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SWF1/YDR126W Single Page Format

This page provides an alternative format to the SGD Locus Summary Page. Note that additional information may be available on or linked from the standard format SGD Locus Summary page.

Contents

Names and Identifiers GO Annotations Pathways Summary Paragraph Mutant Phenotypes Interactions Homologs Protein Info (physical properties, transcript info) PDB Homologs (protein structure info) Motifs Genome-wide Expression (and other large-scale analyses) Locus History (misc. notes) Sequence Retrieval and Analysis Map and Displays Localization Community Annotation Literature Guide

Sequence Coordinates   ChrIV: 703232 to 704242 CDS: 703232 - 704242 Click on map for expanded view SGD ORF map GBrowse

SGD Locus Page

Names and Identifiers [TOP] [NEXT]
Standard Name	Systematic Name	Alias	Feature Type	SGDID
SWF1	YDR126W	PSL10	ORF, Verified	S000002533
This name is reserved with SGD according to the Gene Naming Guidelines agreed upon by the yeast community. Gene name reserved on: 2001-01-09. Gene name expires on 2003-08-15.
Description
Palmitoyltransferase that acts on the SNAREs Snc1p, Syn8p, Tlg1p and likely on all SNAREs; member of a family of putative palmitoyltransferases containing an Asp-His-His-Cys-cysteine rich (DHHC-CRD) domain; may have a role in vacuole fusion

GO Annotations [TOP] [NEXT]
Molecular Function Annotation(s) Reference(s) Evidence Assigned By acyltransferase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0012 Assigned on 2007-05-23 UniProtKB metal ion binding GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0479 Assigned on 2007-05-23 UniProtKB protein-cysteine S-palmitoleyltransferase activity Valdez-Taubas J and Pelham H (2005) Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J 24(14):2524-32          ISS : Inferred from Sequence or structural Similarity IMP : Inferred from Mutant Phenotype Assigned on 2005-10-17 SGD transferase activity GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0808 Assigned on 2007-05-23 UniProtKB zinc ion binding DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.      IEA : Inferred from Electronic Annotation with EBI:IPR001594 Assigned on 2007-05-23 UniProtKB GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0862 Assigned on 2007-05-23 UniProtKB
Biological Process Annotation(s) Reference(s) Evidence Assigned By ascospore wall assembly Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54            IMP : Inferred from Mutant Phenotype Assigned on 2005-05-10 SGD establishment of cell polarity Dighe SA and Kozminski KG (2008) Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, regulates the actin cytoskeleton and polarized secretion independently of its DHHC motif. Mol Biol Cell 19(10):4454-68        IMP : Inferred from Mutant Phenotype Assigned on 2009-04-06 SGD exocytosis Dighe SA and Kozminski KG (2008) Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, regulates the actin cytoskeleton and polarized secretion independently of its DHHC motif. Mol Biol Cell 19(10):4454-68        IMP : Inferred from Mutant Phenotype Assigned on 2009-04-06 SGD protein amino acid palmitoylation Valdez-Taubas J and Pelham H (2005) Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J 24(14):2524-32          IMP : Inferred from Mutant Phenotype Assigned on 2005-10-17 SGD Roth AF, et al. (2006) Global analysis of protein palmitoylation in yeast. Cell 125(5):1003-13          IMP : Inferred from Mutant Phenotype Assigned on 2006-11-13 SGD vacuole fusion, non-autophagic Smotrys JE, et al. (2005) The vacuolar DHHC-CRD protein Pfa3p is a protein acyltransferase for Vac8p. J Cell Biol 170(7):1091-9        IGI : Inferred from Genetic Interaction Assigned on 2005-10-17 SGD
Cellular Component Annotation(s) Reference(s) Evidence Assigned By actin cortical patch Dighe SA and Kozminski KG (2008) Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, regulates the actin cytoskeleton and polarized secretion independently of its DHHC motif. Mol Biol Cell 19(10):4454-68        IDA : Inferred from Direct Assay Assigned on 2009-04-06 SGD actin filament bundle Dighe SA and Kozminski KG (2008) Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, regulates the actin cytoskeleton and polarized secretion independently of its DHHC motif. Mol Biol Cell 19(10):4454-68        IDA : Inferred from Direct Assay Assigned on 2009-04-06 SGD endoplasmic reticulum GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0256 Assigned on 2007-05-23 UniProtKB integral to membrane Bartels DJ, et al. (1999) Erf2, a novel gene product that affects the localization and palmitoylation of Ras2 in Saccharomyces cerevisiae. Mol Cell Biol 19(10):6775-87        ISS : Inferred from Sequence or structural Similarity Assigned on 2002-11-25 SGD GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0812 Assigned on 2007-05-23 UniProtKB GOA curators and UniProt curators (2007) Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping.      IEA : Inferred from Electronic Annotation with EBI:SL-9909 Assigned on 2009-10-01 UniProtKB membrane GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.      IEA : Inferred from Electronic Annotation with EBI:KW-0472 Assigned on 2007-05-23 UniProtKB nuclear envelope-endoplasmic reticulum network Valdez-Taubas J and Pelham H (2005) Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J 24(14):2524-32          IDA : Inferred from Direct Assay Assigned on 2005-10-17 SGD

Pathways [TOP] [NEXT]
No pathways available

Summary Paragraph [TOP] [NEXT]
No summary paragraph available

Basic References [TOP]

BASIC INFORMATION REFERENCES forSWF1/YDR126W for SWF1 1) Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54            2) Valdez-Taubas J and Pelham H (2005) Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J 24(14):2524-32          3) Smotrys JE, et al. (2005) The vacuolar DHHC-CRD protein Pfa3p is a protein acyltransferase for Vac8p. J Cell Biol 170(7):1091-9

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for SWF1/YDR126W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for SWF1/YDR126W

Homologs [TOP] [NEXT]
Comparison Resources PSI-BLAST Results Ashbya Homologs (AGD) BLASTN vs. fungi BLASTP at NCBI BLASTP vs. fungi Candida Homologs (CGD) Candida Homologs (CandidaDB) Fungal Alignment Fungal Orthogroups Repository Ortholog Search (P-POD) PhylomeDB Synteny Viewer Yeast Gene Order Browser (YGOB) eukarYotic OrtholoGY (YOGY)

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations from Predicted Full length Translation N-term MSWNLLF C-term ANLTDLI Length(aa) 336 MW(Da) 39,311 pI 7.33 Amino Acid Composition (full length) GCG tools: PepPlot, Helical Wheel, PepStruct Transcript Translation Calculations Codon Bias -0.039   Codon Adaptation Index 0.108   Frequency of Optimal Codons 0.396   Hydropathicity of Protein 0.177   Aromaticity Score 0.149	10 20 30 40 50 | | | | | MSWNLLFVLLIGFVVLILLSPVFKSTWPFSTFYRNVFQPFLVDDQKYRWK LHLVPLFYTSIYLYLVYTYHMRVESTIKNELFLLERILIVPIIILPPVAL GILAMVSRAEDSKDHKSGSTEEYPYDYLLYYPAIKCSTCRIVKPARSKHC SICNRCVLVADHHCIWINNCIGKGNYLQFYLFLISNIFSMCYAFLRLWYI SLNSTSTLPRAVLTLTILCGCFTIICAIFTYLQLAIVKEGMTTNEQDKWY TIQEYMREGKLVRSLDDDCPSWFFKCTEQKDDAAEPLQDQHVTFYSTNAY DHKHYNLTHYITIKDASEIPNIYDKGTFLANLTDLI*

Protein Structures from PDB: proteins of known structure with sequence similarity to SWF1/YDR126W, based on Smith-Waterman analysis. [TOP] [NEXT]
No protein structure information available.

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]
Functional Analysis Expression Connection Summary Cell cycle and metabolic oscillation Cell cycle transcript profile Cyclebase Genevestigator GermOnline SPELL Microarray Search YGAC Triples Yeast Microarray Global Viewer YeastFunc	You can also search multiple datasets simultaneously using Expression Connection for expression studies or Function Junction for other large scale analyses.

Locus History (misc. notes) [TOP] [NEXT]

Nomenclature History

Standard Name	Date Standardized	Reference
SWF1	2003-08-14	Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54

Nomenclature History Notes

Date	Note
2002-08-15	PSL10 used to be the reserved name for ORF YDR126W. SWF1 is now the reserved name for YDR126W, and PSL10 is now an alias of SWF1/YDR126W.

Sequence Retrieval [TOP] [NEXT]
Sequence Type	Output Format
Genomic DNA	GCG | FASTA | NoHeader
Genomic DNA with 1 kb up and downstream	GCG | FASTA | NoHeader
DNA coding sequence (without introns, without flanking regions)	GCG | FASTA | NoHeader
Protein Translation of ORF	GCG | FASTA | NoHeader
6-Frame Translation(with Restriction Map)	GCG
Restriction Fragment Sizes	GCG
Sequence Analysis Tools BLASTP BLASTN Design Primers FASTA aa FASTA nt Restriction Fragment Map Restriction Fragment Sizes Six-Frame Translation

Sequence from other databases
Sequence ID	Source
YDR126W	SGD Systematic Sequence
851704	NCBI: Gene ID
NP_010411.1	NCBI: RefSeq protein version ID
NP_010411.1	NCBI: RefSeq protein version ID
6320331	NCBI: NCBI protein GI

Map and Displays [TOP] [NEXT]
Physical, Genetic Maps:	Chromosomal Feature Map	GBrowse	Combined Physical and Genetic Map	Genetic Distance vs. Physical Distance Ratios
Similarity Viewers:	Synteny Viewer	Genomic Stripe View	SAGE Results Map

Localization [TOP] [NEXT]
Localization Resources YGAC Triples YeastGFP DB (UCSF) at SGD

Community Annotation [TOP] [NEXT]
No community annotation available.

Literature Guide: papers categorized by topic. [TOP]
Topics	Reference	Other Genes Addressed
16 curated references; 0 references not yet curated
Fungal Related Genes/Proteins Mutants/Phenotypes Non-Fungal Related Genes/Proteins Protein Sequence Features	Gonzalez Montoro A, et al. (2009) A novel motif at the C-terminus of palmitoyltransferases is essential for Swf1 and Pfa3 function in vivo. Biochem J 419(2):301-8	|PFA3
Cellular Location Function/Process Genetic Interactions Mutants/Phenotypes Protein Sequence Features Strains/Constructs	Dighe SA and Kozminski KG (2008) Swf1p, a member of the DHHC-CRD family of palmitoyltransferases, regulates the actin cytoskeleton and polarized secretion independently of its DHHC motif. Mol Biol Cell 19(10):4454-68	|ACT1 |BGL2 |CDC42
Function/Process Genetic Interactions Large-scale genetic interaction Mutants/Phenotypes Strains/Constructs	Hoke SM, et al. (2008) Systematic genetic array analysis links the Saccharomyces cerevisiae SAGA/SLIK and NuA4 component Tra1 to multiple cellular processes. BMC Genet 9:46	|ADA2 |ARL1 |ARL3 |CNB1 |COG5 |EAF7 |GCN5 |GYP1 |MDM34 |MON2 |NGG1 |RIC1 |SMI1 |SPT7 |MORE
Mutants/Phenotypes Strains/Constructs	Ando A, et al. (2007) Identification and classification of genes required for tolerance to freeze-thaw stress revealed by genome-wide screening of Saccharomyces cerevisiae deletion strains. FEMS Yeast Res 7(2):244-53	|AIM4 |AKR1 |ANP1 |BRE1 |BUD19 |CKB2 |CTF4 |CUP5 |DEG1 |DIA2 |EOS1 |ERG24 |FAB1 |GAS1 |MORE
Non-Fungal Related Genes/Proteins Reviews	Nadolski MJ and Linder ME (2007) Protein lipidation. FEBS J 274(20):5202-5210	|AKR1 |AKR2 |CHS3 |ERF2 |LCB4 |PFA3 |PFA4 |PFA5 |RAS2 |SHR5 |TLG1 |TUL1 |VAC8 |YCK2
Mutants/Phenotypes Techniques and Reagents	Freimoser FM, et al. (2006) Systematic screening of polyphosphate (poly P) levels in yeast mutant cells reveals strong interdependence with primary metabolism. Genome Biol 7(11):R109	|ADE1 |ADE3 |AKR1 |ALT2 |APL5 |APL6 |APM3 |APS3 |ARO1 |ARP5 |ATG12 |ATG20 |ATP15 |AVT6 |MORE
Reviews	Mitchell DA, et al. (2006) Protein palmitoylation by a family of DHHC protein S-acyltransferases. J Lipid Res 47(6):1118-27	|AKR1 |ERF2 |PFA3 |PFA4 |PFA5 |VAC8 |YCK1 |YCK2 |YCK3 |YKT6 |YNL155W
Cellular Location Fungal Related Genes/Proteins Non-Fungal Related Genes/Proteins Strains/Constructs	Ohno Y, et al. (2006) Intracellular localization and tissue-specific distribution of human and yeast DHHC cysteine-rich domain-containing proteins. Biochim Biophys Acta 1761(4):474-83	|AKR1 |AKR2 |ERF2 |PFA3 |PFA4 |PFA5
Function/Process Mutants/Phenotypes Strains/Constructs Substrates/Ligands/Cofactors	Roth AF, et al. (2006) Global analysis of protein palmitoylation in yeast. Cell 125(5):1003-13	|AGP1 |AKR1 |AKR2 |ANR2 |BAP2 |BAP3 |BET3 |CDC42 |ENV7 |ERF2 |GAP1 |GNP1 |GPA1 |GPA2 |MORE
Mutants/Phenotypes Strains/Constructs	Hou H, et al. (2005) The DHHC protein Pfa3 affects vacuole-associated palmitoylation of the fusion factor Vac8. Proc Natl Acad Sci U S A 102(48):17366-71	|AKR1 |AKR2 |ERF2 |MEH1 |PFA3 |PFA4 |PFA5 |VAC8 |YCK3
Function/Process Mutants/Phenotypes Strains/Constructs	Smotrys JE, et al. (2005) The vacuolar DHHC-CRD protein Pfa3p is a protein acyltransferase for Vac8p. J Cell Biol 170(7):1091-9	|ERF2 |PFA3 |PFA4 |PFA5
Cellular Location Function/Process Fungal Related Genes/Proteins Mutants/Phenotypes Protein Sequence Features Strains/Constructs	Valdez-Taubas J and Pelham H (2005) Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J 24(14):2524-32	|AKR1 |AKR2 |BSD2 |ERF2 |PFA3 |PFA4 |PFA5 |SNC1 |SYN8 |TLG1 |TUL1
Genetic Interactions Strains/Constructs	Tong AH, et al. (2004) Global mapping of the yeast genetic interaction network. Science 303(5659):808-13	|AAD4 |AAH1 |ABF2 |ACE2 |ADH6 |AEP2 |AFG1 |AGP1 |AHC1 |AHC2 |AIM21 |AIM22 |AIM26 |AIM29 |MORE
Mutants/Phenotypes	Enyenihi AH and Saunders WS (2003) Large-scale functional genomic analysis of sporulation and meiosis in Saccharomyces cerevisiae. Genetics 163(1):47-54	|ADA2 |ADY2 |AKR1 |APS3 |APT1 |ARC1 |ARG82 |ARO2 |ATF1 |ATG11 |ATG15 |ATG16 |ATG5 |BPH1 |MORE
Genetic Interactions Strains/Constructs	Kozminski KG, et al. (2003) Interaction between a Ras and a Rho GTPase couples selection of a growth site to the development of cell polarity in yeast. Mol Biol Cell 14(12):4958-70	|ACT1 |BEM1 |BEM4 |BNI1 |BUD6 |CAP1 |CAP2 |CDC24 |CDC42 |CLA4 |ELP2 |ELP3 |ELP4 |ELP6 |MORE
Cellular Location Genetic Interactions Mutants/Phenotypes Strains/Constructs	Bartels DJ, et al. (1999) Erf2, a novel gene product that affects the localization and palmitoylation of Ras2 in Saccharomyces cerevisiae. Mol Cell Biol 19(10):6775-87	|ERF2 |GPA2 |PFA3 |PFA4 |PFA5 |RAS2 |SHR5

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