Returns:
All transcription factors in the current PGDB (computed
as any protein that is a substrate in a binding reaction where another
substrate is a DNA site).
Arguments:
If Allow-modified-forms? is nil, we return unmodified forms of the
proteins only.
Returns:
T if Protein is a transcription factor in the current
organism. Definition: Protein is a transcription factor if it is a
reactant of a binding-reaction, and another reactant of the same
binding reaction is a DNA-Binding-Site.
Arguments:
Protein: An instance of class Proteins.
Function:
all-cofactors ()
Returns:
All cofactors used by enzymes in the current PGDB.
Function:
all-modulators ()
Returns:
All modulators (activators and inhibitors) that enzymes
in the current PGDB are sensitive to.
Function:
monomers-of-protein (p)
Returns:
A list of the monomers (instances of class Polypeptides) that are
subunits of protein P. If P is itself a monomer, the function returns P.
Arguments:
P: An instance of class Proteins.
Function:
components-of-protein (p &optional coefficient)
Returns:
This function recursively computes all of the components of a protein P.
It returns two values: a list of components (including P) and a list of their coefficients.
Arguments:
P: An instance of class Proteins.
Function:
genes-of-protein (p)
Returns:
All genes that code for protein P and all of the subunits of P.
Arguments:
P: An instance of class Proteins.
Function:
reactions-of-enzyme (e)
Returns:
All reactions that enzyme E is linked to via enzymatic reactions.
Arguments:
E: An instance of class Proteins.
Function:
enzyme? (protein &optional (type :any))
Returns:
Predicate that decides whether a specified protein is an enzyme or not;
returns T or NIL, respectively.
Arguments:
Protein: An instance of class Proteins.
Type [optional]: Can have one of four values to select more precisely what
is meant by an enzyme: :any -- Any protein that catalyzes a reaction is considered an enzyme;
:chemical-change -- If the reactants and products of the catalyzed
reaction differ (not just cellular location), the
protein is considered an enzyme;
:small-molecule -- If the reactants of the catalyzed reaction differ
and are all small molecules, the protein is
considered an enzyme;
:non-transport -- exclude all proteins that only catalyze transport reactions.
Function:
transporter? (protein)
Returns:
T if Protein is a transporter.
Arguments:
Protein: An instance of class Proteins.
Function:
containers-of (protein &optional exclude-self?)
Returns:
All containers of Protein, including itself (unless
Exclude-self? is T). Follows the Component-Of slot.
Arguments:
Protein: An instance of class Proteins.
Exclude-Self?: Boolean indicating whether Protein should be included
in the returned list.
Function:
modified-forms (protein &optional exclude-self?)
Returns:
A list of the modified forms of Protein (including Protein, unless
Exclude-self? is T). Follows the Modified-Forms slot.
Arguments:
Protein: An instance of class Proteins.
Exclude-Self?: Boolean indicating whether Protein should be included
in the returned list.
Function:
modified-containers (protein)
Returns:
Both all containers of a protein (meaning protein complexes of which
this protein is a part) including itself, and
all modified forms of a protein.
Arguments:
Protein: An instance of class Proteins.
Function:
top-containers (protein)
Returns:
Those containers of a protein (meaning protein complexes of which
this protein is a part) that themselves have no containers.
Arguments:
Protein: An instance of class Proteins.
Function:
reactions-of-protein (p)
Returns:
All reactions catalyzed by P or by subunits of P.
Arguments:
Protein: An instance of class Proteins.
Function:
regulon-of-protein (protein)
Returns:
The list of transcription units regulated by any modified
or unmodified form of Protein.
Arguments:
Protein: An instance of class Proteins.
Function:
transcription-units-of-protein (protein)
Returns:
The list of transcription units activated or inhibited by the
supplied protein or modified protein frame (does not consider other
modified or unmodifed forms of Protein as does regulon-of-protein).
Arguments:
Protein: An instance of class Proteins.
Function:
regulator-proteins-of-transcription-unit (tu)
Returns:
All proteins that bind to binding sites within TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
full-enzyme-name (enzyme)
Returns:
A string describing the full name of enzyme, as the concatenation of the
common name of the protein followed by the common names of its
enzymatic reactions. Note that two enzrxns for the same enzyme
could have the same common name, so we avoid including the same
name twice.
Arguments:
Enzyme: An instance of class Proteins.
Function:
enzyme-activity-name (enzyme &optional reaction)
Returns:
A string describing the name of an enzyme -- an enzyme-activity name. If
Reaction is non-nil, then we compute the name of the enzyme in
the context of that reaction, otherwise we return the full enzyme
name, which describes all of the reactions that it catalyzes.
If Reaction is NIL, this function is equivalent to full-enzyme-name.
Arguments:
Enzyme: An instance of class Proteins.
Reaction: An instance of class Reactions.
Gene Operations
Function:
enzymes-of-gene (gene)
Returns:
All enzymes coded for by Gene (meaning both a monomer
product of Gene, and complexes that contain such monomers), meaning
proteins that catalyze some reaction.
Arguments:
Gene: An instance of class Genes.
Function:
all-products-of-gene (gene)
Returns:
All gene products of Gene (including modified forms and complexes),
including those that are not enzymes.
Arguments:
Gene: An instance of class Genes.
Function:
reactions-of-gene (gene)
Returns:
All reactions catalyzed by proteins that are products of Gene
(meaning both monomer products of Gene, and complexes that contain
such monomers).
Arguments:
Gene: An instance of class Genes.
Function:
pathways-of-gene (gene)
Returns:
All pathways containing reactions that are catalyzed by proteins
that are produts of Gene (meaning both monomer products of Gene, and complexes that contain
such monomers).
Arguments:
Gene: An instance of class Genes.
Function:
chromosome-of-gene (gene)
Returns:
The chromosome on which Gene resides.
Arguments:
Gene: An instance of class Genes.
Function:
transcription-units-of-gene (gene)
Returns:
A list of transcription units that form the operon
containing gene.
Arguments:
Gene: An instance of class Genes.
Function:
genes-regulating-gene (gene)
Returns:
A list of genes that regulate transcription or translation of gene
Arguments:
Gene: An instance of class Genes.
Function:
genes-regulated-by-gene (gene)
Returns:
A list of genes whose transcription or translation is regulated by the
product of gene.
Arguments:
Gene: An instance of class Genes.
Function:
terminators-affecting-gene (gene)
Returns:
A list of terminators that are in the same transcription-unit as
gene and are upstream of gene. Anything that regulates these
terminators (i.e. by attenuation) can be assumed to regulate
transcription of gene.
Arguments:
Gene: An instance of class Genes.
Function:
get-gene-sequence (gene)
Returns:
A string containing the nucleotide sequence for the gene (if available).
Arguments:
Gene: An instance of class Genes.
Function:
nucleotide->protein-sequence (sequence &optional (code-num 1))
Returns:
A string containing the translated sequence.
Arguments:
Sequence: A string representing a nucleotide sequence (such as might be
returned by get-gene-sequence).
Code-num: The number of the genetic code to use (an integer from 1 to 15). Defaults to the standard genetic code.
Transcription-Unit Operations
Function:
transcription-unit-promoter (tu)
Returns:
The promoter of the transcription unit TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
transcription-unit-genes (tu)
Returns:
A list of the genes within the transcription unit TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
transcription-unit-binding-sites (tu)
Returns:
A list of the DNA binding sites within the transcription unit TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
transcription-unit-mrna-binding-sites (tu)
Returns:
A list of the mRNA binding sites within the transcription unit TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
transcription-unit-transcription-factors (tu)
Returns:
A list of the transcription factors that control the transcription unit TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
binding-site-transcription-factors (bsite)
Returns:
A list of the transcription factors that bind to the DNA binding site Bsite.
Arguments:
Bsite: An instance of class DNA-Binding-Sites.
Function:
transcription-unit-terminators (tu)
Returns:
A list of the transcription terminator(s) within the transcription unit TU.
Arguments:
TU: An instance of class Transcription-Units.
Function:
transcription-unit-activators (tu)
Returns:
A list of the transcription factors or other regulators
(e.g. small RNAs) that activate transcription or translation of the
transcription unit TU. This does not include regulators of
attenuation (because they regulate only the portion of a transcription
unit downstream of the terminator).
Arguments:
TU: An instance of class Transcription-Units.
Function:
transcription-unit-inhibitors (tu)
Returns:
A list of the transcription factors or other regulators
(e.g. small RNAs) that inhibit transcription or translation of the
transcription unit TU. This does not include regulators of
attenuation (because they regulate only the portion of a transcription
unit downstream of the terminator).
Arguments:
TU: An instance of class Transcription-Units.
Function:
containing-tus (site)
Returns:
A list of transcription units containing site.
Arguments:
Site: An instance of any of the following classes: Genes,
Promoters, Terminators, DNA-Binding-Sites, mRNA-Binding-Sites, Transcription-Units.
Compound Operations
Function:
all-transported-chemicals ()
Returns:
All chemicals that are transported by the set of all defined
transport reactions in the current PGDB.
Arguments:
None.
Function:
reactions-of-compound (cpd)
Returns:
The reactions in which Cpd occurs as a reactant or a product.
Arguments:
Cpd: An instance of class Chemicals.
Regulation Operations
Function:
direct-activators (item)
Returns:
The list of entities (e.g. protein, RNA, small molecule) that
directly activate item.
Arguments:
Item: any frame that can be regulated, e.g. an instance of
Enzymatic-Reactions, Transcription-Units, Promoters, Terminators, etc.
Function:
direct-inhibitors (item)
Returns:
The list of entities (e.g. protein, RNA, small molecule) that
directly inhibit item.
Arguments:
Item: any frame that can be regulated, e.g. an instance of
Enzymatic-Reactions, Transcription-Units, Promoters, Terminators, etc.
General Operations
Function:
create-instance-w-generated-id (class)
Side Effects:
Creates a new instance of Class whose frame ID is generated automatically.
Returns:
The created frame (either its frame name or the frame object).
Arguments:
Class: The parent class of the instance to be created.
Example:
(create-instance-w-generated-id '|Genes|)
Function:
get-name-string (item &key (rxn-eqn-as-name? t) direction name-slot strip-html?)
Returns:
A string name for the frame Item.
This is the standard function for computing the biological name of a frame.
Exact operation depends on what type of entity Item is. For
genes, for example, the fn simply retrieves the value of the
common-name slot, or else the frame ID, if the common-name slot
has no value. For other entities, name generation is more
complex.
Arguments:
Item: The frame whose name is to be computed.
Rxn-eqn-as-name?: Influences how names are computed for reaction
frames. When T, the reaction equation is returned; else the
EC number (or frame name if there is no EC number) is returned.
Direction: Influences how names are computed for reaction
frames. Possible values: :r2l or :l2r.
Name-slot: Overrides use of common-name slot as the slot from
which the name is retrieved.
Strip-Html?: When T causes this fn to strip HTML tags from the resulting
names, which by default will sometimes contain HTML tags such as
italics or subscripts.
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