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 frederiksbergensis ERDD5:01, 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
NZ_CP0178865,4295,174981575,747,498RefSeq:NZ_CP017886
unnamed1348309039371,069RefSeq:NZ_CP017887
Total:5,7775,483981966,118,567
Ortholog data available?Yes
Database Contents
Genes5,777
Pathways354
Enzymatic Reactions1,641
Transport Reactions113
Polypeptides5,483
Protein Complexes69
Enzymes1,115
Transporters545
Compounds1,163
Transcription Units3,701
tRNAs70
Protein Features6,950
GO Terms87
Database Version29.0
Sequence SourceGCF_001874645.1
Synonyms Pseudomonas sp. BDR1P1B1
Pseudomonas sp. BDR1P1B2
Pseudomonas sp. V1D5a
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Pseudomonadales
Pseudomonadaceae
Pseudomonas
Pseudomonas frederiksbergensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05947123
NCBI BioProjectPRJNA224116
NCBI-Taxonomy104087
Environmentglacial stream
Geographic LocationIndia
Latitude/Longitude27.34 N 88.06 E
Altitude (m)4718.0
Collection Date2015-09-28
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-25
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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