Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 20-Sep-2017 from the annotated genome of Pseudomonas aeruginosa PAO1, as obtained from RefSeq (annotation date: 03-AUG-2016). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 21.5) [Karp16, Karp11] using MetaCyc version 21.1 [Caspi16]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutess of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0025165,6965,572105196,264,404RefSeq:NC_002516
Ortholog data available?No
Database Contents
Genes5,697
Pathways284
Enzymatic Reactions1,590
Transport Reactions96
Polypeptides5,572
Protein Complexes18
Enzymes1,073
Transporters525
Compounds1,236
Transcription Units3,787
tRNAs63
Growth Media2
Protein Features14,091
GO Terms44,754
Gene Essentiality Datasets2
Database Version29.0
Synonyms Pseudomonas aeruginosa str. PAO1
Pseudomonas aeruginosa PAO1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
Pseudomonas
Pseudomonas aeruginosa group
Pseudomonas aeruginosa
Pseudomonas aeruginosa PAO1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA57945
NCBI-Taxonomy208964

References

Caspi16: Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD (2016). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases." Nucleic Acids Res 44(D1);D471-80. PMID: 26527732

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

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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