Tier NIL Organism Database Metabolic Map Genome Browser Organism SmartTables Genome Dashboard
Database Authors Jeremy Zucker, PNNL; Neeraj Kumar, PNNL; Bill Cannon, PNNL; Kyle Pomraning, PNNL; Erin Bredeweg, PNNL; Scott Baker, PNNL
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp10 , Karp11 , Caspi14 ] component of Pathway Tools software version 21.0 and MetaCyc version 21.0 on 15-Aug-2017 09:16:11. Citations:
[Kerscher01 ,
Dujon04 ,
Pomraning15 ,
Kerkhoven16 ,
Kerkhoven17 ]
Genome
Database Contents
Genes 7,357 SmartTable Pathways 311 SmartTable Ontology Enzymatic Reactions 2,010 Transport Reactions 71 Ontology Polypeptides 7,156 SmartTable Class Page Protein Complexes 2 SmartTable Class Page Enzymes 1,236 SmartTable Transporters 262 SmartTable Compounds 1,366 SmartTable Ontology tRNAs 0 Ontology
Database Version 29.0
References
Caspi14 : Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315
Dujon04 : Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, De Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, De Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004). "Genome evolution in yeasts." Nature 430(6995);35-44. PMID: 15229592
Karp10 : Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237
Karp11 : Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592
Kerkhoven16 : Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J (2016). "Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica." NPJ Syst Biol Appl 2;16005. PMID: 28725468
Kerkhoven17 : Kerkhoven EJ, Kim YM, Wei S, Nicora CD, Fillmore TL, Purvine SO, Webb-Robertson BJ, Smith RD, Baker SE, Metz TO, Nielsen J (2017). "Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica." MBio 8(3). PMID: 28634240
Kerscher01 : Kerscher S, Durstewitz G, Casaregola S, Gaillardin C, Brandt U (2001). "The complete mitochondrial genome of yarrowia lipolytica." Comp Funct Genomics 2(2);80-90. PMID: 18628906
Pomraning15 : Pomraning KR, Wei S, Karagiosis SA, Kim YM, Dohnalkova AC, Arey BW, Bredeweg EL, Orr G, Metz TO, Baker SE (2015). "Comprehensive Metabolomic, Lipidomic and Microscopic Profiling of Yarrowia lipolytica during Lipid Accumulation Identifies Targets for Increased Lipogenesis." PLoS One 10(4);e0123188. PMID: 25905710
Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17.
hide
show operations
