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P17967

- PDI_YEAST

UniProt

P17967 - PDI_YEAST

Protein

Protein disulfide-isomerase

Gene

PDI1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 149 (01 Oct 2014)
      Sequence version 2 (01 Mar 1992)
      Previous versions | rss
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    Functioni

    Protein disulfide isomerase of ER lumen required for formation of disulfide bonds in secretory and cell-surface proteins and which unscrambles non-native disulfide bonds. Forms a complex with MNL1 to process unfolded protein-bound Man8GlcNAc2 oligosaccharides to Man7GlcNAc2, promoting degradation in unfolded protein response.3 Publications

    Catalytic activityi

    Catalyzes the rearrangement of -S-S- bonds in proteins.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei61 – 611NucleophileBy similarity
    Sitei62 – 621Contributes to redox potential valueBy similarity
    Sitei63 – 631Contributes to redox potential valueBy similarity
    Active sitei64 – 641NucleophileBy similarity
    Sitei126 – 1261Lowers pKa of C-terminal Cys of first active siteBy similarity
    Active sitei406 – 4061NucleophileBy similarity
    Sitei407 – 4071Contributes to redox potential valueBy similarity
    Sitei408 – 4081Contributes to redox potential valueBy similarity
    Active sitei409 – 4091NucleophileBy similarity
    Sitei471 – 4711Lowers pKa of C-terminal Cys of second active siteBy similarity

    GO - Molecular functioni

    1. protein binding Source: IntAct
    2. protein disulfide isomerase activity Source: SGD
    3. protein disulfide oxidoreductase activity Source: SGD
    4. unfolded protein binding Source: SGD

    GO - Biological processi

    1. cell redox homeostasis Source: InterPro
    2. oxidation-reduction process Source: GOC
    3. protein folding Source: SGD

    Keywords - Molecular functioni

    Isomerase

    Enzyme and pathway databases

    BioCyciYEAST:YCL043C-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein disulfide-isomerase (EC:5.3.4.1)
    Short name:
    PDI
    Alternative name(s):
    Thioredoxin-related glycoprotein 1
    Gene namesi
    Name:PDI1
    Synonyms:MFP1, TRG1
    Ordered Locus Names:YCL043C
    ORF Names:YCL313, YCL43C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome III

    Organism-specific databases

    CYGDiYCL043c.
    SGDiS000000548. PDI1.

    Subcellular locationi

    Endoplasmic reticulum lumen PROSITE-ProRule annotation

    GO - Cellular componenti

    1. endoplasmic reticulum lumen Source: SGD

    Keywords - Cellular componenti

    Endoplasmic reticulum

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2828Or 22Sequence AnalysisAdd
    BLAST
    Chaini29 – 522494Protein disulfide-isomerasePRO_0000034218Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Disulfide bondi61 ↔ 64Redox-active1 PublicationPROSITE-ProRule annotation
    Glycosylationi82 – 821N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi117 – 1171N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi155 – 1551N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi174 – 1741N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi406 ↔ 409Redox-active1 PublicationPROSITE-ProRule annotation
    Glycosylationi425 – 4251N-linked (GlcNAc...)Sequence Analysis

    Post-translational modificationi

    The N-terminus is blocked.

    Keywords - PTMi

    Disulfide bond, Glycoprotein

    Proteomic databases

    MaxQBiP17967.
    PaxDbiP17967.
    PeptideAtlasiP17967.

    Expressioni

    Gene expression databases

    GenevestigatoriP17967.

    Interactioni

    Subunit structurei

    Interacts with EPS1, KAR2 and MNL1.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    RNASE1P618232EBI-13012,EBI-908364From a different organism.

    Protein-protein interaction databases

    BioGridi30941. 162 interactions.
    DIPiDIP-4978N.
    IntActiP17967. 10 interactions.
    MINTiMINT-497035.
    STRINGi4932.YCL043C.

    Structurei

    Secondary structure

    1
    522
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Turni39 – 413
    Helixi42 – 465
    Beta strandi50 – 578
    Helixi62 – 7716
    Turni78 – 825
    Beta strandi84 – 896
    Turni90 – 923
    Helixi94 – 996
    Beta strandi104 – 1129
    Beta strandi119 – 1213
    Helixi128 – 13811
    Beta strandi142 – 1454
    Helixi149 – 1557
    Beta strandi162 – 1687
    Helixi171 – 18313
    Turni184 – 1874
    Beta strandi189 – 1946
    Beta strandi201 – 2066
    Beta strandi209 – 2157
    Helixi220 – 2234
    Helixi226 – 23611
    Helixi246 – 2549
    Beta strandi259 – 2668
    Helixi267 – 28317
    Turni284 – 2874
    Beta strandi289 – 2946
    Helixi295 – 2984
    Helixi301 – 3044
    Beta strandi311 – 3188
    Turni319 – 3224
    Beta strandi323 – 3264
    Helixi332 – 3365
    Helixi346 – 35813
    Beta strandi377 – 3815
    Turni383 – 3853
    Helixi386 – 3916
    Beta strandi397 – 4026
    Helixi407 – 42620
    Beta strandi431 – 4366
    Helixi437 – 4393
    Beta strandi448 – 4569
    Helixi473 – 48311
    Helixi490 – 50112

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2B5EX-ray2.40A23-522[»]
    3BOAX-ray3.70A23-522[»]
    ProteinModelPortaliP17967.
    SMRiP17967. Positions 23-494.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17967.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini29 – 141113Thioredoxin 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini356 – 485130Thioredoxin 2PROSITE-ProRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi519 – 5224Prevents secretion from ER

    Sequence similaritiesi

    Belongs to the protein disulfide isomerase family.Curated
    Contains 2 thioredoxin domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Redox-active center, Repeat, Signal

    Phylogenomic databases

    eggNOGiCOG0526.
    GeneTreeiENSGT00740000115037.
    HOGENOMiHOG000162459.
    KOiK09580.
    OMAiHTNNDVD.
    OrthoDBiEOG71CFZN.

    Family and domain databases

    Gene3Di3.40.30.10. 2 hits.
    InterProiIPR005792. Prot_disulphide_isomerase.
    IPR012336. Thioredoxin-like_fold.
    IPR017937. Thioredoxin_CS.
    IPR013766. Thioredoxin_domain.
    [Graphical view]
    PfamiPF00085. Thioredoxin. 2 hits.
    [Graphical view]
    SUPFAMiSSF52833. SSF52833. 4 hits.
    TIGRFAMsiTIGR01130. ER_PDI_fam. 1 hit.
    PROSITEiPS00014. ER_TARGET. 1 hit.
    PS00194. THIOREDOXIN_1. 2 hits.
    PS51352. THIOREDOXIN_2. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P17967-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKFSAGAVLS WSSLLLASSV FAQQEAVAPE DSAVVKLATD SFNEYIQSHD    50
    LVLAEFFAPW CGHCKNMAPE YVKAAETLVE KNITLAQIDC TENQDLCMEH 100
    NIPGFPSLKI FKNSDVNNSI DYEGPRTAEA IVQFMIKQSQ PAVAVVADLP 150
    AYLANETFVT PVIVQSGKID ADFNATFYSM ANKHFNDYDF VSAENADDDF 200
    KLSIYLPSAM DEPVVYNGKK ADIADADVFE KWLQVEALPY FGEIDGSVFA 250
    QYVESGLPLG YLFYNDEEEL EEYKPLFTEL AKKNRGLMNF VSIDARKFGR 300
    HAGNLNMKEQ FPLFAIHDMT EDLKYGLPQL SEEAFDELSD KIVLESKAIE 350
    SLVKDFLKGD ASPIVKSQEI FENQDSSVFQ LVGKNHDEIV NDPKKDVLVL 400
    YYAPWCGHCK RLAPTYQELA DTYANATSDV LIAKLDHTEN DVRGVVIEGY 450
    PTIVLYPGGK KSESVVYQGS RSLDSLFDFI KENGHFDVDG KALYEEAQEK 500
    AAEEADADAE LADEEDAIHD EL 522
    Length:522
    Mass (Da):58,227
    Last modified:March 1, 1992 - v2
    Checksum:i69CF3E05D7F74C94
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti33 – 5220AVVKL…SHDLV → LSLSWPPTLSMNTFSRTTWW in AAA34848. (PubMed:1840696)CuratedAdd
    BLAST
    Sequence conflicti83 – 831I → V in CAA36550. (PubMed:1761554)Curated
    Sequence conflicti83 – 831I → V in AAA35169. (PubMed:1761554)Curated
    Sequence conflicti114 – 1141S → R in CAA38402. (PubMed:1761235)Curated
    Sequence conflicti143 – 1431V → S(PubMed:1761554)Curated
    Sequence conflicti146 – 1461Missing(PubMed:1761554)Curated
    Sequence conflicti168 – 1681K → E in CAA36550. (PubMed:1761554)Curated
    Sequence conflicti168 – 1681K → E in AAA35169. (PubMed:1761554)Curated
    Sequence conflicti197 – 1971D → E in AAA34848. (PubMed:1840696)Curated
    Sequence conflicti215 – 2151V → R AA sequence (PubMed:1761527)Curated
    Sequence conflicti226 – 2261A → V in CAA36550. (PubMed:1761554)Curated
    Sequence conflicti226 – 2261A → V in AAA35169. (PubMed:1761554)Curated
    Sequence conflicti333 – 3331E → S AA sequence (PubMed:1761527)Curated
    Sequence conflicti351 – 3511S → P in AAA34848. (PubMed:1840696)Curated
    Sequence conflicti455 – 4551L → F in AAA34848. (PubMed:1840696)Curated
    Sequence conflicti458 – 4581G → S in CAA36550. (PubMed:1761554)Curated
    Sequence conflicti458 – 4581G → S in AAA35169. (PubMed:1761554)Curated
    Sequence conflicti505 – 5051A → AEADAEAEA(PubMed:1761554)Curated
    Sequence conflicti505 – 5051A → AEADAEAEA(PubMed:1761235)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D00842 Genomic DNA. Translation: BAA00723.1.
    X57712 Genomic DNA. Translation: CAA40883.1.
    M62815 Genomic DNA. Translation: AAA34848.1.
    X52313 Genomic DNA. Translation: CAA36550.1.
    M76982 Genomic DNA. Translation: AAA35169.1.
    X54535 Genomic DNA. Translation: CAA38402.1.
    X59720 Genomic DNA. Translation: CAA42373.1.
    BK006937 Genomic DNA. Translation: DAA07442.1.
    PIRiJX0182. ISBYSS.
    RefSeqiNP_009887.1. NM_001178688.1.

    Genome annotation databases

    EnsemblFungiiYCL043C; YCL043C; YCL043C.
    GeneIDi850314.
    KEGGisce:YCL043C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    D00842 Genomic DNA. Translation: BAA00723.1 .
    X57712 Genomic DNA. Translation: CAA40883.1 .
    M62815 Genomic DNA. Translation: AAA34848.1 .
    X52313 Genomic DNA. Translation: CAA36550.1 .
    M76982 Genomic DNA. Translation: AAA35169.1 .
    X54535 Genomic DNA. Translation: CAA38402.1 .
    X59720 Genomic DNA. Translation: CAA42373.1 .
    BK006937 Genomic DNA. Translation: DAA07442.1 .
    PIRi JX0182. ISBYSS.
    RefSeqi NP_009887.1. NM_001178688.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2B5E X-ray 2.40 A 23-522 [» ]
    3BOA X-ray 3.70 A 23-522 [» ]
    ProteinModelPortali P17967.
    SMRi P17967. Positions 23-494.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 30941. 162 interactions.
    DIPi DIP-4978N.
    IntActi P17967. 10 interactions.
    MINTi MINT-497035.
    STRINGi 4932.YCL043C.

    Proteomic databases

    MaxQBi P17967.
    PaxDbi P17967.
    PeptideAtlasi P17967.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YCL043C ; YCL043C ; YCL043C .
    GeneIDi 850314.
    KEGGi sce:YCL043C.

    Organism-specific databases

    CYGDi YCL043c.
    SGDi S000000548. PDI1.

    Phylogenomic databases

    eggNOGi COG0526.
    GeneTreei ENSGT00740000115037.
    HOGENOMi HOG000162459.
    KOi K09580.
    OMAi HTNNDVD.
    OrthoDBi EOG71CFZN.

    Enzyme and pathway databases

    BioCyci YEAST:YCL043C-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P17967.
    NextBioi 965715.
    PROi P17967.

    Gene expression databases

    Genevestigatori P17967.

    Family and domain databases

    Gene3Di 3.40.30.10. 2 hits.
    InterProi IPR005792. Prot_disulphide_isomerase.
    IPR012336. Thioredoxin-like_fold.
    IPR017937. Thioredoxin_CS.
    IPR013766. Thioredoxin_domain.
    [Graphical view ]
    Pfami PF00085. Thioredoxin. 2 hits.
    [Graphical view ]
    SUPFAMi SSF52833. SSF52833. 4 hits.
    TIGRFAMsi TIGR01130. ER_PDI_fam. 1 hit.
    PROSITEi PS00014. ER_TARGET. 1 hit.
    PS00194. THIOREDOXIN_1. 2 hits.
    PS51352. THIOREDOXIN_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Molecular structure of a yeast gene, PDI1, encoding protein disulfide isomerase that is essential for cell growth."
      Tachikawa H., Miura T., Katakura Y., Mizunaga T.
      J. Biochem. 110:306-313(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PARTIAL PROTEIN SEQUENCE.
      Strain: ATCC 26786 / X2180-1A and TM5.
    2. "Determination of the sequence of the yeast YCL313 gene localized on chromosome III. Homology with the protein disulfide isomerase (PDI gene product) of other organisms."
      Scherens B., Dubois E., Messenguy F.
      Yeast 7:185-193(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    3. "Glycosylation site binding protein and protein disulfide isomerase are identical and essential for cell viability in yeast."
      Lamantia M., Miura T., Tachikawa H., Kaplan H.A., Lennarz W.J., Mizunaga T.
      Proc. Natl. Acad. Sci. U.S.A. 88:4453-4457(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    4. "The Saccharomyces cerevisiae TRG1 gene is essential for growth and encodes a lumenal endoplasmic reticulum glycoprotein involved in the maturation of vacuolar carboxypeptidase."
      Guenther R., Braeuer C., Janetzky B., Foerster H.H., Ehbrecht I.M., Lehle L., Kuentzel H.
      J. Biol. Chem. 266:24557-24563(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    5. "Protein disulfide isomerase is essential for viability in Saccharomyces cerevisiae."
      Farquhar R., Honey N., Murant S.J., Bossier P., Schultz L., Montogomery D., Ellis R.W., Freedman R.B., Tuite M.F.
      Gene 108:81-89(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    6. "The complete sequence of a 9,543 bp segment on the left arm of chromosome III reveals five open reading frames including glucokinase and the protein disulfide isomerase."
      Scherens B., Messenguy F., Gigot D., Dubois E.
      Yeast 8:577-586(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    7. "The complete DNA sequence of yeast chromosome III."
      Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M.
      , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G.
      Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    8. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    9. "Interactions among yeast protein-disulfide isomerase proteins and endoplasmic reticulum chaperone proteins influence their activities."
      Kimura T., Hosoda Y., Sato Y., Kitamura Y., Ikeda T., Horibe T., Kikuchi M.
      J. Biol. Chem. 280:31438-31441(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH EPS1 AND KAR2.
    10. "Htm1 protein generates the N-glycan signal for glycoprotein degradation in the endoplasmic reticulum."
      Clerc S., Hirsch C., Oggier D.M., Deprez P., Jakob C., Sommer T., Aebi M.
      J. Cell Biol. 184:159-172(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH MNL1.
    11. "A complex of Pdi1p and the mannosidase Htm1p initiates clearance of unfolded glycoproteins from the endoplasmic reticulum."
      Gauss R., Kanehara K., Carvalho P., Ng D.T., Aebi M.
      Mol. Cell 42:782-793(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH MNL1.
    12. "The crystal structure of yeast protein disulfide isomerase suggests cooperativity between its active sites."
      Tian G., Xiang S., Noiva R., Lennarz W.J., Schindelin H.
      Cell 124:61-73(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 23-522, DISULFIDE BONDS.

    Entry informationi

    Entry nameiPDI_YEAST
    AccessioniPrimary (citable) accession number: P17967
    Secondary accession number(s): D6VQX3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1990
    Last sequence update: March 1, 1992
    Last modified: October 1, 2014
    This is version 149 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome III
      Yeast (Saccharomyces cerevisiae) chromosome III: entries and gene names

    External Data

    Dasty 3