Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acinetobacter bouvetii CIP 107468, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KB8497271,1721,11934191,245,121RefSeq:NZ_KB849727
NZ_KB8497268167712718877,003RefSeq:NZ_KB849726
NZ_KB849725580557176617,362RefSeq:NZ_KB849725
NZ_KB849730303289122300,845RefSeq:NZ_KB849730
NZ_KB849729175163111176,527RefSeq:NZ_KB849729
NZ_KB84972815615051171,964RefSeq:NZ_KB849728
Total:3,2023,049106473,388,822
Ortholog data available?Yes
Database Contents
Genes3,194
Pathways250
Enzymatic Reactions1,198
Transport Reactions69
Polypeptides3,053
Protein Complexes35
Enzymes694
Transporters289
Compounds902
Transcription Units2,304
tRNAs82
Protein Features3,777
GO Terms9
Database Version29.0
Sequence SourceGCF_000368865.1
Synonyms Acinetobacter bouvetii CIP 107468
Acinetobacter bouvetii CIP 107468 = DSM 14964
Acinetobacter bouvetii DSM 14964
Acinetobacter bouvetii DSM 14964 = CIP 107468
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter bouvetii
Acinetobacter bouvetii DSM 14964 = CIP 107468
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087847
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120925
EnvironmentActivated sludge plant
Geographic LocationAustralia
Collection Date1991
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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