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 15-Oct-2019 from the annotated genome of Pseudomonas chlororaphis ChPhzS140, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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
NZ_CP0277406,4406,237881157,074,317RefSeq:NZ_CP027740
Ortholog data available?Yes
Database Contents
Genes6,440
Pathways338
Enzymatic Reactions1,929
Transport Reactions17
Polypeptides6,239
Protein Complexes33
Enzymes1,098
Transporters784
Compounds1,653
Transcription Units4,282
tRNAs68
Growth Media383
Protein Features8,362
Phenotype Microarray Datasets1
GO Terms655
Database Version29.0
Synonyms Pseudomonas chlororaphis subsp. piscium
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
Pseudomonas
Pseudomonas chlororaphis group
Pseudomonas chlororaphis
Pseudomonas chlororaphis piscium
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN08359202
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1513890
Environmentbulk soil
Geographic LocationFrance
Annotation ProviderNCBI RefSeq
Annotation Date2018-11-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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