Database Authors
Zheng Zhao, Delft University of Technology; Wilbert H. Heijne, DSM Biotechnology Center; Marco A. van den Berg, DSM Biotechnology Center; Liang Wu, DSM Biotechnology Center; Marcel A. van den Broek, Delft University of Technology; Roel A. Bovenberg, DSM Biotechnology Center; Peter J.T. Verheijen, Delft University of Technology; Walter M. van Gulik, Delft University of Technology; S. Aljoscha Wahl, Delft University of Technology; Joseph J. Heijnen, Delft University of Technology
Summary This Pathway/Genome Database (PGDB) for Penicillium rubens Wisconsin 54-1255 was generated by a team from the Delft University of Technology.

The PGDB created from the annotated genome using the PathoLogic component of the Pathway Tools software [Karp11, Karp19] and the MetaCyc reference database [Caspi20]. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

The Penicillium rubens Wisconsin 54-1255| genome sequence used is GenBank accession number NS_000201 [vandenBerg08].

Citations: [Kiel06, Harris09, Jami10]

Genome
Replicon/ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Contig 222,7632,520471966,387,817
Contig 212,4412,280501115,624,362
Contig 121,6961,550381083,988,431
Contig 131,6021,5391623,889,175
Contig 161,5851,418311363,716,833
Contig 201,6131,48534943,652,229
Contig 1868665213211,591,038
Contig 24327281046709,213
Contig 06253229816575,163
Contig 1424123524551,708
Contig 15220199417535,560
Contig 17128107021292,067
Contig 2310392011228,788
Contig 197966112167,906
Contig 0940370373,183
Contig 0332281368,149
Contig 0419180139,849
Contig 49461291631,790
Contig 0714140028,520
Contig 0230301,588
29 Undisplayed Contigs/Replicons39390168,985
Total:13,93112,790262879
Ortholog data available?No
Database Contents
Genes13,933
Pathways293
Enzymatic Reactions1,448
Transport Reactions92
Polypeptides12,794
Protein Complexes1
Enzymes1,294
Transporters663
Compounds984
Transcription Units13,853
tRNAs174
GO Terms86,655
Database Version29.0
Synonyms Penicillium rubens Wisconsin 54-1255
Penicillium chrysogenum Wisconsin 54-1255
Taxonomic Lineage cellular organisms
Eukaryota
Opisthokonta
Fungi
Dikarya
Ascomycota
saccharomyceta
Pezizomycotina
leotiomyceta
Eurotiomycetes
Eurotiomycetidae
Eurotiales
Aspergillaceae
Penicillium
Penicillium chrysogenum species complex
Penicillium rubens
Penicillium rubens Wisconsin 54-1255
Genetic Code Number 1 -- Standard
GOLD0003458
NCBI-Taxonomy500485

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Harris09: Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, Bovenberg RA, Pronk JT, Daran JM (2009). "Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production." BMC Genomics 10;75. PMID: 19203396

Jami10: Jami MS, Barreiro C, Garcia-Estrada C, Martin JF (2010). "Proteome analysis of the penicillin producer Penicillium chrysogenum: Characterization of protein changes during the industrial strain improvement." Mol Cell Proteomics. PMID: 20154335

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

Kiel06: Kiel JA, Veenhuis M, van der Klei IJ (2006). "PEX genes in fungal genomes: common, rare or redundant." Traffic 7(10);1291-303. PMID: 16978390

vandenBerg08: van den Berg MA, Albang R, Albermann K, Badger JH, Daran JM, Driessen AJ, Garcia-Estrada C, Fedorova ND, Harris DM, Heijne WH, Joardar V, Kiel JA, Kovalchuk A, Martin JF, Nierman WC, Nijland JG, Pronk JT, Roubos JA, van der Klei IJ, van Peij NN, Veenhuis M, von Dohren H, Wagner C, Wortman J, Bovenberg RA (2008). "Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum." Nat Biotechnol 26(10);1161-8. PMID: 18820685

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