Gram-negative bacterial post-translational Sec protein export

A reusable bacterial protein-export module in which SecB carries an unfolded precursor to the SecA ATPase, SecA drives the precursor into the SecYEG protein-conducting channel, optional SecDF associated with YajC uses proton motive force to improve late-stage translocation, and signal peptidase I removes the N-terminal signal peptide. The module models the canonical post-translational route used by Gram-negative bacteria. Cotranslational SRP targeting, YidC-dependent membrane insertion, Tat export of folded proteins, lipoprotein maturation, and outer-membrane secretion are neighboring modules.

MODULE:bacterial_sec_posttranslational_protein_exportDRAFTCONCRETEBiological Processmodules/bacterial_sec_posttranslational_protein_export.yaml
protein transport by the Sec complexGO:0043952
GO:0043952
protein transport by the Sec complex
Defines the biological process performed by the Sec export apparatus.
GO:0140309
unfolded protein holdase activity
Defines SecB-mediated carriage of unfolded precursors to the translocon.
GO:0008564
protein-exporting ATPase activity
Defines the ATP-coupled motor activity supplied independently by SecA.
GO:0008320
protein transmembrane transporter activity
Defines the channel-level activity supplied by SecYEG with accessory support from SecDF-YajC.
GO:0009977
proton motive force dependent protein transmembrane transporter activity
Defines the PMF-coupled collective transporter activity contributed by SecD and SecF.
GO:0009003
signal peptidase activity
Defines the LepB signal-peptide cleavage activity.
GO:0016485
protein processing
Defines maturation by peptide-bond cleavage, including LepB removal of a type I signal peptide.
PMID:21562494
Structure and function of a membrane component SecDF that enhances protein export.
Direct biochemical work establishes the PMF-dependent, ATP-independent late-translocation role of SecDF.
In vitro analyses identified an ATP-independent step of protein translocation that requires both SecDF and proton motive force.
PMID:29718185
Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor.
Structural synthesis supports SecDF as a proton-driven completion motor that can act after SecA.
SecDF can complete protein translocation even if SecA function is inactivated by ATP depletion
PMID:24550475
Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG-SecDF-YajC-YidC.
Purification of the bacterial holo-translocon grounds association of SecYEG with SecDF-YajC.
The bacterial version SecYEG interacts with the highly conserved YidC and SecDF-YajC subcomplex, which facilitates translocation into and across the membrane.
PMID:7507921
Genetic and molecular characterization of the Escherichia coli secD operon and its products.
Direct genetics leaves the individual contribution of YajC unresolved and argues against treating it as an obligatory Sec factor.
An analysis of yajC mutations constructed in vitro and recombined onto the chromosome indicates that yajC is neither essential nor a sec gene.
PANTHER:PTN000770133
PAINT bacterial SecA transport node
The local PTHR30612 PAINT table assigns protein transport by the Sec complex to this bacterial node.
PANTHER:PTN000097217
PAINT SecY/Sec61 transporter node
The local PTHR10906 PAINT table assigns protein transmembrane transporter activity to this node.
PANTHER:PTN000763987
PAINT SecD/SecF protein-transport node
The local PTHR30081 PAINT table assigns protein transport to the conserved SecD/SecF node.
file:projects/P_PUTIDA/deep-research/PSEPK__sec-protein-export__ppu03060-deep-research-openscientist.md
OpenScientist PSEPK protein-export pathway synthesis
Species-aware retrieval confirms all KT2440 Sec components and separates the post-translational Sec route from SRP, YidC, Tat, lipoprotein maturation, and Xcp type II secretion.

The module is not specific to Pseudomonas putida. KT2440 supplies a concrete implementation of every role, and reviewed E. coli proteins provide canonical Gram-negative exemplars. SecDF-YajC is an optional accessory assembly rather than the ATPase motor; ATP hydrolysis belongs to SecA, while the individual contribution of YajC remains unresolved. The PTHR30612:SF0 and PTHR43390:SF1 display labels are misleadingly chloroplast-centered, so this module uses the correctly named parent SecA and signal-peptidase I families instead of those subfamily display labels.

6Nodes
5Parts
0Variant Sets
0Variants
9Annotons
4Connections

Derived QC

Recommended-field compliance

53.8% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)

Module deep research

✗ none found

No MODULE:bacterial_sec_posttranslational_protein_export deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (10/18 grounded genes reviewed)

10 complete review(s) · 2 with deep research · 8 missing review · 8 reviewed but lacking deep research

Gene Review Complete Deep research
lepB Q88MY6 ✓ ✓ ✗
E. coli LepB P00803 ✗ — —
E. coli YajC P0ADZ7 ✗ — —
E. coli SecD P0AG90 ✗ — —
E. coli SecF P0AG93 ✗ — —
E. coli SecE P0AG96 ✗ — —
E. coli SecG P0AG99 ✗ — —
E. coli SecY P0AGA2 ✗ — —
E. coli SecA P10408 ✗ — —
secA Q88N69 ✓ ✓ ✓
SecB P0AG86 ✓ ✓ ✓
secB Q88CX7 ✓ ✓ ✗
secD Q88PL5 ✓ ✓ ✗
secE Q88QP7 ✓ ✓ ✗
secF Q88PL4 ✓ ✓ ✗
secG A0A140FWQ9 ✓ ✓ ✗
secY Q88QL5 ✓ ✓ ✗
yajC Q88PL6 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
Gram-negative bacterial post-translational Sec protein exportBiological Processbacterial_sec_posttranslational_protein_export
protein transport by the Sec complexGO:0043952
Context
bacteriaNCBITaxon:2

Connections

seca_atpase_motor -> secyeg_channel Provides Input For
SecDF uses proton motive force to improve late-stage translocation through SecYEG; this accessory route is not obligatory for every substrate.
Part 1: ATP-independent precursor carriage and SecA delivery
SecB carriage of an unfolded export precursorBiological Processsecb_precursor_carriage

Annotons

SecB unfolded-preprotein carrier
secb_carrier_activity
Participant: Family: bacterial SecB family
Family:
bacterial SecB familyPANTHER:PTHR36918:SF1
Representative Members: PSEPK SecBUniProtKB:Q88CX7 E. coli SecBUniProtKB:P0AG86
Required Function:
unfolded protein holdase activityGO:0140309

Function

unfolded protein holdase activityGO:0140309
Substrates: unfolded Sec precursor protein
Products: SecB-bound translocation-competent precursor

Processes

protein transport by the Sec complexGO:0043952

Locations

cytoplasmGO:0005737

Prevents premature precursor folding and carries the substrate to the SecA motor.

Part 2: ATP-driven precursor engagement and translocation motor
SecA ATP-driven protein-export motorReactionseca_atpase_motor

Annotons

SecA protein-exporting ATPase
seca_export_atpase_activity
Participant: Family: bacterial SecA family
Family:
bacterial SecA familyPANTHER:PTHR30612
Representative Members: PSEPK SecAUniProtKB:Q88N69 E. coli SecAUniProtKB:P10408
Required Function:
protein-exporting ATPase activityGO:0008564

Function

protein-exporting ATPase activityGO:0008564
Substrates: SecB-bound translocation-competent precursor ATP water
Products: SecA-engaged precursor at SecYEG ADP phosphate

Processes

protein transport by the Sec complexGO:0043952

Locations

plasma membraneGO:0005886

Receives SecB-bound precursors and couples ATP hydrolysis to stepwise channel translocation.

Part 3: inner-membrane protein-conducting channel
SecYEG protein-conducting channelProtein Complexsecyeg_channel

Annotons

SecY pore-forming channel subunit
secy_channel_activity
Participant: Family: SecY/Sec61-alpha family
Family:
SecY/Sec61-alpha familyPANTHER:PTHR10906
Representative Members: PSEPK SecYUniProtKB:Q88QL5 E. coli SecYUniProtKB:P0AGA2
Required Function:
protein transmembrane transporter activityGO:0008320

Function

protein transmembrane transporter activityGO:0008320
Substrates: SecA-engaged precursor at SecYEG
Products: partially translocated Sec precursor

Processes

protein transport by the Sec complexGO:0043952

Locations

plasma membraneGO:0005886

Forms the gated aqueous pore and lateral gate through which the polypeptide moves.

SecE channel-clamp subunit
sece_clamp_activity
Participant: Family: bacterial SecE family
Family:
bacterial SecE familyPANTHER:PTHR33910:SF1
Representative Members: PSEPK SecEUniProtKB:Q88QP7 E. coli SecEUniProtKB:P0AG96
Required Function:
contributes to protein transmembrane transporter activityGO:0008320

Function

contributes to protein transmembrane transporter activityGO:0008320

Processes

protein transport by the Sec complexGO:0043952

Locations

plasma membraneGO:0005886

Clamps the two halves of SecY and supports channel gating.

SecG channel accessory subunit
secg_channel_accessory_activity
Participant: Family: bacterial SecG family
Family:
bacterial SecG familyPANTHER:PTHR34182:SF1
Representative Members: PSEPK SecGUniProtKB:A0A140FWQ9 E. coli SecGUniProtKB:P0AG99
Required Function:
contributes to protein transmembrane transporter activityGO:0008320

Function

contributes to protein transmembrane transporter activityGO:0008320

Processes

protein transport by the Sec complexGO:0043952

Locations

plasma membraneGO:0005886

Supports efficient early translocation without independently hydrolyzing ATP.

Part 4: proton-motive-force-assisted translocation completion (optional)
SecDF-YajC accessory translocation complexProtein Complexsecdf_yajc_accessory_complex

Annotons

SecD PMF-coupled accessory subunit
secd_pmf_accessory_activity
Participant: Family: bacterial SecD subfamily
Family:
bacterial SecD subfamilyPANTHER:PTHR30081:SF1
Representative Members: PSEPK SecDUniProtKB:Q88PL5 E. coli SecDUniProtKB:P0AG90
Required Function:
contributes to proton motive force dependent protein transmembrane transporter activityGO:0009977

Function

contributes to proton motive force dependent protein transmembrane transporter activityGO:0009977
Substrates: partially translocated Sec precursor
Products: translocated precursor with uncleaved signal peptide

Processes

protein transport by the Sec complexGO:0043952

Locations

plasma membraneGO:0005886

Forms the large periplasmic SecDF component that couples proton motive force to late translocation.

SecF PMF-coupled accessory subunit
secf_pmf_accessory_activity
Participant: Family: bacterial SecF subfamily
Family:
bacterial SecF subfamilyPANTHER:PTHR30081:SF8
Representative Members: PSEPK SecFUniProtKB:Q88PL4 E. coli SecFUniProtKB:P0AG93
Required Function:
contributes to proton motive force dependent protein transmembrane transporter activityGO:0009977

Function

contributes to proton motive force dependent protein transmembrane transporter activityGO:0009977

Processes

protein transport by the Sec complexGO:0043952

Locations

plasma membraneGO:0005886

Partners with SecD in the PMF-coupled accessory complex.

YajC complex-associated subunit
yajc_accessory_activity
Participant: Family: bacterial YajC family
Family:
bacterial YajC familyPANTHER:PTHR33909:SF1
Representative Members: PSEPK YajCUniProtKB:Q88PL6 E. coli YajCUniProtKB:P0ADZ7

Locations

plasma membraneGO:0005886

Small membrane subunit found in SecDF-YajC and holo-translocon assemblies; its individual mechanistic contribution is unresolved.

Part 5: type I signal-peptide cleavage
LepB cleavage of the type I signal peptideReactionlepb_signal_peptide_processing

Annotons

LepB signal peptidase I
lepb_signal_peptidase_activity
Participant: Family: bacterial signal peptidase I family
Family:
bacterial signal peptidase I familyPANTHER:PTHR43390
Representative Members: PSEPK LepBUniProtKB:Q88MY6 E. coli LepBUniProtKB:P00803
Required Function:
signal peptidase activityGO:0009003

Function

signal peptidase activityGO:0009003
Substrates: translocated precursor with uncleaved signal peptide
Products: mature exported protein cleaved type I signal peptide

Processes

protein processingGO:0016485

Locations

plasma membraneGO:0005886

Cleaves the type I signal peptide from the translocated non-lipoprotein precursor.