SecA is the essential ATP-driven motor protein of the bacterial Sec translocase (EC 7.4.2.8) that powers post-translational protein secretion through the SecYEG channel. As a P-type polypeptide translocase ATPase, SecA couples ATP binding and hydrolysis to mechanical translocation of preproteins bearing N-terminal signal peptides across the cytoplasmic membrane. The protein cycles between cytoplasmic and membrane-associated states, interacting with the SecYEG preprotein-conducting channel to drive stepwise translocation of polypeptide chains. SecA undergoes conformational changes upon nucleotide binding and hydrolysis that push polypeptide segments through SecYEG. In B. subtilis, SecA localizes to discrete membrane-proximal "secretion zones" during high-level secretion of proteins like alpha-amylase. The protein functions as part of the holotranslocon complex comprising SecYEG with SecDF-YajC and YidC, and cooperates with TerC family proteins (MeeF/MeeY) for co-translocational metalation of secreted enzymes. SecA binds zinc as a cofactor through a C-terminal SEC-C motif and contains helicase-like ATP-binding domains characteristic of the superfamily 2 helicases. The protein can exist as both monomers and various homodimeric forms, with a single SecA monomer interacting with SecY in the functional translocation channel. SecA is essential for bacterial viability and has been proposed as an antibiotic target.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005886
plasma membrane
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecA is a peripheral membrane protein that associates with the plasma membrane on the cytoplasmic side during active protein translocation. UniProt states SecA is localized to Cell membrane as a Peripheral membrane protein on the Cytoplasmic side with experimental evidence from PMID:27362352. The deep research confirms SecA binds to the inner leaflet and SecYEG at the cytoplasmic membrane and cycles into a membrane-inserted state during active translocation.
Reason: Plasma membrane localization is well-established for SecA as part of its core function in protein translocation. SecA cycles between cytoplasm and membrane, associating with the membrane during translocation via SecYEG interaction. IBA annotation is appropriate and consistent with experimental evidence.
Supporting Evidence:
file:BACSU/secA/secA-deep-research-falcon.md
SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane; it cycles into a membrane-inserted state during active translocation and interacts with anionic phospholipids
|
|
GO:0005524
ATP binding
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: ATP binding is a core molecular function of SecA. The protein contains well-characterized ATP-binding sites with multiple residues directly involved in nucleotide coordination. Mutagenesis of K106 abolishes activity (PMID:8440733). Crystal structures demonstrate ADP/ATP binding.
Reason: ATP binding is fundamental to SecA function as an ATPase motor. The protein belongs to the superfamily 2 helicases with helicase-like ATP-binding domains (IPR014001, IPR001650). UniProt records multiple ATP binding residues with structural evidence. This is a core function annotation.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane
file:BACSU/secA/secA-deep-research-falcon.md
ATP binding/hydrolysis by SecA produces conformational changes that push polypeptide segments through SecYEG
|
|
GO:0031522
cell envelope Sec protein transport complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecA is an integral component of the Sec protein transport complex. UniProt states SecA is Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. The deep research confirms SecA operates within the holotranslocon as a dynamic secretion machine.
Reason: SecA is definitionally a component of the Sec protein transport complex. This cellular component annotation accurately captures SecA's localization as part of the functional translocase machinery at the membrane. The IBA annotation is appropriate.
Supporting Evidence:
UniProt:P28366
Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF
file:BACSU/secA/secA-deep-research-falcon.md
The functional secretion unit in Gram-positive bacteria (holotranslocon) comprises SecYEG with SecDF-YajC and YidC; SecA powers translocation into/through SecYEG
|
|
GO:0043952
protein transport by the Sec complex
|
IBA
GO_REF:0000033 |
ACCEPT |
Summary: SecA drives protein transport through the Sec complex as the ATP-dependent motor. The deep research states SecA has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane.
Reason: This biological process annotation accurately captures the primary function of SecA - driving protein transport through the Sec translocase. SecA is the motor that powers Sec-dependent translocation. This is a core function.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
file:BACSU/secA/secA-deep-research-falcon.md
SecA is the ATP-driven motor of the bacterial Sec translocase that post-translationally drives preprotein movement through the SecYEG channel
|
|
GO:0000166
nucleotide binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: SecA binds nucleotides (ATP/ADP) as part of its catalytic cycle. This IEA annotation from UniProtKB keyword mapping is accurate but too general compared to the more specific GO:0005524 (ATP binding) annotations also present.
Reason: While this annotation is correct, it is broader than the ATP binding annotations already present. Since duplicates with different evidence codes are acceptable and this IEA provides complementary computational evidence, it can be retained. The annotation is not wrong, just less specific than the IBA ATP binding annotation.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane
|
|
GO:0005524
ATP binding
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is a duplicate ATP binding annotation with IEA evidence from combined automated annotation. The IBA annotation with the same GO ID provides phylogenetically-based evidence for the same function.
Reason: Duplicate annotations with different evidence codes are acceptable. This IEA annotation provides complementary computational support for the core ATP binding function of SecA.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor
|
|
GO:0005737
cytoplasm
|
IEA
GO_REF:0000044 |
ACCEPT |
Summary: SecA is a cytoplasmic protein that cycles to the membrane during active translocation. UniProt states subcellular location includes Cytoplasm with the note Distribution is 50-50 between cytoplasm and membrane. The deep research confirms SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane.
Reason: Cytoplasmic localization is accurate - SecA exists in equilibrium between cytoplasm and membrane. The protein is soluble in the cytoplasm and peripherally associates with the membrane during translocation.
Supporting Evidence:
UniProt:P28366
Note=Distribution is 50-50
file:BACSU/secA/secA-deep-research-falcon.md
SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane; it cycles into a membrane-inserted state during active translocation
|
|
GO:0005886
plasma membrane
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: This is a duplicate plasma membrane annotation with IEA evidence. The IBA annotation with the same GO ID is also present with phylogenetic evidence.
Reason: Duplicate annotations with different evidence codes are acceptable. Both IBA and IEA evidence support plasma membrane localization as a core aspect of SecA function.
Supporting Evidence:
file:BACSU/secA/secA-deep-research-falcon.md
SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane
|
|
GO:0006605
protein targeting
|
IEA
GO_REF:0000120 |
ACCEPT |
Summary: SecA is involved in targeting preproteins to the translocation apparatus. The protein recognizes signal peptide-bearing preproteins and delivers them to SecYEG for translocation. This is part of the broader Sec-dependent secretion pathway.
Reason: Protein targeting is a valid biological process for SecA, as it recognizes and directs preproteins to the SecYEG channel. This is broader than but consistent with the more specific "protein transport by the Sec complex" annotation.
Supporting Evidence:
file:BACSU/secA/secA-deep-research-falcon.md
SecA recognizes preproteins with N-terminal signal peptides that engage the lateral gate of SecY
|
|
GO:0006886
intracellular protein transport
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: SecA participates in intracellular protein transport by moving preproteins from the cytoplasm to the membrane/extracellular space via SecYEG. This InterPro-derived annotation captures the transport function.
Reason: This annotation is accurate but very general. SecA does participate in intracellular protein transport as part of the Sec pathway. The more specific annotation "protein transport by the Sec complex" (GO:0043952) better captures the specificity of SecA function, but this broader term is not incorrect.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane
|
|
GO:0008564
protein-exporting ATPase activity
|
IEA
GO_REF:0000003 |
ACCEPT |
Summary: This is the most specific and accurate molecular function annotation for SecA. EC 7.4.2.8 maps to protein-exporting ATPase activity. UniProt records the catalytic activity with experimental evidence from PMID:8440733.
Reason: This is the core molecular function of SecA. The EC number 7.4.2.8 corresponds to protein-translocating ATPase activity. SecA couples ATP hydrolysis to the mechanical work of pushing polypeptides through SecYEG. This annotation should be retained as a core function.
Supporting Evidence:
UniProt:P28366
Reaction=ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2.; EC=7.4.2.8
file:BACSU/secA/secA-deep-research-falcon.md
SecA is a P-type polypeptide translocase ATPase (EC 7.4.2.8) that couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane via SecYEG
|
|
GO:0015031
protein transport
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: SecA is involved in protein transport as the motor driving secretion through SecYEG. This annotation is accurate but very general compared to the more specific "protein transport by the Sec complex" (GO:0043952).
Reason: This general protein transport annotation is accurate. SecA mediates protein transport across membranes. While less specific than GO:0043952, it is not incorrect and provides keyword-based evidence.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane
|
|
GO:0016020
membrane
|
IEA
GO_REF:0000002 |
ACCEPT |
Summary: SecA associates with membranes as a peripheral membrane protein. This InterPro-derived annotation is accurate but very general - the more specific GO:0005886 (plasma membrane) annotations are also present.
Reason: This general membrane annotation is technically correct but less informative than the specific plasma membrane annotations. It can be retained as complementary evidence from InterPro.
Supporting Evidence:
file:BACSU/secA/secA-deep-research-falcon.md
SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane
|
|
GO:0017038
protein import
|
IEA
GO_REF:0000002 |
REMOVE |
Summary: This annotation appears to be an error or overly generic mapping from InterPro. SecA is involved in protein EXPORT (secretion) not import. The Sec pathway translocates proteins from the cytoplasm to the periplasm/extracellular space, which is export, not import.
Reason: SecA is a protein EXPORTER, not importer. The Sec translocase moves preproteins from the cytoplasm out through the membrane. "Protein import" implies movement into the cytoplasm, which is the opposite of SecA's function. This annotation should be removed as it is misleading.
Supporting Evidence:
UniProt:P28366
Reaction=ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2.; EC=7.4.2.8
file:BACSU/secA/secA-deep-research-falcon.md
SecA is a P-type polypeptide translocase ATPase that couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane
|
|
GO:0045121
membrane raft
|
IEA
GO_REF:0000044 |
KEEP AS NON CORE |
Summary: UniProt records membrane raft localization based on PMID:27362352, which studied flotillin-associated membrane microdomains in B. subtilis. However, the UniProt subunit comment notes SecA only shows some colocalization with FloA or FloT membrane assemblies suggesting limited association with lipid rafts.
Reason: The annotation is based on experimental evidence from PMID:27362352, but the evidence indicates only partial colocalization with membrane rafts. This is not a core localization for SecA function - the primary functional location is at SecYEG translocon sites. The membrane raft association may represent a subset of SecA molecules or a regulatory aspect.
Supporting Evidence:
UniProt:P28366
Only shows some colocalization with FloA or FloT membrane assemblies (PubMed:27362352)
|
|
GO:0046872
metal ion binding
|
IEA
GO_REF:0000043 |
ACCEPT |
Summary: SecA binds zinc through its C-terminal SEC-C motif. UniProt records that SecA may bind 1 zinc ion per subunit through conserved cysteine residues.
Reason: Metal ion binding (specifically zinc) is a documented property of SecA. The SEC-C motif at the C-terminus contains conserved cysteines that coordinate zinc. While the precise functional role of zinc binding is less clear than the ATPase activity, this is a legitimate molecular function annotation based on structural and sequence evidence.
Supporting Evidence:
UniProt:P28366
May bind 1 zinc ion per subunit
|
|
GO:0065002
intracellular protein transmembrane transport
|
IEA
GO_REF:0000104 |
ACCEPT |
Summary: SecA drives transmembrane transport of proteins through SecYEG. This annotation captures the essence of SecA function - moving proteins across the membrane. The term is appropriate for SecA's role in translocation.
Reason: This annotation accurately describes SecA's function in driving protein transport across the cytoplasmic membrane. SecA powers the movement of preproteins through the SecYEG channel, which is intracellular protein transmembrane transport.
Supporting Evidence:
UniProt:P28366
Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane
file:BACSU/secA/secA-deep-research-falcon.md
SecA couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane via SecYEG
|
Exported on March 22, 2026 at 02:26 AM
Organism: Bacillus subtilis
Sequence:
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEIENNLEREEVVQGQTTAHQPQEGDDNKKAKKAPVRKVVDIGRNAPCHCGSGKKYKNCCGRTE
I begin by dissecting the InterPro architecture and its order along the sequence. The N-terminus is dominated by ATPase/helicase-like modules: IPR014018 (SecA motor DEAD domain, residues 1–570) and IPR027417 (P-loop containing nucleoside triphosphate hydrolase superfamily, residues 6–570) define a classical NTPase engine. This engine is refined by IPR011115 (SecA DEAD-like, N-terminal, residues 5–382) and the embedded IPR014001 (Helicase superfamily 1/2, ATP-binding domain, residues 87–257), which together specify a RecA/DEAD-like ATP-binding and hydrolysis core. Midway, a cargo-engagement module appears: IPR036670 (SecA preprotein cross-linking domain superfamily, residues 225–348) and its specific instance IPR011130 (SecA preprotein cross-linking domain, residues 226–338) create a clamp that binds unfolded preproteins and couples them to the channel. The catalytic cycle is completed by the C-terminal helicase-like elements: IPR044722 (SecA, C-terminal helicase domain, residues 397–565) and IPR001650 (Helicase, C-terminal domain-like, residues 421–575), reinforced by a conserved catalytic patch IPR020937 (SecA conserved site, residues 480–495). Downstream, the architecture transitions into the assembly and targeting scaffold: IPR011116 (SecA Wing/Scaffold, residues 568–778) and IPR036266 (SecA Wing/Scaffold superfamily, residues 571–829) build a winged scaffold that mediates protein-protein interactions and membrane association. The extreme C-terminus carries IPR004027 (SEC-C motif, residues 821–839), a hallmark of SecA that tunes assembly and membrane-proximal function. The entire arrangement is encompassed by IPR000185 (Protein translocase subunit SecA family, residues 4–807), confirming that the full-length polypeptide is a canonical SecA-type motor.
This ordered layout causally dictates molecular function. The NTPase/helicase modules (IPR014018, IPR027417, IPR011115, IPR014001) generate ATP-dependent conformational cycles that drive mechanical work. The preprotein cross-linking domain pair (IPR036670/IPR011130) forms a clamp for unfolded secretory precursors, while the C-terminal helicase-like region (IPR044722/IPR001650) and conserved catalytic site (IPR020937) coordinate ATP hydrolysis with substrate handling. The wing/scaffold (IPR011116/IPR036266) and SEC-C motif (IPR004027) anchor the motor to partner complexes and membranes. Together, this architecture enforces ATP-coupled translocation of polypeptides, establishing GO:0005515 as the operative molecular function term that captures ATP-driven activity within the translocation machinery.
From molecular function, the biological process follows directly. The preprotein clamp and SecA motor architecture are specialized for post-translational movement of secretory and membrane proteins through the protein-conducting channel. This defines the process of protein secretion via the Sec pathway, i.e., GO:0009306 protein secretion. The scaffold that recruits partner subunits ensures efficient handoff from ribosomes/translocons to the extracytoplasmic space, aligning the enzyme’s activity with the broader secretory pathway.
Cellular localization is implied by the soluble, multidomain motor lacking transmembrane segments and by its scaffold that binds membrane partners rather than embedding in the bilayer. The wing/scaffold and SEC-C motif mediate peripheral association with the membrane-embedded translocon while the bulk of the protein remains soluble; thus the predominant residence is cytoplasmic, with transient membrane-proximal engagement. This supports GO:0005737 cytoplasm and explains the experimentally observed cytoplasmic localization.
Mechanistically, ATP binding and hydrolysis in the DEAD-like core power cyclical clamp-and-release motions that ratchet preproteins through the Sec channel. The preprotein cross-linking domain captures signal peptides and unstructured segments, while the wing/scaffold organizes assemblies with SecYEG/SecYE and chaperones. I therefore hypothesize that the protein forms transient complexes with the membrane translocon and accessory modules to drive vectorial secretion in Bacillus subtilis. Likely interaction partners include the SecYEG channel and its Bacillus-specific paralog SecYE, the signal peptidase complex for luminal processing, and soluble chaperones that stabilize export substrates; together these assemblies couple ATP-fueled cycles to directional translocation and secretion fidelity.
An ATP-driven motor of the bacterial secretory pathway that binds unfolded preproteins and powers their post-translational translocation through the membrane channel. It operates as a soluble cytoplasmic factor that transiently associates with membrane translocons via a winged scaffold and conserved C-terminal elements, using cycles of nucleotide binding and hydrolysis to clamp, ratchet, and release substrates during secretion.
Part of the Sec complex required for protein secretion. May be the energy-transducing component of the system.
IPR014018, domain) — residues 1-570IPR000185, family) — residues 4-807IPR011115, domain) — residues 5-382IPR027417, homologous_superfamily) — residues 6-570IPR014001, domain) — residues 87-257IPR036670, homologous_superfamily) — residues 225-348IPR011130, domain) — residues 226-338IPR044722, domain) — residues 397-565IPR001650, domain) — residues 421-575IPR020937, conserved_site) — residues 480-495IPR011116, domain) — residues 568-778IPR036266, homologous_superfamily) — residues 571-829IPR004027, conserved_site) — residues 821-839Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), protein binding (GO:0005515)
Biological Process: biological_process (GO:0008150), biological regulation (GO:0065007), localization (GO:0051179), regulation of biological process (GO:0050789), homeostatic process (GO:0042592), cellular process (GO:0009987), negative regulation of biological process (GO:0048519), chemical homeostasis (GO:0048878), cellular localization (GO:0051641), cellular homeostasis (GO:0019725), negative regulation of transport (GO:0051051), transmembrane transport (GO:0055085), regulation of localization (GO:0032879), regulation of pH (GO:0006885), regulation of cellular process (GO:0050794), establishment of localization (GO:0051234), cellular component organization or biogenesis (GO:0071840), negative regulation of cellular process (GO:0048523), monoatomic ion homeostasis (GO:0050801), intracellular chemical homeostasis (GO:0055082), regulation of transport (GO:0051049), cellular component biogenesis (GO:0044085), negative regulation of cellular component organization (GO:0051129), intracellular transport (GO:0046907), cell redox homeostasis (GO:0045454), regulation of sequestering of calcium ion (GO:0051282), inorganic ion transmembrane transport (GO:0098660), transport (GO:0006810), establishment of localization in cell (GO:0051649), cellular component organization (GO:0016043), inorganic ion homeostasis (GO:0098771), regulation of cellular component organization (GO:0051128), regulation of cellular component biogenesis (GO:0044087), negative regulation of protein-containing complex assembly (GO:0031333), monoatomic cation transmembrane transport (GO:0098655), negative regulation of organelle organization (GO:0010639), import into cell (GO:0098657), inorganic cation transmembrane transport (GO:0098662), monoatomic cation homeostasis (GO:0055080), regulation of cell projection organization (GO:0031344), iron import into cell (GO:0033212), regulation of organelle organization (GO:0033043), organic substance transport (GO:0071702), intracellular monoatomic ion homeostasis (GO:0006873), vacuolar transport (GO:0007034), organelle organization (GO:0006996), monoatomic ion transport (GO:0006811), regulation of cell projection assembly (GO:0060491), cellular component assembly (GO:0022607), organelle assembly (GO:0070925), regulation of plasma membrane bounded cell projection assembly (GO:0120032), monoatomic cation transport (GO:0006812), negative regulation of cytoskeleton organization (GO:0051494), regulation of plasma membrane bounded cell projection organization (GO:0120035), negative regulation of plasma membrane bounded cell projection assembly (GO:0120033), lysosomal transport (GO:0007041), calcium ion transport (GO:0006816), intracellular calcium ion homeostasis (GO:0006874), intracellular pH reduction (GO:0051452), proton transmembrane transport (GO:1902600), intracellular monoatomic cation homeostasis (GO:0030003), metal ion transport (GO:0030001), non-membrane-bounded organelle assembly (GO:0140694), regulation of neuron projection development (GO:0010975)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), host cellular component (GO:0018995), host cell part (GO:0033643), host cell (GO:0043657), host intracellular part (GO:0033646), host intracellular region (GO:0043656), host cell cytoplasm (GO:0030430)
Generated by BioReason
Exported on March 22, 2026 at 02:26 AM
Organism: Bacillus subtilis
Sequence:
MLGILNKMFDPTKRTLNRYEKIANDIDAIRGDYENLSDDALKHKTIEFKERLEKGATTDDLLVEAFAVVREASRRVTGMFPFKVQLMGGVALHDGNIAEMKTGEGKTLTSTLPVYLNALTGKGVHVVTVNEYLASRDAEQMGKIFEFLGLTVGLNLNSMSKDEKREAYAADITYSTNNELGFDYLRDNMVLYKEQMVQRPLHFAVIDEVDSILIDEARTPLIISGQAAKSTKLYVQANAFVRTLKAEKDYTYDIKTKAVQLTEEGMTKAEKAFGIDNLFDVKHVALNHHINQALKAHVAMQKDVDYVVEDGQVVIVDSFTGRLMKGRRYSEGLHQAIEAKEGLEIQNESMTLATITFQNYFRMYEKLAGMTGTAKTEEEEFRNIYNMQVVTIPTNRPVVRDDRPDLIYRTMEGKFKAVAEDVAQRYMTGQPVLVGTVAVETSELISKLLKNKGIPHQVLNAKNHEREAQIIEEAGQKGAVTIATNMAGRGTDIKLGEGVKELGGLAVVGTERHESRRIDNQLRGRSGRQGDPGITQFYLSMEDELMRRFGAERTMAMLDRFGMDDSTPIQSKMVSRAVESSQKRVEGNNFDSRKQLLQYDDVLRQQREVIYKQRFEVIDSENLREIVENMIKSSLERAIAAYTPREELPEEWKLDGLVDLINTTYLDEGALEKSDIFGKEPDEMLELIMDRIITKYNEKEEQFGKEQMREFEKVIVLRAVDSKWMDHIDAMDQLRQGIHLRAYAQTNPLREYQMEGFAMFEHMIESIEDEVAKFVMKAEIENNLEREEVVQGQTTAHQPQEGDDNKKAKKAPVRKVVDIGRNAPCHCGSGKKYKNCCGRTE
I begin by dissecting the InterPro architecture and its order along the sequence. The N-terminus is dominated by ATPase/helicase-like modules: IPR014018 (SecA motor DEAD domain, residues 1–570) and IPR027417 (P-loop containing nucleoside triphosphate hydrolase superfamily, residues 6–570) define a classical NTPase engine. This engine is refined by IPR011115 (SecA DEAD-like, N-terminal, residues 5–382) and the embedded IPR014001 (Helicase superfamily 1/2, ATP-binding domain, residues 87–257), which together specify a RecA/DEAD-like ATP-binding and hydrolysis core. Midway, a cargo-engagement module appears: IPR036670 (SecA preprotein cross-linking domain superfamily, residues 225–348) and its specific instance IPR011130 (SecA preprotein cross-linking domain, residues 226–338) create a clamp that binds unfolded preproteins and couples them to the channel. The catalytic cycle is completed by the C-terminal helicase-like elements: IPR044722 (SecA, C-terminal helicase domain, residues 397–565) and IPR001650 (Helicase, C-terminal domain-like, residues 421–575), reinforced by a conserved catalytic patch IPR020937 (SecA conserved site, residues 480–495). Downstream, the architecture transitions into the assembly and targeting scaffold: IPR011116 (SecA Wing/Scaffold, residues 568–778) and IPR036266 (SecA Wing/Scaffold superfamily, residues 571–829) build a winged scaffold that mediates protein-protein interactions and membrane association. The extreme C-terminus carries IPR004027 (SEC-C motif, residues 821–839), a hallmark of SecA that tunes assembly and membrane-proximal function. The entire arrangement is encompassed by IPR000185 (Protein translocase subunit SecA family, residues 4–807), confirming that the full-length polypeptide is a canonical SecA-type motor.
This ordered layout causally dictates molecular function. The NTPase/helicase modules (IPR014018, IPR027417, IPR011115, IPR014001) generate ATP-dependent conformational cycles that drive mechanical work. The preprotein cross-linking domain pair (IPR036670/IPR011130) forms a clamp for unfolded secretory precursors, while the C-terminal helicase-like region (IPR044722/IPR001650) and conserved catalytic site (IPR020937) coordinate ATP hydrolysis with substrate handling. The wing/scaffold (IPR011116/IPR036266) and SEC-C motif (IPR004027) anchor the motor to partner complexes and membranes. Together, this architecture enforces ATP-coupled translocation of polypeptides, establishing GO:0005515 as the operative molecular function term that captures ATP-driven activity within the translocation machinery.
From molecular function, the biological process follows directly. The preprotein clamp and SecA motor architecture are specialized for post-translational movement of secretory and membrane proteins through the protein-conducting channel. This defines the process of protein secretion via the Sec pathway, i.e., GO:0009306 protein secretion. The scaffold that recruits partner subunits ensures efficient handoff from ribosomes/translocons to the extracytoplasmic space, aligning the enzyme’s activity with the broader secretory pathway.
Cellular localization is implied by the soluble, multidomain motor lacking transmembrane segments and by its scaffold that binds membrane partners rather than embedding in the bilayer. The wing/scaffold and SEC-C motif mediate peripheral association with the membrane-embedded translocon while the bulk of the protein remains soluble; thus the predominant residence is cytoplasmic, with transient membrane-proximal engagement. This supports GO:0005737 cytoplasm and explains the experimentally observed cytoplasmic localization.
Mechanistically, ATP binding and hydrolysis in the DEAD-like core power cyclical clamp-and-release motions that ratchet preproteins through the Sec channel. The preprotein cross-linking domain captures signal peptides and unstructured segments, while the wing/scaffold organizes assemblies with SecYEG/SecYE and chaperones. I therefore hypothesize that the protein forms transient complexes with the membrane translocon and accessory modules to drive vectorial secretion in Bacillus subtilis. Likely interaction partners include the SecYEG channel and its Bacillus-specific paralog SecYE, the signal peptidase complex for luminal processing, and soluble chaperones that stabilize export substrates; together these assemblies couple ATP-fueled cycles to directional translocation and secretion fidelity.
An ATP-driven motor of the bacterial secretory pathway that binds unfolded preproteins and powers their post-translational translocation through the membrane channel. It operates as a soluble cytoplasmic factor that transiently associates with membrane translocons via a winged scaffold and conserved C-terminal elements, using cycles of nucleotide binding and hydrolysis to clamp, ratchet, and release substrates during secretion.
Part of the Sec complex required for protein secretion. May be the energy-transducing component of the system.
IPR014018, domain) — residues 1-570IPR000185, family) — residues 4-807IPR011115, domain) — residues 5-382IPR027417, homologous_superfamily) — residues 6-570IPR014001, domain) — residues 87-257IPR036670, homologous_superfamily) — residues 225-348IPR011130, domain) — residues 226-338IPR044722, domain) — residues 397-565IPR001650, domain) — residues 421-575IPR020937, conserved_site) — residues 480-495IPR011116, domain) — residues 568-778IPR036266, homologous_superfamily) — residues 571-829IPR004027, conserved_site) — residues 821-839Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), protein binding (GO:0005515)
Biological Process: biological_process (GO:0008150), biological regulation (GO:0065007), localization (GO:0051179), regulation of biological process (GO:0050789), homeostatic process (GO:0042592), cellular process (GO:0009987), negative regulation of biological process (GO:0048519), chemical homeostasis (GO:0048878), cellular localization (GO:0051641), cellular homeostasis (GO:0019725), negative regulation of transport (GO:0051051), transmembrane transport (GO:0055085), regulation of localization (GO:0032879), regulation of pH (GO:0006885), regulation of cellular process (GO:0050794), establishment of localization (GO:0051234), cellular component organization or biogenesis (GO:0071840), negative regulation of cellular process (GO:0048523), monoatomic ion homeostasis (GO:0050801), intracellular chemical homeostasis (GO:0055082), regulation of transport (GO:0051049), cellular component biogenesis (GO:0044085), negative regulation of cellular component organization (GO:0051129), intracellular transport (GO:0046907), cell redox homeostasis (GO:0045454), regulation of sequestering of calcium ion (GO:0051282), inorganic ion transmembrane transport (GO:0098660), transport (GO:0006810), establishment of localization in cell (GO:0051649), cellular component organization (GO:0016043), inorganic ion homeostasis (GO:0098771), regulation of cellular component organization (GO:0051128), regulation of cellular component biogenesis (GO:0044087), negative regulation of protein-containing complex assembly (GO:0031333), monoatomic cation transmembrane transport (GO:0098655), negative regulation of organelle organization (GO:0010639), import into cell (GO:0098657), inorganic cation transmembrane transport (GO:0098662), monoatomic cation homeostasis (GO:0055080), regulation of cell projection organization (GO:0031344), iron import into cell (GO:0033212), regulation of organelle organization (GO:0033043), organic substance transport (GO:0071702), intracellular monoatomic ion homeostasis (GO:0006873), vacuolar transport (GO:0007034), organelle organization (GO:0006996), monoatomic ion transport (GO:0006811), regulation of cell projection assembly (GO:0060491), cellular component assembly (GO:0022607), organelle assembly (GO:0070925), regulation of plasma membrane bounded cell projection assembly (GO:0120032), monoatomic cation transport (GO:0006812), negative regulation of cytoskeleton organization (GO:0051494), regulation of plasma membrane bounded cell projection organization (GO:0120035), negative regulation of plasma membrane bounded cell projection assembly (GO:0120033), lysosomal transport (GO:0007041), calcium ion transport (GO:0006816), intracellular calcium ion homeostasis (GO:0006874), intracellular pH reduction (GO:0051452), proton transmembrane transport (GO:1902600), intracellular monoatomic cation homeostasis (GO:0030003), metal ion transport (GO:0030001), non-membrane-bounded organelle assembly (GO:0140694), regulation of neuron projection development (GO:0010975)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), host cellular component (GO:0018995), host cell part (GO:0033643), host cell (GO:0043657), host intracellular part (GO:0033646), host intracellular region (GO:0043656), host cell cytoplasm (GO:0030430)
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organism: BACSU
gene_id: secA
gene_symbol: secA
uniprot_accession: P28366
protein_description: 'RecName: Full=Protein translocase subunit SecA {ECO:0000255|HAMAP-Rule:MF_01382};
EC=7.4.2.8 {ECO:0000255|HAMAP-Rule:MF_01382, ECO:0000305|PubMed:8440733};'
gene_info: Name=secA {ECO:0000255|HAMAP-Rule:MF_01382}; Synonyms=div+; OrderedLocusNames=BSU35300;
organism_full: Bacillus subtilis (strain 168).
protein_family: Belongs to the SecA family. {ECO:0000255|HAMAP-
protein_domains: Helicase_ATP-bd. (IPR014001); Helicase_C-like. (IPR001650); P-loop_NTPase.
(IPR027417); SEC_C_motif. (IPR004027); SecA. (IPR000185)
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BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'secA' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene secA (gene ID: secA, UniProt: P28366) in BACSU.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Question: You are an expert researcher providing comprehensive, well-cited information.
Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies
Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.
BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.
DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'secA' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information
Please provide a comprehensive research report on the gene secA (gene ID: secA, UniProt: P28366) in BACSU.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
Plan and verification
- Identity check: secA in Bacillus subtilis (strain 168) encodes the cytosolic/peripheral membrane ATPase motor (SecA) of the general Sec protein translocation machinery, consistent with UniProt P28366, EC 7.4.2.8. Mechanistic and structural reviews and Bacillus-focused experimental studies confirm SecA’s role at the SecYEG channel in B. subtilis and other bacteria (nijeholt2012thebacterialsectranslocase pages 3-5, strach2023proteinsecretionzones pages 1-2). The protein operates at the cytoplasmic membrane, cycles on/off SecYEG, and binds anionic phospholipids, in line with a peripheral membrane ATPase motor; this matches the UniProt functional annotation and family assignment (SecA) (nijeholt2012thebacterialsectranslocase pages 5-6, nijeholt2012thebacterialsectranslocase pages 3-5).
Comprehensive research report
1) Key concepts and definitions with current understanding
- Core role of SecA: SecA is the ATP-driven motor of the bacterial Sec translocase that post-translationally drives preprotein movement through the SecYEG channel. ATP binding/hydrolysis by SecA produces conformational changes that push polypeptide segments through SecYEG; SecA’s oligomeric state (monomer/dimer) and lipid interactions modulate activity (Philosophical Transactions R. Soc. B, 2012, https://doi.org/10.1098/rstb.2011.0201, Apr 2012) (nijeholt2012thebacterialsectranslocase pages 13-14, nijeholt2012thebacterialsectranslocase pages 5-6, nijeholt2012thebacterialsectranslocase pages 3-5).
- Translocon architecture: SecY forms the protein-conducting channel with a hydrophobic constriction and a movable plug; the lateral gate opens to accept signal peptides or transmembrane segments. Constraining the lateral gate impairs translocation and alters SecA ATPase activity, evidencing tight allosteric coupling between SecA’s catalytic cycle and SecY gating (Philosophical Transactions R. Soc. B, 2012, https://doi.org/10.1098/rstb.2011.0201, Apr 2012) (nijeholt2012thebacterialsectranslocase pages 3-5, nijeholt2012thebacterialsectranslocase pages 5-6).
- Holotranslocon and accessory partners: The functional secretion unit in Gram-positive bacteria (holotranslocon) comprises SecYEG with SecDF–YajC and YidC; SecA powers translocation into/through SecYEG. Bacillus subtilis TerC family proteins MeeF (YceF) and MeeY (YkoY) physically associate with this complex and facilitate co-translocational metalation of secreted enzymes (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-41896-1, Oct 2023) (he2023tercproteinsfunction pages 6-8).
- Localization: In B. subtilis, SecA localizes at discrete membrane-proximal “secretion zones” during high-level secretion; single-molecule tracking reveals multiple diffusive states, consistent with SecA cycling between substrate-bound, translocon-bound, and free states (BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (strach2023proteinsecretionzones pages 1-2).
2) Recent developments and latest research (2023–2024 prioritized)
- Spatial secretion zones and SecA dynamics in B. subtilis: Overexpression of the secreted α-amylase (AmyE) reveals stable secretion patches within the Gram-positive cell wall that overlap SecA signals. SecA exhibits three diffusive states whose populations shift with secretion load, yet without overwhelming the translocase, refining our view of how SecA is deployed in vivo (BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (strach2023proteinsecretionzones pages 1-2).
- Co-translocational metalation via TerC proteins: Deletion of MeeF and MeeY impairs protein export and reduces Mn in the secreted proteome; MeeF/MeeY co-purify with Sec pathway components, indicating a SecA/SecYEG/SecDF–YajC–YidC–TerC functional unit that supports maturation of Mn-dependent extracytoplasmic enzymes (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-41896-1, Oct 2023) (he2023tercproteinsfunction pages 6-8).
- Translational arrest-peptide regulation of Sec components: High-resolution work on arrest peptides shows how regulatory nascent chains stall translation to modulate expression of Sec machinery components. For SecM in E. coli, a 2.0 Å structure reveals stabilization of the A-site Pro-tRNA that prevents peptide bond formation; relief occurs when mechanical pulling forces (e.g., by SecA/translocon) act on the nascent chain. RAPP-motif arrest peptides were structurally defined in both B. subtilis and E. coli, demonstrating a conserved “short-circuit” of peptidyltransferase activity that likely tunes Sec-related gene expression in Firmicutes (Nature Communications, 2024, https://doi.org/10.1038/s41467-024-46762-2, Mar 2024; Nature Communications, 2024, https://doi.org/10.1038/s41467-024-46761-3, Mar 2024) (jensen2025incelldiscoveryand pages 25-27).
- Review integration for Gram-positives: A 2024 expert review synthesizes emerging links between Sec-dependent export and extracytoplasmic metalation, highlighting SecA and SecDF as central elements in maintaining envelope homeostasis and the function of metal-dependent exoenzymes (Annual Review of Microbiology, 2024, https://doi.org/10.1146/annurev-micro-041522-091507, Nov 2024) (he2023tercproteinsfunction pages 6-8).
3) Current applications and real-world implementations
- Industrial secretion in Bacillus: Bacillus spp. are major hosts for secreted enzyme production. In a high-yield B. subtilis mutant for nattokinase, transcriptomics indicated upregulation of Sec pathway components correlating with higher extracellular enzyme titers, aligning with the concept that tuning SecA/SecDF/associated factors boosts secretion capacity (Foods, 2025, https://doi.org/10.3390/foods14050898, Mar 2025). The study reported 300.0 ± 4.7 FU/mL nattokinase activity in the engineered strain, a 1.84-fold increase over the parent (guo2025genomicandtranscriptomic pages 19-19). Complementary microscopy in B. subtilis shows secretion zones overlapping SecA signals during high amylase production, providing spatial targets for engineering secretion efficiency (BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (strach2023proteinsecretionzones pages 1-2).
- Accessory folding support: The lipoprotein foldase PrsA is critical for post-translocation folding and secretion of enzymes like α-amylase, indicating that SecA-driven export must be matched by extracytoplasmic folding capacity for industrial performance (BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (strach2023proteinsecretionzones pages 1-2).
4) Expert opinions and analysis from authoritative sources
- Mechanism: Structural-mechanistic analyses converge on a model where SecA cycles at SecYEG, with ATPase activity allosterically coupled to lateral-gate opening and polypeptide diffusion through the hydrophobic constriction. These insights provide a robust mechanistic framework for Gram-positive SecA, including B. subtilis (Philosophical Transactions R. Soc. B, 2012, https://doi.org/10.1098/rstb.2011.0201, Apr 2012) (nijeholt2012thebacterialsectranslocase pages 3-5, nijeholt2012thebacterialsectranslocase pages 5-6).
- System-level integration: Recent expert synthesis emphasizes the holotranslocon (SecYEG–SecDF–YajC–YidC) as a dynamic secretion machine, with TerC family proteins interfacing co-translocational metalation and quality control. This positions SecA’s activity within a broader envelope homeostasis network in B. subtilis (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-41896-1, Oct 2023) (he2023tercproteinsfunction pages 6-8).
- Regulatory logic: Structural work on SecM and RAPP-like arrest peptides illustrates a conserved feedback where force generated by SecA-dependent translocation can relieve stalls, thereby coupling translocase workload to expression of its components. This is increasingly seen as a general regulatory motif across bacteria, including B. subtilis (Nature Communications, 2024, https://doi.org/10.1038/s41467-024-46762-2, Mar 2024; Nature Communications, 2024, https://doi.org/10.1038/s41467-024-46761-3, Mar 2024) (jensen2025incelldiscoveryand pages 25-27).
5) Relevant statistics and data from recent studies
- Secretion dynamics in vivo: B. subtilis shows discrete, long-lived secretion zones during AmyE overexpression; SecA displays three distinct diffusive states whose distributions shift with secretion demand, indicating regulated allocation of SecA to translocon engagement versus free states (BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (strach2023proteinsecretionzones pages 1-2).
- TerC–dependent metalation: ΔmeeF ΔmeeY mutants exhibit reduced export capacity and a large reduction of Mn in the secreted proteome, providing quantitative proteomic evidence that the Sec translocase cooperates with metal-handling factors during export (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-41896-1, Oct 2023) (he2023tercproteinsfunction pages 6-8).
- Bioprocess titers: Engineered B. subtilis for nattokinase showed 300.0 ± 4.7 FU/mL and a 1.84× increase over the starting strain; genes of the Sec pathway were broadly upregulated, consistent with increased export throughput (Foods, 2025, https://doi.org/10.3390/foods14050898, Mar 2025) (guo2025genomicandtranscriptomic pages 19-19).
Mechanism, substrates, and localization of B. subtilis SecA (functional annotation)
- Primary function and reaction: SecA is a P-type polypeptide translocase ATPase (EC 7.4.2.8) that couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane via SecYEG (Philosophical Transactions R. Soc. B, 2012, https://doi.org/10.1098/rstb.2011.0201, Apr 2012) (nijeholt2012thebacterialsectranslocase pages 3-5, nijeholt2012thebacterialsectranslocase pages 13-14).
- Substrate specificity: SecA recognizes preproteins with N-terminal signal peptides that engage the lateral gate of SecY; signal peptides are cleaved by signal peptidases after translocation initiation, with subsequent folding often assisted by extracytoplasmic factors (Philosophical Transactions R. Soc. B, 2012, https://doi.org/10.1098/rstb.2011.0201, Apr 2012; BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (nijeholt2012thebacterialsectranslocase pages 3-5, strach2023proteinsecretionzones pages 1-2).
- Localization: SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane; it cycles into a membrane-inserted state during active translocation and interacts with anionic phospholipids. In B. subtilis, SecA signal overlaps discrete secretion zones near/within the cell wall during high secretion (Philosophical Transactions R. Soc. B, 2012, https://doi.org/10.1098/rstb.2011.0201, Apr 2012; BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (nijeholt2012thebacterialsectranslocase pages 5-6, strach2023proteinsecretionzones pages 1-2).
- Pathway context and interacting partners: SecA functions with SecYEG, SecDF–YajC, and YidC; in B. subtilis, PrsA assists post-translocation folding, and TerC proteins (MeeF/MeeY) participate in co-translocational metalation and interface with envelope homeostasis (Nature Communications, 2023, https://doi.org/10.1038/s41467-023-41896-1, Oct 2023; BMC Biology, 2023, https://doi.org/10.1186/s12915-023-01684-1, Oct 2023) (he2023tercproteinsfunction pages 6-8, strach2023proteinsecretionzones pages 1-2).
- Regulation: Translation arrest peptides (e.g., SecM-like and RAPP-type) provide feedback that can modulate SecA/Sec machinery expression by stalling elongation; mechanical pulling by translocation relieves stalling, coordinating expression with translocase workload (Nature Communications, 2024, https://doi.org/10.1038/s41467-024-46762-2, Mar 2024; Nature Communications, 2024, https://doi.org/10.1038/s41467-024-46761-3, Mar 2024) (jensen2025incelldiscoveryand pages 25-27).
Embedded summary table
| Topic | Specific finding/claim | Organism / context | Key quantitative / mechanistic detail | Year | Source (journal) | URL | Citation ID |
|---|---|---:|---|---:|---|---|---|
| SecA identity & catalytic role | SecA is the ATP-driven motor of the Sec translocase (EC 7.4.2.8), delivering preproteins to the SecYEG channel and using ATP hydrolysis to power translocation | General bacteria (including Bacillus subtilis) | ATP-dependent cycles of SecA binding/hydrolysis drive conformational changes that push polypeptides through SecYEG; SecA oligomeric state (dimer/monomer) modulates activity | 2012 | Philosophical Transactions R. Soc. B | https://doi.org/10.1098/rstb.2011.0201 | (nijeholt2012thebacterialsectranslocase pages 13-14) |
| SecA dynamics & "secretion zones" | SecA localizes to membrane-associated secretion zones during high AmyE expression; single-molecule tracking reveals multiple diffusive states of SecA that change with secretion load | Bacillus subtilis (AmyE overexpression) | Discrete low-dynamics secretion zones in cell wall overlap SecA signals; single-particle tracking shows three diffusive states of SecA without system saturation | 2023 | BMC Biology | https://doi.org/10.1186/s12915-023-01684-1 | (strach2023proteinsecretionzones pages 1-2) |
| Holotranslocon composition & TerC association | The holotranslocon comprises SecYEG + SecDF-YajC + YidC; TerC family proteins (MeeF/MeeY) associate with the complex and facilitate co-translocational metalation and efficient secretion | Bacillus subtilis | ΔmeeF ΔmeeY strains show reduced protein export and decreased Mn in the secreted proteome; TerC proteins co-purify with Sec pathway components, implicating a role in co-translocational metalation | 2023 | Nature Communications | https://doi.org/10.1038/s41467-023-41896-1 | (he2023tercproteinsfunction pages 6-8) |
| Metalation & envelope homeostasis (sec-linked) | Metalation of extracytoplasmic enzymes is coupled to Sec-dependent export; SecDF and associated factors support translocation and maturation of metallo-exoenzymes | Gram-positive bacteria (notably Bacillus subtilis) | Lipoteichoic acid (LTA) synthesis enzymes require Mn; exporters/chaperones and translocon-associated factors enable co-translocational metalation to ensure active exoenzymes | 2023 | Nature Communications / review context | https://doi.org/10.1038/s41467-023-41896-1 | (he2023tercproteinsfunction pages 6-8) |
| Translation-arrest peptides regulate SecA expression | Monitoring peptides (e.g., SecM, RAPP-containing motifs) induce translational stalling that controls expression of Sec components and responds to pulling forces from SecA to relieve arrest | Bacillus subtilis and other bacteria (comparative structural evidence) | Cryo-EM + MD show arrest motifs stabilize A/P-site tRNA geometry to prevent peptide-bond formation; mechanical pulling (by SecA/translocon) can relieve stall and feedback-regulate SecA expression | 2024 | Nature Communications (structural studies on arrest peptides) | https://doi.org/10.1038/s41467-024-46762-2 | (jensen2025incelldiscoveryand pages 25-27, jensen2025incelldiscoveryand pages 27-29) |
| SecYEG channel architecture & coupling to SecA | SecY contains a plug helix, hydrophobic constriction and lateral gate (TMS2/7); lateral-gate opening is allosterically coupled to SecA ATPase activity during translocation | Various bacterial systems (structural/mechanistic studies including B. subtilis context) | Crosslinking of lateral gate residues affects SecA ATP hydrolysis and translocation; lateral gate opening accommodates signal peptides and membrane segments | 2012 | Philosophical Transactions R. Soc. B | https://doi.org/10.1098/rstb.2011.0201 | (nijeholt2012thebacterialsectranslocase pages 3-5) |
| Industrial secretion & pathway tuning | Bacillus spp. are industrial secretion hosts; tuning Sec pathway components (SecA, SecDF, PrsA) and understanding secretion zones can improve heterologous protein yields | Bacillus subtilis and industrial Bacillus spp. | High-yield strains show upregulation of Sec-pathway genes; secretion-zone biology (spatial localization) provides targets for engineering secretion efficiency | 2023–2025 | BMC Biology; Genomic/transcriptomic studies (Foods) | https://doi.org/10.1186/s12915-023-01684-1 ; https://doi.org/10.3390/foods14050898 | (strach2023proteinsecretionzones pages 1-2, guo2025genomicandtranscriptomic pages 19-19) |
| Accessory foldase PrsA requirement | PrsA (membrane-anchored foldase/chaperone) is required for efficient post-translocation folding and high-level secretion (e.g., α-amylase) in B. subtilis | Bacillus subtilis | PrsA copes with secreted protein folding load; absence/reduction of PrsA limits secretion capacity and enzyme activity at cell surface | 2023 | BMC Biology (experimental context referencing PrsA) | https://doi.org/10.1186/s12915-023-01684-1 | (strach2023proteinsecretionzones pages 1-2) |
Table: Compact, evidence-linked summary of functional annotation and recent findings for Bacillus subtilis SecA (UniProt P28366), combining mechanistic, structural, regulatory, and applied (industrial/metalation) literature for rapid reference.
Notes on antibiotic targeting
- Although SecA has long been proposed as an antibiotic target, the most directly supported, recent Bacillus-subtilis–centric advances here are indirect, via the emerging understanding of SecA’s integration in the holotranslocon and its coupling to metalation/quality control. Direct, recent inhibitor studies specific to B. subtilis SecA were not identified in the curated 2023–2024 evidence above; thus, we refrain from making specific inhibitor claims while noting the rationale (essentiality, centrality to secretion) (he2023tercproteinsfunction pages 6-8, strach2023proteinsecretionzones pages 1-2).
Conclusion
- Collectively, the recent literature refines the functional annotation of B. subtilis SecA (P28366): a peripheral membrane ATPase motor that powers Sec-dependent protein export at SecYEG, operating within a holotranslocon that includes SecDF–YajC and YidC and interfaces with TerC-dependent metalation. New live-cell and structural studies in 2023–2024 have added spatial (secretion zones), systems (metalation/quality control), and regulatory (arrest peptides) layers to this core function, with clear implications for industrial secretion engineering in Bacillus (strach2023proteinsecretionzones pages 1-2, he2023tercproteinsfunction pages 6-8, jensen2025incelldiscoveryand pages 25-27, nijeholt2012thebacterialsectranslocase pages 3-5).
References
(nijeholt2012thebacterialsectranslocase pages 3-5): Jelger A. Lycklama a Nijeholt and Arnold J. M. Driessen. The bacterial sec-translocase: structure and mechanism. Philosophical Transactions of the Royal Society B: Biological Sciences, 367:1016-1028, Apr 2012. URL: https://doi.org/10.1098/rstb.2011.0201, doi:10.1098/rstb.2011.0201. This article has 235 citations and is from a domain leading peer-reviewed journal.
(strach2023proteinsecretionzones pages 1-2): Manuel Strach, Felicitas Koch, Svenja Fiedler, Klaus Liebeton, and Peter L. Graumann. Protein secretion zones during overexpression of amylase within the gram-positive cell wall. BMC Biology, Oct 2023. URL: https://doi.org/10.1186/s12915-023-01684-1, doi:10.1186/s12915-023-01684-1. This article has 10 citations and is from a domain leading peer-reviewed journal.
(nijeholt2012thebacterialsectranslocase pages 5-6): Jelger A. Lycklama a Nijeholt and Arnold J. M. Driessen. The bacterial sec-translocase: structure and mechanism. Philosophical Transactions of the Royal Society B: Biological Sciences, 367:1016-1028, Apr 2012. URL: https://doi.org/10.1098/rstb.2011.0201, doi:10.1098/rstb.2011.0201. This article has 235 citations and is from a domain leading peer-reviewed journal.
(nijeholt2012thebacterialsectranslocase pages 13-14): Jelger A. Lycklama a Nijeholt and Arnold J. M. Driessen. The bacterial sec-translocase: structure and mechanism. Philosophical Transactions of the Royal Society B: Biological Sciences, 367:1016-1028, Apr 2012. URL: https://doi.org/10.1098/rstb.2011.0201, doi:10.1098/rstb.2011.0201. This article has 235 citations and is from a domain leading peer-reviewed journal.
(he2023tercproteinsfunction pages 6-8): Bixi He, Ankita J. Sachla, and John D. Helmann. Terc proteins function during protein secretion to metalate exoenzymes. Nature Communications, Oct 2023. URL: https://doi.org/10.1038/s41467-023-41896-1, doi:10.1038/s41467-023-41896-1. This article has 22 citations and is from a highest quality peer-reviewed journal.
(jensen2025incelldiscoveryand pages 25-27): Rasmus K. Jensen, Liang Xue, Federico Marotta, Joseph C. Somody, Joel Selkrig, Swantje Lenz, Juri Rappsilber, Mikhail M. Savitski, Jan Kosinski, Athanasios Typas, Maria Zimmermann-Kogadeeva, Peer Bork, and Julia Mahamid. In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex. bioRxiv, Apr 2025. URL: https://doi.org/10.1101/2025.04.25.650208, doi:10.1101/2025.04.25.650208. This article has 2 citations and is from a poor quality or predatory journal.
(guo2025genomicandtranscriptomic pages 19-19): Liuyu Guo, Yang Chen, Zhiyong He, Zhaojun Wang, Qiuming Chen, Jie Chen, Fatih Oz, Zhimin Xu, and Maomao Zeng. Genomic and transcriptomic analysis of mutant bacillus subtilis with enhanced nattokinase production via artp mutagenesis. Foods, 14:898, Mar 2025. URL: https://doi.org/10.3390/foods14050898, doi:10.3390/foods14050898. This article has 4 citations and is from a poor quality or predatory journal.
(jensen2025incelldiscoveryand pages 27-29): Rasmus K. Jensen, Liang Xue, Federico Marotta, Joseph C. Somody, Joel Selkrig, Swantje Lenz, Juri Rappsilber, Mikhail M. Savitski, Jan Kosinski, Athanasios Typas, Maria Zimmermann-Kogadeeva, Peer Bork, and Julia Mahamid. In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex. bioRxiv, Apr 2025. URL: https://doi.org/10.1101/2025.04.25.650208, doi:10.1101/2025.04.25.650208. This article has 2 citations and is from a poor quality or predatory journal.
Source: secA-deep-research-bioreason-rl.md
The BioReason functional summary reads:
An ATP-driven motor of the bacterial secretory pathway that binds unfolded preproteins and powers their post-translational translocation through the membrane channel. It operates as a soluble cytoplasmic factor that transiently associates with membrane translocons via a winged scaffold and conserved C-terminal elements, using cycles of nucleotide binding and hydrolysis to clamp, ratchet, and release substrates during secretion.
This is a highly accurate summary that captures the essence of SecA function. The description of SecA as an ATP-driven motor for protein secretion matches the curated core molecular function of protein-exporting ATPase activity (GO:0008564, EC 7.4.2.8). The description of preprotein binding, membrane channel association, and ATP hydrolysis-driven translocation aligns with protein transport by the Sec complex (GO:0043952). The cytoplasmic-to-membrane cycling is correctly noted, matching the dual localization of cytoplasm (GO:0005737) and plasma membrane (GO:0005886).
The thinking trace provides excellent domain-by-domain analysis, correctly identifying the DEAD-like ATPase core, preprotein cross-linking domain, helicase-like C-terminal region, wing/scaffold domain, and SEC-C motif. The mechanistic description of "clamp, ratchet, and release" is an apt summary of the translocation mechanism.
One minor issue: the BioReason functional summary correctly assigns "protein binding" (GO:0005515) as the molecular function in its GO terms section, but the narrative makes clear this is ATP-driven translocation activity. The curated review's more specific GO:0008564 (protein-exporting ATPase activity) better captures the function. BioReason also misses the zinc binding through the SEC-C motif (metal ion binding, GO:0046872) and the association with the Sec protein transport complex (GO:0031522).
Comparison with interpro2go:
The interpro2go annotations for secA include intracellular protein transport (GO:0006886), membrane localization (GO:0016020), and protein import (GO:0017038). The curated review flags GO:0017038 (protein import) as incorrect -- SecA is a protein EXPORTER. BioReason avoids this error entirely, correctly describing SecA's function as secretion/export. BioReason significantly outperforms interpro2go here by providing accurate mechanistic context and avoiding the import/export confusion.
The trace walks through the 13 InterPro domains systematically and builds a coherent mechanistic model. The reasoning from the ATPase engine through the preprotein clamp to the wing/scaffold is logically sound. The inference about transient membrane association from the soluble architecture with membrane-binding motifs is well-executed.
id: P28366
gene_symbol: secA
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:224308
label: Bacillus subtilis (strain 168)
description: >-
SecA is the essential ATP-driven motor protein of the bacterial Sec translocase
(EC 7.4.2.8) that powers post-translational protein secretion through the SecYEG
channel. As a P-type polypeptide translocase ATPase, SecA couples ATP binding and
hydrolysis to mechanical translocation of preproteins bearing N-terminal signal
peptides across the cytoplasmic membrane. The protein cycles between cytoplasmic
and membrane-associated states, interacting with the SecYEG preprotein-conducting
channel to drive stepwise translocation of polypeptide chains. SecA undergoes
conformational changes upon nucleotide binding and hydrolysis that push polypeptide
segments through SecYEG. In B. subtilis, SecA localizes to discrete membrane-proximal
"secretion zones" during high-level secretion of proteins like alpha-amylase.
The protein functions as part of the holotranslocon complex comprising SecYEG
with SecDF-YajC and YidC, and cooperates with TerC family proteins (MeeF/MeeY)
for co-translocational metalation of secreted enzymes. SecA binds zinc as a
cofactor through a C-terminal SEC-C motif and contains helicase-like ATP-binding
domains characteristic of the superfamily 2 helicases. The protein can exist as
both monomers and various homodimeric forms, with a single SecA monomer interacting
with SecY in the functional translocation channel. SecA is essential for bacterial
viability and has been proposed as an antibiotic target.
existing_annotations:
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecA is a peripheral membrane protein that associates with the plasma membrane
on the cytoplasmic side during active protein translocation. UniProt states
SecA is localized to Cell membrane as a Peripheral membrane protein on the
Cytoplasmic side with experimental evidence from PMID:27362352. The deep research
confirms SecA binds to the inner leaflet and SecYEG at the cytoplasmic membrane
and cycles into a membrane-inserted state during active translocation.
action: ACCEPT
reason: >-
Plasma membrane localization is well-established for SecA as part of its core
function in protein translocation. SecA cycles between cytoplasm and membrane,
associating with the membrane during translocation via SecYEG interaction.
IBA annotation is appropriate and consistent with experimental evidence.
supported_by:
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane; it cycles into a membrane-inserted state during active translocation and interacts with anionic phospholipids"
- term:
id: GO:0005524
label: ATP binding
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
ATP binding is a core molecular function of SecA. The protein contains
well-characterized ATP-binding sites with multiple residues directly
involved in nucleotide coordination. Mutagenesis of K106 abolishes activity
(PMID:8440733). Crystal structures demonstrate ADP/ATP binding.
action: ACCEPT
reason: >-
ATP binding is fundamental to SecA function as an ATPase motor. The protein
belongs to the superfamily 2 helicases with helicase-like ATP-binding domains
(IPR014001, IPR001650). UniProt records multiple ATP binding residues with
structural evidence. This is a core function annotation.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "ATP binding/hydrolysis by SecA produces conformational changes that push polypeptide segments through SecYEG"
- term:
id: GO:0031522
label: cell envelope Sec protein transport complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecA is an integral component of the Sec protein transport complex. UniProt
states SecA is Part of the essential Sec protein translocation apparatus
which comprises SecA, SecYEG and auxiliary proteins SecDF. The deep research
confirms SecA operates within the holotranslocon as a dynamic secretion machine.
action: ACCEPT
reason: >-
SecA is definitionally a component of the Sec protein transport complex.
This cellular component annotation accurately captures SecA's localization
as part of the functional translocase machinery at the membrane. The IBA
annotation is appropriate.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "The functional secretion unit in Gram-positive bacteria (holotranslocon) comprises SecYEG with SecDF-YajC and YidC; SecA powers translocation into/through SecYEG"
- term:
id: GO:0043952
label: protein transport by the Sec complex
evidence_type: IBA
original_reference_id: GO_REF:0000033
review:
summary: >-
SecA drives protein transport through the Sec complex as the ATP-dependent
motor. The deep research states SecA has a central role in coupling the
hydrolysis of ATP to the transfer of proteins into and across the cell
membrane, serving as an ATP-driven molecular motor driving the stepwise
translocation of polypeptide chains across the membrane.
action: ACCEPT
reason: >-
This biological process annotation accurately captures the primary function
of SecA - driving protein transport through the Sec translocase. SecA is
the motor that powers Sec-dependent translocation. This is a core function.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is the ATP-driven motor of the bacterial Sec translocase that post-translationally drives preprotein movement through the SecYEG channel"
- term:
id: GO:0000166
label: nucleotide binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
SecA binds nucleotides (ATP/ADP) as part of its catalytic cycle. This IEA
annotation from UniProtKB keyword mapping is accurate but too general
compared to the more specific GO:0005524 (ATP binding) annotations also present.
action: ACCEPT
reason: >-
While this annotation is correct, it is broader than the ATP binding annotations
already present. Since duplicates with different evidence codes are acceptable
and this IEA provides complementary computational evidence, it can be retained.
The annotation is not wrong, just less specific than the IBA ATP binding annotation.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane"
- term:
id: GO:0005524
label: ATP binding
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This is a duplicate ATP binding annotation with IEA evidence from combined
automated annotation. The IBA annotation with the same GO ID provides
phylogenetically-based evidence for the same function.
action: ACCEPT
reason: >-
Duplicate annotations with different evidence codes are acceptable. This
IEA annotation provides complementary computational support for the core
ATP binding function of SecA.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor"
- term:
id: GO:0005737
label: cytoplasm
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
SecA is a cytoplasmic protein that cycles to the membrane during active
translocation. UniProt states subcellular location includes Cytoplasm
with the note Distribution is 50-50 between cytoplasm and membrane.
The deep research confirms SecA is cytosolic but binds to the inner
leaflet and SecYEG at the cytoplasmic membrane.
action: ACCEPT
reason: >-
Cytoplasmic localization is accurate - SecA exists in equilibrium between
cytoplasm and membrane. The protein is soluble in the cytoplasm and
peripherally associates with the membrane during translocation.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Note=Distribution is 50-50"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane; it cycles into a membrane-inserted state during active translocation"
- term:
id: GO:0005886
label: plasma membrane
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
This is a duplicate plasma membrane annotation with IEA evidence. The IBA
annotation with the same GO ID is also present with phylogenetic evidence.
action: ACCEPT
reason: >-
Duplicate annotations with different evidence codes are acceptable. Both
IBA and IEA evidence support plasma membrane localization as a core
aspect of SecA function.
supported_by:
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane"
- term:
id: GO:0006605
label: protein targeting
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
summary: >-
SecA is involved in targeting preproteins to the translocation apparatus.
The protein recognizes signal peptide-bearing preproteins and delivers
them to SecYEG for translocation. This is part of the broader Sec-dependent
secretion pathway.
action: ACCEPT
reason: >-
Protein targeting is a valid biological process for SecA, as it recognizes
and directs preproteins to the SecYEG channel. This is broader than but
consistent with the more specific "protein transport by the Sec complex"
annotation.
supported_by:
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA recognizes preproteins with N-terminal signal peptides that engage the lateral gate of SecY"
- term:
id: GO:0006886
label: intracellular protein transport
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
SecA participates in intracellular protein transport by moving preproteins
from the cytoplasm to the membrane/extracellular space via SecYEG. This
InterPro-derived annotation captures the transport function.
action: ACCEPT
reason: >-
This annotation is accurate but very general. SecA does participate in
intracellular protein transport as part of the Sec pathway. The more
specific annotation "protein transport by the Sec complex" (GO:0043952)
better captures the specificity of SecA function, but this broader term
is not incorrect.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane"
- term:
id: GO:0008564
label: protein-exporting ATPase activity
evidence_type: IEA
original_reference_id: GO_REF:0000003
review:
summary: >-
This is the most specific and accurate molecular function annotation for
SecA. EC 7.4.2.8 maps to protein-exporting ATPase activity. UniProt
records the catalytic activity with experimental evidence from PMID:8440733.
action: ACCEPT
reason: >-
This is the core molecular function of SecA. The EC number 7.4.2.8
corresponds to protein-translocating ATPase activity. SecA couples ATP
hydrolysis to the mechanical work of pushing polypeptides through SecYEG.
This annotation should be retained as a core function.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Reaction=ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2.; EC=7.4.2.8"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is a P-type polypeptide translocase ATPase (EC 7.4.2.8) that couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane via SecYEG"
- term:
id: GO:0015031
label: protein transport
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
SecA is involved in protein transport as the motor driving secretion
through SecYEG. This annotation is accurate but very general compared
to the more specific "protein transport by the Sec complex" (GO:0043952).
action: ACCEPT
reason: >-
This general protein transport annotation is accurate. SecA mediates
protein transport across membranes. While less specific than GO:0043952,
it is not incorrect and provides keyword-based evidence.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane, serving as an ATP-driven molecular motor driving the stepwise translocation of polypeptide chains across the membrane"
- term:
id: GO:0016020
label: membrane
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
SecA associates with membranes as a peripheral membrane protein. This
InterPro-derived annotation is accurate but very general - the more
specific GO:0005886 (plasma membrane) annotations are also present.
action: ACCEPT
reason: >-
This general membrane annotation is technically correct but less
informative than the specific plasma membrane annotations. It can be
retained as complementary evidence from InterPro.
supported_by:
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is cytosolic but binds to the inner leaflet and SecYEG at the cytoplasmic membrane"
- term:
id: GO:0017038
label: protein import
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
summary: >-
This annotation appears to be an error or overly generic mapping from
InterPro. SecA is involved in protein EXPORT (secretion) not import.
The Sec pathway translocates proteins from the cytoplasm to the
periplasm/extracellular space, which is export, not import.
action: REMOVE
reason: >-
SecA is a protein EXPORTER, not importer. The Sec translocase moves
preproteins from the cytoplasm out through the membrane. "Protein import"
implies movement into the cytoplasm, which is the opposite of SecA's
function. This annotation should be removed as it is misleading.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Reaction=ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2.; EC=7.4.2.8"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is a P-type polypeptide translocase ATPase that couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane"
- term:
id: GO:0045121
label: membrane raft
evidence_type: IEA
original_reference_id: GO_REF:0000044
review:
summary: >-
UniProt records membrane raft localization based on PMID:27362352, which
studied flotillin-associated membrane microdomains in B. subtilis.
However, the UniProt subunit comment notes SecA only shows some
colocalization with FloA or FloT membrane assemblies suggesting
limited association with lipid rafts.
action: KEEP_AS_NON_CORE
reason: >-
The annotation is based on experimental evidence from PMID:27362352,
but the evidence indicates only partial colocalization with membrane
rafts. This is not a core localization for SecA function - the primary
functional location is at SecYEG translocon sites. The membrane raft
association may represent a subset of SecA molecules or a regulatory
aspect.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Only shows some colocalization with FloA or FloT membrane assemblies (PubMed:27362352)"
- term:
id: GO:0046872
label: metal ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000043
review:
summary: >-
SecA binds zinc through its C-terminal SEC-C motif. UniProt records that
SecA may bind 1 zinc ion per subunit through conserved cysteine residues.
action: ACCEPT
reason: >-
Metal ion binding (specifically zinc) is a documented property of SecA.
The SEC-C motif at the C-terminus contains conserved cysteines that
coordinate zinc. While the precise functional role of zinc binding is
less clear than the ATPase activity, this is a legitimate molecular
function annotation based on structural and sequence evidence.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "May bind 1 zinc ion per subunit"
- term:
id: GO:0065002
label: intracellular protein transmembrane transport
evidence_type: IEA
original_reference_id: GO_REF:0000104
review:
summary: >-
SecA drives transmembrane transport of proteins through SecYEG. This
annotation captures the essence of SecA function - moving proteins
across the membrane. The term is appropriate for SecA's role in
translocation.
action: ACCEPT
reason: >-
This annotation accurately describes SecA's function in driving protein
transport across the cytoplasmic membrane. SecA powers the movement of
preproteins through the SecYEG channel, which is intracellular protein
transmembrane transport.
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Has a central role in coupling the hydrolysis of ATP to the transfer of proteins into and across the cell membrane"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins bearing N-terminal signal peptides across the cytoplasmic membrane via SecYEG"
core_functions:
- molecular_function:
id: GO:0008564
label: protein-exporting ATPase activity
description: >-
SecA is the ATP-driven motor (EC 7.4.2.8) that powers post-translational
protein translocation through SecYEG. Multiple crystal structures show ATP
binding sites; mutagenesis of K106 abolishes function (PMID:8440733).
directly_involved_in:
- id: GO:0043952
label: protein transport by the Sec complex
locations:
- id: GO:0005886
label: plasma membrane
in_complex:
id: GO:0031522
label: cell envelope Sec protein transport complex
supported_by:
- reference_id: UniProt:P28366
supporting_text: "Reaction=ATP + H2O + cellular proteinSide 1 = ADP + phosphate + cellular proteinSide 2.; EC=7.4.2.8"
- reference_id: file:BACSU/secA/secA-deep-research-falcon.md
supporting_text: "SecA is a P-type polypeptide translocase ATPase (EC 7.4.2.8) that couples ATP hydrolysis to mechanical translocation of mostly unfolded preproteins"
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO terms
findings: []
- id: GO_REF:0000003
title: Gene Ontology annotation based on Enzyme Commission mapping
findings:
- statement: EC 7.4.2.8 maps to protein-exporting ATPase activity
- id: GO_REF:0000033
title: Annotation inferences using phylogenetic trees
findings:
- statement: IBA annotations for SecA based on PANTHER family PTHR30612
- id: GO_REF:0000043
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
findings: []
- id: GO_REF:0000044
title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
vocabulary mapping, accompanied by conservative changes to GO terms applied by
UniProt
findings: []
- id: GO_REF:0000104
title: Electronic Gene Ontology annotations created by transferring manual GO annotations
between related proteins based on shared sequence features
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: file:BACSU/secA/secA-deep-research-falcon.md
title: Deep research on SecA function in Bacillus subtilis
findings:
- statement: Comprehensive review of SecA structure and mechanism
- statement: SecA cycles between cytoplasm and membrane during translocation
- statement: ATP hydrolysis drives conformational changes pushing polypeptides through SecYEG
- id: PMID:8440733
title: Lysine 106 of the putative catalytic ATP-binding site of the Bacillus subtilis SecA protein is required for functional complementation of Escherichia coli secA mutants in vivo.
findings:
- statement: Mutagenesis demonstrates K106 is essential for SecA ATPase activity
supporting_text: "Replacement of a lysine residue at position 106, which corresponds to an invariable amino acid residue, in the consensus motif by asparagine (K106N) resulted in the loss of the ability of the B. subtilis SecA protein to complement the growth and secretion defects of E. coli secA mutants"
- statement: Experimental evidence for catalytic activity EC 7.4.2.8
supporting_text: "We conclude that lysine 106 is part of the catalytic ATP-binding site of the B. subtilis SecA protein, which is required for protein translocation in vivo"
- id: PMID:12242434
title: Nucleotide control of interdomain interactions in the conformational reaction cycle of SecA.
findings:
- statement: Crystal structure of SecA with and without ADP
supporting_text: "We have determined the crystal structure of SecA with and without magnesium-adenosine diphosphate bound to the high-affinity ATPase site at 3.0 and 2.7 angstrom resolution, respectively"
- statement: Reveals conformational changes upon nucleotide binding
supporting_text: "Comparisons with structurally related ATPases, including superfamily I and II ATP-dependent helicases, suggest that the interaction geometry of the tandem motor domains in SecA is modulated by nucleotide binding"
- id: PMID:27362352
title: Super Resolution Fluorescence Microscopy and Tracking of Bacterial Flotillin (Reggie) Paralogs Provide Evidence for Defined-Sized Protein Microdomains within the Bacterial Membrane but Absence of Clusters Containing Detergent-Resistant Proteins.
findings:
- statement: SecA shows some colocalization with FloA/FloT membrane assemblies
supporting_text: "B. subtilis flotillins can be co-isolated with NfeD proteins of unknown function, with the signaling receptor KinC [26], cell wall synthesis enzyme Pbp5, secretory protein SecY, membrane transporters like FhuD"
- statement: Experimental evidence for membrane raft localization
supporting_text: "flotillins have been suggested to set up microdomains within the membrane, by recruiting other proteins and possibly specific lipids into the special structures"