Transport And Transporters

Process: Transport and Localization

This area of the biological process ontology covers the processes involved in positioning a substance or cellular entity and maintaining it in that location.

Terms and Structure

The processes that influence the location of a substance or entity in or outside the cell fall under the general term localization. Localization is split into two parts; there is the establishment of localization, which covers transport and/or autonomous movement of substances or cellular components, as well as orienting a protein or organelle. The maintenance of localization covers sequestering and active retrieval processes.

The structure to represent the localization of a substance or entity is shown below.

  • x localization
    • [p] establishment of x localization
      • [i] establishment of x orientation
      • [i] x movement
      • [i] x transport
        • [i] x export
        • [i] x import
        • [i] x secretion
    • [p] maintenance of x localization
      • [i] sequestering of x

Standard Definitions

Note that not all localization terms have standard definitions at present; as a guide to term usage, x movement should be used to refer to the change in position of entities that can propel themselves, whilst x intended for substances that are moved by another entity. Storage, retention or sequestration are represented by the term sequestering of x.
x localization
The processes by which x (where x is a substance or cellular entity, such as a protein complex or organelle) is transported to, and maintained in, a specific location.
establishment of x localization
The directed movement of x to a specific location.
maintenance of x localization
The processes by which x is maintained in a location and prevented from moving elsewhere.
x secretion
The regulated release of x from a cell or group of cells.
x transport
The directed movement of x into, out of or within a cell, or between cells.
x export
The directed movement of x out of a cell or organelle.
x import
The directed movement of x into a cell or organelle.
establishment of x orientation
The processes that set the alignment of x relative to other cellular structures.

Function: Transporter activity

Terms and Structure

  • [i]transmembrane transporter activity
    • [i]active transporter activity
      • [i]primary active transporter activity
        • [i]decarboxylation-driven active transporter activity
        • [i]light-driven active transporter activity
        • [i]methyl transfer-driven active transporter activity
        • [i]oxidoreduction-driven active transporter activity
        • [i]P-P-bond-hydrolysis-driven transporter activity
      • [i]secondary active transporter activity
        • [i]antiporter activity
        • [i]symporter activity
        • [i]uniporter activity

  • [i]transmembrane transporter activity
    • [i]passive transmembrane transporter activity
      • [i]channel activity
        • [i]gated channel activity
          • [i]dephosphorylation-gated channel activity
          • [i]ion gated channel activity
          • [i]ligand-gated channel activity
          • [i]mechanically gated channel activity
          • [i]phosphorylation-gated channel activity
          • [i]voltage-gated channel activity

  • [i]transporter activity
    • [i]substrate-specific transporter activity
      • [i]substrate-specific transmembrane transporter activity
    • [i]transmembrane transporter activity
      • [i]substrate-specific transmembrane transporter activity

  • [i]transmembrane transporter activity
    • [i]efflux transmembrane transporter activity
    • [i]uptake transmembrane transporter activity

Transporter Standard Definitions

Active Transporters

X transmembrane transporter activity
Catalysis of the transfer of X from one side of the membrane to the other. X is [insert description].
X uptake transmembrane transporter activity
Catalysis of the transfer of X from the outside of a cell to the inside of a cell across a membrane. X is [insert description].
X efflux transmembrane transporter activity
Catalysis of the transfer of X from the inside of a cell to the outside of the cell across a membrane. X is [insert description].
active transmembrane X transporter activity
Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction. X is [insert description].
primary active transmembrane X transporter activity
Catalysis of the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a primary energy source. Primary energy sources known to be coupled to transport are chemical, electrical and solar sources. X is [insert description].
decarboxylation-driven active transmembrane X transporter activity
Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by decarboxylation of a cytoplasmic substrate. X is [insert description].
light-driven active transmembrane X transporter activity
Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by light. X is [insert description].
methyl transfer-driven active transmembrane X transporter activity
Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by a methyl transfer reaction. X is [insert description].
oxidoreduction-driven active transmembrane X transporter activity
Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by an exothermic flow of electrons from a reduced substrate to an oxidized substrate. X is [insert description].
P-P-bond-hydrolysis-driven transmembrane X transporter activity
Enables the transport of X across a membrane, up the solute's concentration gradient, by binding the solute and undergoing a series of conformational changes. Transport works equally well in either direction and is driven by the hydrolysis of the diphosphate bond of inorganic pyrophosphate, ATP, or another nucleoside triphosphate. The transport protein may or may not be transiently phosphorylated, but the substrate is not phosphorylated. X is [insert description].
secondary active transmembrane X transporter activity
Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy. Chemiosmotic sources of energy include uniport, symport or antiport. X is [insert description].
X:solute antiporter activity
Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a antiport mechanism whereby two or more species are transported in opposite directions in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].
X:solute symporter activity
Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a symport mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy. X is [insert description].
X uniporter activity
Catalysis of the transfer of X from one side of the membrane to the other, up the solute's concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a uniport mechanism which is independent of the movement of any other molecular species. X is [insert description].
In secondary active transporter defs include a reaction where possible. For example:

Catalysis of the reaction: sugar(out) + H+(out) = sugar(in) + H+(in). Catalysis of the reaction: solute(out) + H+(out) = solute(in) + H+(in).

Passive Transporters

passive transmembrane X transporter activity
Catalysis of the transfer of X from one side of the membrane to the other, down the solute's concentration gradient. X is [insert description].
X channel activity
Catalysis of facilitated diffusion of X (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
gated X channel activity
Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific stimulus.
dephosphorylation-gated X channel activity
Catalysis of the transmembrane transfer of X by a channel that opens in response to dephosphorylation of one of its constituent parts.
ion-gated X channel activity
Catalysis of the transmembrane transfer of X by a channel that opens in response to a specific ion stimulus.
ligand-gated X channel activity
Catalysis of the transmembrane transfer of X by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts.
mechanically-gated X channel activity
Catalysis of the transmembrane transfer of X by a channel that opens in response to a mechanical stress.
phosphorylation-gated X channel activity
Catalysis of the transmembrane transfer of X by a channel that opens in response to phosphorylation of one of its constituent parts.
voltage-gated X channel activity
Catalysis of the transmembrane transfer of X by a channel whose open state is dependent on the voltage across the membrane in which it is embedded.
X channel activity
Catalysis of facilitated diffusion of X (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
x gated y channel activity
Catalysis of the transmembrane transfer of y by a channel that opens in response to stimulus by x. Transport by a channel involves catalysis of facilitated diffusion of a solute (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel, without evidence for a carrier-mediated mechanism.

Other standard definitions

L-amino acid
L-Y is the levorotatory isomer of [insert systematic name].
D-amino acid
D-Y is the dextrorotatory isomer of [insert systematic name].
constitutive activity
This activity is constitutive and therfore always present, regardless of demand.
inducible activity
This activity is inducible and therefore only present when there is demand.
high affinity
In high affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations.
low affinity
In low affinity transport the transporter is able to bind the solute only if it is present at very high concentrations.