the MDL molfile format, but it is currently not used. Instead, this slot could be recycled later for describing stereocenters according to the CIP system. This slot describes what is known about the element balance state of this reaction. Its possible values are : NIL -- The balance state is unknown :BALANCED -- The last time the reaction-balancing code checked this reaction, it was balanced. :UNBALANCED-UNKNOWN -- The reaction is unbalanced, and the curation team cannot determine how to balance it. :UNBALANCED-INCOMPLETE -- The reaction is unbalanced because the complete reaction equation is not known. :UNBALANCED-DIFFERING-R-GROUPS -- The reaction is unbalanced because it contains substrates with R-groups where the structures of the two R-groups differ. A number indicating the transcription of the promoter in the absence of any regulator. This slot stores the net charge of a chemical, which must be an integer. Lists the empirical formula for this compound. Each value of this slot is a list of the form ATOM COUNT where ATOM is the ID of a frame for the corresponding element, and COUNT is the number of occurrences of that atom in this compound. For example, water would be represented as two slot values :The first value is the list H 2 . The second value is the list O 1 . This slot applies to both small molecular weight compounds, and to proteins. In the case of proteins, it is used to encode chemical modifications to proteins, such as methylation. In this case, one of the ATOMs would be the ID of a protein frame. This slot lists general citations pertaining to the object containing the slot. Citations may or may not have evidence codes attached to them. Each value of the slot is a string of the form either \ @[reference-id]" or "[reference-id:evidence-code:timestamp:curator:probability]", where: reference-id = a PubMed/Medline identifier we prefer the PubMed id or id for a Publication frame w/o the leading \ @PUB-") evidence-code = the frame id of some subclass of |Evidence|, e.g. EV-EXP timestamp = a lisp universal time corresponding to the time the evidence code was assigned curator = the username of the curator who assigned the evidence code probability = a number between 0 and 1 describing the probability that the evidence is correct Any of the above components may be omitted, but it is meaningless to supply a timestamp, curator or probability if the evidence-code is omitted. Trailing colons should be omitted, but if a value contains an evidence-code with no accompanying citation, the leading colon must be present. The square brackets are optional. Examples : [ 123456 ] -- a PubMed or Medline reference [ SMITH95 ] -- a non-PubMed reference [ 123456 :EV-IDA ] -- an evidence code with associated PubMed reference [ :EV-HINF ] -- an evidence code with no associated reference [ 123456 :EV-IGI :9876543 :paley ] -- a time- and user-stamped evidence code with associated reference [ 123456 :EV-AINF :9876543 :paley :0.75 ] -- a fully instantiated evidence code and reference Each value of this slot is a reaction in the pathway. Two annotations in addition to the usual possibilities are available on this slot : REACTANT-INSTANCES and PRODUCT-INSTANCES, whose values are compounds. If one of the reactants of the slot-value reaction is a class C and the REACTANT-INSTANCES are instances of C, then the instances are drawn as part of the pathway, with identity links to the class. The PRODUCT-INSTANCES are treated similarly. The Comment slot stores a general comment about the object that contains the slot. A comment for internal purposes that is not released to the pubilc. The primary name by which an object is known to scientists -- a widely used and familiar name in some cases arbitrary choices must be made . This slot specifies an object that contains this object as a smaller part. For example, this slot points from a monomer to a larger complex that contains it. This slot lists the components of some physical assembly, such as the subunits of a protein complex or the genes within a chromosome. The coefficient of each component when known is listed as an annotation of the component value under the label coefficient. When a modified protein is created to reflect a chemically modified alternate form of the protein, if that protein is a complex, its subunit structure need not be mirrored in the modified-protein frame. The subunit structure should be defined only once, for the frame that represents the unmodified form of the protein. The :Creation-Date slot stores the date on which the current frame was created, as a Lisp universal time integer. The :Creator slot stores the userid of the creator of the current frame. Stores links to information about the same object in other DBs. Each value is a list of the form (DB-NAME DB-UNIQUE-ID) This slot contains the change in Gibbs free energy for the reaction in the direction the reaction is written. Compounds or proteins known to depress or inhibit a non-enzymatic reaction. Often the mechanism is unknown -- the action may even be indirect. When true, this slot disables display of the pathway graph for a pathway. This slot lists coordinates for the display of the chemical structure of this compound in two dimensions. The values of this slot correspond one-to-one to the values of slot Structure-Atoms. Each value of this slot is of the form X Y and consists of the X-Y display coordinate of the corresponding atom in Structure-Atoms. The coordinates are real numbers with no specified minimum or maximum values -- they are re-scaled at display time. This slot records info about retired and transfered EC numbers. The enzyme commission (EC) number of the reaction. Links a reaction frame to the enzymatic reaction frame(s) that connect to enzymes that catalyze this reaction. This slot allows us to specify that specific enzymes are the only enzymes that catalyze a specified reaction within the current pathway. That is, in the context of pathway P, we might want to specify that for reaction R, only two of the three known isozymes for R actually catalyze R in this pathway. This slot is used when it is specifically known that some enzymes in an organism specifically do not catalyze a given reaction in the context of some pathway, usually because of regulation. Each value of this slot is a tuple of the form R ER1 ... ERn where R is a reaction frame ID, and the one or more ERi are the IDs of enzymatic reaction frames. A given tuple specifies that the enzyme linked to ER1 catalyzes R. The equilibrium constant for a reaction. The standard Gibbs free energy of formation of the compound. The values are in units of kcal/mol, assuming the common state in aqueous solution at pH = 7 and T = 25C. Contains a textual history of changes made to this frame. Each item is either a string or a note frame. A list of reactions in this pathway that are considered hypothetical, probably because presence of the enzyme, reactants, or products have not been demonstrated. This slot specifies the pathways that a reaction occurs in. Values of this slot are tuples containing a transcription factor and a DNA binding site. Presence of the transcription factor bound to the DNA binding site inhibits this RNA-Polymerase binding reaction, and therefore inhibits transcription. This is an own slot on classes that specifies a template for generating a frame id for instances of the class; it may contain a wildcard character * for which a number gets substituted when an instance name is generated. Specifies which slot (if any) in a given frame contains a key for indexing that frame. Usually defined on a per-class basis. A set of keyword-value pairs that advise the pathway layout algorithms how best to lay out the pathway. Currently supported advice keywords are : :CYCLE-TOP-CPD -- The advice is a compound key. In pathways containing a cycle, the cycle will be rotated so that the specified comound is positioned at twelve o'clock. :CASCADE-RXN-ORDERING -- The advice is a list of reactions that form a partial order for reactions in a cascade pathway i.e. the 2-component signalling pathways . The compounds produced by this reaction. The coefficients of these compounds that are not equal to 1 are stored in annotations on the values of this slot, under the annotation label COEFFICIENT. This is a slot on classes that specifies a sort function for ordering the presentation of subclasses and instances of the class within a user interface display; it should name a function of two arguments that returns non-nil if the arguments are in correct sorted order, and nil otherwise. This slot lists the molecular weight of a chemical, in daltons. Compounds transported into the cell. Compounds transported out of the cell. For a polymeric compound, the name to use when displaying it in its N-1 form For a polymeric compound, the name to use when displaying it in its N form For a polymeric compound, the name to use when displaying it in its N+1 form This is a computed slot that returns the union of all names of this frame, by appending names from all other name slots. This slot specifies the net chemical transformation accomplished by a pathway, including the stoichiometry, and is written in the form of a reaction equation. The value of this slot is NO if the current reaction either was not defined by the enzyme commission at all, or if the current equation stored for that reaction is not the equation assigned by the EC such as if we have corrected the EC equation . Otherwise, the value is YES, which is the default inherited value. This slot indicates whether the current reaction is an orphan reaction. An orphan reaction is one for which no enzyme that catalyzes the reaction or a cognate gene for that enzyme has been sequenced. Thus, if an enzyme that catalyzes this reaction in any species has ever been sequenced, the value is :NO. Values :NO -- When this reaction was analyzed, at least one cognate DNA or protein sequence for an enzyme that catalyzes the reaction was found in at least one species. The analysis could have be performed either manually or computationally. :YES-CONFIRMED -- When this reaction was analyzed, the analytical process conclusively determined that the object is truly an orphan. :YES-PUTATIVE -- When this reaction was analyzed, the analytical process could not conclusively determine whether the reaction was truly an orphan, although the analysis suggested that it is. :UNKNOWN -- When this reaction was analyzed, it was not known whether at least one cognate DNA or protein sequence in at least one species was associated with it. NIL or no value -- No analysis of the orphan status for this reaction has been performed, so that status is not known. Describes how an object should be drawn in the overview graph This slot holds a comment that describes interactions between this pathway and other biochemical pathways, such as those pathways that supply an important precurser. Each value is of the form (compound other-pathway*) or (compound (other-pathway . [:INCOMING|:OUTGOING])*) where compound is a compound in the current pathway and all the other-pathways. The link directionality should be supplied only if it is not otherwise obvious e.g. if the compound is an internal compound in both pathways . If no other-pathways are specified, then all other pathways that contain compound are implied. Ionization constant of the first site in this compound to ionize. Ionization constant of the second site in this compound to ionize. Ionization constant of the third site in this compound to ionize. Each value of this slot is of the form cpd-class product-rxn reactant-rxn . When both reactions are non-nil, an identity link is created between the polymer compound class cpd-class, a product of product-rxn, and the same compound class as a reactant of reactant-rxn. The PRODUCT-NAME-SLOT and REACTANT-NAME-SLOT annotations specify which slot should be used to derive the compound label in product-rxn and reactant-rxn above respectively --- if one or both are omitted, COMMON-NAME is assumed. Either reaction above may be nil ; in this case, no identity link is created --- this form is used solely in conjunction with one of the name-slot annotations to specify a name-slot other than COMMON-NAME for a polymer compound class in a reaction of the pathway. This slot describes the linked reactions that comprise the current pathway. Each value of this slot is of the form reaction-id pred-id * . Each pred-id is the id of a reaction frame that is a direct predecessor of reaction-id in the pathway. When drawing a pathway, EcoCyc usually computes automatically which compounds are primaries mains and which compounds are secondaries sides . Occasionally, the heuristics we use are not sufficient to make the correct distinction. This slot is used to specify a list of primary reactants, primary products, or both for a particular reaction in the pathway. Values are of the form reaction-id primary-reactant-id-1 ... primary-reactant-id-n primary-product-id-1 ... primary-product-id-n The compounds to be bound by this reaction. A list of reaction layout instructions, one for each reaction in the pathway; each instruction is a list containing the following elements : 1 the rxn frame or ID, 2 a list of the left primaries, 3 the reaction direction in the pathway, and 4 a list of the right primaries. This slot lists all reactions in the current pathway, in no particular order. It is automatically computed from the predecessors slot. This slot is n