Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
Saccharomyces cerevisiae Reference Assembly Panel Database (ScRAPdb)
A searchable table of the S. cerevisiae pangenome ORFs defined in Peter et al. (2018) Nature (LINK) is provided below. The listed core/accessory classification and origin assignment are based on the original study. Click on the PanORF ID to find out the detailed presence/absence pattern of the corresponding pangenome ORF in both ScRAPdb and the 1002ScGP strain collections (which were recalculated by ScRAPdb).
| PanORF ID | SGD systematic Name | SGD standard name | Alias | Description | Type | Origin assignment | Mostly likely origin species | NCBI megablast hit |
|---|---|---|---|---|---|---|---|---|
| 5258-YKL186C | YKL186C | MTR2 | NA | mRNA transport regulator; essential nuclear protein; Mex67p and Mtr2p form a mRNA export complex which binds to RNA | Core | NA | NA | NA |
| 5259-YKL187C | YKL187C | FAT3 | NA | Protein required for fatty acid uptake; protein abundance increases in cortical patches in response to oleate exposure; the authentic, non-tagged protein is detected in a phosphorylated state in highly purified mitochondria in high-throughput studies; FAT3 has a paralog, YLR413W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5260-YKL188C | YKL188C | PXA2 | ATP-binding cassette long-chain fatty acid transporter PXA2|PAT1 | Subunit of heterodimeric peroxisomal ABC transport complex, with Pxa1p; required for import of long-chain fatty acids into peroxisomes; similar to human adrenoleukodystrophy transportesr ABCD1 and ABCD2, and ALD-related proteins; mutations in ABCD1 cause X-linked adrenoleukodystrophy (X-ALD), a peroxisomal disorder; human ABCD1 and ABCD2 can each partially complement yeast pxa1 pxa2 double null mutant | Core | NA | NA | NA |
| 5261-YKL189W | YKL189W | HYM1 | NA | Component of the RAM signaling network; is involved in regulation of Ace2p activity and cellular morphogenesis, interacts with Kic1p and Sog2p, localizes to sites of polarized growth during budding and during the mating response | Core | NA | NA | NA |
| 5262-YKL190W | YKL190W | CNB1 | calcineurin regulatory subunit B|YCN2|CRV1 | Calcineurin B; regulatory subunit of calcineurin, a Ca++/calmodulin-regulated type 2B protein phosphatase which regulates Crz1p (stress-response transcription factor); other calcineurin subunit encoded by CNA1 and/or CMP1; regulates function of Aly1p alpha-arrestin; myristoylation by Nmt1p reduces calcineurin activity in response to submaximal Ca signals, is needed to prevent constitutive phosphatase activity; protein abundance increases in response to DNA replication stress | Core | NA | NA | NA |
| 5263-YKL191W | YKL191W | DPH2 | NA | Protein required for synthesis of diphthamide; required along with Dph1p, Kti11p, Jjj3p, and Dph5p; diphthamide is a modified histidine residue of translation elongation factor 2 (Eft1p or Eft2p); may act in a complex with Dph1p and Kti11p | Core | NA | NA | NA |
| 5264-YKL192C | YKL192C | ACP1 | acyl carrier protein | Mitochondrial matrix acyl carrier protein; involved in biosynthesis of octanoate, which is a precursor to lipoic acid; activated by phosphopantetheinylation catalyzed by Ppt2p | Core | NA | NA | NA |
| 5265-YKL193C | YKL193C | SDS22 | type 1 protein phosphatase-activating protein SDS22|EGP1 | Regulatory subunit of the type 1 protein phosphatase (PP1) Glc7p; whether it functions as a positive or negative regulator of Glc7p is controversial; involved in the regulation of Glc7p nuclear localization and function | Core | NA | NA | NA |
| 5266-YKL194C | YKL194C | MST1 | threonine--tRNA ligase MST1 | Mitochondrial threonyl-tRNA synthetase; aminoacylates both the canonical threonine tRNA tT(UGU)Q1 and the unusual threonine tRNA tT(UAG)Q2 in vitro; lacks a typical editing domain, but has pre-transfer editing activity stimulated by the unusual tRNA-Thr | Core | NA | NA | NA |
| 5267-YKL195W | YKL195W | MIA40 | TIM40|FMP15 | Import and assembly protein in mitochondrial intermembrane space; component of MIA pathway which mediates import and oxidative folding of substrates including small proteins containing twin cysteine motifs; acts in concert with Erv1p, which oxidizes the cysteine residues of Mia40p to comprise a disulfide relay system that catalyzes import; also mediates folding of Atp23p via a chaperone-like activity; forms a dimer that binds iron-sulfur cluster in vitro | Core | NA | NA | NA |
| 5268-YKL196C | YKL196C | YKT6 | palmitoyltransferase YKT6 | Vesicle membrane protein (v-SNARE) with acyltransferase activity; involved in trafficking to and within the Golgi, endocytic trafficking to the vacuole, and vacuolar fusion; membrane localization due to prenylation at the carboxy-terminus; human homolog YKT6 can complement yeast ykt6 mutant | Core | NA | NA | NA |
| 5269-YKL197C | YKL197C | PEX1 | AAA family ATPase peroxin 1|PAS1 | AAA-peroxin; heterodimerizes with AAA-peroxin Pex6p and participates in the recycling of peroxisomal signal receptor Pex5p from the peroxisomal membrane to the cystosol; induced by oleic acid and upregulated during anaerobiosis; mutations in human PEX1 can lead to severe peroxisomal disorders and early death | Core | NA | NA | NA |
| 5270-YKL198C | YKL198C | PTK1 | putative serine/threonine protein kinase PTK1|POT1|YKT9|YKL199C|STK1|KKT8 | Putative serine/threonine protein kinase; regulates spermine uptake; involved in polyamine transport; possible mitochondrial protein; PTK1 has a paralog, PTK2, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5271-YKL201C_NumOfGenes_2 | YKL201C | MNN4 | YKL200C | Putative positive regulator of mannosylphosphate transferase Mnn6p; involved in mannosylphosphorylation of N-linked oligosaccharides; expression increases in late-logarithmic and stationary growth phases; coding sequence contains length polymorphisms in different strains; MNN4 has a paralog, YJR061W, that arose from the whole genome duplication | Core | NA | NA | NA |
| 5272-YKL203C | YKL203C | TOR2 | phosphatidylinositol kinase-related protein kinase TOR2|DRR2 | PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis; TOR2 has a paralog, TOR1, that arose from the whole genome duplication | Core | NA | NA | NA |