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 soli GFJ2, 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_CP0168963,2263,08999383,438,298RefSeq:NZ_CP016896
pGFJ1766601086,373RefSeq:NZ_CP016897
pGFJ285830278,649RefSeq:NZ_CP016898
pGFJ312110110,453RefSeq:NZ_CP016899
pGFJ41313009,416RefSeq:NZ_CP016900
pGFJ544005,086RefSeq:NZ_CP016901
pGFJ666004,066RefSeq:NZ_CP016902
pGFJ744004,008RefSeq:NZ_CP016903
Total:3,4263,27699513,636,349
Ortholog data available?Yes
Database Contents
Genes3,426
Pathways265
Enzymatic Reactions1,274
Transport Reactions86
Polypeptides3,278
Protein Complexes45
Enzymes765
Transporters328
Compounds964
Transcription Units2,234
tRNAs74
Protein Features4,115
GO Terms15
Database Version29.0
Sequence SourceGCF_001953195.1
Synonyms Acinetobacter sp. Ba6
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter soli
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05554081
NCBI BioProjectPRJNA224116
NCBI-Taxonomy487316
Environmentsoil
Geographic LocationThailand
Collection Date2011-12-31/2011-01-1
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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