identifier: METPO:1000702
label: motile
definition: A motility in which an organism has the ability to move independently
  using metabolic energy.
definition_source: DOI:10.1038/s41579-021-00626-4
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000701
synonyms:
- synonym_text: 'yes'
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1038/s41579-021-00626-4
  snippet: physical and molecular mechanisms that allow bacteria to move around
  notes: Supports motile bacteria as organisms whose movement is mediated by specific
    molecular machines.
- reference: PMID:34680106
  snippet: Pseudomonas aeruginosa is a motile bacterium
  notes: 'Organism example: Pseudomonas aeruginosa is described as motile.'
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "flagellar swimming motility"
  reference: PMID:32449734
- taxon_id: NCBITaxon:287
  taxon_label: Pseudomonas aeruginosa
  note: "flagellar + pilus motility"
  reference: PMID:11029417
causal_graphs:
- graph_id: motile_energy_dependent_locomotion
  title: Energy-dependent bacterial locomotion
  description: Evidence-backed causal sketch linking motile phenotype to metabolic
    energy, ion motive force, flagella, pili, and directional regulation.
  nodes:
  - node_id: motile_trait
    label: motile
    node_type: TRAIT
    grounding: METPO:1000702
    description: Ability to move independently using metabolic energy.
  - node_id: metabolic_energy
    label: metabolic energy
    node_type: BIOLOGICAL_PROCESS
    description: Energy generated by cellular metabolism and converted into ion gradients
      or ATP-dependent movement.
  - node_id: ion_motive_force
    label: ion motive force
    node_type: BIOLOGICAL_PROCESS
    description: Electrochemical gradient used by many motility motors.
  - node_id: flagellar_motor
    label: flagellar motor
    node_type: GENE_OR_PROTEIN
    description: Rotary motor that turns bacterial flagella.
  - node_id: type_iv_pilus
    label: type IV pilus
    node_type: GENE_OR_PROTEIN
    description: Pilus machinery that extends, adheres, and retracts.
    grounding: UniProtKB:R6TBR9
  - node_id: chemotaxis_signaling
    label: chemotaxis signaling
    node_type: BIOLOGICAL_PROCESS
    description: Regulatory system that biases movement toward favorable conditions.
    grounding: GO:0006935
  - node_id: motab_stator
    label: MotA-MotB stator complex
    node_type: GENE_OR_PROTEIN
    description: Membrane-embedded stator complex of the flagellar motor that conducts
      ions.
  - node_id: stator_proton_channel
    label: transmembrane H+ channel activity
    node_type: MOLECULAR_FUNCTION
    description: Proton-conducting channel function of the MotA-MotB stator across
      the cytoplasmic membrane.
  - node_id: motor_torque
    label: flagellar motor torque
    node_type: BIOLOGICAL_PROCESS
    description: Rotational torque generated by ion flux through the stator acting
      on the rotor.
  - node_id: flig_rotor
    label: FliG rotor protein
    node_type: GENE_OR_PROTEIN
    description: C-ring rotor protein that electrostatically interacts with the stator
      to generate torque.
  - node_id: chea_kinase
    label: CheA histidine kinase
    node_type: GENE_OR_PROTEIN
    description: Autophosphorylating chemotaxis histidine kinase.
    grounding: UniProtKB:G0HQV3
  - node_id: chey_response_regulator
    label: CheY response regulator
    node_type: GENE_OR_PROTEIN
    description: Response regulator that, when phosphorylated, binds the flagellar
      switch.
    grounding: UniProtKB:A0A2X5A7X5
  - node_id: flagellar_c_ring
    label: flagellar C-ring switch complex
    node_type: GENE_OR_PROTEIN
    description: Switch complex (FliM/FliN/FliG) that controls direction of motor
      rotation.
  - node_id: pilb_atpase
    label: PilB extension ATPase
    node_type: GENE_OR_PROTEIN
    description: ATPase that powers type IV pilus extension/assembly.
  - node_id: pilt_atpase
    label: PilT retraction ATPase
    node_type: GENE_OR_PROTEIN
    description: ATPase that powers type IV pilus retraction/disassembly.
  - node_id: t4p_extension
    label: type IV pilus extension
    node_type: BIOLOGICAL_PROCESS
    description: Assembly-driven elongation of the type IV pilus.
  - node_id: t4p_retraction
    label: type IV pilus retraction
    node_type: BIOLOGICAL_PROCESS
    description: Disassembly-driven shortening of the type IV pilus.
  - node_id: twitching_motility
    label: twitching motility
    node_type: BIOLOGICAL_PROCESS
    description: Surface translocation powered by cycles of type IV pilus extension
      and retraction.
    grounding: GO:0043107
  - node_id: sprb_adhesin_movement
    label: SprB adhesin surface movement
    node_type: BIOLOGICAL_PROCESS
    description: Movement of the SprB cell-surface adhesin along the outer membrane.
  - node_id: gliding_motility
    label: gliding motility
    node_type: BIOLOGICAL_PROCESS
    description: Non-flagellar surface motility driven by adhesin surface movement.
  edges:
  - subject: metabolic_energy
    predicate: generates
    object: ion_motive_force
    description: Metabolism supports ion gradients that can power motility.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.659464
      snippet: ion motive force powering the bacterial flagellar motor
      notes: Supports energy transduction from ion gradients into motor function.
    predicate_id: biolink:produces
  - subject: ion_motive_force
    predicate: enables
    object: flagellar_motor
    description: Ion motive force powers rotation of the flagellar motor.
    evidence:
    - reference: DOI:10.3389/fmicb.2021.659464
      snippet: The Dynamic Ion Motive Force Powering
      notes: Review directly addresses ion motive force powering flagellar motors.
    predicate_id: RO:0002327
  - subject: flagellar_motor
    predicate: enables
    object: motile_trait
    description: Flagellar rotation enables independent bacterial movement.
    evidence:
    - reference: DOI:10.3390/biom9070279
      snippet: responsible for motility
      notes: Supports flagella-driven motility.
    predicate_id: RO:0002327
  - subject: type_iv_pilus
    predicate: enables
    object: motile_trait
    description: Type IV pilus extension and retraction enable surface motility.
    evidence:
    - reference: DOI:10.1038/s41579-019-0195-4
      snippet: enable T4P to perform
      notes: Supports pilus-mediated twitching and related motility functions.
    predicate_id: RO:0002327
  - subject: chemotaxis_signaling
    predicate: directs
    object: motile_trait
    description: Chemotaxis signaling regulates motility direction in response to
      environmental changes.
    evidence:
    - reference: DOI:10.3390/biom9070279
      snippet: migrate towards more desirable environments
      notes: Supports chemotaxis regulation of motile behavior.
    predicate_id: RO:0002211
  - subject: motab_stator
    predicate: acts as
    object: stator_proton_channel
    description: The MotA-MotB stator acts as a transmembrane H+ channel.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: it can act as a transmembrane H+ channel
  - subject: stator_proton_channel
    predicate: generates
    object: motor_torque
    description: H+ flux through the stator generates torque via electrostatic interaction
      with FliG.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: conducts H+ through the channel to generate torque by electrostatic interactions
        between MotA and FliG
    predicate_id: biolink:produces
  - subject: motor_torque
    predicate: acts on
    object: flig_rotor
    description: Torque is generated by electrostatic interaction between the stator
      and the FliG rotor.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: electrostatic interactions between MotA and FliG generate torque on the
        rotor
  - subject: motor_torque
    predicate: enables
    object: flagellar_motor
    description: Torque generation drives rotation of the flagellar motor.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: a membrane-embedded rotary motor fueled by an ion motive force across
        the cytoplasmic membrane
    predicate_id: RO:0002327
  - subject: chea_kinase
    predicate: phosphorylates
    object: chey_response_regulator
    description: Phosphorylated CheA transfers phosphate to the response regulator
      CheY.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: Phosphorylated CheA transfers its phosphate group to a response regulator
        called CheY
  - subject: chey_response_regulator
    predicate: binds
    object: flagellar_c_ring
    description: Phosphorylated CheY binds the C-ring switch complex to control rotation
      direction.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: Phosphorylated CheY (CheY-P) binds to the C-ring
  - subject: flagellar_c_ring
    predicate: regulates
    object: chemotaxis_signaling
    description: CheY-P binding to the C-ring switches motor rotation direction, implementing
      chemotactic responses.
    evidence:
    - reference: DOI:10.3390/biom14121488
      notes: allowing the motor to switch the direction of rotation from CCW to CW
    predicate_id: RO:0002211
  - subject: pilb_atpase
    predicate: promotes
    object: t4p_extension
    description: PilB ATPase powers type IV pilus extension/assembly.
    evidence:
    - reference: DOI:10.1128/msphere.00390-24
      notes: PilB (extension ATPase)
    predicate_id: RO:0002213
  - subject: pilt_atpase
    predicate: promotes
    object: t4p_retraction
    description: PilT ATPase powers type IV pilus retraction/disassembly.
    evidence:
    - reference: DOI:10.1128/msphere.00390-24
      notes: PilT (retraction ATPase)
    predicate_id: RO:0002213
  - subject: t4p_extension
    predicate: enables
    object: twitching_motility
    description: Cycles of T4P extension and retraction power twitching surface motility.
    evidence:
    - reference: DOI:10.1128/msphere.00390-24
      notes: recurrent cycles of T4P assembly (extension) and disassembly (retraction)
        power surface movement
    predicate_id: RO:0002327
  - subject: t4p_retraction
    predicate: enables
    object: twitching_motility
    description: Cycles of T4P extension and retraction power twitching surface motility.
    evidence:
    - reference: DOI:10.1128/msphere.00390-24
      notes: recurrent cycles of T4P assembly (extension) and disassembly (retraction)
        power surface movement
    predicate_id: RO:0002327
  - subject: twitching_motility
    predicate: enables
    object: motile_trait
    description: Twitching motility is a form of independent surface movement.
    evidence:
    - reference: DOI:10.1128/msphere.00390-24
      notes: recurrent cycles of T4P assembly and disassembly power surface movement
        (twitching motility)
    predicate_id: RO:0002327
  - subject: sprb_adhesin_movement
    predicate: drives
    object: gliding_motility
    description: Movement of the SprB adhesin along the outer membrane drives gliding
      motility.
    evidence:
    - reference: DOI:10.1128/jb.00068-24
      notes: gliding... is driven by the surface movement of adhesins (notably SprB)
        along the outer membrane
  - subject: gliding_motility
    predicate: enables
    object: motile_trait
    description: Gliding motility is a non-flagellar mechanism of independent movement.
    evidence:
    - reference: DOI:10.1128/jb.00068-24
      notes: gliding is a form of surface motility driven by adhesin movement
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.905197+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-06T14:40:41-07:00'
  curator: codex
  action: CURATED_WITH_ORGANISM_EXAMPLE
  changes: Added Pseudomonas aeruginosa organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-11T00:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Replaced PMID definition source with DOI-backed motility review and added
    causal graph for energy-dependent locomotion by flagella, type IV pili, ion motive
    force, and chemotaxis.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×2).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:produces×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:15Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:R6TBR9×1).
  llm_assisted: true
- timestamp: '2026-05-26T05:00:48Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    powers → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-16T06:54:40Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0006935×1).
  llm_assisted: true
- timestamp: '2026-06-17T04:09:44Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 14 evidence-backed generic edges (14 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 9 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×5, RO:0002213×2, biolink:produces×1, RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0043107×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:G0HQV3×1, UniProtKB:A0A2X5A7X5×1).
  llm_assisted: true