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 dispersus NCCP 16014, 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_CP0419703,7533,59397634,024,840RefSeq:NZ_CP041970
Ortholog data available?Yes
Database Contents
Genes3,753
Pathways253
Enzymatic Reactions1,252
Transport Reactions78
Polypeptides3,595
Protein Complexes42
Enzymes749
Transporters376
Compounds938
Transcription Units2,609
tRNAs74
Protein Features4,428
GO Terms9
Database Version29.0
Sequence SourceGCF_009884975.1
Synonyms Acinetobacter genomosp. 17
Acinetobacter genomosp. 17BJ
Acinetobacter genomosp. BJ17
Acinetobacter genomospecies 17
Acinetobacter sp. group 17
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter dispersus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN12340932
NCBI BioProjectPRJNA224116
NCBI-Taxonomy70348
Environmentsputum
Geographic LocationSouth Korea
Latitude/Longitude37.46258 N 126.642944 E
Collection Date2014-01-1
HostHomo sapiens
Human Microbiome Body Siteoral
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-23
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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