SecY is the central channel-forming subunit of the bacterial SecYEG protein translocase complex. It forms a heterotrimeric complex with SecE and SecG that constitutes the core protein-conducting channel in the cytoplasmic membrane. SecY consists of 10 transmembrane helices organized into two halves (TMs 1-5 and TMs 6-10) that form a lateral gate, which can open to allow insertion of transmembrane segments into the lipid bilayer. The channel is sealed by a pore ring of hydrophobic residues and a plug helix on the extracellular side. SecY functions in two modes: (1) post-translational translocation of secretory proteins driven by the SecA ATPase, and (2) co-translational insertion of membrane proteins via the SRP (signal recognition particle) pathway. In B. subtilis, SecY localizes to the plasma membrane and is found in detergent-resistant membrane domains (membrane rafts), where it interacts with the flotillin homolog FloT. SecY is essential for protein secretion and membrane protein biogenesis in bacteria.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: SecY is an integral membrane protein with 10 transmembrane helices that localizes to the cytoplasmic (plasma) membrane of B. subtilis. UniProt reports cell membrane localization based on experimental evidence from PMID:23651456, which demonstrated SecY presence in the B. subtilis membrane. Reason: This is a core annotation for SecY. The protein is an integral component of the plasma membrane where it forms the protein-conducting channel of the Sec translocon. The deep research confirms SecY is localized to the cytoplasmic membrane, and UniProt cites experimental evidence (PMID:23651456) for cell membrane localization. IBA inference is consistent with extensive biochemical and structural data across bacteria. Supporting Evidence: UniProt:P16336 SUBCELLULAR LOCATION: Cell membrane file:BACSU/secY/secY-deep-research-falcon.md SecY is the channel-forming subunit of the bacterial SecYEG translocon |
| GO:0005048 signal sequence binding | IBA GO_REF:0000033 | ACCEPT | Summary: SecY binds to signal sequences on preproteins during translocation. The signal sequence interacts with the lateral gate of SecY, which can open to release transmembrane segments into the lipid bilayer. Reason: This is a core molecular function of SecY. Signal sequence binding is integral to SecY's role in recognizing and translocating secretory proteins. Structural studies have shown that signal sequences interact with the lateral gate region of SecY between TMs 2 and 7. The deep research confirms that substrates are signal peptide-bearing preproteins. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md Substrates are unfolded polypeptides bearing N-terminal signal peptides (secretory proteins) or topogenic sequences (membrane protein TM helices) UniProt:P16336 These two domains form a lateral gate at the front which open onto the bilayer between TMs 2 and 7 |
| GO:0006616 SRP-dependent cotranslational protein targeting to membrane, translocation | IBA GO_REF:0000033 | ACCEPT | Summary: SecY participates in co-translational protein targeting via the SRP pathway. The ribosome-nascent chain complex is targeted to SecYEG by SRP and its receptor, and SecY mediates insertion of transmembrane segments into the membrane. Reason: This is a well-established function of SecY. While post-translational translocation (SecA-dependent) is the dominant mode for secretory proteins, membrane protein insertion is typically co-translational and SRP-dependent. SecY functions as the translocon in both pathways. The deep research explicitly states that co-translational insertion is mediated by SRP-ribosome targeting. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md co-translational routes can also target substrates to SecYEG via SRP-ribosome interactions file:BACSU/secY/secY-deep-research-falcon.md membrane protein insertion is typically co-translational |
| GO:0008320 protein transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: SecY has protein transmembrane transporter activity, enabling the transfer of unfolded polypeptides across the cytoplasmic membrane. This is the central molecular function of the SecY channel. Reason: This is the core molecular function of SecY. The protein forms the actual channel through which preproteins are translocated. The GO term definition "Enables the transfer of a protein from one side of a membrane to the other" precisely describes SecY's function as the protein-conducting channel of the Sec translocon. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane (secretion) and supports insertion of membrane proteins UniProt:P16336 The central subunit of the protein translocation channel SecYEG |
| GO:0031522 cell envelope Sec protein transport complex | IBA GO_REF:0000033 | ACCEPT | Summary: SecY is a core component of the cell envelope Sec protein transport complex (SecYEG translocon). This complex includes SecY, SecE, SecG, and associated factors like SecA and SecDF. Reason: This is the appropriate cellular component annotation for SecY. The GO term definition explicitly mentions SecY as a component of the Sec complex. SecY forms the heterotrimeric SecYEG complex with SecE and SecG, which is the core translocon. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md SecY is the channel-forming subunit of the bacterial SecYEG translocon UniProt:P16336 Component of the Sec protein translocase complex. Heterotrimer consisting of SecY, SecE and SecG subunits |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: IEA annotation for plasma membrane localization, which is consistent with the experimentally validated IBA annotation above. Reason: This annotation is redundant with the IBA annotation but is not incorrect. SecY is indeed an integral plasma membrane protein. The IEA annotation provides additional automated support for what is well-established experimentally. Supporting Evidence: UniProt:P16336 SUBCELLULAR LOCATION: Cell membrane |
| GO:0006605 protein targeting | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: SecY participates in protein targeting by receiving signal sequence-bearing proteins targeted by the SRP pathway or post-translationally by SecA. Reason: While SecY is involved in protein targeting as part of the translocation machinery, this term is quite general. The more specific terms like GO:0043952 (protein transport by the Sec complex) and GO:0006616 (SRP-dependent cotranslational protein targeting) are more informative. This annotation is not wrong but represents a higher-level categorization rather than a core specific function. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md Substrates are signal peptide-bearing preproteins (secretory) or nascent TM helices (membrane proteins) |
| GO:0015031 protein transport | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: SecY is involved in protein transport across the cytoplasmic membrane. Reason: This is a general parent term for the more specific protein transport processes that SecY participates in. While accurate, the more specific terms (GO:0043952, GO:0006616, GO:0065002) are more informative about SecY's actual role. Keeping as non-core since it is not incorrect, just less specific. Supporting Evidence: UniProt:P16336 The central subunit of the protein translocation channel SecYEG |
| GO:0016020 membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: SecY is a membrane protein. Reason: This is a very general cellular component term. While accurate, the more specific term GO:0005886 (plasma membrane) provides more informative localization. This annotation is acceptable but not a core annotation as it lacks specificity. Supporting Evidence: UniProt:P16336 Multi-pass membrane protein |
| GO:0043952 protein transport by the Sec complex | IEA GO_REF:0000104 | ACCEPT | Summary: SecY is a core component of the Sec complex and directly participates in protein transport by this complex. This biological process term accurately describes SecY's role in translocating unfolded proteins across the membrane via the SecYEG translocon. Reason: This is a highly appropriate and specific annotation for SecY. The GO term definition explicitly mentions that it is for annotating proteins that compose the transport complex. SecY is the central channel subunit and directly conducts proteins across the membrane as part of the Sec complex. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md SecY is the channel-forming subunit of the bacterial SecYEG translocon. It conducts preproteins across the cytoplasmic membrane UniProt:P16336 Component of the Sec protein translocase complex |
| GO:0045121 membrane raft | IEA GO_REF:0000044 | ACCEPT | Summary: SecY localizes to membrane rafts (detergent-resistant membrane domains) in B. subtilis. This is based on experimental evidence from Bach & Bramkamp 2013 (PMID:23651456) which showed SecY is found in DRM fractions and interacts with the flotillin homolog FloT. Reason: This annotation is supported by experimental evidence in B. subtilis. UniProt cites PMID:23651456 which demonstrated that SecY is present in detergent-resistant membrane fractions (bacterial membrane rafts) and interacts with FloT. While membrane rafts are a secondary localization relative to plasma membrane, this is a valid specific annotation. Supporting Evidence: UniProt:P16336 Present in detergent-resistant membrane (DRM) fractions that may be equivalent to eukaryotic membrane rafts UniProt:P16336 Interacts with FloT (PubMed:23651456) |
| GO:0065002 intracellular protein transmembrane transport | IEA GO_REF:0000104 | ACCEPT | Summary: SecY mediates the translocation of proteins across the cytoplasmic membrane, which constitutes intracellular protein transmembrane transport. Reason: This is an accurate biological process annotation for SecY. The term describes the directed movement of proteins across a membrane, which is exactly what SecY does as the protein-conducting channel. In bacteria, this involves transport from the cytoplasm across the plasma membrane to the periplasm or cell exterior. Supporting Evidence: file:BACSU/secY/secY-deep-research-falcon.md conducts preproteins across the cytoplasmic membrane (secretion) file:BACSU/secY/secY-deep-research-falcon.md AFM observation of protein translocation mediated by one unit of SecYEG-SecA complex |
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