Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Pseudomonas aeruginosa , as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. 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 Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome PA14OR6,0295,90380466,541,482RefSeq:NZ_LT608330
Ortholog data available?Yes
Database Contents
Genes6,029
Pathways420
Enzymatic Reactions1,879
Transport Reactions132
Polypeptides5,903
Protein Complexes71
Enzymes1,231
Transporters700
Compounds1,351
Transcription Units3,819
tRNAs63
Protein Features8,010
GO Terms2,607
Database Version29.0
Sequence SourceGCF_900095805.1
Synonyms Bacillus aeruginosus
Bacillus pyocyaneus
Bacterium aeruginosum
bacterium ASFP-37
bacterium ASFP-38
bacterium ASFP-45
bacterium ASFP-46
bacterium ASFP-48
bacterium CRM125
Bacterium pyocyaneum
Micrococcus pyocyaneus
probable synonym or variety: "Pseudomonas polycolor" Clara 1930
Pseudomonas polycolor
Pseudomonas pyocyanea
Pseudomonas sp. 2_1_26
Pseudomonas sp. ACP_02
Pseudomonas sp. CRRI 93
Pseudomonas sp. HSA1/2016
Pseudomonas sp. NCIM 2036
Pseudomonas sp. NCIM 2862
Pseudomonas sp. PR_01
Pseudomonas sp. PSE5
Pseudomonas sp. RV3
Pseudomonas sp. UFT2/2016
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
Pseudomonas
Pseudomonas aeruginosa group
Pseudomonas aeruginosa
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA4393802
NCBI BioProjectPRJNA224116
NCBI-Taxonomy287
Annotation ProviderNCBI RefSeq
Annotation Date2020-12-13
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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

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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