Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Paraburkholderia acidophila ATCC 31433, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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 13,4913,38674313,737,663RefSeq:NZ_CP020737
Chromosome 23,0102,92614703,308,659RefSeq:NZ_CP020738
Chromosome 3501485511641,159RefSeq:NZ_CP020739
pATCC3143317016604153,349RefSeq:NZ_CP020740
Total:7,1726,963931167,840,830
Ortholog data available?Yes
Database Contents
Genes7,172
Pathways361
Enzymatic Reactions1,746
Transport Reactions99
Polypeptides6,963
Protein Complexes162
Enzymes1,213
Transporters696
Compounds1,280
Transcription Units4,864
tRNAs71
Protein Features8,822
GO Terms764
Database Version29.0
Sequence SourceGCF_002097715.1
Synonyms Burkholderia sp. ATCC 31433
Pseudomonas mesoacidophila ATCC 31433
Pseudomonas mesoacidophila
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Burkholderiaceae
Paraburkholderia
Paraburkholderia acidophila
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06690200
NCBI BioProjectPRJNA224116
NCBI-Taxonomy265293
Environmentsoil
Geographic LocationJapan
Collection Date1980
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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