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 01-June-2020 from the annotated genome of Acinetobacter calcoaceticus CA16, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_CP0200003,9093,77787454,110,074RefSeq:NZ_CP020000
pCA1676015,920RefSeq:NZ_CP020001
Total:3,9163,78387464,115,994
Ortholog data available?Yes
Database Contents
Genes3,916
Pathways287
Enzymatic Reactions1,348
Transport Reactions88
Polypeptides3,785
Protein Complexes49
Enzymes830
Transporters423
Compounds1,000
Transcription Units2,743
tRNAs65
Protein Features4,667
GO Terms36
Database Version29.0
Sequence SourceGCF_002055515.1
Synonyms Acinetobacter genomosp. 1
Acinetobacter genomospecies 1
Acinetobacter sp. AV6
Acinetobacter sp. HNR
Acinetobacter sp. STB1
Micrococcus calcoaceticus
Moraxella calcoacetica
Neisseria winogradskyi
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter calcoaceticus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06197019
NCBI BioProjectPRJNA224116
NCBI-Taxonomy471
EnvironmentCanola Roots
Geographic LocationCanada
Collection Date2015-07-30
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-18
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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