DAL4/YIR028W 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

ChrIX: 408465 to 410372
CDS: 408465 - 410372
Genetic position: 34 cM
Genetic Map Data

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

DAL4 YIR028W ORF, Verified S000001467

Description
Allantoin permease; expression sensitive to nitrogen catabolite repression and induced by allophanate, an intermediate in allantoin degradation

GO Annotations [TOP] [NEXT]
Molecular Function
Annotation(s) Reference(s) Evidence Assigned By
allantoin uptake transmembrane transporter activity Cooper TG, et al. (1979) A cluster of three genes responsible for allantoin degradation in Saccharomyces cerevisiae. Genetics 92(2):383-96
     IMP : Inferred from Mutant Phenotype
Assigned on 2007-10-02 SGD
Yoo HS, et al. (1992) The allantoin and uracil permease gene sequences of Saccharomyces cerevisiae are nearly identical. Yeast 8(12):997-1006
     ISS : Inferred from Sequence or structural Similarity
Assigned on 2002-09-27 SGD
nucleobase transmembrane transporter activity DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR001248 , EBI:IPR012681
Assigned on 2007-05-23 UniProtKB
Biological Process
Annotation(s) Reference(s) Evidence Assigned By
allantoin catabolic process Cooper TG, et al. (1979) A cluster of three genes responsible for allantoin degradation in Saccharomyces cerevisiae. Genetics 92(2):383-96
     IMP : Inferred from Mutant Phenotype
Assigned on 2009-05-07 SGD
allantoin transport Chisholm VT, et al. (1987) Regulation of allantoate transport in wild-type and mutant strains of Saccharomyces cerevisiae. J Bacteriol 169(4):1684-90
     IMP : Inferred from Mutant Phenotype
Assigned on 2007-10-02 SGD
Cooper TG, et al. (1979) A cluster of three genes responsible for allantoin degradation in Saccharomyces cerevisiae. Genetics 92(2):383-96
     IMP : Inferred from Mutant Phenotype
Assigned on 2009-05-07 SGD
heterocycle metabolic process Huttenhower C and Troyanskaya OG (2009) Prediction of Gene Ontology annotations by integrating high-throughput datasets
   RCA : Reviewed Computational Analysis
Assigned on 2009-08-06 bioPIXIE_MEFIT
nucleobase, nucleoside, nucleotide and nucleic acid transport DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR001248 , EBI:IPR012681
Assigned on 2007-05-23 UniProtKB
purine base metabolic process GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0659
Assigned on 2007-05-23 UniProtKB
transmembrane transport DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR001248 , EBI:IPR012681
Assigned on 2009-10-01 UniProtKB
transport GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0813
Assigned on 2007-05-23 UniProtKB
Cellular Component
Annotation(s) Reference(s) Evidence Assigned By
integral to membrane 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 Yoo HS, et al. (1992) The allantoin and uracil permease gene sequences of Saccharomyces cerevisiae are nearly identical. Yeast 8(12):997-1006
     ISS : Inferred from Sequence or structural Similarity
Assigned on 2002-09-27 SGD
DDB, et al. (2001) Gene Ontology annotation through association of InterPro records with GO terms.
     IEA : Inferred from Electronic Annotation with EBI:IPR012681 , EBI:IPR001248
Assigned on 2009-06-17 UniProtKB
GOA curators (2000) Gene Ontology annotation based on Swiss-Prot keyword mapping.
     IEA : Inferred from Electronic Annotation with EBI:KW-0472
Assigned on 2009-06-29 UniProtKB

Pathways [TOP] [NEXT]
No pathways available

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

Basic References [TOP]
BASIC INFORMATION REFERENCES forDAL4/YIR028W for DAL4
1) Dorrington RA and Cooper TG (1993) The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS). Nucleic Acids Res 21(16):3777-84

2) Yoo HS, et al. (1992) The allantoin and uracil permease gene sequences of Saccharomyces cerevisiae are nearly identical. Yeast 8(12):997-1006

Mutant Phenotypes [TOP] [NEXT]
Phenotype page for DAL4/YIR028W

Interactions: genetic, physical, and other gene-gene links. [TOP] [NEXT]
Interaction page for DAL4/YIR028W

Homologs [TOP] [NEXT]

Comparison Resources

Physical Properties and Transcript Information: predicted from sequence [TOP] [NEXT]
Protein Sequence Calculations
from Predicted Full length Translation

N-term MANDALS

C-term TEEKIVY

Length(aa) 635

MW(Da) 71,755

pI 7.78

Amino Acid Composition (full length)

GCG tools: PepPlot, Helical Wheel, PepStruct

Transcript Translation Calculations

Codon Bias 0.144

Codon Adaptation Index 0.163

Frequency of Optimal Codons 0.492

Hydropathicity of Protein 0.349

Aromaticity Score 0.167

10 20 30 40 50 | | | | | MANDALSAIFSNPSRKGVQPSTSIVSYTNNEDDIIDVENGKFNKNKNINT NVYVDNSSIEESEVVPLPETKSIWSKIYYDFIVLDKTTLNVSLKESFLYN RDLKPVEEERRCWSWFNYLYFWLADCFNINTWQIAGTGLQLGLNWWQCWL TVWIGYTFAGIFVVLNSRFGSAYHLSFPITVRASFGIFFSMWPIINRVVM AIVWYAVQAWLGATPVALMLKSIFGKNLEDRIPNHFGSPNSTTFEFMCFF IFWVVSIPFVLVAPHKIRHLFTVKAALIPFAAFGFLIWALKKSHGKIELG TLNDYSPHGSEFSWIFVRSLMACVANFAALIINAPDFGRFAKNPQASLWP QLVAIPLFFAITCLIGIIVTAAGYHLYGVNYWSPLDVLGQFLETTYTRGT RAGVFLISFVFALAQLGTNISANSLACGADMTALFPRYINIRRGSLFCVA MALCICPWNLMASSSKFTSALGAYAIFLSSIAGVICADYFVVRRGYVKLT HLFLAQKGSFYMFGNKFGANWRAFVAYICGIAPNLPGFIGDVGAPKITVS EGAMRLYYLGYPVGFFISAVIYLILCYFFPVPGTPVTNFLTEKGWFQRWA YVEDFEQDWKNELRRDDLCDDTVSIYDGTEEKIVY*

Protein Structures from PDB: proteins of known structure with sequence similarity to DAL4/YIR028W, based on Smith-Waterman analysis. [TOP] [NEXT]
PDB protein structure(s) homologous to DAL4 Homolog Source (per PDB) Protein Alignment: DAL4 vs. Homolog External Links
P-Value %Identical %Similar Alignment
2jlo ( Chain: A)
Structure of mhp1, a nucleobase-cation-symport-1 family transporter, in a closed conformation with benzylhydantoin
PDB_Info
PDB_Structure
Microbacterium liquefaciens 4.8e-20 24 30 View alignment SCOP
MMDB
CATH
2jln ( Chain: A)
Structure of mhp1, a nucleobase-cation-symport-1 family transporter
PDB_Info
PDB_Structure
Microbacterium liquefaciens 4.8e-20 24 30 View alignment SCOP
MMDB
CATH

Genome-wide Expression and Other Large-Scale Analyses [TOP] [NEXT]

Functional Analysis
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 Reference
DAL4 SGD (2007) Information without a citation in SGD

Standard Name	Reference
DAL4	SGD (2007) Information without a citation in SGD

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
Sequence from other databases

Sequence ID Source

YIR028W SGD Systematic Sequence

854846 NCBI: Gene ID

NP_012294.1 NCBI: RefSeq protein version ID

NP_012294.1 NCBI: RefSeq protein version ID

6322219 NCBI: NCBI protein GI

Sequence from other databases
Sequence ID	Source
YIR028W	SGD Systematic Sequence
854846	NCBI: Gene ID
NP_012294.1	NCBI: RefSeq protein version ID
NP_012294.1	NCBI: RefSeq protein version ID
6322219	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

Community Annotation [TOP] [NEXT]
DNA & RNA Details
Topic Research Highlight Reference Contributor
Other DNA & RNA Details Description: Specifically higher expression in nitrogen limited chemostat cultures versus nitrogen excess.
otherTopic: expression
Boer VM, et al. (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278(5):3265-74
Viktor Boer
2003-07-25

Literature Guide: papers categorized by topic. [TOP]
Topics Reference Other Genes Addressed
26 curated references; 0 references not yet curated
DNA/RNA Sequence Features
Fungal Related Genes/Proteins
Gordon JL, et al. (2009) Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet 5(5):e1000485
           |ABM1 |ADH1 |ADH2 |ARI1 |ASP3-1 |ASP3-2 |ASP3-3 |ASP3-4 |AUS1 |AXL2 |AZR1 |CCT2 |DAL7 |DIA3 |MORE
Evolution
Fungal Related Genes/Proteins
Hamari Z, et al. (2009) Convergent evolution and orphan genes in the Fur4p-like family and characterization of a general nucleoside transporter in Aspergillus nidulans. Mol Microbiol 73(1):43-57
       |FCY2 |FCY21 |FCY22 |FUI1 |FUN26 |FUR4 |NRT1 |THI7 |THI72 |TPN1
Reviews
Osbourn AE and Field B (2009) Operons. Cell Mol Life Sci 66(23):3755-75
       |DAL1 |DAL2 |DAL3 |DAL7 |DCG1 |HTZ1 |SUM1
RNA Levels and Processing
Zhang YQ and Rao R (2007) Global disruption of cell cycle progression and nutrient response by the antifungal agent amiodarone. J Biol Chem 282(52):37844-53
       |ACS1 |ALD4 |CAT8 |CNB1 |CRZ1 |CTA1 |CYB2 |CYR1 |DAL7 |DAL80 |ECI1 |FAA2 |FDH1 |FOX2 |MORE
Evolution
Fungal Related Genes/Proteins
De Hertogh B, et al. (2006) Emergence of species-specific transporters during evolution of the hemiascomycete phylum. Genetics 172(2):771-81
       |AAC1 |AAC3 |ACS2 |ADP1 |ADY2 |AGC1 |AGP1 |AGP2 |AGP3 |ALP1 |ALR1 |ALR2 |ANT1 |AQR1 |MORE
Function/Process
Fungal Related Genes/Proteins
Mutants/Phenotypes
Substrates/Ligands/Cofactors
Paluszynski JP, et al. (2006) Various cytosine/adenine permease homologues are involved in the toxicity of 5-fluorocytosine in Saccharomyces cerevisiae. Yeast 23(9):707-15
       |FCY1 |FCY2 |FCY21 |FCY22 |FUI1 |FUR4 |NRT1 |TPN1
RNA Levels and Processing
Usaite R, et al. (2006) Global transcriptional and physiological responses of Saccharomyces cerevisiae to ammonium, L-alanine, or L-glutamine limitation. Appl Environ Microbiol 72(9):6194-203
         |ACS1 |ADH5 |ALT1 |BAT2 |CAT8 |CHA1 |CIT2 |CPA1 |DAL1 |DAL7 |DCG1 |DIP5 |FOL1 |GDH2 |MORE
Non-Fungal Related Genes/Proteins
Suzuki S, et al. (2005) Molecular Cloning and Expression of the hyu Genes from Microbacterium liquefaciens AJ 3912, Responsible for the Conversion of 5-Substituted Hydantoins to alpha-Amino Acids, in Escherichia coli. Biosci Biotechnol Biochem 69(8):1473-82

DNA/RNA Sequence Features
Fungal Related Genes/Proteins
Wong S and Wolfe KH (2005) Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet 37(7):777-82
       |DAL1 |DAL2 |DAL3 |DAL7 |DCG1 |HST1 |SUM1
Function/Process
RNA Levels and Processing
Regulation of
Techniques and Reagents
Transcription
Boer VM, et al. (2003) The genome-wide transcriptional responses of Saccharomyces cerevisiae grown on glucose in aerobic chemostat cultures limited for carbon, nitrogen, phosphorus, or sulfur. J Biol Chem 278(5):3265-74
           |ADH2 |ADY2 |AGP3 |ATO2 |ATO3 |BDS1 |CIT3 |CPS1 |CTA1 |CTR3 |DAL5 |DAL80 |FBP1 |FDH1 |MORE
Computational analysis
Baudouin-Cornu P, et al. (2001) Molecular evolution of protein atomic composition. Science 293(5528):297-300
             |CDC19 |CYS3 |CYS4 |DAL1 |DAL2 |DAL3 |DAL5 |DAL7 |DAL81 |DUR1,2 |DUR3 |ENO1 |ENO2 |FBA1 |MORE
Function/Process
Regulation of
Transcription
van der Merwe GK, et al. (2001) Ammonia regulates VID30 expression and Vid30p function shifts nitrogen metabolism toward glutamate formation especially when Saccharomyces cerevisiae is grown in low concentrations of ammonia. J Biol Chem 276(31):28659-66
       |CAN1 |DAL1 |DAL5 |DAL80 |GAT1 |GDH1 |GDH3 |GLN3 |GLT1 |MEP2 |URE2 |VID30
DNA/RNA Sequence Features
Regulation of
Transcription
van der Merwe GK, et al. (2001) Cis-acting sites contributing to expression of divergently transcribed DAL1 and DAL4 genes in S. cerevisiae: a word of caution when correlating cis-acting sequences with genome-wide expression analyses. Curr Genet 39(3):156-65
       |DAL1 |DAL82 |GAT1 |GLN3
Reviews
ter Schure EG, et al. (2000) The role of ammonia metabolism in nitrogen catabolite repression in Saccharomyces cerevisiae. FEMS Microbiol Rev 24(1):67-83
       |ASP3-1 |ASP3-2 |ASP3-3 |ASP3-4 |BAS1 |CAN1 |CAR1 |DAL1 |DAL2 |DAL7 |DAL80 |DSD1 |FUR4 |GAP1 |MORE
Fungal Related Genes/Proteins
Wagner R, et al. (1998) The ORF YBL042 of Saccharomyces cerevisiae encodes a uridine permease. FEMS Microbiol Lett 159(1):69-75
       |FUI1 |FUR4
Fungal Related Genes/Proteins
Protein Sequence Features
de Montigny J, et al. (1998) The uracil permease of Schizosaccharomyces pombe: a representative of a family of 10 transmembrane helix transporter proteins of yeasts. Yeast 14(11):1051-9
       |FUI1 |FUR4 |NRT1 |THI7
Fungal Related Genes/Proteins
Nelissen B, et al. (1995) Phylogenetic classification of the major superfamily of membrane transport facilitators, as deduced from yeast genome sequencing. FEBS Lett 377(2):232-6
       |DUR3 |FCY2 |FEN2 |FUI1 |FUR4 |HOL1 |HXT11 |HXT12 |HXT17 |HXT9 |PHO84 |PTR2 |SGE1 |SNF3 |MORE
Fungal Related Genes/Proteins
De Wergifosse P, et al. (1994) The sequence of a 22.4 kb DNA fragment from the left arm of yeast chromosome II reveals homologues to bacterial proline synthetase and murine alpha-adaptin, as well as a new permease and a DNA-binding protein. Yeast 10(11):1489-96
     |COR1 |EDE1 |ERD2 |FUI1 |FUR4 |PRE7 |UBP5 |URA7
Regulation of
Transcription
Daugherty JR, et al. (1993) Regulatory circuit for responses of nitrogen catabolic gene expression to the GLN3 and DAL80 proteins and nitrogen catabolite repression in Saccharomyces cerevisiae. J Bacteriol 175(1):64-73
     |CAN1 |DAL1 |DAL2 |DAL5 |DAL7 |DAL80 |GAP1 |GDH1 |GDH2 |GLN1 |GLN3 |PUT1 |PUT2 |PUT4 |MORE
Regulation of
Transcription
Dorrington RA and Cooper TG (1993) The DAL82 protein of Saccharomyces cerevisiae binds to the DAL upstream induction sequence (UIS). Nucleic Acids Res 21(16):3777-84
     |DAL2 |DAL7 |DAL81 |DAL82 |DUR1,2 |DUR3
DNA/RNA Sequence Features
Fungal Related Genes/Proteins
Protein Sequence Features
Regulation of
Transcription
Yoo HS, et al. (1992) The allantoin and uracil permease gene sequences of Saccharomyces cerevisiae are nearly identical. Yeast 8(12):997-1006
     |FUR4
Regulation of
Transcription
van Vuuren HJ, et al. (1991) Upstream induction sequence, the cis-acting element required for response to the allantoin pathway inducer and enhancement of operation of the nitrogen-regulated upstream activation sequence in Saccharomyces cerevisiae. J Bacteriol 173(22):7186-95
     |CAR2 |DAL2 |DAL7 |DAL81 |DAL82 |DUR1,2 |DUR3
Function/Process
Genetic Interactions
Mutants/Phenotypes
Regulation of
Transcription
Chisholm VT, et al. (1987) Regulation of allantoate transport in wild-type and mutant strains of Saccharomyces cerevisiae. J Bacteriol 169(4):1684-90
     |DAL5
Function/Process
Regulation of
Transcription
Cooper TG, et al. (1987) Allantoin transport in Saccharomyces cerevisiae is regulated by two induction systems. J Bacteriol 169(10):4660-7
     |DAL81
Mapping
Mutants/Phenotypes
Cooper TG, et al. (1979) A cluster of three genes responsible for allantoin degradation in Saccharomyces cerevisiae. Genetics 92(2):383-96
     |DAL1 |DAL2 |LYS1
Function/Process
Regulation of
Substrates/Ligands/Cofactors
Sumrada R, et al. (1978) Induction and inhibition of the allantoin permease in Saccharomyces cerevisiae. J Bacteriol 135(2):498-510
     |RNA1

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