lcb1

Summary: Serine palmitoyltransferase activity (PAINT/EC/similarity); the Lcb1-Lcb2 heterodimer is the catalytic SPT (contributes).

Reason: The SPT activity is assigned by similarity to S. cerevisiae LCB1 (UniProtKB:P25045; the UniProt FUNCTION and CATALYTIC ACTIVITY notes carry ECO:0000250|UniProtKB:P25045) and by membership of the PANTHER SPT1 subfamily. This is ortholog evidence, not an S. pombe assay. Lcb1 is the non-catalytic partner of the Lcb1-Lcb2 heterodimer, so the activity belongs to the complex (contributes_to), as the core function records.

Summary: Serine palmitoyltransferase activity (PAINT/EC/similarity); the Lcb1-Lcb2 heterodimer is the catalytic SPT (contributes).

Reason: The SPT activity is assigned by similarity to S. cerevisiae LCB1 (UniProtKB:P25045; the UniProt FUNCTION and CATALYTIC ACTIVITY notes carry ECO:0000250|UniProtKB:P25045) and by membership of the PANTHER SPT1 subfamily. This is ortholog evidence, not an S. pombe assay. Lcb1 is the non-catalytic partner of the Lcb1-Lcb2 heterodimer, so the activity belongs to the complex (contributes_to), as the core function records.

Summary: Serine palmitoyltransferase activity (PAINT/EC/similarity); the Lcb1-Lcb2 heterodimer is the catalytic SPT (contributes).

Reason: The SPT activity is assigned by similarity to S. cerevisiae LCB1 (UniProtKB:P25045; the UniProt FUNCTION and CATALYTIC ACTIVITY notes carry ECO:0000250|UniProtKB:P25045) and by membership of the PANTHER SPT1 subfamily. This is ortholog evidence, not an S. pombe assay. Lcb1 is the non-catalytic partner of the Lcb1-Lcb2 heterodimer, so the activity belongs to the complex (contributes_to), as the core function records.

Summary: Cytoplasm is true but generic; SPT is an ER membrane complex, and the more specific ER location is asserted (ACCEPT) elsewhere in this review.

Reason: The ER is part of the cytoplasm, so this row is entailed by the endoplasmic reticulum annotation, which rests on the S. pombe ORFeome localisation screen (UniProt ECO:0000269|PubMed:16823372). The UniProt cytoplasm statement itself is by similarity to S. cerevisiae LCB1 (ECO:0000250|UniProtKB:P25045). Changed from KEEP_AS_NON_CORE because the term is correct but general and the specific descendant is on the gene.

Summary: Cytoplasm is true but generic; SPT is an ER membrane complex, and the more specific ER location is asserted (ACCEPT) elsewhere in this review.

Reason: The ER is part of the cytoplasm, so this row is entailed by the endoplasmic reticulum annotation, which rests on the S. pombe ORFeome localisation screen (UniProt ECO:0000269|PubMed:16823372). The ISS source is S. cerevisiae LCB1 (UniProtKB:P25045). Changed from KEEP_AS_NON_CORE for consistency with the IEA cytoplasm row, because the term is correct but general and the specific descendant is on the gene.

Summary: ORFeome screen: ER.

Summary: PAINT inference.

Reason: UniProt records the ER location from the S. pombe ORFeome localisation screen (ECO:0000269|PubMed:16823372), and the record has three predicted TRANSMEM segments; this agrees with the PAINT placement of the SPT clade in the ER.

Summary: Mapping.

Reason: The SubCell mapping rests on the UniProt ER location, which is experimental for S. pombe (ORFeome screen, ECO:0000269|PubMed:16823372).

Summary: Broad parent; the specific ceramide biosynthetic process (ACCEPT) is asserted elsewhere in this review.

Reason: SPT catalyses the committed step of de novo sphingolipid synthesis, which the review captures as ceramide biosynthetic process (GO:0046513), a descendant of this term. The supporting statement is by similarity to S. cerevisiae LCB1 (ECO:0000250|UniProtKB:P25045), not an S. pombe assay.

Summary: Membrane is correct but generic; Lcb1 is a multi-pass protein of the ER, so the supported location is the ER membrane.

Reason: Two independent lines place Lcb1 in the ER membrane. The sequence has three predicted transmembrane helices (FT TRANSMEM, ECO:0000255), and the S. pombe ORFeome localisation screen places it in the ER (ECO:0000269|PubMed:16823372). Changed from KEEP_AS_NON_CORE to MODIFY because the term is correct but general and a specific descendant is supported.

Proposed replacements: endoplasmic reticulum membrane

Summary: Subunit of the SPT complex (with the small subunit Tsc3-like SPAC23A1.05).

Reason: Subunit composition is by similarity to S. cerevisiae LCB1 (UniProtKB:P25045; SUBUNIT and FUNCTION notes carry ECO:0000250|UniProtKB:P25045). Ortholog evidence, not a pombe complex purification.

Summary: PLP cofactor of the SPT heterodimer; Lcb2 carries the catalytic PLP-binding lysine, Lcb1 is the non-catalytic partner.

Reason: The PLP cofactor is assigned by similarity to S. cerevisiae LCB1 (COFACTOR, ECO:0000250|UniProtKB:P25045) and by membership of the class-II PLP-dependent aminotransferase family (Pfam PF00155). Lcb1 lacks the catalytic lysine, so PLP binding is a property of the heterodimer to which Lcb1 contributes rather than a core Lcb1 activity.

Summary: PAINT inference of sphingosine biosynthesis; SPT makes 3-ketosphinganine, the first long-chain base of the sphingoid base pathway.

Reason: The IBA follows from Lcb1's membership of the PANTHER SPT1 subfamily, and nothing places the target outside the PAINT clade. SPT forms the long-chain base 3-ketosphinganine (by similarity to S. cerevisiae LCB1, ECO:0000250|UniProtKB:P25045), the precursor of the sphingoid bases. Kept as non-core because the core process recorded is ceramide biosynthesis.

Summary: PAINT inference: first step of de novo ceramide (sphingolipid) synthesis.

Reason: SPT makes 3-ketosphinganine, the committed step of de novo sphingolipid synthesis, which feeds ceramide synthesis. The role is by similarity to S. cerevisiae LCB1 (ECO:0000250|UniProtKB:P25045).